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Bordini J, Lenzi C, Frenquelli M, Morabito A, Pseftogas A, Belloni D, Mansouri L, Tsiolas G, Perotta E, Ranghetti P, Gandini F, Genova F, Hägerstrand D, Gavriilidis G, Keisaris S, Pechlivanis N, Davi F, Kay NE, Langerak AW, Pospisilova S, Scarfò L, Makris A, Psomopoulos FE, Stamatopoulos K, Rosenquist R, Campanella A, Ghia P. IκBε deficiency accelerates disease development in chronic lymphocytic leukemia. Leukemia 2024:10.1038/s41375-024-02236-4. [PMID: 38575671 DOI: 10.1038/s41375-024-02236-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 03/11/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024]
Abstract
The NFKBIE gene, which encodes the NF-κB inhibitor IκBε, is mutated in 3-7% of patients with chronic lymphocytic leukemia (CLL). The most recurrent alteration is a 4-bp frameshift deletion associated with NF-κB activation in leukemic B cells and poor clinical outcome. To study the functional consequences of NFKBIE gene inactivation, both in vitro and in vivo, we engineered CLL B cells and CLL-prone mice to stably down-regulate NFKBIE expression and investigated its role in controlling NF-κB activity and disease expansion. We found that IκBε loss leads to NF-κB pathway activation and promotes both migration and proliferation of CLL cells in a dose-dependent manner. Importantly, NFKBIE inactivation was sufficient to induce a more rapid expansion of the CLL clone in lymphoid organs and contributed to the development of an aggressive disease with a shortened survival in both xenografts and genetically modified mice. IκBε deficiency was associated with an alteration of the MAPK pathway, also confirmed by RNA-sequencing in NFKBIE-mutated patient samples, and resistance to the BTK inhibitor ibrutinib. In summary, our work underscores the multimodal relevance of the NF-κB pathway in CLL and paves the way to translate these findings into novel therapeutic options.
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Affiliation(s)
| | - Chiara Lenzi
- IRCSS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | | | - Alessia Morabito
- IRCSS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Athanasios Pseftogas
- IRCSS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Daniela Belloni
- IRCSS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Larry Mansouri
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - George Tsiolas
- Centre for Research & Technology, Hellas (CERTH), Thessaloniki, Greece
| | | | | | - Francesca Gandini
- IRCSS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | | | - Daniel Hägerstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | | | - Sofoklis Keisaris
- Centre for Research & Technology, Hellas (CERTH), Thessaloniki, Greece
| | | | - Frederic Davi
- Institution Université Pierre et Marie Curie & Hôpital Pitié-Salpêtrière, Paris, France
| | | | | | - Sarka Pospisilova
- University Hospital Brno, Brno, Czech Republic
- Masaryk University, Brno, Czech Republic
| | - Lydia Scarfò
- IRCSS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Antonios Makris
- Centre for Research & Technology, Hellas (CERTH), Thessaloniki, Greece
| | | | | | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Alessandro Campanella
- IRCSS Ospedale San Raffaele, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
| | - Paolo Ghia
- IRCSS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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Navrkalova V, Plevova K, Radova L, Porc J, Pal K, Malcikova J, Pavlova S, Doubek M, Panovska A, Kotaskova J, Pospisilova S. Integrative NGS testing reveals clonal dynamics of adverse genomic defects contributing to a natural progression in treatment-naïve CLL patients. Br J Haematol 2024; 204:240-249. [PMID: 38062779 DOI: 10.1111/bjh.19191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/17/2023] [Accepted: 10/25/2023] [Indexed: 01/11/2024]
Abstract
Large-scale next-generation sequencing (NGS) studies revealed extensive genetic heterogeneity, driving a highly variable clinical course of chronic lymphocytic leukaemia (CLL). The evolution of subclonal populations contributes to diverse therapy responses and disease refractoriness. Besides, the dynamics and impact of subpopulations before therapy initiation are not well understood. We examined changes in genomic defects in serial samples of 100 untreated CLL patients, spanning from indolent to aggressive disease. A comprehensive NGS panel LYNX, which provides targeted mutational analysis and genome-wide chromosomal defect assessment, was employed. We observed dynamic changes in the composition and/or proportion of genomic aberrations in most patients (62%). Clonal evolution of gene variants prevailed over the chromosomal alterations. Unsupervised clustering based on aberration dynamics revealed four groups of patients with different clinical behaviour. An adverse cluster was associated with fast progression and early therapy need, characterized by the expansion of TP53 defects, ATM mutations, and 18p- alongside dynamic SF3B1 mutations. Our results show that clonal evolution is active even without therapy pressure and that repeated genetic testing can be clinically relevant during long-term patient monitoring. Moreover, integrative NGS testing contributes to the consolidated evaluation of results and accurate assessment of individual patient prognosis.
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Affiliation(s)
- Veronika Navrkalova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Lenka Radova
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jakub Porc
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Karol Pal
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jitka Malcikova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jana Kotaskova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
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3
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Chatzikonstantinou T, Scarfò L, Karakatsoulis G, Minga E, Chamou D, Iacoboni G, Kotaskova J, Demosthenous C, Smolej L, Mulligan S, Alcoceba M, Al-Shemari S, Aurran-Schleinitz T, Bacchiarri F, Bellido M, Bijou F, Calleja A, Medina A, Khan MA, Cassin R, Chatzileontiadou S, Collado R, Christian A, Davis Z, Dimou M, Donaldson D, Santos GD, Dreta B, Efstathopoulou M, El-Ashwah S, Enrico A, Fresa A, Galimberti S, Galitzia A, García-Serra R, Gimeno E, González-Gascón-y-Marín I, Gozzetti A, Guarente V, Guieze R, Gogia A, Gupta R, Harrop S, Hatzimichael E, Herishanu Y, Hernández-Rivas JÁ, Inchiappa L, Jaksic O, Janssen S, Kalicińska E, Kamel L, Karakus V, Kater AP, Kho B, Kislova M, Konstantinou E, Koren-Michowitz M, Kotsianidis I, Kreitman RJ, Labrador J, Lad D, Levin MD, Levy I, Longval T, Lopez-Garcia A, Marquet J, Martin-Rodríguez L, Maynadié M, Maslejova S, Mayor-Bastida C, Mihaljevic B, Milosevic I, Miras F, Moia R, Morawska M, Murru R, Nath UK, Navarro-Bailón A, Oliveira AC, Olivieri J, Oscier D, Panovska-Stavridis I, Papaioannou M, Papajík T, Kubova Z, Phumphukhieo P, Pierie C, Puiggros A, Rani L, Reda G, Rigolin GM, Ruchlemer R, Daniel de Deus Santos M, Schipani M, Schiwitza A, Shen Y, Simkovic M, Smirnova S, Abdelrahman Soliman DS, Spacek M, Tadmor T, Tomic K, Tse E, Vassilakopoulos T, Visentin A, Vitale C, von Tresckow J, Vrachiolias G, Vukovic V, Walewska R, Wasik-Szczepanek E, Xu Z, Yagci M, Yañez L, Yassin M, Zuchnicka J, Angelopoulou M, Antic D, Biderman B, Catherwood M, Claus R, Coscia M, Cuneo A, Demirkan F, Espinet B, Gaidano G, Kalashnikova OB, Laurenti L, Nikitin E, Pangalis GA, Panagiotidis P, Popov VM, Pospisilova S, Sportoletti P, Stavroyianni N, Tam C, Trentin L, Chatzidimitriou A, Bosch F, Doubek M, Ghia P, Stamatopoulos K. Other malignancies in the history of CLL: an international multicenter study conducted by ERIC, the European Research Initiative on CLL, in HARMONY. EClinicalMedicine 2023; 65:102307. [PMID: 38033506 PMCID: PMC10685149 DOI: 10.1016/j.eclinm.2023.102307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 12/02/2023] Open
Abstract
Background Patients with chronic lymphocytic leukemia (CLL) have a higher risk of developing other malignancies (OMs) compared to the general population. However, the impact of CLL-related risk factors and CLL-directed treatment is still unclear and represents the focus of this work. Methods We conducted a retrospective international multicenter study to assess the incidence of OMs and detect potential risk factors in 19,705 patients with CLL, small lymphocytic lymphoma, or high-count CLL-like monoclonal B-cell lymphocytosis, diagnosed between 2000 and 2016. Data collection took place between October 2020 and March 2022. Findings In 129,254 years of follow-up after CLL diagnosis, 3513 OMs were diagnosed (27.2 OMs/1000 person-years). The most common hematological OMs were Richter transformation, myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Non-melanoma skin (NMSC) and prostate cancers were the most common solid tumors (STs).The only predictor for MDS and AML development was treatment with fludarabine and cyclophosphamide with/without rituximab (FC ± R) (OR = 3.7; 95% CI = 2.79-4.91; p < 0.001). STs were more frequent in males and patients with unmutated immunoglobulin heavy variable genes (OR = 1.77; 95% CI = 1.49-2.11; p < 0.001/OR = 1.89; 95% CI = 1.6-2.24; p < 0.001).CLL-directed treatment was associated with non-melanoma skin and prostate cancers (OR = 1.8; 95% CI = 1.36-2.41; p < 0.001/OR = 2.11; 95% CI = 1.12-3.97; p = 0.021). In contrast, breast cancers were more frequent in untreated patients (OR = 0.17; 95% CI = 0.08-0.33; p < 0.001).Patients with CLL and an OM had inferior overall survival (OS) than those without. AML and MDS conferred the worst OS (p < 0.001). Interpretation OMs in CLL impact on OS. Treatment for CLL increased the risk for AML/MDS, prostate cancer, and NMSC. FCR was associated with increased risk for AML/MDS. Funding AbbVie, and EU/EFPIAInnovative Medicines Initiative Joint Undertaking HARMONY grant n° 116026.
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Affiliation(s)
| | - Lydia Scarfò
- Università Vita-Salute San Raffaele and IRCCS Ospedale San Raffaele, Milan, Italy
| | - Georgios Karakatsoulis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
- Department of Mathematics, University of Ioannina, Ioannina, Greece
| | - Eva Minga
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Dimitra Chamou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Gloria Iacoboni
- Department of Haematology, University Hospital Vall d'Hebron, Autonomous University, Barcelona, Spain
| | - Jana Kotaskova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | | | - Lukas Smolej
- 4th Department of Internal Medicine-Haematology, University Hospital and Faculty of Medicine, Hradec Králové, Czech Republic
| | | | - Miguel Alcoceba
- Department of Haematology, University Hospital of Salamanca (HUS-IBSAL), CIBERONC (CB16/12/00233) and Cancer Research Centre (CIC-IBMCC, USAL-CSIC), Salamanca, Spain
| | - Salem Al-Shemari
- Faculty of Medicine, Department of Medicine, Kuwait University, Kuwait City, Kuwait
| | | | | | - Mar Bellido
- Hematology Department, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Anne Calleja
- Department of Hemato-Oncology, Institut Paoli Calmettes, Marseille, France
| | | | - Mehreen Ali Khan
- Department of Hematology and Stem Cell Transplant, Armed Forces Bone Marrow Transplant Center/National Institute of Blood and Marrow Transplant, Rawalpindi, Pakistan
| | - Ramona Cassin
- Hematology Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico of Milan, Milan, Italy
| | - Sofia Chatzileontiadou
- Hematology Unit, 1st Dept of Internal Medicine, AUTH, AHEPA Hospital, Thessaloniki, Greece
| | - Rosa Collado
- Servicio de Hematología, Consorcio Hospital General Universitario de Valencia, Fundación de Investigación Hospital General Universitario de Valencia, Valencia, Spain
| | - Amy Christian
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, United Kingdom
| | - Zadie Davis
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, United Kingdom
| | - Maria Dimou
- Department of Hematology and Bone Marrow Transplantation Unit, National and Kapodistrian University of Athens, Laikon General Hospital, Athens, Greece
| | - David Donaldson
- Clinical Haematology, Belfast City Hospital, Belfast, United Kingdom
| | | | - Barbara Dreta
- Division of Hematology, Department of Internal Medicine, University Hospital Center Zagreb, Zagreb, Croatia
| | - Maria Efstathopoulou
- Department of Haematology, Athens Medical Center-Psychikon Branch, Athens, Greece
| | | | | | - Alberto Fresa
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Sara Galimberti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Andrea Galitzia
- Hematology and Stem Cell Transplantation Unit, Ospedale Oncologico A. Businco, ARNAS "G. Brotzu", Cagliari, Italy
| | - Rocío García-Serra
- Servicio de Hematología, Consorcio Hospital General Universitario de Valencia, Fundación de Investigación Hospital General Universitario de Valencia, Valencia, Spain
| | - Eva Gimeno
- Department of Hematology, Hospital del Mar, Barcelona, Spain
| | | | | | - Valerio Guarente
- Institute of Hematology and Center for Hemato-Oncology Research, University of Perugia and Santa Maria della Misericordia Hospital, Perugia, Italy
| | - Romain Guieze
- Department of Hematology and Cell Therapy, Estaing University Hospital, Clermont-Ferrand, France
| | - Ajay Gogia
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Sean Harrop
- Peter MacCallum Cancer Centre, St Vincent's Hospital, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Eleftheria Hatzimichael
- Faculty of Medicine, Department of Haematology, School of Health Sciences, University of Ioannina, Stavros Niarchos Avenue, Ioannina 45110, Greece
| | - Yair Herishanu
- Department of Hematology, Tel Aviv Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Luca Inchiappa
- Department of Hemato-Oncology, Institut Paoli Calmettes, Marseille, France
| | - Ozren Jaksic
- Department of Hematology, University Hospital Dubrava, Zagreb, Croatia
| | - Susanne Janssen
- Dept of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Elżbieta Kalicińska
- Department and Clinic of Hematology, Blood Neoplasms and Bone Marrow Transplantation Wroclaw Medical University, Wroclaw, Poland
| | - Laribi Kamel
- Department of Hematology, Centre Hospitalier Le Mans, Le Mans, France
| | | | - Arnon P. Kater
- Dept of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Bonnie Kho
- Department of Medicine, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China
| | - Maria Kislova
- Department of Hematology, Oncology, and Chemotherapy, S. P. Botkin's City Hospital, Moscow, Russia
| | | | - Maya Koren-Michowitz
- Department of Hematology, Shamir Medical Center, Zerifin, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Ioannis Kotsianidis
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Robert J. Kreitman
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jorge Labrador
- Department of Hematology, Hospital Universitario de Burgos, Burgos, Spain
| | - Deepesh Lad
- Department of Internal Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Mark-David Levin
- Department of Internal Medicine, Albert Schweitzer Hospital, Dordrecht, the Netherlands
| | - Ilana Levy
- Hematology, Bnai-Zion Medical Center, Haifa, Israel
| | - Thomas Longval
- Service d'Hématologie Oncologie, Centre Hospitalier de Versailles, Le Chesnay, France
| | - Alberto Lopez-Garcia
- Fundacion Jimenez Diaz University Hospital, Health Research Institute IIS-FJD, Madrid, Spain
| | - Juan Marquet
- Hematology Department, Ramón y Cajal University Hospital, Madrid, Spain
| | - Lucia Martin-Rodríguez
- Department of Haematology, University Hospital Vall d'Hebron, Autonomous University, Barcelona, Spain
| | - Marc Maynadié
- Biological Haematology Department, Dijon Bourgogne University Hospital, Haematological Malignancies Registry, LNC UMR 1231, Dijon 21000, France
| | - Stanislava Maslejova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | | | - Biljana Mihaljevic
- Clinic for Hematology, University Clinical Center of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ivana Milosevic
- Faculty of Medicine, Clinical Centre of Vojvodina, University of Novi Sad, Novi Sad, Serbia
| | - Fatima Miras
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Riccardo Moia
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Marta Morawska
- Experimental Hematooncology Department, Medical University of Lublin, Lublin, Poland
- Hematology Department, St. John's Cancer Center, Lublin, Poland
| | - Roberta Murru
- Hematology and Stem Cell Transplantation Unit, Ospedale Oncologico A. Businco, ARNAS "G. Brotzu", Cagliari, Italy
| | - Uttam Kumar Nath
- Department of Medical Oncology & Hematology, All India Institute of Medical Sciences, Rishikesh, India
| | - Almudena Navarro-Bailón
- Department of Haematology, University Hospital of Salamanca (HUS-IBSAL), CIBERONC (CB16/12/00233) and Cancer Research Centre (CIC-IBMCC, USAL-CSIC), Salamanca, Spain
| | - Ana C. Oliveira
- Department of Clinical Hematology, ICO, Hospital Duran i Reynals, IDIBELL, Barcelona, Spain
| | | | - David Oscier
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, United Kingdom
| | - Irina Panovska-Stavridis
- Medical Faculty, University Clinic of Hematology, University Ss. Cyril and Methodius, Skopje, North Macedonia
| | - Maria Papaioannou
- Hematology Unit, 1st Dept of Internal Medicine, AUTH, AHEPA Hospital, Thessaloniki, Greece
| | - Tomas Papajík
- Faculty of Medicine and Dentistry, Department of Hemato-Oncology, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
| | - Zuzana Kubova
- Faculty of Medicine and Dentistry, Department of Hemato-Oncology, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
| | | | - Cheyenne Pierie
- Dept of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Anna Puiggros
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar and Translational Research on Hematological Neoplasms Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Lata Rani
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Gianluigi Reda
- Hematology Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico of Milan, Milan, Italy
| | | | - Rosa Ruchlemer
- Department of Hematology, Shaare-Zedek Medical Center, Affiliated with the Hebrew University Medical School, Jerusalem, Israel
| | | | - Mattia Schipani
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Annett Schiwitza
- Hematology and Oncology, Faculty of Medicine, University of Augsburg, Stenglinstrasse 2, Augsburg 86156, Germany
| | - Yandong Shen
- Royal North Shore Hospital, Sydney, NSW, Australia
| | - Martin Simkovic
- 4th Department of Internal Medicine-Haematology, University Hospital and Faculty of Medicine, Hradec Králové, Czech Republic
| | - Svetlana Smirnova
- Consultative Hematology Department with a Day Hospital for Intensive High-Dose Chemotherapy, National Medical Research Center for Hematology, Moscow, Russia
| | | | - Martin Spacek
- First Faculty of Medicine, 1st Department of Medicine - Hematology, Charles University and General Hospital in Prague, Czech Republic
| | - Tamar Tadmor
- Hematology, Bnai-Zion Medical Center, Haifa, Israel
| | - Kristina Tomic
- Clinic for Hematology, University Clinical Center of Serbia, Belgrade, Serbia
| | - Eric Tse
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | | | - Andrea Visentin
- Hematology and Clinical Immunology Unit, Department of Medicine, University of Padova, Padova, Italy
| | - Candida Vitale
- Division of Hematology, A.O.U. Città della Salute e della Scienza di Torino and Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Julia von Tresckow
- Clinic for Hematology and Stem Cell Transplantation, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - George Vrachiolias
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Vojin Vukovic
- Clinic for Hematology, University Clinical Center of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Renata Walewska
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, United Kingdom
| | - Ewa Wasik-Szczepanek
- Dept. Hematooncology and Bone Marrow Transplantation, Medical University in Lublin, Lublin, Poland
| | - Zhenshu Xu
- Fujian Provincial Key Laboratory of Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou 350001, China
| | - Munci Yagci
- Gazi University Medical Faculty, Ankara, Turkey
| | - Lucrecia Yañez
- Department of Hematology, University Hospital Marqués de Valdecilla, Santander, Spain
- Department of Hematological Malignancies and Stem Cell Transplantation, Research Institute of Marques de Valdecilla (IDIVAL), Santander, Spain
| | - Mohamed Yassin
- Hematology Section, Department of Medical Oncology, National Center for Cancer Care and Research, Doha, Qatar
| | - Jana Zuchnicka
- Department of Haematooncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - Maria Angelopoulou
- Haematology, University of Athens, Laikon General Hospital, Athens, Greece
| | - Darko Antic
- Clinic for Hematology, University Clinical Center of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Bella Biderman
- Department of Molecular Hematology, National Medical Research Center for Hematology, Moscow, Russia
| | - Mark Catherwood
- Clinical Haematology, Belfast City Hospital, Belfast, United Kingdom
| | - Rainer Claus
- Pathology, Faculty of Medicine, University of Augsburg, Stenglinstrasse 2, Augsburg 86156, Germany
- Faculty of Medicine, Comprehensive Cancer Center Augsburg, University of Augsburg, Stenglinstrasse 2, Augsburg 86156, Germany
| | - Marta Coscia
- Division of Hematology, A.O.U. Città della Salute e della Scienza di Torino and Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | | | - Fatih Demirkan
- Division of Hematology, Dokuz Eylul University, Izmir, Turkey
| | - Blanca Espinet
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar and Translational Research on Hematological Neoplasms Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Olga B. Kalashnikova
- Federal State Budgetary Educational Institution of Higher Education Academician I.P. Pavlov First St. Petersburg State Medical University of the Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
| | - Luca Laurenti
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Eugene Nikitin
- Department of Hematology, Oncology, and Chemotherapy, S. P. Botkin's City Hospital, Moscow, Russia
| | | | - Panagiotis Panagiotidis
- Department of Hematology and Bone Marrow Transplantation Unit, National and Kapodistrian University of Athens, Laikon General Hospital, Athens, Greece
| | - Viola Maria Popov
- Hematology Department, Colentina Clinical Hospital, Bucharest, Romania
| | - Sarka Pospisilova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Paolo Sportoletti
- Institute of Hematology and Center for Hemato-Oncology Research, University of Perugia and Santa Maria della Misericordia Hospital, Perugia, Italy
| | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Constantine Tam
- Peter MacCallum Cancer Centre, St Vincent's Hospital, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Livio Trentin
- Hematology and Clinical Immunology Unit, Department of Medicine, University of Padova, Padova, Italy
| | | | - Francesc Bosch
- Department of Haematology, University Hospital Vall d'Hebron, Autonomous University, Barcelona, Spain
| | - Michael Doubek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Paolo Ghia
- Università Vita-Salute San Raffaele and IRCCS Ospedale San Raffaele, Milan, Italy
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
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4
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Mansouri L, Thorvaldsdottir B, Sutton LA, Karakatsoulis G, Meggendorfer M, Parker H, Nadeu F, Brieghel C, Laidou S, Moia R, Rossi D, Catherwood M, Kotaskova J, Delgado J, Rodríguez-Vicente AE, Benito R, Rigolin GM, Bonfiglio S, Scarfo L, Mattsson M, Davis Z, Gogia A, Rani L, Baliakas P, Foroughi-Asl H, Jylhä C, Skaftason A, Rapado I, Miras F, Martinez-Lopez J, de la Serna J, Rivas JMH, Thornton P, Larráyoz MJ, Calasanz MJ, Fésüs V, Mátrai Z, Bödör C, Smedby KE, Espinet B, Puiggros A, Gupta R, Bullinger L, Bosch F, Tazón-Vega B, Baran-Marszak F, Oscier D, Nguyen-Khac F, Zenz T, Terol MJ, Cuneo A, Hernández-Sánchez M, Pospisilova S, Mills K, Gaidano G, Niemann CU, Campo E, Strefford JC, Ghia P, Stamatopoulos K, Rosenquist R. Different prognostic impact of recurrent gene mutations in chronic lymphocytic leukemia depending on IGHV gene somatic hypermutation status: a study by ERIC in HARMONY. Leukemia 2023; 37:339-347. [PMID: 36566271 PMCID: PMC9898037 DOI: 10.1038/s41375-022-01802-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/08/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022]
Abstract
Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. In this study, we assessed the impact of nine recurrently mutated genes (BIRC3, EGR2, MYD88, NFKBIE, NOTCH1, POT1, SF3B1, TP53, and XPO1) in pre-treatment samples from 4580 patients with CLL, using time-to-first-treatment (TTFT) as the primary end-point in relation to IGHV gene SHM status. Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3-9.8% with mutations in NOTCH1 being the most frequent. In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. Our findings underscore the need for a compartmentalized approach to identify high-risk patients, particularly among M-CLL patients, with potential implications for stratified management.
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Affiliation(s)
- Larry Mansouri
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Birna Thorvaldsdottir
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Lesley-Ann Sutton
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Georgios Karakatsoulis
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
- Department of Mathematics, University of Ioannina, Ioannina, Greece
| | | | - Helen Parker
- Cancer Genomics, School for Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Christian Brieghel
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Stamatia Laidou
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
| | - Riccardo Moia
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - Davide Rossi
- Division of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Laboratory of Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
| | - Mark Catherwood
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Jana Kotaskova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Julio Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Ana E Rodríguez-Vicente
- Cancer Research Center (IBMCC) CSIC-University of Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica (IBSAL), Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Rocío Benito
- Cancer Research Center (IBMCC) CSIC-University of Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica (IBSAL), Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Gian Matteo Rigolin
- Hematology-Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Silvia Bonfiglio
- Università Vita Salute San Raffaele and IRCCS Ospedale San Raffaele, Milano, Italy
| | - Lydia Scarfo
- Università Vita Salute San Raffaele and IRCCS Ospedale San Raffaele, Milano, Italy
| | - Mattias Mattsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Zadie Davis
- Molecular Pathology Department, University Hospitals Dorset, Bournemouth, UK
| | - Ajay Gogia
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Lata Rani
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Hassan Foroughi-Asl
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Cecilia Jylhä
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Aron Skaftason
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Inmaculada Rapado
- Hospital Universitario 12 Octubre, Madrid, Spain
- Spanish National Cancer Research (CNIO), Madrid, Spain
| | - Fatima Miras
- Hospital Universitario 12 Octubre, Madrid, Spain
| | - Joaquín Martinez-Lopez
- Hospital Universitario 12 Octubre, Madrid, Spain
- Spanish National Cancer Research (CNIO), Madrid, Spain
| | - Javier de la Serna
- Hospital Universitario 12 Octubre, Madrid, Spain
- Spanish National Cancer Research (CNIO), Madrid, Spain
| | - Jesús María Hernández Rivas
- Cancer Research Center (IBMCC) CSIC-University of Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica (IBSAL), Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | | | - María José Larráyoz
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - María José Calasanz
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Viktória Fésüs
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Zoltán Mátrai
- Central Hospital of Southern Pest-National Institute of Hematology and Infectious Diseases, Budapest, Hungary
| | - Csaba Bödör
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Karin E Smedby
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Blanca Espinet
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar and Translational Research on Hematological Neoplasms Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Anna Puiggros
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar and Translational Research on Hematological Neoplasms Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Ritu Gupta
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Lars Bullinger
- Department of Hematology, Oncology and Cancer Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Francesc Bosch
- Department of Hematology, Hospital Universitari Vall d'Hebron (HUVH), Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Bárbara Tazón-Vega
- Department of Hematology, Hospital Universitari Vall d'Hebron (HUVH), Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Fanny Baran-Marszak
- Service d'hématologie Biologique Hôpital Avicenne Assistance Publique des Hôpitaux de Paris, Bobigny, France
| | - David Oscier
- Molecular Pathology Department, University Hospitals Dorset, Bournemouth, UK
| | - Florence Nguyen-Khac
- Sorbonne Université, Service d'Hématologie Clinique, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Thorsten Zenz
- Department of Oncology and Haematology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Maria Jose Terol
- Department of Hematology, INCLIVA Research Insitute, University of Valencia, Valencia, Spain
| | - Antonio Cuneo
- Hematology-Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - María Hernández-Sánchez
- Cancer Research Center (IBMCC) CSIC-University of Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica (IBSAL), Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Sarka Pospisilova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ken Mills
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - Carsten U Niemann
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Jonathan C Strefford
- Cancer Genomics, School for Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Paolo Ghia
- Università Vita Salute San Raffaele and IRCCS Ospedale San Raffaele, Milano, Italy
| | - Kostas Stamatopoulos
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden.
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5
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Mansouri L, Thorvaldsdottir B, Sutton LA, Karakatsoulis G, Meggendorfer M, Parker H, Nadeu F, Brieghel C, Laidou S, Moia R, Rossi D, Catherwood M, Kotaskova J, Delgado J, Rodríguez-Vicente AE, Benito R, Rigolin GM, Bonfiglio S, Scarfo L, Mattsson M, Davis Z, Gogia A, Rani L, Baliakas P, Foroughi-Asl H, Jylhä C, Skaftason A, Rapado I, Miras F, Martinez-Lopez J, de la Serna J, Rivas JMH, Thornton P, Larráyoz MJ, Calasanz MJ, Fésüs V, Mátrai Z, Bödör C, Smedby KE, Espinet B, Puiggros A, Gupta R, Bullinger L, Bosch F, Tazón-Vega B, Baran-Marszak F, Oscier D, Nguyen-Khac F, Zenz T, Terol MJ, Cuneo A, Hernández-Sánchez M, Pospisilova S, Mills K, Gaidano G, Niemann CU, Campo E, Strefford JC, Ghia P, Stamatopoulos K, Rosenquist R. Correction: Different prognostic impact of recurrent gene mutations in chronic lymphocytic leukemia depending on IGHV gene somatic hypermutation status: a study by ERIC in HARMONY. Leukemia 2023; 37:504. [PMID: 36635392 PMCID: PMC9898025 DOI: 10.1038/s41375-023-01813-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Larry Mansouri
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Birna Thorvaldsdottir
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Lesley-Ann Sutton
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Georgios Karakatsoulis
- grid.423747.10000 0001 2216 5285Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece ,grid.9594.10000 0001 2108 7481Department of Mathematics, University of Ioannina, Ioannina, Greece
| | - Manja Meggendorfer
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Munich, Germany
| | - Helen Parker
- grid.5491.90000 0004 1936 9297Cancer Genomics, School for Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Ferran Nadeu
- grid.10403.360000000091771775Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain ,grid.510933.d0000 0004 8339 0058Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Christian Brieghel
- grid.4973.90000 0004 0646 7373Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Stamatia Laidou
- grid.423747.10000 0001 2216 5285Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
| | - Riccardo Moia
- grid.16563.370000000121663741Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - Davide Rossi
- grid.419922.5Division of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland ,grid.419922.5Laboratory of Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
| | - Mark Catherwood
- grid.4777.30000 0004 0374 7521Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
| | - Jana Kotaskova
- grid.412554.30000 0004 0609 2751Department of Internal Medicine—Hematology and Oncology, University Hospital Brno, Brno, Czech Republic ,grid.10267.320000 0001 2194 0956Faculty of Medicine, Masaryk University, Brno, Czech Republic ,grid.10267.320000 0001 2194 0956Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Julio Delgado
- grid.10403.360000000091771775Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain ,grid.510933.d0000 0004 8339 0058Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain ,grid.410458.c0000 0000 9635 9413Hospital Clínic of Barcelona, Barcelona, Spain ,grid.5841.80000 0004 1937 0247Universitat de Barcelona, Barcelona, Spain
| | - Ana E. Rodríguez-Vicente
- grid.11762.330000 0001 2180 1817Cancer Research Center (IBMCC) CSIC—University of Salamanca, Salamanca, Spain ,grid.452531.4Instituto de Investigación Biomédica (IBSAL), Salamanca, Spain ,grid.411258.bDepartment of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Rocío Benito
- grid.11762.330000 0001 2180 1817Cancer Research Center (IBMCC) CSIC—University of Salamanca, Salamanca, Spain ,grid.452531.4Instituto de Investigación Biomédica (IBSAL), Salamanca, Spain ,grid.411258.bDepartment of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Gian Matteo Rigolin
- grid.8484.00000 0004 1757 2064Hematology—Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Silvia Bonfiglio
- grid.15496.3f0000 0001 0439 0892Università Vita Salute San Raffaele and IRCCS Ospedale San Raffaele, Milano, Italy
| | - Lydia Scarfo
- grid.15496.3f0000 0001 0439 0892Università Vita Salute San Raffaele and IRCCS Ospedale San Raffaele, Milano, Italy
| | - Mattias Mattsson
- grid.8993.b0000 0004 1936 9457Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Zadie Davis
- Molecular Pathology Department, University Hospitals Dorset, Bournemouth, UK
| | - Ajay Gogia
- grid.413618.90000 0004 1767 6103All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Lata Rani
- grid.413618.90000 0004 1767 6103All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Panagiotis Baliakas
- grid.8993.b0000 0004 1936 9457Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Hassan Foroughi-Asl
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Cecilia Jylhä
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Aron Skaftason
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Inmaculada Rapado
- grid.144756.50000 0001 1945 5329Hospital Universitario 12 Octubre, Madrid, Spain ,grid.7719.80000 0000 8700 1153Spanish National Cancer Research (CNIO), Madrid, Spain
| | - Fatima Miras
- grid.144756.50000 0001 1945 5329Hospital Universitario 12 Octubre, Madrid, Spain
| | - Joaquín Martinez-Lopez
- grid.144756.50000 0001 1945 5329Hospital Universitario 12 Octubre, Madrid, Spain ,grid.7719.80000 0000 8700 1153Spanish National Cancer Research (CNIO), Madrid, Spain
| | - Javier de la Serna
- grid.144756.50000 0001 1945 5329Hospital Universitario 12 Octubre, Madrid, Spain ,grid.7719.80000 0000 8700 1153Spanish National Cancer Research (CNIO), Madrid, Spain
| | - Jesús María Hernández Rivas
- grid.11762.330000 0001 2180 1817Cancer Research Center (IBMCC) CSIC—University of Salamanca, Salamanca, Spain ,grid.452531.4Instituto de Investigación Biomédica (IBSAL), Salamanca, Spain ,grid.411258.bDepartment of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Patrick Thornton
- grid.414315.60000 0004 0617 6058Haematology Department, Beaumont Hospital, Dublin, Ireland
| | - María José Larráyoz
- grid.5924.a0000000419370271Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain ,grid.508840.10000 0004 7662 6114IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - María José Calasanz
- grid.5924.a0000000419370271Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain ,grid.508840.10000 0004 7662 6114IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Viktória Fésüs
- grid.11804.3c0000 0001 0942 9821HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Zoltán Mátrai
- Central Hospital of Southern Pest—National Institute of Hematology and Infectious Diseases, Budapest, Hungary
| | - Csaba Bödör
- grid.11804.3c0000 0001 0942 9821HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Karin E. Smedby
- grid.4714.60000 0004 1937 0626Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Blanca Espinet
- grid.411142.30000 0004 1767 8811Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar and Translational Research on Hematological Neoplasms Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Anna Puiggros
- grid.411142.30000 0004 1767 8811Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar and Translational Research on Hematological Neoplasms Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Ritu Gupta
- grid.413618.90000 0004 1767 6103All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Lars Bullinger
- grid.6363.00000 0001 2218 4662Department of Hematology, Oncology and Cancer Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Francesc Bosch
- grid.411083.f0000 0001 0675 8654Department of Hematology, Hospital Universitari Vall d’Hebron (HUVH), Experimental Hematology, Vall d’Hebron Institute of Oncology (VHIO), Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Bárbara Tazón-Vega
- grid.411083.f0000 0001 0675 8654Department of Hematology, Hospital Universitari Vall d’Hebron (HUVH), Experimental Hematology, Vall d’Hebron Institute of Oncology (VHIO), Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Fanny Baran-Marszak
- grid.50550.350000 0001 2175 4109Service d’hématologie Biologique Hôpital Avicenne Assistance Publique des Hôpitaux de Paris, Bobigny, France
| | - David Oscier
- Molecular Pathology Department, University Hospitals Dorset, Bournemouth, UK
| | - Florence Nguyen-Khac
- grid.462844.80000 0001 2308 1657Sorbonne Université, Service d’Hématologie Clinique, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Thorsten Zenz
- grid.7400.30000 0004 1937 0650Department of Oncology and Haematology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Maria Jose Terol
- grid.5338.d0000 0001 2173 938XDepartment of Hematology, INCLIVA Research Insitute, University of Valencia, Valencia, Spain
| | - Antonio Cuneo
- grid.8484.00000 0004 1757 2064Hematology—Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - María Hernández-Sánchez
- grid.11762.330000 0001 2180 1817Cancer Research Center (IBMCC) CSIC—University of Salamanca, Salamanca, Spain ,grid.452531.4Instituto de Investigación Biomédica (IBSAL), Salamanca, Spain ,grid.411258.bDepartment of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Sarka Pospisilova
- grid.412554.30000 0004 0609 2751Department of Internal Medicine—Hematology and Oncology, University Hospital Brno, Brno, Czech Republic ,grid.10267.320000 0001 2194 0956Faculty of Medicine, Masaryk University, Brno, Czech Republic ,grid.10267.320000 0001 2194 0956Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ken Mills
- grid.4777.30000 0004 0374 7521Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
| | - Gianluca Gaidano
- grid.16563.370000000121663741Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - Carsten U. Niemann
- grid.4973.90000 0004 0646 7373Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Elias Campo
- grid.10403.360000000091771775Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain ,grid.510933.d0000 0004 8339 0058Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain ,grid.410458.c0000 0000 9635 9413Hospital Clínic of Barcelona, Barcelona, Spain ,grid.5841.80000 0004 1937 0247Universitat de Barcelona, Barcelona, Spain
| | - Jonathan C. Strefford
- grid.5491.90000 0004 1936 9297Cancer Genomics, School for Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Paolo Ghia
- grid.15496.3f0000 0001 0439 0892Università Vita Salute San Raffaele and IRCCS Ospedale San Raffaele, Milano, Italy
| | - Kostas Stamatopoulos
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden ,grid.423747.10000 0001 2216 5285Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
| | - Richard Rosenquist
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Clinical Genetics, Karolinska University Hospital, Solna, Sweden
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6
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Mancikova V, Pesova M, Pavlova S, Helma R, Zavacka K, Hejret V, Taus P, Hynst J, Plevova K, Malcikova J, Pospisilova S. Distinct p53 phosphorylation patterns in chronic lymphocytic leukemia patients are reflected in the activation of circumjacent pathways upon DNA damage. Mol Oncol 2022; 17:82-97. [PMID: 36334078 PMCID: PMC9812841 DOI: 10.1002/1878-0261.13337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/21/2022] [Accepted: 11/04/2022] [Indexed: 11/06/2022] Open
Abstract
TP53 gene abnormalities represent the most important biomarker in chronic lymphocytic leukemia (CLL). Altered protein modifications could also influence p53 function, even in the wild-type protein. We assessed the impact of p53 protein phosphorylations on p53 functions as an alternative inactivation mechanism. We studied p53 phospho-profiles induced by DNA-damaging agents (fludarabine, doxorubicin) in 71 TP53-intact primary CLL samples. Doxorubicin induced two distinct phospho-profiles: profile I (heavily phosphorylated) and profile II (hypophosphorylated). Profile II samples were less capable of activating p53 target genes upon doxorubicin exposure, resembling TP53-mutant samples at the transcriptomic level, whereas standard p53 signaling was triggered in profile I. ATM locus defects were more common in profile II. The samples also differed in the basal activity of the hypoxia pathway: the highest level was detected in TP53-mutant samples, followed by profile II and profile I. Our study suggests that wild-type TP53 CLL cells with less phosphorylated p53 show TP53-mutant-like behavior after DNA damage. p53 hypophosphorylation and the related lower ability to respond to DNA damage are linked to ATM locus defects and the higher basal activity of the hypoxia pathway.
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Affiliation(s)
- Veronika Mancikova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
| | - Michaela Pesova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
| | - Sarka Pavlova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
| | - Robert Helma
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
| | - Kristyna Zavacka
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
| | - Vaclav Hejret
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Petr Taus
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Jakub Hynst
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Karla Plevova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic,Institute of Medical Genetics and Genomics, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
| | - Jitka Malcikova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic,Institute of Medical Genetics and Genomics, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
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7
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Kaufman M, Yan XJ, Li W, Ghia EM, Langerak AW, Rassenti LZ, Belessi C, Kay NE, Davi F, Byrd JC, Pospisilova S, Brown JR, Catherwood M, Davis Z, Oscier D, Montillo M, Trentin L, Rosenquist R, Ghia P, Barrientos JC, Kolitz JE, Allen SL, Rai KR, Stamatopoulos K, Kipps TJ, Neuberg D, Chiorazzi N. Impact of the Types and Relative Quantities of IGHV Gene Mutations in Predicting Prognosis of Patients With Chronic Lymphocytic Leukemia. Front Oncol 2022; 12:897280. [PMID: 35903706 PMCID: PMC9315922 DOI: 10.3389/fonc.2022.897280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Patients with CLL with mutated IGHV genes (M-CLL) have better outcomes than patients with unmutated IGHVs (U-CLL). Since U-CLL usually express immunoglobulins (IGs) that are more autoreactive and more effectively transduce signals to leukemic B cells, B-cell receptor (BCR) signaling is likely at the heart of the worse outcomes of CLL cases without/few IGHV mutations. A corollary of this conclusion is that M-CLL follow less aggressive clinical courses because somatic IGHV mutations have altered BCR structures and no longer bind stimulatory (auto)antigens and so cannot deliver trophic signals to leukemic B cells. However, the latter assumption has not been confirmed in a large patient cohort. We tried to address the latter by measuring the relative numbers of replacement (R) mutations that lead to non-conservative amino acid changes (Rnc) to the combined numbers of conservative (Rc) and silent (S) amino acid R mutations that likely do not or cannot change amino acids, "(S+Rc) to Rnc IGHV mutation ratio". When comparing time-to-first-treatment (TTFT) of patients with (S+Rc)/Rnc ≤ 1 and >1, TTFTs were similar, even after matching groups for equal numbers of samples and identical numbers of mutations per sample. Thus, BCR structural change might not be the main reason for better outcomes for M-CLL. Since the total number of IGHV mutations associated better with longer TTFT, better clinical courses appear due to the biologic state of a B cell having undergone many stimulatory events leading to IGHV mutations. Analyses of larger patient cohorts will be needed to definitively answer this question.
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Affiliation(s)
- Matthew Kaufman
- Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Xiao-Jie Yan
- Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Wentian Li
- The Robert S. Boas Center for Genomics & Human Genetics, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Emanuela M. Ghia
- Center for Novel Therapeutics, Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
| | - Anton W. Langerak
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Laura Z. Rassenti
- Center for Novel Therapeutics, Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
| | | | - Neil E. Kay
- Division of Hematology, Mayo Clinic, Rochester, MN, United States
| | - Frederic Davi
- Department of Biological Hematology, Hôpital Pitié-Salpêtrière (AP-HP), Sorbonne Université, Paris, France
| | - John C. Byrd
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology and Department of Medical Genetics and Genomics, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Jennifer R. Brown
- Chronic Lymphocytic Leukemia Center, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Mark Catherwood
- Clinical Hematology, Belfast City Hospital, Belfast, Ireland
| | - Zadie Davis
- Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, United Kingdom
| | - David Oscier
- Department of Hematology, Royal Bournemouth Hospital, Bournemouth, United Kingdom
| | - Marco Montillo
- Department of Hematology & Oncology, Niguarda Cancer Center, Niguarda Hospital, Milan, Italy
| | - Livio Trentin
- Hematology Unit, Department of Medicine-(DIMED), University of Padua University Hospital, Padua, Italy
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Paolo Ghia
- Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Jacqueline C. Barrientos
- Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
- Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Uniondale, NY, United States
- Departments of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Uniondale, NY, United States
- Northwell Health Cancer Institute, Lake Success, NY, United States
| | - Jonathan E. Kolitz
- Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
- Northwell Health Cancer Institute, Lake Success, NY, United States
| | - Steven L. Allen
- Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
- Northwell Health Cancer Institute, Lake Success, NY, United States
| | - Kanti R. Rai
- Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
- Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Uniondale, NY, United States
- Departments of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Uniondale, NY, United States
- Northwell Health Cancer Institute, Lake Success, NY, United States
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Thomas J. Kipps
- Center for Novel Therapeutics, Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
| | - Donna Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Nicholas Chiorazzi
- Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
- Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Uniondale, NY, United States
- Departments of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Uniondale, NY, United States
- Northwell Health Cancer Institute, Lake Success, NY, United States
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8
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Dreyling M, André M, Gökbuget N, Tilly H, Jerkeman M, Gribben J, Ferreri A, Morel P, Stilgenbauer S, Fox C, Maria Ribera J, Zweegman S, Aurer I, Bödör C, Burkhardt B, Buske C, Dollores Caballero M, Campo E, Chapuy B, Davies A, de Leval L, Doorduijn J, Federico M, Gaulard P, Gay F, Ghia P, Grønbæk K, Goldschmidt H, Kersten MJ, Kiesewetter B, Landman-Parker J, Le Gouill S, Lenz G, Leppä S, Lopez-Guillermo A, Macintyre E, Mantega MVM, Moreau P, Moreno C, Nadel B, Okosun J, Owen R, Pospisilova S, Pott C, Robak T, Spina M, Stamatopoulos K, Stary J, Tarte K, Tedeschi A, Thieblemont C, Trappe RU, Trümper LH, Salles G. The EHA Research Roadmap: Malignant Lymphoid Diseases. Hemasphere 2022; 6:e726. [PMID: 35620592 PMCID: PMC9126526 DOI: 10.1097/hs9.0000000000000726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/21/2022] [Indexed: 12/11/2022] Open
Affiliation(s)
| | - Marc André
- Université Catholique de Louvain, CHU UcL Namur, Yvoir, Belgium
| | - Nicola Gökbuget
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Hervé Tilly
- INSERM U1245, Department of Hematology, Centre Henri Becquerel and Université de Rouen, France
| | | | - John Gribben
- Barts Cancer Institute, Queen Mary University of London, United Kingdom
| | - Andrés Ferreri
- Lymphoma Unit, Department of Onco-hematology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Pierre Morel
- Service Hematologie Clinique Therapie Cellulaire, CHU Amiens Picardie, Amiens, France
| | - Stephan Stilgenbauer
- Comprehensive Cancer Center Ulm (CCCU), Sektion CLL Klinik für Innere Medizin III, Universität Ulm, Germany
| | - Christopher Fox
- School of Medicine, University of Nottingham, United Kingdom
| | - José Maria Ribera
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Badalona, Spain
| | - Sonja Zweegman
- Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, the Netherlands
| | - Igor Aurer
- University Hospital Centre Zagreb and Medical School, University of Zagreb, Croatia
| | - Csaba Bödör
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Birgit Burkhardt
- Experimentelle und Translationale päd. Hämatologie u Onkologie, Leitung der Bereiche Lymphome und Stammzelltransplantation, Universitätsklinikum Münster (UKM), Klinik für Kinder- und Jugendmedizin, Pädiatrische Hämatologie und Onkologie, Munich, Germany
| | - Christian Buske
- Institute of Experimental Cancer Research, CCC Ulm, University Hospital Ulm, Germany
| | - Maria Dollores Caballero
- Clinical and Transplant Unit, University Hospital of Salamanca, Spain
- Department of Medicine at the University of Salamanca, Spain
- El Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Elias Campo
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Bjoern Chapuy
- Department of Hematology, Oncology and Tumor Immunology, Charité, University Medical Center Berlin, Campus Benjamin Franklin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Andrew Davies
- Southampton NCRI/UK Experimental Cancer Medicines Centre, Faculty of Medicine, University of Southampton, United Kingdom
| | - Laurence de Leval
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Jeanette Doorduijn
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | - Philippe Gaulard
- Département de Pathologie, Hôpital Henri Mondor, AP-HP, Créteil, France
| | - Francesca Gay
- Clinical Trial Unit, Division of Hematology 1, AOU Città Della Salute e Della Scienza, University of Torino, Italy
| | - Paolo Ghia
- Università Vita Salute San Raffaele and IRCCS Ospedale San Raffaele, Milano, Italy
| | - Kirsten Grønbæk
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Denmark
| | - Hartmut Goldschmidt
- University Hospital Heidelberg, Internal Medicine V and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Marie-Jose Kersten
- Department of Hematology, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam and LYMMCARE, Amsterdam, the Netherlands
| | - Barbara Kiesewetter
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Austria
| | - Judith Landman-Parker
- Pediatric Hematology Oncology, Sorbonne Université APHP/hôpital A Trousseau, Paris, France
| | - Steven Le Gouill
- Service d’Hématologie, Clinique du Centre Hospitalier Universitaire (CHU) de Nantes, France
| | - Georg Lenz
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Germany
| | - Sirpa Leppä
- University of Helsinki and Helsinki University Hospital Comprehensive Cancer Centre, Helsinki, Finland
| | | | - Elizabeth Macintyre
- Onco-hematology, Université de Paris and Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, France
| | | | - Philippe Moreau
- Hematology Department, University Hospital Hotel-Dieu, Nantes, France
| | - Carol Moreno
- Hospital de la Santa Creu I Sant Pau, Autonomous University of Barcelona, Spain
| | - Bertrand Nadel
- Aix Marseille Univ, CNRS, INSERM, CIML, Marseille, France
| | - Jessica Okosun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, United Kingdom
| | - Roger Owen
- St James’s Institute of Oncology, Leeds, United Kingdom
| | - Sarka Pospisilova
- Department of Internal Medicine—Hematology and Oncology and Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
| | - Christiane Pott
- Klinisch-experimentelle Hämatologie, Medizinische Klinik II, Hämatologie und Internistische Onkologie, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Germany
| | | | - Michelle Spina
- Division of Medical Oncology and Immune-related Tumors, National Cancer Institute, Aviano, Italy
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Jan Stary
- Department of Pediatric Hematology and Oncology 2nd Faculty of Medicine, Charles University Prague University Hospital, Prague, Czech Republic
| | - Karin Tarte
- Immunology and Cell Therapy Lab at Rennes University Hospital, Rennes, France
| | | | - Catherine Thieblemont
- Department of Hemato-Oncology, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Ralf Ulrich Trappe
- Department of Internal Medicine II: Haematology and Oncology, DIAKO Hospital Bremen, Germany
| | - Lorenz H. Trümper
- Hematology and Medical Oncology, University Medicine Goettingen, Germany
| | - Gilles Salles
- Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medicine, New York, NY, USA
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9
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Limberger T, Schlederer M, Trachtová K, Garces de Los Fayos Alonso I, Yang J, Högler S, Sternberg C, Bystry V, Oppelt J, Tichý B, Schmeidl M, Kodajova P, Jäger A, Neubauer HA, Oberhuber M, Schmalzbauer BS, Pospisilova S, Dolznig H, Wadsak W, Culig Z, Turner SD, Egger G, Lagger S, Kenner L. KMT2C methyltransferase domain regulated INK4A expression suppresses prostate cancer metastasis. Mol Cancer 2022; 21:89. [PMID: 35354467 PMCID: PMC8966196 DOI: 10.1186/s12943-022-01542-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/17/2022] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Frequent truncation mutations of the histone lysine N-methyltransferase KMT2C have been detected by whole exome sequencing studies in various cancers, including malignancies of the prostate. However, the biological consequences of these alterations in prostate cancer have not yet been elucidated. METHODS To investigate the functional effects of these mutations, we deleted the C-terminal catalytic core motif of Kmt2c specifically in mouse prostate epithelium. We analysed the effect of Kmt2c SET domain deletion in a Pten-deficient PCa mouse model in vivo and of truncation mutations of KMT2C in a large number of prostate cancer patients. RESULTS We show here for the first time that impaired KMT2C methyltransferase activity drives proliferation and PIN formation and, when combined with loss of the tumour suppressor PTEN, triggers loss of senescence, metastatic dissemination and dramatically reduces life expectancy. In Kmt2c-mutated tumours we show enrichment of proliferative MYC gene signatures and loss of expression of the cell cycle repressor p16INK4A. In addition, we observe a striking reduction in disease-free survival of patients with KMT2C-mutated prostate cancer. CONCLUSIONS We identified truncating events of KMT2C as drivers of proliferation and PIN formation. Loss of PTEN and KMT2C in prostate cancer results in loss of senescence, metastatic dissemination and reduced life expectancy. Our data demonstrate the prognostic significance of KMT2C mutation status in prostate cancer patients. Inhibition of the MYC signalling axis may be a viable treatment option for patients with KMT2C truncations and therefore poor prognosis.
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Affiliation(s)
- Tanja Limberger
- Division of Experimental and Translational Pathology, Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria.,CBmed-Center for Biomarker Research in Medicine GmbH, 8010, Graz, Austria
| | - Michaela Schlederer
- Division of Experimental and Translational Pathology, Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
| | - Karolina Trachtová
- Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic.,Christian Doppler Laboratory for Applied Metabolomics, 1090, Vienna, Austria.,Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090, Vienna, Austria
| | - Ines Garces de Los Fayos Alonso
- Division of Experimental and Translational Pathology, Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria.,Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Jiaye Yang
- Division of Experimental and Translational Pathology, Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
| | - Sandra Högler
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Christina Sternberg
- Division of Experimental and Translational Pathology, Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria.,Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.,Institute of Biochemistry, Christian-Albrechts-University Kiel, 24118, Kiel, Germany
| | - Vojtech Bystry
- Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
| | - Jan Oppelt
- Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
| | - Boris Tichý
- Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
| | - Margit Schmeidl
- Division of Experimental and Translational Pathology, Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
| | - Petra Kodajova
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Anton Jäger
- Division of Experimental and Translational Pathology, Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
| | - Heidi A Neubauer
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Monika Oberhuber
- CBmed-Center for Biomarker Research in Medicine GmbH, 8010, Graz, Austria
| | - Belinda S Schmalzbauer
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
| | - Helmut Dolznig
- Institute of Medical Genetics, Medical University of Vienna, 1090, Vienna, Austria
| | - Wolfgang Wadsak
- CBmed-Center for Biomarker Research in Medicine GmbH, 8010, Graz, Austria.,Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090, Vienna, Austria
| | - Zoran Culig
- Department of Urology, Innsbruck Medical University, 6020, Innsbruck, Austria
| | - Suzanne D Turner
- Department of Pathology, University Cambridge, Cambridge, UK.,CEITEC, Masaryk University, Brno, Czech Republic
| | - Gerda Egger
- Division of Experimental and Translational Pathology, Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria.,Ludwig Boltzmann Institute Applied Diagnostics, 1090, Vienna, Austria
| | - Sabine Lagger
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Lukas Kenner
- Division of Experimental and Translational Pathology, Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria. .,CBmed-Center for Biomarker Research in Medicine GmbH, 8010, Graz, Austria. .,Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090, Vienna, Austria. .,Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
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10
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Poppova L, Pavlova S, Gonzalez B, Kotaskova J, Plevova K, Dumbovic G, Janovska P, Bystry V, Panovska A, Bezdekova L, Maslejova S, Brychtova Y, Doubek M, Krzyzankova M, Borsky M, Mayer J, Bryja V, Alonso S, Pospisilova S. Memory B-cell like chronic lymphocytic leukaemia is associated with specific methylation profile of WNT5A promoter and undetectable expression of WNT5A gene. Epigenetics 2022; 17:1628-1635. [PMID: 35333703 PMCID: PMC9621079 DOI: 10.1080/15592294.2022.2050004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Genome methylation profiles define naïve-like (n-CLL), memory-like (m-CLL), and intermediate (i-CLL) subsets of chronic lymphocytic leukaemia (CLL). The profiles can be easily determined by the analysis of the five-CpG signature. m-CLL, i-CLL, and n-CLL with the good, intermediate, and poor prognoses, respectively, differ by the somatic hypermutation status of the immunoglobulin heavy chain variable gene (IGHV), a widely used prognostic predictor in CLL. We have previously shown that the expression of WNT5A, encoding a ROR1 ligand, distinguishes patients with the worse outcome within the prognostically favourable IGHV-mutated subgroup. To analyse the mechanisms controlling WNT5A expression, we investigated the methylation status of 54 CpG sites within the WNT5A promoter and its relation to the WNT5A gene expression. In a cohort of 59 CLL patients balanced for combinations of IGHV and WNT5A statuses, we identified three promoter CpG sites whose methylation level correlated with the WNT5A expression within the IGHV-mutated subgroup. Further, we complemented our data with the methylation status of the five-CpG signature. IGHV-mutated/WNT5A-negative and IGHV-mutated/WNT5A-positive cases overlapped with m‑CLL and i‑CLL methylation subgroups, respectively, while most IGHV‑unmutated samples were assigned to n-CLL. Median methylation levels of all the three CpG sites in the WNT5A promoter were lowest in i-CLL. Finally, a detailed analysis of m-CLL and i-CLL showed that undetectable WNT5A expression predicts longer treatment-free survival with higher statistical significance than the classification according to the five-CpG signature. To conclude, a favourable m-CLL subgroup is associated with mutated IGHV and undetectable WNT5A expression due to its promoter methylation.
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Affiliation(s)
- Lucie Poppova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Beatriz Gonzalez
- IGTP-PMPPC: Program of Predictive and Personalized Medicine of Cancer, Germans Trias I Pujol Research Institute, Badalona, Spain
| | - Jana Kotaskova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Institute of Medical Genetics and Genomics, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Gabrijela Dumbovic
- IGTP-PMPPC: Program of Predictive and Personalized Medicine of Cancer, Germans Trias I Pujol Research Institute, Badalona, Spain.,Institute for Cardiovascular Regeneration, Center for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Pavlina Janovska
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Vojtech Bystry
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lucie Bezdekova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Stanislava Maslejova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Yvona Brychtova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Institute of Medical Genetics and Genomics, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marcela Krzyzankova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Marek Borsky
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jiri Mayer
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Vitezslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Sergio Alonso
- IGTP-PMPPC: Program of Predictive and Personalized Medicine of Cancer, Germans Trias I Pujol Research Institute, Badalona, Spain
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Institute of Medical Genetics and Genomics, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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11
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Arpas T, Jelinkova H, Hrabovsky S, Orsulova M, Vrzalova Z, Navrkalova V, Brhelova E, Bryjova L, Bulikova A, Ondrouskova E, Sejnohova M, Folber F, Sedová P, Mayer J, Pospisilova S, Jarosova M, Doubek M. Very rare near‐haploid acute lymphoblastic leukemia resistant to immunotherapy and CAR‐T therapy in 19‐year‐old male patient. Clin Case Rep 2022; 10:e05545. [PMID: 35280086 PMCID: PMC8894580 DOI: 10.1002/ccr3.5545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/17/2022] [Accepted: 02/06/2022] [Indexed: 02/02/2023] Open
Abstract
Near‐haploid acute lymphoblastic leukemia is rare subgroup of the disease, which is very important due to very poor prognosis and resistance to treatment including novel monoclonal antibodies and CAR‐T therapy.
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Affiliation(s)
- Tomas Arpas
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Hana Jelinkova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Stepan Hrabovsky
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Martina Orsulova
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Zuzana Vrzalova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
- Central European Institute of Technology (CEITEC) Masaryk University Brno Czechia
| | - Veronika Navrkalova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Eva Brhelova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Lenka Bryjova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Alena Bulikova
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
- Department of Clinical Hematology University Hospital Brno Czechia
| | - Eva Ondrouskova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Marketa Sejnohova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Frantisek Folber
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Petra Sedová
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Jiri Mayer
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Sarka Pospisilova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
- Central European Institute of Technology (CEITEC) Masaryk University Brno Czechia
- Department of Medical Genetics and Genomics University Hospital and Faculty of Medicine Brno Czechia
| | - Marie Jarosova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
- Department of Medical Genetics and Genomics University Hospital and Faculty of Medicine Brno Czechia
| | - Michael Doubek
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
- Central European Institute of Technology (CEITEC) Masaryk University Brno Czechia
- Department of Medical Genetics and Genomics University Hospital and Faculty of Medicine Brno Czechia
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12
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Olbertova H, Plevova K, Pavlova S, Malcikova J, Kotaskova J, Stranska K, Spunarova M, Trbusek M, Navrkalova V, Dvorackova B, Tom N, Pal K, Jarosova M, Brychtova Y, Panovska A, Doubek M, Pospisilova S. Evolution of TP53 abnormalities during CLL disease course is associated with telomere length changes. BMC Cancer 2022; 22:137. [PMID: 35114947 PMCID: PMC8812042 DOI: 10.1186/s12885-022-09221-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 01/19/2022] [Indexed: 11/10/2022] Open
Abstract
Background Telomeres are protective structures at chromosome ends which shorten gradually with increasing age. In chronic lymphocytic leukemia (CLL), short telomeres have been associated with unfavorable disease outcome, but the link between clonal evolution and telomere shortening remains unresolved. Methods We investigated relative telomere length (RTL) in a well-characterized cohort of 198 CLL patients by qPCR and focused in detail on a subgroup 26 patients who underwent clonal evolution of TP53 mutations (evolTP53). In the evolTP53 subgroup we explored factors influencing clonal evolution and corresponding changes in telomere length through measurements of telomerase expression, lymphocyte doubling time, and BCR signaling activity. Results At baseline, RTL of the evolTP53 patients was scattered across the entire RTL spectrum observed in our CLL cohort. RTL changed in the follow-up samples of 16/26 (62%) evolTP53 cases, inclining to reach intermediate RTL values, i.e., longer telomeres shortened compared to baseline while shorter ones prolonged. For the first time we show that TP53 clonal shifts are linked to RTL change, including unexpected RTL prolongation. We further investigated parameters associated with RTL changes. Unstable telomeres were significantly more frequent among younger patients (P = 0.032). Shorter telomeres were associated with decreased activity of the B-cell receptor signaling components p-ERK1/2, p-ZAP-70/SYK, and p-NFκB (P = 0.04, P = 0.01, and P = 0.02, respectively). Conclusions Our study revealed that changes of telomere length reflect evolution in leukemic subclone proportion, and are associated with specific clinico-biological features of the explored cohort. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09221-z.
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Affiliation(s)
- Helena Olbertova
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics and Genomics Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pavlova
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jitka Malcikova
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jana Kotaskova
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Kamila Stranska
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michaela Spunarova
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Martin Trbusek
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Veronika Navrkalova
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Barbara Dvorackova
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Nikola Tom
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Karol Pal
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Marie Jarosova
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics and Genomics Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Yvona Brychtova
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michael Doubek
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics and Genomics Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic. .,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic. .,Department of Medical Genetics and Genomics Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic.
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13
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Mancikova V, Peschelova H, Kozlova V, Ledererova A, Ladungova A, Verner J, Loja T, Folber F, Mayer J, Pospisilova S, Smida M. Performance of anti-CD19 chimeric antigen receptor T cells in genetically defined classes of chronic lymphocytic leukemia. J Immunother Cancer 2021; 8:jitc-2019-000471. [PMID: 32217767 PMCID: PMC7206910 DOI: 10.1136/jitc-2019-000471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 01/25/2023] Open
Abstract
Background While achieving prolonged remissions in other B cell-derived malignancies, chimeric antigen receptor (CAR) T cells still underperform when injected into patients with chronic lymphocytic leukemia (CLL). We studied the influence of genetics on CLL response to anti-CD19 CAR T-cell therapy. Methods First, we studied 32 primary CLL samples composed of 26 immunoglobulin heavy-chain gene variable (IGHV)-unmutated (9 ATM-mutated, 8 TP53-mutated, and 9 without mutations in ATM, TP53, NOTCH1 or SF3B1) and 6 IGHV-mutated samples without mutations in the above-mentioned genes. Then, we mimicked the leukemic microenvironment in the primary cells by ‘2S stimulation’ through interleukin-2 and nuclear factor kappa B. Finally, CRISPR/Cas9-generated ATM-knockout and TP53-knockout clones (four and seven, respectively) from CLL-derived cell lines MEC1 and HG3 were used. All these samples were exposed to CAR T cells. In vivo survival study in NSG mice using HG3 wild-type (WT), ATM-knockout or TP53-knockout cells was also performed. Results Primary unstimulated CLL cells were specifically eliminated after >24 hours of coculture with CAR T cells. ‘2S’ stimulated cells showed increased survival when exposed to CAR T cells compared with unstimulated ones, confirming the positive effect of this stimulation on CLL cells’ in vitro fitness. After 96 hours of coculture, there was no difference in survival among the genetic classes. Finally, CAR T cells were specifically activated in vitro in the presence of target knockout cell lines as shown by the production of interferon-γ when compared with control (CTRL) T cells (p=0.0020), but there was no difference in knockout cells’ survival. In vivo, CAR T cells prolonged the survival of mice injected with WT, TP53-knockout and ATM-knockout HG3 tumor cells as compared with CTRL T cells (p=0.0485, 0.0204 and <0.0001, respectively). When compared with ATM-knockout, TP53-knockout disease was associated with an earlier time of onset (p<0.0001), higher tumor burden (p=0.0002) and inefficient T-cell engraftment (p=0.0012). Conclusions While in vitro no differences in survival of CLL cells of various genetic backgrounds were observed, CAR T cells showed a different effectiveness at eradicating tumor cells in vivo depending on the driver mutation. Early disease onset, high-tumor burden and inefficient T-cell engraftment, associated with TP53-knockout tumors in our experimental setting, ultimately led to inferior performance of CAR T cells.
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Affiliation(s)
- Veronika Mancikova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic .,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Helena Peschelova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Veronika Kozlova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Aneta Ledererova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Adriana Ladungova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Jan Verner
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Tomas Loja
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Frantisek Folber
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jiri Mayer
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Smida
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic .,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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14
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Ledererova A, Dostalova L, Kozlova V, Peschelova H, Ladungova A, Culen M, Loja T, Verner J, Pospisilova S, Smida M, Mancikova V. Hypermethylation of CD19 promoter enables antigen-negative escape to CART-19 in vivo and in vitro. J Immunother Cancer 2021; 9:jitc-2021-002352. [PMID: 34413165 PMCID: PMC8378389 DOI: 10.1136/jitc-2021-002352] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2021] [Indexed: 12/13/2022] Open
Abstract
Background Anti-CD19 chimeric antigen receptor T cells (CART-19) frequently induce remissions in hemato-oncological patients with recurred and/or refractory B-cell tumors. However, malignant cells sometimes escape the immunotherapeutic targeting by CD19 gene mutations, alternative splicing or lineage switch, commonly causing lack of CD19 expression on the surface of neoplastic cells. We assumed that, in addition to the known mechanisms, other means could act on CD19 to drive antigen-negative relapse. Methods Herein, we studied the mechanism of antigen loss in an in vivo CD19-negative recurrence model of chronic lymphocytic leukemia (CLL) to CART-19, established using NOD-scid IL2Rgnull mice and HG3 cell line. We validated our findings in vitro in immortalized B-cell lines and primary CLL cells. Results In our in vivo CLL recurrence model, up to 70% of CART-19-treated mice eventually recurred with CD19-negative disease weeks after initial positive response. We found that the lack of CD19 expression was caused by promoter DNA hypermethylation. Importantly, the expression loss was partially reversible by treatment with a demethylating agent. Moreover, this escape mechanism was common for 3 B-cell immortalized lines as well as primary CLL cells, as assessed by in vitro coculture experiments. Conclusions Epigenetically driven antigen escape could represent a novel, yet at least partially reversible, means of CD19 loss to CART-19 in B-cell tumors.
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Affiliation(s)
- Aneta Ledererova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Oncology and Hematology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Dostalova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Veronika Kozlova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Oncology and Hematology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Helena Peschelova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Adriana Ladungova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin Culen
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Oncology and Hematology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Tomas Loja
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jan Verner
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Oncology and Hematology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Oncology and Hematology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Smida
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic .,Department of Internal Medicine - Oncology and Hematology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Veronika Mancikova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic .,Department of Internal Medicine - Oncology and Hematology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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15
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Kozubik KS, Radova L, Reblova K, Smida M, Zaliova Kubricanova M, Baloun J, Pesova M, Vrzalova Z, Folber F, Mejstrikova S, Pospisilova S, Doubek M. Functional analysis of germline ETV6 W380R mutation causing inherited thrombocytopenia and secondary acute lymphoblastic leukemia or essential thrombocythemia. Platelets 2021; 32:838-841. [PMID: 32819174 DOI: 10.1080/09537104.2020.1802416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/02/2020] [Accepted: 07/10/2020] [Indexed: 10/23/2022]
Abstract
Germline mutations in ETV6 gene cause inherited thrombocytopenia with leukemia predisposition. Here, we report on functional validation of ETV6 W380R mutation segregating with thrombocytopenia in a family where two family members also suffered from acute lymphoblastic leukemia (ALL) or essential thrombocythemia (ET). In-silico analysis predicted impaired DNA binding due to W380R mutation. Functional analysis showed that this mutation prevents the ETV6 protein from localizing into the cell nucleus and impairs the transcriptional repression activity of ETV6. Based on the germline ETV6 mutation, ET probably started with somatic JAK2 V617F mutation, whereas ALL could be caused by diverse mechanisms: high-hyperdiploidity; somatic deletion of exon 1 IKZF1 gene; or somatic mutations of other genes found by exome sequencing of the ALL sample taken at the diagnosis.
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Affiliation(s)
- Katerina Stano Kozubik
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University (CEITEC MU), Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, University Hospital and Medical Faculty, Masaryk University, Brno, Czech Republic
| | - Lenka Radova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University (CEITEC MU), Brno, Czech Republic
| | - Kamila Reblova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University (CEITEC MU), Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, University Hospital and Medical Faculty, Masaryk University, Brno, Czech Republic
| | - Michal Smida
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University (CEITEC MU), Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, University Hospital and Medical Faculty, Masaryk University, Brno, Czech Republic
| | - Marketa Zaliova Kubricanova
- Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Jiri Baloun
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University (CEITEC MU), Brno, Czech Republic
| | - Michaela Pesova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University (CEITEC MU), Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, University Hospital and Medical Faculty, Masaryk University, Brno, Czech Republic
| | - Zuzana Vrzalova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University (CEITEC MU), Brno, Czech Republic
| | - Frantisek Folber
- Department of Internal Medicine - Haematology and Oncology, University Hospital and Medical Faculty, Masaryk University, Brno, Czech Republic
| | - Sona Mejstrikova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University (CEITEC MU), Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, University Hospital and Medical Faculty, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University (CEITEC MU), Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, University Hospital and Medical Faculty, Masaryk University, Brno, Czech Republic
| | - Michael Doubek
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University (CEITEC MU), Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, University Hospital and Medical Faculty, Masaryk University, Brno, Czech Republic
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16
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Sandova V, Pavlasova GM, Seda V, Cerna KA, Sharma S, Palusova V, Brychtova Y, Pospisilova S, Fernandes SM, Panovska A, Doubek M, Davids MS, Brown JR, Mayer J, Mraz M. IL4-STAT6 signaling induces CD20 in chronic lymphocytic leukemia and this axis is repressed by PI3Kδ inhibitor idelalisib. Haematologica 2021; 106:2995-2999. [PMID: 34196167 PMCID: PMC8561290 DOI: 10.3324/haematol.2021.278644] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Indexed: 12/05/2022] Open
Affiliation(s)
- Veronika Sandova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | | | - Vaclav Seda
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Katerina Amruz Cerna
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sonali Sharma
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Veronika Palusova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Yvona Brychtova
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anna Panovska
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Matthew S Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jiri Mayer
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.
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17
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Taus P, Pospisilova S, Plevova K. Identification of Clinically Relevant Subgroups of Chronic Lymphocytic Leukemia Through Discovery of Abnormal Molecular Pathways. Front Genet 2021; 12:627964. [PMID: 34262590 PMCID: PMC8273263 DOI: 10.3389/fgene.2021.627964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common form of adult leukemia in the Western world with a highly variable clinical course. Its striking genetic heterogeneity is not yet fully understood. Although the CLL genetic landscape has been well-described, patient stratification based on mutation profiles remains elusive mainly due to the heterogeneity of data. Here we attempted to decrease the heterogeneity of somatic mutation data by mapping mutated genes in the respective biological processes. From the sequencing data gathered by the International Cancer Genome Consortium for 506 CLL patients, we generated pathway mutation scores, applied ensemble clustering on them, and extracted abnormal molecular pathways with a machine learning approach. We identified four clusters differing in pathway mutational profiles and time to first treatment. Interestingly, common CLL drivers such as ATM or TP53 were associated with particular subtypes, while others like NOTCH1 or SF3B1 were not. This study provides an important step in understanding mutational patterns in CLL.
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Affiliation(s)
- Petr Taus
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czechia.,Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czechia.,Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University, Brno, Czechia.,Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czechia.,Faculty of Medicine, Masaryk University, Brno, Czechia
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18
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Navrkalova V, Plevova K, Hynst J, Pal K, Mareckova A, Reigl T, Jelinkova H, Vrzalova Z, Stranska K, Pavlova S, Panovska A, Janikova A, Doubek M, Kotaskova J, Pospisilova S. LYmphoid NeXt-Generation Sequencing (LYNX) Panel: A Comprehensive Capture-Based Sequencing Tool for the Analysis of Prognostic and Predictive Markers in Lymphoid Malignancies. J Mol Diagn 2021; 23:959-974. [PMID: 34082072 DOI: 10.1016/j.jmoldx.2021.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 04/21/2021] [Accepted: 05/03/2021] [Indexed: 02/07/2023] Open
Abstract
B-cell neoplasms represent a clinically heterogeneous group of hematologic malignancies with considerably diverse genomic architecture recently endorsed by next-generation sequencing (NGS) studies. Because multiple genetic defects have a potential or confirmed clinical impact, a tendency toward more comprehensive testing of diagnostic, prognostic, and predictive markers is desired. This study introduces the design, validation, and implementation of an integrative, custom-designed, capture-based NGS panel titled LYmphoid NeXt-generation sequencing (LYNX) for the analysis of standard and novel molecular markers in the most common lymphoid neoplasms (chronic lymphocytic leukemia, acute lymphoblastic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma). A single LYNX test provides the following: i) accurate detection of mutations in all coding exons and splice sites of 70 lymphoma-related genes with a sensitivity of 5% variant allele frequency, ii) reliable identification of large genome-wide (≥6 Mb) and recurrent chromosomal aberrations (≥300 kb) in at least 20% of the clonal cell fraction, iii) the assessment of immunoglobulin and T-cell receptor gene rearrangements, and iv) lymphoma-specific translocation detection. Dedicated bioinformatic pipelines were designed to detect all markers mentioned above. The LYNX panel represents a comprehensive, up-to-date tool suitable for routine testing of lymphoid neoplasms with research and clinical applicability. It allows a wide adoption of capture-based targeted NGS in clinical practice and personalized management of patients with lymphoproliferative diseases.
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Affiliation(s)
- Veronika Navrkalova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jakub Hynst
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karol Pal
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Department of Internal Medicine II - Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andrea Mareckova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Tomas Reigl
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Hana Jelinkova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Zuzana Vrzalova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Kamila Stranska
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Andrea Janikova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jana Kotaskova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic.
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19
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Larose H, Prokoph N, Matthews JD, Schlederer M, Högler S, Alsulami AF, Ducray SP, Nuglozeh E, Fazaludeen MF, Elmouna A, Ceccon M, Mologni L, Gambacorti-Passerini C, Hoefler G, Lobello C, Pospisilova S, Janikova A, Woessmann W, Welk CD, Zimmermann MT, Fedorova A, Malone A, Smith O, Wasik M, Inghirami G, Lamant L, Blundell TL, Klapper W, Merkel O, Burke GAA, Mian S, Ashankyty I, Kenner L, Turner SD. Whole Exome Sequencing reveals NOTCH1 mutations in anaplastic large cell lymphoma and points to Notch both as a key pathway and a potential therapeutic target. Haematologica 2021; 106:1693-1704. [PMID: 32327503 PMCID: PMC8168516 DOI: 10.3324/haematol.2019.238766] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
Patients diagnosed with Anaplastic Large Cell Lymphoma (ALCL) are still treated with toxic multi-agent chemotherapy and as many as 25-50% of patients relapse. To understand disease pathology and to uncover novel targets for therapy, Whole-Exome Sequencing (WES) of Anaplastic Lymphoma Kinase (ALK)+ ALCL was performed as well as Gene-Set Enrichment Analysis. This revealed that the T-cell receptor (TCR) and Notch pathways were the most enriched in mutations. In particular, variant T349P of NOTCH1, which confers a growth advantage to cells in which it is expressed, was detected in 12% of ALK+ and ALK- ALCL patient samples. Furthermore, we demonstrate that NPM-ALK promotes NOTCH1 expression through binding of STAT3 upstream of NOTCH1. Moreover, inhibition of NOTCH1 with γ-secretase inhibitors (GSIs) or silencing by shRNA leads to apoptosis; co-treatment in vitro with the ALK inhibitor Crizotinib led to additive/synergistic anti-tumour activity suggesting this may be an appropriate combination therapy for future use in the circumvention of ALK inhibitor resistance. Indeed, Crizotinib-resistant and sensitive ALCL were equally sensitive to GSIs. In conclusion, we show a variant in the extracellular domain of NOTCH1 that provides a growth advantage to cells and confirm the suitability of the Notch pathway as a second-line druggable target in ALK+ ALCL.
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Affiliation(s)
- Hugo Larose
- Department of Pathology, University of Cambridge, Cambridge, UK
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
| | - Nina Prokoph
- Department of Pathology, University of Cambridge, Cambridge, UK
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
| | | | | | - Sandra Högler
- Unit of Laborator y Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ali F. Alsulami
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Stephen P. Ducray
- Department of Pathology, University of Cambridge, Cambridge, UK
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
| | - Edem Nuglozeh
- Molecular Diagnostics and Personalised Therapeutics Unit, Colleges of Medicine and Applied Medical Sciences, University of Ha’il, Ha’il, Saudi Arabia
| | - Mohammad Feroze Fazaludeen
- Neuroinflammation Research Group, Depar tment of Neurobiology, A.I Virtanen Institute for Molecular Sciences, University of Eastern Finland, Finland
| | - Ahmed Elmouna
- Molecular Diagnostics and Personalised Therapeutics Unit, Colleges of Medicine and Applied Medical Sciences, University of Ha’il, Ha’il, Saudi Arabia
| | - Monica Ceccon
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- University of Milano-Bicocca, Monza, Italy
| | - Luca Mologni
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- University of Milano-Bicocca, Monza, Italy
| | - Carlo Gambacorti-Passerini
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- University of Milano-Bicocca, Monza, Italy
| | - Gerald Hoefler
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Cosimo Lobello
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- Center of Molecular Medicine, CEITEC, Masar yk University, Brno, Czech Republic
| | - Sarka Pospisilova
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- Center of Molecular Medicine, CEITEC, Masar yk University, Brno, Czech Republic
- Department of Internal Medicine – Hematology and Oncology, University Hospital Brno, Czech Republic
| | - Andrea Janikova
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- Department of Internal Medicine – Hematology and Oncology, University Hospital Brno, Czech Republic
| | - Wilhelm Woessmann
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- University Hospital Hamburg-Eppendor f, Pediatric Hematology and Oncology, Hamburg, Germany
| | - Christine Damm- Welk
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- University Hospital Hamburg-Eppendor f, Pediatric Hematology and Oncology, Hamburg, Germany
| | - Mar tin Zimmermann
- Department of Pediatric Hematology/Oncology and Blood Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Alina Fedorova
- Belarusian Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | | | - Owen Smith
- Our Lady’s Children’s Hospital, Crumlin, Ireland
| | - Mariusz Wasik
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- Perelman School of Medicine, Philadelphia, PA, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Cornell University, New York, NY USA
| | - Laurence Lamant
- Institut Universitaire du Cancer Toulouse, Oncopole et Universite Paul-Sabatier, Toulouse, France
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Wolfram Klapper
- Department of Pathology, Hematopathology Section, UKSH Campus Kiel, Kiel, Germany
| | - Olaf Merkel
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - G. A. Amos Burke
- Department of Paediatric Oncology, Addenbrooke’s Hospital, Cambridge, UK
| | - Shahid Mian
- Molecular Diagnostics and Personalised Therapeutics Unit, Colleges of Medicine and Applied Medical Sciences, University of Ha’il, Ha’il, Saudi Arabia
| | - Ibraheem Ashankyty
- Department of Medical Technology Laboratory, College of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Lukas Kenner
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- Department of Pathology, Medical University of Vienna, Vienna, Austria
- Ludwig-Boltzmann Institute for Cancer Research, Vienna, Austria
| | - Suzanne D. Turner
- Department of Pathology, University of Cambridge, Cambridge, UK
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- Center of Molecular Medicine, CEITEC, Masar yk University, Brno, Czech Republic
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20
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Hrabovsky S, Vrzalova Z, Stika J, Jelinkova H, Jarosova M, Navrkalova V, Martenek J, Folber F, Salek C, Horacek JM, Pospisilova S, Mayer J, Doubek M. Genomic landscape of B-other acute lymphoblastic leukemia in an adult retrospective cohort with a focus on BCR-ABL1-like subtype. Acta Oncol 2021; 60:760-770. [PMID: 33750258 DOI: 10.1080/0284186x.2021.1900908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION BCR-ABL1-like acute lymphoblastic leukemia (ALL) is a high-risk disease with a complex genomic background. Though extensively studied, data on the frequency and mutual associations of present mutations are still incomplete in adult patients. This retrospective study aims to map the genomic landscape of B-other ALL in a cohort of adult patients with a focus on the BCR-ABL1-like ALL subtype. METHODS We analyzed bone marrow and peripheral blood samples of adult B-other ALL patients treated consecutively at three major Czech teaching hospitals. Samples were analyzed by cytogenetic methods, gene expression profiling, multiplex ligation-dependent probe amplification (MLPA), and next-generation sequencing (NGS). RESULTS Fifty-eight B-other ALL patients (not BCR-ABL1, KMT2A-rearranged, ETV6-RUNX1, TCF3-PBX1, or iAMP21) were included in the study. Median follow-up was 23.8 months. Samples from 33 patients were available for a gene expression analysis, 48.9% identified as BCR-ABL1-like ALL. Of the BCR-ABL1-like ALL cases, 18.8% harbored IGH-CRLF2 and 12.5% P2RY8-CRLF2 fusion gene. We observed a higher MRD failure rate in BCR-ABL1-like than in non-BCR-ABL1-like ALL patients after the induction treatment (50.0 vs. 13.3%, p=.05). There was a trend to worse progression-free and overall survival in the BCR-ABL1-like group, though not statistically significant. Deletions in IKZF1 gene were found in 31.3% of BCR-ABL1-like cases. Patients with concurrent IKZF1 and CDKN2A/B, PAX5 or PAR1 region deletions (IKZF1plus profile) had significantly worse progression-free survival than those with sole IKZF1 deletion or IKZF1 wild-type (p=.02). NGS analysis was performed in 54 patients and identified 99 short variants in TP53, JAK2, NRAS, PAX5, CREBBP, NF1, FLT3, ATM, KRAS, RUNX1, and other genes. Seventy-five of these gene variants have not yet been described in B-cell precursor ALL to date. CONCLUSION This study widens existing knowledge of the BCR-ABL1-like and B-other ALL genomic landscape in the adult population, supports previous findings, and identifies a number of novel gene variants.
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Affiliation(s)
- Stepan Hrabovsky
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czechia
- Faculty of Medicine, Masaryk University, Brno, Czechia
- Czech Leukemia Study Group – for Life (CELL), Brno, Czechia
| | - Zuzana Vrzalova
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czechia
- Central European Institute of Technology (CEITEC), Brno, Czechia
| | - Jiri Stika
- Central European Institute of Technology (CEITEC), Brno, Czechia
| | - Hana Jelinkova
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czechia
| | - Marie Jarosova
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czechia
- Faculty of Medicine, Masaryk University, Brno, Czechia
- Central European Institute of Technology (CEITEC), Brno, Czechia
| | - Veronika Navrkalova
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czechia
- Central European Institute of Technology (CEITEC), Brno, Czechia
| | - Jiri Martenek
- Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Frantisek Folber
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czechia
- Faculty of Medicine, Masaryk University, Brno, Czechia
- Czech Leukemia Study Group – for Life (CELL), Brno, Czechia
| | - Cyril Salek
- Czech Leukemia Study Group – for Life (CELL), Brno, Czechia
- Institute of Hematology and Blood Transfusion, Prague, Czechia
- Institute of Clinical and Experimental Hematology, First Faculty of Medicine, Charles University, Prague, Czechia
| | - Jan M. Horacek
- Czech Leukemia Study Group – for Life (CELL), Brno, Czechia
- Fourth Department of Internal Medicine – Hematology, University Hospital Hradec Kralove, Hradec Kralove, Czechia
- Department of Military Internal Medicine and Hygiene, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czechia
| | - Sarka Pospisilova
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czechia
- Faculty of Medicine, Masaryk University, Brno, Czechia
- Czech Leukemia Study Group – for Life (CELL), Brno, Czechia
- Central European Institute of Technology (CEITEC), Brno, Czechia
| | - Jiri Mayer
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czechia
- Faculty of Medicine, Masaryk University, Brno, Czechia
- Czech Leukemia Study Group – for Life (CELL), Brno, Czechia
- Central European Institute of Technology (CEITEC), Brno, Czechia
| | - Michael Doubek
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czechia
- Faculty of Medicine, Masaryk University, Brno, Czechia
- Czech Leukemia Study Group – for Life (CELL), Brno, Czechia
- Central European Institute of Technology (CEITEC), Brno, Czechia
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21
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Bencurova P, Baloun J, Hynst J, Oppelt J, Kubova H, Pospisilova S, Brazdil M. Dynamic miRNA changes during the process of epileptogenesis in an infantile and adult-onset model. Sci Rep 2021; 11:9649. [PMID: 33958654 PMCID: PMC8102630 DOI: 10.1038/s41598-021-89084-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 04/12/2021] [Indexed: 02/03/2023] Open
Abstract
Temporal lobe epilepsy (TLE) is the most common epilepsy type. TLE onset in infancy aggravates features like severity, drug responsiveness, or development of comorbidities. These aggravations may arise from altered micro RNA (miRNA) expression specific to the early onset of the disease. Although the miRNA involvement in TLE is widely studied, the relationship between the onset-age and miRNA expression has not been addressed. Here, we investigated the miRNA profile of infantile and adult-onset TLE in rats combining sequencing and PCR. Since miRNA expression changes with the disease progression, we scrutinized miRNA dynamics across three stages: acute, latent, and chronic. We report that infantile-onset TLE leads to changes in the expression of fewer miRNAs across these stages. Interestingly, the miRNA profile in the acute stage of infantile-onset TLE overlaps in dysregulation of miR-132-5p, -205, and -211-3p with the chronic stage of the disease starting in adulthood. The analysis of putative targets linked the majority of dysregulated miRNAs with pathways involved in epilepsy. Our profiling uncovered miRNA expression characteristic for infantile and adulthood-onset epileptogenesis, suggesting the distinct biology underlying TLE in the onset age-dependent matter. Our results indicate the necessity of addressing the onset age as an important parameter in future epilepsy research.
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Affiliation(s)
- Petra Bencurova
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.412752.70000 0004 0608 7557Brno Epilepsy Center, Department of Neurology, St. Anne’s University Hospital and Medical Faculty of Masaryk University, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Baloun
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jakub Hynst
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jan Oppelt
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, 19104-6100 Philadelphia, PA USA
| | - Hana Kubova
- grid.418095.10000 0001 1015 3316Department of Developmental Epileptology, Institute of Physiology, Academy of Sciences Czech Republic, Videnska 1083, 14220 Prague, Czech Republic
| | - Sarka Pospisilova
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Milan Brazdil
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.412752.70000 0004 0608 7557Brno Epilepsy Center, Department of Neurology, St. Anne’s University Hospital and Medical Faculty of Masaryk University, Pekarska 53, 656 91 Brno, Czech Republic
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22
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Doffe F, Carbonnier V, Tissier M, Leroy B, Martins I, Mattsson JSM, Micke P, Pavlova S, Pospisilova S, Smardova J, Joerger AC, Wiman KG, Kroemer G, Soussi T. Identification and functional characterization of new missense SNPs in the coding region of the TP53 gene. Cell Death Differ 2021; 28:1477-1492. [PMID: 33257846 PMCID: PMC8166836 DOI: 10.1038/s41418-020-00672-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023] Open
Abstract
Infrequent and rare genetic variants in the human population vastly outnumber common ones. Although they may contribute significantly to the genetic basis of a disease, these seldom-encountered variants may also be miss-identified as pathogenic if no correct references are available. Somatic and germline TP53 variants are associated with multiple neoplastic diseases, and thus have come to serve as a paradigm for genetic analyses in this setting. We searched 14 independent, globally distributed datasets and recovered TP53 SNPs from 202,767 cancer-free individuals. In our analyses, 19 new missense TP53 SNPs, including five novel variants specific to the Asian population, were recurrently identified in multiple datasets. Using a combination of in silico, functional, structural, and genetic approaches, we showed that none of these variants displayed loss of function compared to the normal TP53 gene. In addition, classification using ACMG criteria suggested that they are all benign. Considered together, our data reveal that the TP53 coding region shows far more polymorphism than previously thought and present high ethnic diversity. They furthermore underline the importance of correctly assessing novel variants in all variant-calling pipelines associated with genetic diagnoses for cancer.
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Affiliation(s)
- Flora Doffe
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
- Department of Oncology-Pathology, Bioclinicum, Karolinska Institutet, Stockholm, Sweden
| | - Vincent Carbonnier
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
| | - Manon Tissier
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
| | - Bernard Leroy
- Department of Life Science, Sorbonne Université, Paris, France
| | - Isabelle Martins
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Johanna S M Mattsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sarka Pavlova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jana Smardova
- Faculty of Science, Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Klas G Wiman
- Department of Oncology-Pathology, Bioclinicum, Karolinska Institutet, Stockholm, Sweden
| | - Guido Kroemer
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
- Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
| | - Thierry Soussi
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France.
- Department of Oncology-Pathology, Bioclinicum, Karolinska Institutet, Stockholm, Sweden.
- Department of Life Science, Sorbonne Université, Paris, France.
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
- Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France.
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23
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Hynst J, Navrkalova V, Pal K, Pospisilova S. Bioinformatic strategies for the analysis of genomic aberrations detected by targeted NGS panels with clinical application. PeerJ 2021; 9:e10897. [PMID: 33850640 PMCID: PMC8019320 DOI: 10.7717/peerj.10897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/13/2021] [Indexed: 01/21/2023] Open
Abstract
Molecular profiling of tumor samples has acquired importance in cancer research, but currently also plays an important role in the clinical management of cancer patients. Rapid identification of genomic aberrations improves diagnosis, prognosis and effective therapy selection. This can be attributed mainly to the development of next-generation sequencing (NGS) methods, especially targeted DNA panels. Such panels enable a relatively inexpensive and rapid analysis of various aberrations with clinical impact specific to particular diagnoses. In this review, we discuss the experimental approaches and bioinformatic strategies available for the development of an NGS panel for a reliable analysis of selected biomarkers. Compliance with defined analytical steps is crucial to ensure accurate and reproducible results. In addition, a careful validation procedure has to be performed before the application of NGS targeted assays in routine clinical practice. With more focus on bioinformatics, we emphasize the need for thorough pipeline validation and management in relation to the particular experimental setting as an integral part of the NGS method establishment. A robust and reproducible bioinformatic analysis running on powerful machines is essential for proper detection of genomic variants in clinical settings since distinguishing between experimental noise and real biological variants is fundamental. This review summarizes state-of-the-art bioinformatic solutions for careful detection of the SNV/Indels and CNVs for targeted sequencing resulting in translation of sequencing data into clinically relevant information. Finally, we share our experience with the development of a custom targeted NGS panel for an integrated analysis of biomarkers in lymphoproliferative disorders.
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Affiliation(s)
- Jakub Hynst
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics and Genomics, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic
| | - Veronika Navrkalova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic
| | - Karol Pal
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sarka Pospisilova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics and Genomics, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic
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24
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Sutton LA, Ljungström V, Enjuanes A, Cortese D, Skaftason A, Tausch E, Stano Kozubik K, Nadeu F, Armand M, Malcikova J, Pandzic T, Forster J, Davis Z, Oscier D, Rossi D, Ghia P, Strefford JC, Pospisilova S, Stilgenbauer S, Davi F, Campo E, Stamatopoulos K, Rosenquist R, On Behalf Of The European Research Initiative On Cll Eric. Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study. Haematologica 2021; 106:682-691. [PMID: 32273480 PMCID: PMC7927885 DOI: 10.3324/haematol.2019.234716] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) has transitioned from research to clinical routine, yet the comparability of different technologies for mutation profiling remains an open question. We performed a European multicenter (n=6) evaluation of three amplicon-based NGS assays targeting 11 genes recurrently mutated in chronic lymphocytic leukemia. Each assay was assessed by two centers using 48 pre-characterized chronic lymphocytic leukemia samples; libraries were sequenced on the Illumina MiSeq instrument and bioinformatics analyses were centralized. Across all centers the median percentage of target reads ≥100x ranged from 94.2-99.8%. In order to rule out assay-specific technical variability, we first assessed variant calling at the individual assay level i.e., pairwise analysis of variants detected amongst partner centers. After filtering for variants present in the paired normal sample and removal of PCR/sequencing artefacts, the panels achieved 96.2% (Multiplicom), 97.7% (TruSeq) and 90% (HaloPlex) concordance at a variant allele frequency (VAF) >0.5%. Reproducibility was assessed by looking at the inter-laboratory variation in detecting mutations and 107 of 115 (93% concordance) mutations were detected by all six centers, while the remaining eight variants (7%) were undetected by a single center. Notably, 6 of 8 of these variants concerned minor subclonal mutations (VAF <5%). We sought to investigate low-frequency mutations further by using a high-sensitivity assay containing unique molecular identifiers, which confirmed the presence of several minor subclonal mutations. Thus, while amplicon-based approaches can be adopted for somatic mutation detection with VAF >5%, after rigorous validation, the use of unique molecular identifiers may be necessary to reach a higher sensitivity and ensure consistent and accurate detection of low-frequency variants.
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Affiliation(s)
- Lesley-Ann Sutton
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Viktor Ljungström
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Enjuanes
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Diego Cortese
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Aron Skaftason
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Eugen Tausch
- Department of Internal Medicine III, Ulm University,Ulm, Germany
| | - Katerina Stano Kozubik
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ferran Nadeu
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Marine Armand
- AP-HP, Hopital Pitie-Salpetriere, Department of Hematology, Sorbonne Université, Paris, France
| | - Jikta Malcikova
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jade Forster
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Zadie Davis
- Department of Hematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - David Oscier
- Department of Hematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Davide Rossi
- Hematology Department, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Paolo Ghia
- Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Jonathan C Strefford
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sarka Pospisilova
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Frederic Davi
- AP-HP, Hopital Pitie-Salpetriere, Department of Hematology, Sorbonne Université, Paris, France
| | - Elias Campo
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Kostas Stamatopoulos
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Institute of Applied Biosciences, Center for Research and Technology, Thessaloniki, Greec
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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25
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Leeksma AC, Derks IAM, Kasem MH, Kilic E, de Klein A, Jager MJ, van de Loosdrecht AA, Jansen JH, Navrkalova V, Faber LM, Zaborsky N, Egle A, Zenz T, Pospisilova S, Abdel-Wahab O, Kater AP, Eldering E. The Effect of SF3B1 Mutation on the DNA Damage Response and Nonsense-Mediated mRNA Decay in Cancer. Front Oncol 2021; 10:609409. [PMID: 33585229 PMCID: PMC7880055 DOI: 10.3389/fonc.2020.609409] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/01/2020] [Indexed: 01/08/2023] Open
Abstract
Recurrent mutations in splicing factor 3B subunit 1 (SF3B1) have been identified in several malignancies and are associated with an increased expression of 3' cryptic transcripts as a result of alternative branchpoint recognition. A large fraction of cryptic transcripts associated with SF3B1 mutations is expected to be sensitive for RNA degradation via nonsense-mediated mRNA decay (NMD). Several studies indicated alterations in various signaling pathways in SF3B1-mutated cells, including an impaired DNA damage response (DDR) in chronic lymphocytic leukemia (CLL). In this study, we investigated isogenic cell lines and treatment naïve primary CLL samples without any TP53 and/or ATM defect, and found no significant effects of SF3B1 mutations on the ATM/p53 response, phosphorylation of H2AX and sensitivity to fludarabine. Cryptic transcripts associated with SF3B1 mutation status were observed at relatively low levels compared to the canonical transcripts and were validated as target for mRNA degradation via NMD. Expression of cryptic transcripts increased after NMD inhibition. In conclusion, our results confirm involvement of NMD in the biological effects of SF3B1 mutations. Further studies may elucidate whether SF3B1-mutant patients could benefit from NMD modulatory agents.
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Affiliation(s)
- Alexander C. Leeksma
- Department of Hematology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Cancer Center Amsterdam (CCA) and Amsterdam Infection and Immunity Institute (AIII), Amsterdam, Netherlands
| | - Ingrid A. M. Derks
- Department of Experimental Immunology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Cancer Center Amsterdam (CCA) and Amsterdam Infection and Immunity Institute (AIII), Amsterdam, Netherlands
| | - M. Haidar Kasem
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Emine Kilic
- Department of Ophthalmology and Clinical Genetics Erasmus MC, Rotterdam, Netherlands
| | - Annelies de Klein
- Department of Ophthalmology and Clinical Genetics Erasmus MC, Rotterdam, Netherlands
| | | | | | - Joop H. Jansen
- Laboratory of Hematology, Department Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Veronika Navrkalova
- Center of Molecular Biology and Gene Therapy, Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Center of Molecular Medicine, CEITEC, Masaryk University, Brno, Czechia
| | - Laura M. Faber
- Department of Internal Medicine, Rode Kruis Ziekenhuis, Beverwijk, Netherlands
| | - Nadja Zaborsky
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria
- Department of Internal Medicine III with Haematology, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Salzburg, Austria
- Department of Internal Medicine III with Haematology, Cancer Cluster Salzburg, Salzburg, Austria
| | - Alexander Egle
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria
- Department of Internal Medicine III with Haematology, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Salzburg, Austria
- Department of Internal Medicine III with Haematology, Cancer Cluster Salzburg, Salzburg, Austria
| | - Thorsten Zenz
- Department of Oncology and Haematology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Sarka Pospisilova
- Center of Molecular Biology and Gene Therapy, Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Center of Molecular Medicine, CEITEC, Masaryk University, Brno, Czechia
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Arnon P. Kater
- Department of Hematology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Eric Eldering
- Department of Experimental Immunology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Cancer Center Amsterdam (CCA) and Amsterdam Infection and Immunity Institute (AIII), Amsterdam, Netherlands
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26
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Leeksma AC, Baliakas P, Moysiadis T, Puiggros A, Plevova K, Van der Kevie-Kersemaekers AM, Posthuma H, Rodriguez-Vicente AE, Tran AN, Barbany G, Mansouri L, Gunnarsson R, Parker H, Van den Berg E, Bellido M, Davis Z, Wall M, Scarpelli I, Österborg A, Hansson L, Jarosova M, Ghia P, Poddighe P, Espinet B, Pospisilova S, Tam C, Ysebaert L, Nguyen-Khac F, Oscier D, Haferlach C, Schoumans J, Stevens-Kroef M, Eldering E, Stamatopoulos K, Rosenquist R, Strefford JC, Mellink C, Kater AP. Genomic arrays identify high-risk chronic lymphocytic leukemia with genomic complexity: a multi-center study. Haematologica 2021; 106:87-97. [PMID: 31974198 PMCID: PMC7776256 DOI: 10.3324/haematol.2019.239947] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/22/2020] [Indexed: 01/15/2023] Open
Abstract
Complex karyotype (CK) identified by chromosome-banding analysis (CBA) has shown prognostic value in chronic lymphocytic leukemia (CLL). Genomic arrays offer high-resolution genome-wide detection of copy-number alterations (CNAs) and could therefore be well equipped to detect the presence of a CK. Current knowledge on genomic arrays in CLL is based on outcomes of single center studies, in which different cutoffs for CNA calling were used. To further determine the clinical utility of genomic arrays for CNA assessment in CLL diagnostics, we retrospectively analyzed 2293 arrays from 13 diagnostic laboratories according to established standards. CNAs were found outside regions captured by CLL FISH probes in 34% of patients, and several of them including gains of 8q, deletions of 9p and 18p (p<0.01) were linked to poor outcome after correction for multiple testing. Patients (n=972) could be divided in three distinct prognostic subgroups based on the number of CNAs. Only high genomic complexity (high-GC), defined as ≥5 CNAs emerged as an independent adverse prognosticator on multivariable analysis for time to first treatment (Hazard ratio: 2.15, 95% CI: 1.36-3.41; p=0.001) and overall survival (Hazard ratio: 2.54, 95% CI: 1.54-4.17; p<0.001; n=528). Lowering the size cutoff to 1 Mb in 647 patients did not significantly improve risk assessment. Genomic arrays detected more chromosomal abnormalities and performed at least as well in terms of risk stratification compared to simultaneous chromosome banding analysis as determined in 122 patients. Our findings highlight genomic array as an accurate tool for CLL risk stratification.
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Affiliation(s)
| | - Panagiotis Baliakas
- Dept of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Theodoros Moysiadis
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | | | - Karla Plevova
- University Hospital Brno, Masaryk University, Brno, Czech Republic
| | | | - Hidde Posthuma
- Dept of Clinical Genetics, Amsterdam University Medical Centers, Univ of Amsterdam, The Netherlands
| | | | - Anh Nhi Tran
- Dept of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Gisela Barbany
- Dept of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Larry Mansouri
- Dept of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Rebeqa Gunnarsson
- Division of Clinical Genetics, Dept of Laboratory Medicine, Lund University, Lund, Sweden
| | - Helen Parker
- Cancer Genomics, Academic Unit of Cancer Sciences, University of Southampton, Southampton, UK
| | - Eva Van den Berg
- Dept of Genetics, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Mar Bellido
- Dept of Genetics, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Zadie Davis
- Dept of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Meaghan Wall
- Cytogenetics department, St Vincent Hospital Melbourne, Victoria, Australia
| | - Ilaria Scarpelli
- Oncogenomic laboratory, Dept of Hematology, Lausanne University Hospital (CHUV), Switzerland
| | - Anders Österborg
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Lotta Hansson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm
| | - Marie Jarosova
- University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Paolo Ghia
- Dept. of Experimental Oncology, IRCCS Ospedale San Raffaele, Università Vita-Salute, Milan
| | - Pino Poddighe
- Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, The Netherlands
| | - Blanca Espinet
- Laboratori de Citogenetica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | - Sarka Pospisilova
- CEITEC, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Constantine Tam
- St Vincent Hospital Melbourne, Peter MacCallum Cancer Center, University of Melbourne, Australia
| | - Loïc Ysebaert
- Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Florence Nguyen-Khac
- Service d'Hematologie Biologique, Hopital Pitié-Salpetriere, APHP, Paris, France
| | - David Oscier
- Dept of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | | | - Jacqueline Schoumans
- Oncogenomic laboratory, Dept of Hematology, Lausanne University Hospital (CHUV), Switzerland
| | - Marian Stevens-Kroef
- Radboud University Medical Center, Dept of Human Genetics, Nijmegen, The Netherlands
| | - Eric Eldering
- Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Richard Rosenquist
- Dept of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Clemens Mellink
- Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| | - Arnon P Kater
- Hematology, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
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27
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Lobello C, Tichy B, Bystry V, Radova L, Filip D, Mraz M, Montes-Mojarro IA, Prokoph N, Larose H, Liang HC, Sharma GG, Mologni L, Belada D, Kamaradova K, Fend F, Gambacorti-Passerini C, Merkel O, Turner SD, Janikova A, Pospisilova S. STAT3 and TP53 mutations associate with poor prognosis in anaplastic large cell lymphoma. Leukemia 2020; 35:1500-1505. [PMID: 33247178 PMCID: PMC8102183 DOI: 10.1038/s41375-020-01093-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 10/01/2020] [Accepted: 11/09/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Cosimo Lobello
- Center of Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Boris Tichy
- Center of Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Vojtech Bystry
- Center of Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Lenka Radova
- Center of Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Daniel Filip
- Center of Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Medical Faculty MU, Brno, Czech Republic
| | - Marek Mraz
- Center of Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Medical Faculty MU, Brno, Czech Republic
| | - Ivonne-Aidee Montes-Mojarro
- Institute of Pathology and Neuropathology and Comprehensive Cancer Center Tübingen, Eberhard Karls University, Tübingen, Germany
| | - Nina Prokoph
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Hugo Larose
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Huan-Chang Liang
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Geeta G Sharma
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Luca Mologni
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - David Belada
- 4th Department of Internal Medicine-Hematology, Charles University Hospital and Faculty of Medicine, Hradec Králové, Czech Republic
| | - Katerina Kamaradova
- Fingerland Department of Pathology, Charles University Hospital and Faculty of Medicine, Hradec Králové, Czech Republic
| | - Falko Fend
- Institute of Pathology and Neuropathology and Comprehensive Cancer Center Tübingen, Eberhard Karls University, Tübingen, Germany
| | | | - Olaf Merkel
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Suzanne D Turner
- Center of Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Andrea Janikova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Medical Faculty MU, Brno, Czech Republic
| | - Sarka Pospisilova
- Center of Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic. .,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Medical Faculty MU, Brno, Czech Republic.
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28
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Aksoy O, Pencik J, Hartenbach M, Moazzami AA, Schlederer M, Balber T, Varady A, Philippe C, Baltzer PA, Mazumder B, Whitchurch JB, Roberts CJ, Haitel A, Herac M, Susani M, Mitterhauser M, Marculescu R, Stangl-Kremser J, Hassler MR, Kramer G, Shariat SF, Turner SD, Tichy B, Oppelt J, Pospisilova S, Hartenbach S, Tangermann S, Egger G, Neubauer HA, Moriggl R, Culig Z, Greiner G, Hoermann G, Hacker M, Heery DM, Merkel O, Kenner L. Thyroid and androgen receptor signaling are antagonized by μ-Crystallin in prostate cancer. Int J Cancer 2020; 148:731-747. [PMID: 33034050 PMCID: PMC7756625 DOI: 10.1002/ijc.33332] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/02/2020] [Indexed: 12/29/2022]
Abstract
Androgen deprivation therapy (ADT) remains a key approach in the treatment of prostate cancer (PCa). However, PCa inevitably relapses and becomes ADT resistant. Besides androgens, there is evidence that thyroid hormone thyroxine (T4) and its active form 3,5,3'-triiodo-L-thyronine (T3) are involved in the progression of PCa. Epidemiologic evidences show a higher incidence of PCa in men with elevated thyroid hormone levels. The thyroid hormone binding protein μ-Crystallin (CRYM) mediates intracellular thyroid hormone action by sequestering T3 and blocks its binding to cognate receptors (TRα/TRβ) in target tissues. We show in our study that low CRYM expression levels in PCa patients are associated with early biochemical recurrence and poor prognosis. Moreover, we found a disease stage-specific expression of CRYM in PCa. CRYM counteracted thyroid and androgen signaling and blocked intracellular choline uptake. CRYM inversely correlated with [18F]fluoromethylcholine (FMC) levels in positron emission tomography/magnetic resonance imaging of PCa patients. Our data suggest CRYM as a novel antagonist of T3- and androgen-mediated signaling in PCa. The role of CRYM could therefore be an essential control mechanism for the prevention of aggressive PCa growth.
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Affiliation(s)
- Osman Aksoy
- Department of Pathology, Medical University Vienna, Vienna, Austria
| | - Jan Pencik
- Department of Pathology, Medical University Vienna, Vienna, Austria.,Center for Biomarker Research in Medicine (CBmed), Graz, Austria.,Present address: Jan Pencik, Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Markus Hartenbach
- Department of Biomedical Imaging and Image Guided Therapy, Medical University Vienna, Vienna, Austria
| | - Ali A Moazzami
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Theresa Balber
- Department of Biomedical Imaging and Image Guided Therapy, Medical University Vienna, Vienna, Austria.,Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria.,Department for Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria
| | - Adam Varady
- Department of Pathology, Medical University Vienna, Vienna, Austria
| | - Cecile Philippe
- Department of Biomedical Imaging and Image Guided Therapy, Medical University Vienna, Vienna, Austria
| | - Pascal A Baltzer
- Department of Biomedical Imaging and Image Guided Therapy, Medical University Vienna, Vienna, Austria
| | - Bismoy Mazumder
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | | | | | - Andrea Haitel
- Department of Pathology, Medical University Vienna, Vienna, Austria
| | - Merima Herac
- Department of Pathology, Medical University Vienna, Vienna, Austria
| | - Martin Susani
- Department of Pathology, Medical University Vienna, Vienna, Austria
| | - Markus Mitterhauser
- Department of Biomedical Imaging and Image Guided Therapy, Medical University Vienna, Vienna, Austria.,Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria
| | - Rodrig Marculescu
- Department of Laboratory Medicine, Medical University Vienna, Vienna, Austria
| | | | | | - Gero Kramer
- Department of Urology, Medical University Vienna, Vienna, Austria
| | - Shahrokh F Shariat
- Department of Urology, Medical University Vienna, Vienna, Austria.,Division of Urology, Department of Special Surgery, Jordan University Hospital, The University of Jordan, Amman, Jordan.,Institute for Urology and Reproductive Health, Sechenov University, Moscow, Russia.,Departments of Urology, Weill Cornell Medical College, New York, New York, USA.,Department of Urology, University of Texas Southwestern, Dallas, Texas, USA.,Department of Urology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Suzanne D Turner
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK.,Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Boris Tichy
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jan Oppelt
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sabrina Hartenbach
- Histo Consulting Inc., Ulm, Germany.,Department of Pathology, Rudolfinerhaus Privatklinik Gmbh, Vienna, Austria
| | - Simone Tangermann
- Unit for Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Gerda Egger
- Department of Pathology, Medical University Vienna, Vienna, Austria.,Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria
| | - Heidi A Neubauer
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Zoran Culig
- Department of Urology, Innsbruck Medical University, Innsbruck, Austria
| | - Georg Greiner
- Department of Laboratory Medicine, Medical University Vienna, Vienna, Austria
| | - Gregor Hoermann
- Department of Laboratory Medicine, Medical University Vienna, Vienna, Austria.,MLL Munich Leukemia Laboratory, Munich, Germany
| | - Marcus Hacker
- Center for Biomarker Research in Medicine (CBmed), Graz, Austria.,Department of Biomedical Imaging and Image Guided Therapy, Medical University Vienna, Vienna, Austria
| | - David M Heery
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Olaf Merkel
- Department of Pathology, Medical University Vienna, Vienna, Austria
| | - Lukas Kenner
- Department of Pathology, Medical University Vienna, Vienna, Austria.,Center for Biomarker Research in Medicine (CBmed), Graz, Austria.,Unit for Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria.,Christian Doppler Laboratory for Applied Metabolomics (CDL-AM), Medical University of Vienna, Vienna, Austria
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29
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Baloun J, Bencurova P, Totkova T, Kubova H, Hermanova M, Hendrych M, Pail M, Pospisilova S, Brazdil M. Epilepsy miRNA Profile Depends on the Age of Onset in Humans and Rats. Front Neurosci 2020; 14:924. [PMID: 33041753 PMCID: PMC7522367 DOI: 10.3389/fnins.2020.00924] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 08/11/2020] [Indexed: 12/27/2022] Open
Abstract
Temporal lobe epilepsy (TLE) is a severe neurological disorder accompanied by recurrent spontaneous seizures. Although the knowledge of TLE onset is still incomplete, TLE pathogenesis most likely involves the aberrant expression of microRNAs (miRNAs). miRNAs play an essential role in organism homeostasis and are widely studied in TLE as potential therapeutics and biomarkers. However, many discrepancies in discovered miRNAs occur among TLE studies due to model-specific miRNA expression, different onset ages of epilepsy among patients, or technology-related bias. We employed a massive parallel sequencing approach to analyze brain tissues from 16 adult mesial TLE (mTLE)/hippocampal sclerosis (HS) patients, 8 controls and 20 rats with TLE-like syndrome, and 20 controls using the same workflow and categorized these subjects based on the age of epilepsy onset. All categories were compared to discover overlapping miRNAs with an aberrant expression, which could be involved in TLE. Our cross-comparative analyses showed distinct miRNA profiles across the age of epilepsy onset and found that the miRNA profile in rats with adult-onset TLE shows the closest resemblance to the profile in mTLE/HS patients. Additionally, this analysis revealed overlapping miRNAs between patients and the rat model, which should participate in epileptogenesis and ictogenesis. Among the overlapping miRNAs stand out miR-142-5p and miR-142-3p, which regulate immunomodulatory agents with pro-convulsive effects and suppress neuronal growth. Our cross-comparison study enhanced the insight into the effect of the age of epilepsy onset on miRNA expression and deepened the knowledge of epileptogenesis. We employed the same methodological workflow in both patients and the rat model, thus improving the reliability and accuracy of our results.
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Affiliation(s)
- Jiri Baloun
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Petra Bencurova
- Central European Institute of Technology, Masaryk University, Brno, Czechia.,Brno Epilepsy Center, Department of Neurology, Medical Faculty of Masaryk University, St. Anne's University Hospital, Brno, Czechia
| | - Tereza Totkova
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Hana Kubova
- Department of Developmental Epileptology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czechia
| | - Marketa Hermanova
- First Department of Pathology, Medical Faculty of Masaryk University, St. Anne's University Hospital, Brno, Czechia
| | - Michal Hendrych
- First Department of Pathology, Medical Faculty of Masaryk University, St. Anne's University Hospital, Brno, Czechia
| | - Martin Pail
- Brno Epilepsy Center, Department of Neurology, Medical Faculty of Masaryk University, St. Anne's University Hospital, Brno, Czechia
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Milan Brazdil
- Central European Institute of Technology, Masaryk University, Brno, Czechia.,Brno Epilepsy Center, Department of Neurology, Medical Faculty of Masaryk University, St. Anne's University Hospital, Brno, Czechia
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30
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Pospisilova S, Malik I, Curillova J, Michnova H, Cerna L, Padrtova T, Hosek J, Pecher D, Cizek A, Jampilek J. Insight into antimicrobial activity of substituted phenylcarbamoyloxypiperazinylpropanols. Bioorg Chem 2020; 102:104060. [PMID: 32663668 DOI: 10.1016/j.bioorg.2020.104060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/20/2020] [Accepted: 06/26/2020] [Indexed: 12/23/2022]
Abstract
3-[4-(Substituted)phenyl-/4-(diphenylmethyl)phenylpiperazin-1-yl]-2-hydroxypropyl-1-[(substituted)phenyl]carbamates and their salts with hydrochloric acid were synthesized, characterized, and tested in vitro against Staphylococcus aureus ATCC 29213 and Enterococcus faecalis ATCC 29212 as reference and quality control strains, against three methicillin-resistant isolates of S. aureus, and three isolates of vancomycin-resistant E. faecalis. All the compounds were evaluated against Mycobacterium tuberculosis H37Ra/ATCC 25177, M. kansasii DSM 44162, and M. smegmatis ATCC 700084. All of the tested compounds demonstrated very good activity against all the tested strains/isolates comparable with or better than that of clinically used drugs (ampicillin, ciprofloxacin, vancomycin, isoniazid). 1-[{(3-Trifluoromethyl)phenyl}carbamoyloxy-2-hydroxypropyl]-4-(3,4-dichlorophenyl)piperazin-1-ium chloride demonstrated the highest potency against all the tested strains/isolates (MICs ranged from 3.78 to 30.2 µM), and 1-[{(3-trifluoromethyl)phenyl}carbamoyloxy-2-hydroxypropyl]-4-(diphenylmethyl)piperazin-1-ium chloride was the most effective against all the screened mycobacterial strains (MICs ranged from 3.64 to 14.5 µM). All the investigated derivatives had strong antibiofilm activity against S. aureus ATCC 29123 and a synergistic or additive effect with gentamicin against isolates of E. faecalis with both intrinsic and acquired resistance to gentamicin. The screening of the cytotoxicity of the compounds was performed using human monocytic leukemia THP-1 cells. The IC50 values of the most effective compounds ranged from ca. 2.8 to 7.3 µM; thus, it can be stated that the antimicrobial effect is closely connected with their cytotoxicity. These observations disqualify these compounds from further development as antimicrobial agents, but they can be considered potential multi-target drugs with a preferred anticancer effect with good water solubility and additional anti-infectious activity.
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Affiliation(s)
- Sarka Pospisilova
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic
| | - Ivan Malik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, 832 32 Bratislava, Slovak Republic.
| | - Jana Curillova
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, 832 32 Bratislava, Slovak Republic
| | - Hana Michnova
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic
| | - Lucie Cerna
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic
| | - Tereza Padrtova
- Department of Chemical Drugs, Faculty of Pharmacy, Masaryk University, Palackeho 1946/1, 612 00 Brno, Czech Republic
| | - Jan Hosek
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic
| | - Daniel Pecher
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, 832 32 Bratislava, Slovak Republic
| | - Alois Cizek
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Palackeho 1946/1, 612 42 Brno, Czech Republic
| | - Josef Jampilek
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic.
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31
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Condoluci A, Terzi di Bergamo L, Langerbeins P, Hoechstetter MA, Herling CD, De Paoli L, Delgado J, Rabe KG, Gentile M, Doubek M, Mauro FR, Chiodin G, Mattsson M, Bahlo J, Cutrona G, Kotaskova J, Deambrogi C, Smedby KE, Spina V, Bruscaggin A, Wu W, Moia R, Bianchi E, Gerber B, Zucca E, Gillessen S, Ghielmini M, Cavalli F, Stussi G, Hess MA, Baumann TS, Neri A, Ferrarini M, Rosenquist R, Forconi F, Foà R, Pospisilova S, Morabito F, Stilgenbauer S, Döhner H, Parikh SA, Wierda WG, Montserrat E, Gaidano G, Hallek M, Rossi D. International prognostic score for asymptomatic early-stage chronic lymphocytic leukemia. Blood 2020; 135:1859-1869. [PMID: 32267500 DOI: 10.1182/blood.2019003453] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/12/2020] [Indexed: 02/08/2023] Open
Abstract
Most patients with chronic lymphocytic leukemia (CLL) are diagnosed with early-stage disease and managed with active surveillance. The individual course of patients with early-stage CLL is heterogeneous, and their probability of needing treatment is hardly anticipated at diagnosis. We aimed at developing an international prognostic score to predict time to first treatment (TTFT) in patients with CLL with early, asymptomatic disease (International Prognostic Score for Early-stage CLL [IPS-E]). Individual patient data from 11 international cohorts of patients with early-stage CLL (n = 4933) were analyzed to build and validate the prognostic score. Three covariates were consistently and independently correlated with TTFT: unmutated immunoglobulin heavy variable gene (IGHV), absolute lymphocyte count higher than 15 × 109/L, and presence of palpable lymph nodes. The IPS-E was the sum of the covariates (1 point each), and separated low-risk (score 0), intermediate-risk (score 1), and high-risk (score 2-3) patients showing a distinct TTFT. The score accuracy was validated in 9 cohorts staged by the Binet system and 1 cohort staged by the Rai system. The C-index was 0.74 in the training series and 0.70 in the aggregate of validation series. By meta-analysis of the training and validation cohorts, the 5-year cumulative risk for treatment start was 8.4%, 28.4%, and 61.2% among low-risk, intermediate-risk, and high-risk patients, respectively. The IPS-E is a simple and robust prognostic model that predicts the likelihood of treatment requirement in patients with early-stage CLL. The IPS-E can be useful in clinical management and in the design of early intervention clinical trials.
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MESH Headings
- Aged
- Biomarkers, Tumor/genetics
- Clinical Trials as Topic/statistics & numerical data
- Combined Modality Therapy
- Disease Progression
- Female
- Follow-Up Studies
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Male
- Mutation
- Nomograms
- Prognosis
- Retrospective Studies
- Survival Rate
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Affiliation(s)
- Adalgisa Condoluci
- Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | | | - Petra Langerbeins
- Center of Integrated Oncology Cologne Bonn and German CLL Study Group, University of Cologne, Cologne, Germany
| | | | - Carmen D Herling
- Center of Integrated Oncology Cologne Bonn and German CLL Study Group, University of Cologne, Cologne, Germany
| | - Lorenzo De Paoli
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | | | | | | | - Michael Doubek
- Interní Hematologická a Onkologická Klinika (IHOK), University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Giorgia Chiodin
- Cancer Sciences Division, University of Southampton, Southampton, United Kingdom
| | | | - Jasmin Bahlo
- Center of Integrated Oncology Cologne Bonn and German CLL Study Group, University of Cologne, Cologne, Germany
| | | | - Jana Kotaskova
- Interní Hematologická a Onkologická Klinika (IHOK), University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Clara Deambrogi
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | | | - Valeria Spina
- Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Alessio Bruscaggin
- Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Wei Wu
- Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
- The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Riccardo Moia
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Elena Bianchi
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Bernhard Gerber
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Emanuele Zucca
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Silke Gillessen
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | | | - Franco Cavalli
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Georg Stussi
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Mark A Hess
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Antonino Neri
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Manlio Ferrarini
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | | | - Francesco Forconi
- Cancer Sciences Division, University of Southampton, Southampton, United Kingdom
- Southampton University Hospital Trust, Southampton, United Kingdom
| | - Robin Foà
- Division of Hematology, Sapienza University, Rome, Italy
| | - Sarka Pospisilova
- Interní Hematologická a Onkologická Klinika (IHOK), University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Fortunato Morabito
- Biotechnology Research Unit Aprigliano, Cosenza, Italy
- Augusta Victoria Hospital, Jerusalem, Israel
| | - Stephan Stilgenbauer
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany; and
| | - Hartmut Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany; and
| | | | | | - Emili Montserrat
- Hospital Clinic, Barcelona, Spain
- Institute of Hematology and Oncology, University of Barcelona, Barcelona, Spain
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Michael Hallek
- Center of Integrated Oncology Cologne Bonn and German CLL Study Group, University of Cologne, Cologne, Germany
| | - Davide Rossi
- Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
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32
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Kozlova V, Ledererova A, Ladungova A, Peschelova H, Janovska P, Slusarczyk A, Domagala J, Kopcil P, Vakulova V, Oppelt J, Bryja V, Doubek M, Mayer J, Pospisilova S, Smida M. CD20 is dispensable for B-cell receptor signaling but is required for proper actin polymerization, adhesion and migration of malignant B cells. PLoS One 2020; 15:e0229170. [PMID: 32210425 PMCID: PMC7094844 DOI: 10.1371/journal.pone.0229170] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/31/2020] [Indexed: 11/19/2022] Open
Abstract
Surface protein CD20 serves as the critical target of immunotherapy in various B-cell malignancies for decades, however its biological function and regulation remain largely elusive. Better understanding of CD20 function may help to design improved rational therapies to prevent development of resistance. Using CRISPR/Cas9 technique, we have abrogated CD20 expression in five different malignant B-cell lines. We show that CD20 deletion has no effect upon B-cell receptor signaling or calcium flux. Also B-cell survival and proliferation is unaffected in the absence of CD20. On the contrary, we found a strong defect in actin cytoskeleton polymerization and, consequently, defective cell adhesion and migration in response to homeostatic chemokines SDF1α, CCL19 and CCL21. Mechanistically, we could identify a reduction in chemokine-triggered PYK2 activation, a calcium-activated signaling protein involved in activation of MAP kinases and cytoskeleton regulation. These cellular defects in consequence result in a severely disturbed homing of B cells in vivo.
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MESH Headings
- Actins/metabolism
- Animals
- Antigens, CD20/genetics
- Antigens, CD20/metabolism
- Antigens, CD20/physiology
- B-Lymphocytes/pathology
- B-Lymphocytes/physiology
- Cell Adhesion/physiology
- Cell Line, Tumor
- Cell Movement/physiology
- Gene Knockdown Techniques
- Humans
- Leukemia, B-Cell/metabolism
- Leukemia, B-Cell/pathology
- Lymphoma, B-Cell/metabolism
- Lymphoma, B-Cell/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Mice, Transgenic
- Polymerization
- Protein Multimerization/physiology
- Receptors, Antigen, B-Cell/metabolism
- Signal Transduction/immunology
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Affiliation(s)
- Veronika Kozlova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Medical Faculty of Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Aneta Ledererova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Medical Faculty of Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Adriana Ladungova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Helena Peschelova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Pavlina Janovska
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Joanna Domagala
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Pavel Kopcil
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Viera Vakulova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Jan Oppelt
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Vitezslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michael Doubek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Medical Faculty of Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jiri Mayer
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Medical Faculty of Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Medical Faculty of Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Michal Smida
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Medical Faculty of Masaryk University and University Hospital Brno, Brno, Czech Republic
- * E-mail:
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33
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Pospisilova S, Marvanova P, Treml J, Moricz AM, Ott PG, Mokry P, Odehnalova K, Sedo O, Cizek A, Jampilek J. Activity of N-Phenylpiperazine Derivatives Against Bacterial and Fungal Pathogens. Curr Protein Pept Sci 2020; 20:1119-1129. [PMID: 31518219 DOI: 10.2174/1389203720666190913114041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/01/2019] [Accepted: 04/04/2019] [Indexed: 01/21/2023]
Abstract
BACKGROUND As the bacterial resistance to antibacterial chemotherapeutics is one of the greatest problems in modern medicine, efforts are made to develop new antimicrobial drugs. Compounds with a piperazine ring have proved to be promising agents against various pathogens. OBJECTIVE The aim of the study was to prepare a series of new N-phenylpiperazines and determine their activity against various pathogens. METHOD Target compounds were prepared by multi-step synthesis starting from an appropriate substituted acid to an oxirane intermediate reacting with 1-(4-nitrophenyl)piperazine. Lipophilicity and pKa values were experimentally determined. Other molecular parameters were calculated. The inhibitory activity of the target compounds against Staphylococcus aureus, four mycobacteria strains, Bipolaris sorokiniana, and Fusarium avenaceum was tested. In vitro antiproliferative activity was determined on a THP-1 cell line, and toxicity against plant was determined using Nicotiana tabacum. RESULTS In general, most compounds demonstrated only moderate effects. 1-(2-Hydroxy-3-{[4-(propan- 2-yloxy)benzoyl]oxy}propyl)-4-(4-nitrophenyl)piperazinediium dichloride and 1-{3-[(4-butoxybenzoyl)- oxy]-2-hydroxypropyl}-4-(4-nitrophenyl)piperazinediium dichloride showed the highest inhibition activity against M. kansasii (MIC = 15.4 and 15.0 µM, respectively) and the latter also against M. marinum (MIC = 15.0 µM). 1-(2-Hydroxy-3-{[4-(2-propoxyethoxy)benzoyl]oxy}propyl)-4-(4-nitrophenyl)piperazinediium dichloride had the highest activity against F. avenaceum (MIC = 14.2 µM). All the compounds showed only insignificant toxic effects on human and plant cells. CONCLUSION Ten new 1-(4-nitrophenyl)piperazine derivatives were prepared and analyzed, and their antistaphylococcal, antimycobacterial, and antifungal activities were determined. The activity against M. kansasii was positively influenced by higher lipophilicity, the electron-donor properties of substituent R and a lower dissociation constant. The exact mechanism of action will be investigated in follow-up studies.
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Affiliation(s)
- Sarka Pospisilova
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Pavlina Marvanova
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Jakub Treml
- Department of Molecular Biology and Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Agnes M Moricz
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Peter G Ott
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Petr Mokry
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Klara Odehnalova
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Ondrej Sedo
- Research Group of Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Alois Cizek
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Josef Jampilek
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc, Czech Republic
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Laidou S, Alanis-Lobato G, Pribyl J, Raskó T, Tichy B, Mikulasek K, Tsagiopoulou M, Oppelt J, Kastrinaki G, Lefaki M, Singh M, Zink A, Chondrogianni N, Psomopoulos F, Prigione A, Ivics Z, Pospisilova S, Skladal P, Izsvák Z, Andrade-Navarro MA, Petrakis S. Nuclear inclusions of pathogenic ataxin-1 induce oxidative stress and perturb the protein synthesis machinery. Redox Biol 2020; 32:101458. [PMID: 32145456 PMCID: PMC7058924 DOI: 10.1016/j.redox.2020.101458] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/29/2020] [Accepted: 02/06/2020] [Indexed: 12/20/2022] Open
Abstract
Spinocerebellar ataxia type-1 (SCA1) is caused by an abnormally expanded polyglutamine (polyQ) tract in ataxin-1. These expansions are responsible for protein misfolding and self-assembly into intranuclear inclusion bodies (IIBs) that are somehow linked to neuronal death. However, owing to lack of a suitable cellular model, the downstream consequences of IIB formation are yet to be resolved. Here, we describe a nuclear protein aggregation model of pathogenic human ataxin-1 and characterize IIB effects. Using an inducible Sleeping Beauty transposon system, we overexpressed the ATXN1(Q82) gene in human mesenchymal stem cells that are resistant to the early cytotoxic effects caused by the expression of the mutant protein. We characterized the structure and the protein composition of insoluble polyQ IIBs which gradually occupy the nuclei and are responsible for the generation of reactive oxygen species. In response to their formation, our transcriptome analysis reveals a cerebellum-specific perturbed protein interaction network, primarily affecting protein synthesis. We propose that insoluble polyQ IIBs cause oxidative and nucleolar stress and affect the assembly of the ribosome by capturing or down-regulating essential components. The inducible cell system can be utilized to decipher the cellular consequences of polyQ protein aggregation. Our strategy provides a broadly applicable methodology for studying polyQ diseases.
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Affiliation(s)
- Stamatia Laidou
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece
| | - Gregorio Alanis-Lobato
- Faculty of Biology, Johannes Gutenberg University Mainz, 55122, Mainz, Germany; Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Jan Pribyl
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Tamás Raskó
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany
| | - Boris Tichy
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Kamil Mikulasek
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500, Brno, Czech Republic
| | - Maria Tsagiopoulou
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece
| | - Jan Oppelt
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Georgia Kastrinaki
- Aerosol and Particle Technology Laboratory/Chemical Process & Energy Resources Institute/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece
| | - Maria Lefaki
- Institute of Biology, Medicinal Chemistry & Biotechnology/National Hellenic Research Foundation, 11365, Athens, Greece
| | - Manvendra Singh
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany
| | - Annika Zink
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany; Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Niki Chondrogianni
- Institute of Biology, Medicinal Chemistry & Biotechnology/National Hellenic Research Foundation, 11365, Athens, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece; Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Alessandro Prigione
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany; Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225, Langen, Germany
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Petr Skladal
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Zsuzsanna Izsvák
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany.
| | | | - Spyros Petrakis
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece.
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35
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Tsagiopoulou M, Papakonstantinou N, Moysiadis T, Mansouri L, Ljungström V, Duran-Ferrer M, Malousi A, Queirós AC, Plevova K, Bhoi S, Kollia P, Oscier D, Anagnostopoulos A, Trentin L, Ritgen M, Pospisilova S, Stavroyianni N, Ghia P, Martin-Subero JI, Pott C, Rosenquist R, Stamatopoulos K. DNA methylation profiles in chronic lymphocytic leukemia patients treated with chemoimmunotherapy. Clin Epigenetics 2019; 11:177. [PMID: 31791414 PMCID: PMC6889736 DOI: 10.1186/s13148-019-0783-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/19/2019] [Indexed: 01/01/2023] Open
Abstract
Background In order to gain insight into the contribution of DNA methylation to disease progression of chronic lymphocytic leukemia (CLL), using 450K Illumina arrays, we determined the DNA methylation profiles in paired pre-treatment/relapse samples from 34 CLL patients treated with chemoimmunotherapy, mostly (n = 31) with the fludarabine-cyclophosphamide-rituximab (FCR) regimen. Results The extent of identified changes in CLL cells versus memory B cells from healthy donors was termed “epigenetic burden” (EB) whereas the number of changes between the pre-treatment versus the relapse sample was termed “relapse changes” (RC). Significant (p < 0.05) associations were identified between (i) high EB and short time-to-first-treatment (TTFT); and, (ii) few RCs and short time-to-relapse. Both the EB and the RC clustered in specific genomic regions and chromatin states, including regulatory regions containing binding sites of transcription factors implicated in B cell and CLL biology. Conclusions Overall, we show that DNA methylation in CLL follows different dynamics in response to chemoimmunotherapy. These epigenetic alterations were linked with specific clinical and biological features.
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Affiliation(s)
- Maria Tsagiopoulou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, 6th km Charilaou-Thermi Rd, 57001, Thermi, Thessaloniki, GR, Greece.,Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikos Papakonstantinou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, 6th km Charilaou-Thermi Rd, 57001, Thermi, Thessaloniki, GR, Greece
| | - Theodoros Moysiadis
- Institute of Applied Biosciences, Center for Research and Technology Hellas, 6th km Charilaou-Thermi Rd, 57001, Thermi, Thessaloniki, GR, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Larry Mansouri
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Martí Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain
| | - Andigoni Malousi
- Laboratory of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ana C Queirós
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain
| | - Karla Plevova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Medical Faculty of Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sujata Bhoi
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Panagoula Kollia
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - David Oscier
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | | | - Livio Trentin
- Department of Medicine, Hematology and Clinical Immunology Branch, Padua University School of Medicine, Padua, Italy
| | - Matthias Ritgen
- Second Medical Department, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Sarka Pospisilova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Medical Faculty of Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Paolo Ghia
- Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy
| | - Jose I Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas, 6th km Charilaou-Thermi Rd, 57001, Thermi, Thessaloniki, GR, Greece. .,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
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36
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Komkov A, Miroshnichenkova A, Nugmanov G, Popov A, Pogorelyy M, Zapletalova E, Jelinkova H, Pospisilova S, Lebedev Y, Chudakov D, Olshanskaya Y, Plevova K, Maschan M, Mamedov I. High‐throughput sequencing of T‐cell receptor alpha chain clonal rearrangements at the DNA level in lymphoid malignancies. Br J Haematol 2019; 188:723-731. [DOI: 10.1111/bjh.16230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/04/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Alexander Komkov
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Anna Miroshnichenkova
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Gaiaz Nugmanov
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
| | - Alexander Popov
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Mikhail Pogorelyy
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Department of Molecular Technologies Pirogov Russian National Research Medical University Moscow Russia
| | - Eva Zapletalova
- Department of Internal Medicine, Haematology and Oncology University Hospital Brno and Faculty of Medicine Masaryk University Brno Czech Republic
| | - Hana Jelinkova
- Department of Internal Medicine, Haematology and Oncology University Hospital Brno and Faculty of Medicine Masaryk University Brno Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine, Haematology and Oncology University Hospital Brno and Faculty of Medicine Masaryk University Brno Czech Republic
- Central European Institute of Technology Masaryk University Brno Czech Republic
| | - Yuri Lebedev
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Department of Molecular Technologies Pirogov Russian National Research Medical University Moscow Russia
| | - Dmitriy Chudakov
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Department of Molecular Technologies Pirogov Russian National Research Medical University Moscow Russia
- Central European Institute of Technology Masaryk University Brno Czech Republic
| | - Yulia Olshanskaya
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Karla Plevova
- Department of Internal Medicine, Haematology and Oncology University Hospital Brno and Faculty of Medicine Masaryk University Brno Czech Republic
- Central European Institute of Technology Masaryk University Brno Czech Republic
| | - Michael Maschan
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Ilgar Mamedov
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
- Department of Molecular Technologies Pirogov Russian National Research Medical University Moscow Russia
- Central European Institute of Technology Masaryk University Brno Czech Republic
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37
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Stranska K, Plevova K, Skuhrova Francova H, Skabrahova H, von Jagwitz-Biegnitz M, Radova L, Panovska A, Hrobkova S, Brychtova Y, Urbanova R, Smolej L, Simkovic M, Zuchnicka J, Mohammadova L, Spacek M, Mayer J, Pospisilova S, Doubek M. Profiling of biological and environmental risk factors in immunogenetic subgroups of chronic lymphocytic leukemia - Czech national study. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2019; 164:425-434. [PMID: 31558845 DOI: 10.5507/bp.2019.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/04/2019] [Indexed: 11/23/2022] Open
Abstract
AIMS This is a nation-wide survey of chronic lymphocytic leukemia (CLL) patients at six large hematology centers in the Czech Republic. The aim was to identify specific populations, social, and health characteristics of CLL subgroups divided according to the immunogenetic features of their B cell receptors (BCRs) and clonality. PATIENTS AND METHODS Questionnaires directed to specific health, social, and environmental conditions were collected in a cohort of 573 CLL patients. For these patients, immunoglobulin heavy chain gene rearrangements were also analyzed in order to gain information about their clonality, IGHV mutational status, and the presence of stereotyped BCRs. Data extracted from the questionnaires were analyzed statistically in the context of immunogenetic features of the cohort. RESULTS There were no statistically significant differences in the data collected in the survey between patients with mutated and patients with unmutated IGHV. However, patients with oligoclonal CLL reported health conditions such as hypercholesterolemia, hypertension, herpes simplex, tumors, and also, separately, CLL in 1st degree relatives, more often than their monoclonal counterparts. In patients with stereotyped BCRs, we found more frequent alcohol consumption and gastric infections in subset #1 cases and frequent cholecystectomies and familial CLL in subset #2 cases. CONCLUSION To the best of our knowledge, this study is the first to investigate CLL immunogenetic features and clonality in the context of epidemiological data. We reported statistically significant associations suggesting the influence of certain health and social conditions on a number of clonal populations expanding in CLL and also on characteristic BCR features, especially stereotypy.
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Affiliation(s)
- Kamila Stranska
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Hana Skuhrova Francova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Hana Skabrahova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Magdalena von Jagwitz-Biegnitz
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Radova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Stanislava Hrobkova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Yvona Brychtova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Renata Urbanova
- Department of Hemato-Oncology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Czech Republic
| | | | | | - Jana Zuchnicka
- Department of Hematooncology, University Hospital Ostrava, Czech Republic
| | - Lekaa Mohammadova
- Department of Hematology and Oncology, University Hospital Pilsen, Czech Republic
| | | | - Jiri Mayer
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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38
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Bereshchenko O, Lo Re O, Nikulenkov F, Flamini S, Kotaskova J, Mazza T, Le Pannérer MM, Buschbeck M, Giallongo C, Palumbo G, Li Volti G, Pazienza V, Cervinek L, Riccardi C, Krejci L, Pospisilova S, Stewart AF, Vinciguerra M. Deficiency and haploinsufficiency of histone macroH2A1.1 in mice recapitulate hematopoietic defects of human myelodysplastic syndrome. Clin Epigenetics 2019; 11:121. [PMID: 31439048 PMCID: PMC6704528 DOI: 10.1186/s13148-019-0724-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/12/2019] [Indexed: 12/19/2022] Open
Abstract
Background Epigenetic regulation is important in hematopoiesis, but the involvement of histone variants is poorly understood. Myelodysplastic syndromes (MDS) are heterogeneous clonal hematopoietic stem cell (HSC) disorders characterized by ineffective hematopoiesis. MacroH2A1.1 is a histone H2A variant that negatively correlates with the self-renewal capacity of embryonic, adult, and cancer stem cells. MacroH2A1.1 is a target of the frequent U2AF1 S34F mutation in MDS. The role of macroH2A1.1 in hematopoiesis is unclear. Results MacroH2A1.1 mRNA levels are significantly decreased in patients with low-risk MDS presenting with chromosomal 5q deletion and myeloid cytopenias and tend to be decreased in MDS patients carrying the U2AF1 S34F mutation. Using an innovative mouse allele lacking the macroH2A1.1 alternatively spliced exon, we investigated whether macroH2A1.1 regulates HSC homeostasis and differentiation. The lack of macroH2A1.1 decreased while macroH2A1.1 haploinsufficiency increased HSC frequency upon irradiation. Moreover, bone marrow transplantation experiments showed that both deficiency and haploinsufficiency of macroH2A1.1 resulted in enhanced HSC differentiation along the myeloid lineage. Finally, RNA-sequencing analysis implicated macroH2A1.1-mediated regulation of ribosomal gene expression in HSC homeostasis. Conclusions Together, our findings suggest a new epigenetic process contributing to hematopoiesis regulation. By combining clinical data with a discrete mutant mouse model and in vitro studies of human and mouse cells, we identify macroH2A1.1 as a key player in the cellular and molecular features of MDS. These data justify the exploration of macroH2A1.1 and associated proteins as therapeutic targets in hematological malignancies. Electronic supplementary material The online version of this article (10.1186/s13148-019-0724-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oxana Bereshchenko
- Department of Medicine, Department of Philosophy, Social Sciences and Education, University of Perugia, Perugia, Italy.
| | - Oriana Lo Re
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Fedor Nikulenkov
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sara Flamini
- Department of Medicine, Department of Philosophy, Social Sciences and Education, University of Perugia, Perugia, Italy
| | - Jana Kotaskova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Tommaso Mazza
- IRCCS Casa Sollievo della Sofferenza, Bioinformatics unit, San Giovanni Rotondo, Italy
| | - Marguerite-Marie Le Pannérer
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Campus ICO-Germans Trias I Pujol, Badalona, Spain.,Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Marcus Buschbeck
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Campus ICO-Germans Trias I Pujol, Badalona, Spain.,Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Cesarina Giallongo
- Division of Hematology, A.O.U. Policlinico-OVE, University of Catania, Catania, Italy
| | - Giuseppe Palumbo
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, Catania, Italy
| | - Giovanni Li Volti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Valerio Pazienza
- Gastroenterology unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Libor Cervinek
- Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Carlo Riccardi
- Department of Medicine, Department of Philosophy, Social Sciences and Education, University of Perugia, Perugia, Italy
| | - Lumir Krejci
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Manlio Vinciguerra
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.
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Moysiadis T, Baliakas P, Rossi D, Catherwood M, Strefford JC, Delgado J, Anagnostopoulos A, Belessi C, Stavroyianni N, Pospisilova S, Oscier D, Gaidano G, Campo E, Rosenquist R, Ghia P, Stamatopoulos K. Different time-dependent changes of risk for evolution in chronic lymphocytic leukemia with mutated or unmutated antigen B cell receptors. Leukemia 2019; 33:1801-1805. [PMID: 30679797 DOI: 10.1038/s41375-018-0322-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Theodoros Moysiadis
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Davide Rossi
- Division of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Mark Catherwood
- Department of Hemato-Oncology, Belfast City Hospital, Belfast, UK
| | - Jonathan C Strefford
- Cancer Genomics, Academic Unit of Cancer Sciences, Cancer Research UK Centre and Experimental Cancer Medicine Centre, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Julio Delgado
- Hematology Department, Hospital Clinic, Barcelona, Spain
| | | | | | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - David Oscier
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Elias Campo
- Hematopathology Section, Laboratory of Pathology, Hospital Clinic of Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Paolo Ghia
- Division of experimental Oncology, IRCCS Istituto Scientfico San Raffaele and Università Vita-Salute San Raffaele, Milan, Italy
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece.
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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40
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Hynst J, Plevova K, Radova L, Bystry V, Pal K, Pospisilova S. Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants. PeerJ 2019; 7:e7071. [PMID: 31223530 PMCID: PMC6571010 DOI: 10.7717/peerj.7071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 05/06/2019] [Indexed: 11/21/2022] Open
Abstract
Background Extensive genome rearrangements, known as chromothripsis, have been recently identified in several cancer types. Chromothripsis leads to complex structural variants (cSVs) causing aberrant gene expression and the formation of de novo fusion genes, which can trigger cancer development, or worsen its clinical course. The functional impact of cSVs can be studied at the RNA level using whole transcriptome sequencing (total RNA-Seq). It represents a powerful tool for discovering, profiling, and quantifying changes of gene expression in the overall genomic context. However, bioinformatic analysis of transcriptomic data, especially in cases with cSVs, is a complex and challenging task, and the development of proper bioinformatic tools for transcriptome studies is necessary. Methods We designed a bioinformatic workflow for the analysis of total RNA-Seq data consisting of two separate parts (pipelines): The first pipeline incorporates a statistical solution for differential gene expression analysis in a biologically heterogeneous sample set. We utilized results from transcriptomic arrays which were carried out in parallel to increase the precision of the analysis. The second pipeline is used for the identification of de novo fusion genes. Special attention was given to the filtering of false positives (FPs), which was achieved through consensus fusion calling with several fusion gene callers. We applied the workflow to the data obtained from ten patients with chronic lymphocytic leukemia (CLL) to describe the consequences of their cSVs in detail. The fusion genes identified by our pipeline were correlated with genomic break-points detected by genomic arrays. Results We set up a novel solution for differential gene expression analysis of individual samples and de novo fusion gene detection from total RNA-Seq data. The results of the differential gene expression analysis were concordant with results obtained by transcriptomic arrays, which demonstrates the analytical capabilities of our method. We also showed that the consensus fusion gene detection approach was able to identify true positives (TPs) efficiently. Detected coordinates of fusion gene junctions were in concordance with genomic breakpoints assessed using genomic arrays. Discussion Byapplying our methods to real clinical samples, we proved that our approach for total RNA-Seq data analysis generates results consistent with other genomic analytical techniques. The data obtained by our analyses provided clues for the study of the biological consequences of cSVs with far-reaching implications for clinical outcome and management of cancer patients. The bioinformatic workflow is also widely applicable for addressing other research questions in different contexts, for which transcriptomic data are generated.
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Affiliation(s)
- Jakub Hynst
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Lenka Radova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vojtech Bystry
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karol Pal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
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41
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Condoluci A, Terzi di Bergamo L, Langerbeins P, Hoechstetter M, Herling C, De Paoli L, Delgado J, Gentile M, Doubek M, Mauro F, Chiodin G, Mattsson M, Bahlo J, Cutrona G, Kotaskova J, Deambrogi C, Moia R, Gerber B, Zucca E, Ghielmini M, Cavalli F, Stüssi G, Neri A, Ferrarini M, Rosenquist R, Forconi F, Foà R, Pospisilova S, Morabito F, Wierda W, Montserrat E, Gaidano G, Hallek M, Rossi D. INTERNATIONAL PROGNOSTIC SCORE FOR EARLY STAGE CHRONIC LYMPHOCYTIC LEUKEMIA (IPS-A). Hematol Oncol 2019. [DOI: 10.1002/hon.51_2629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- A. Condoluci
- Experimental Hematology; Institute of Oncology Research; Oncology Institute of Southern Switzerland; Bellinzona Switzerland
| | - L. Terzi di Bergamo
- Experimental Hematology; Institute of Oncology Research; Bellinzona Switzerland
| | - P. Langerbeins
- University of Cologne; Center of Integrated Oncology Cologne-Bonn, German CLL Study Group; Köln Germany
| | - M. Hoechstetter
- University of Cologne; Center of Integrated Oncology Cologne-Bonn, German CLL Study Group; Köln Germany
| | - C. Herling
- University of Cologne; Center of Integrated Oncology Cologne-Bonn, German CLL Study Group; Köln Germany
| | - L. De Paoli
- Translational Medicine; University of Eastern Piedmont; Novara Italy
| | - J. Delgado
- Hematology; Hospital Clínic de Barcelona; Barcelona Spain
| | - M. Gentile
- Hematology; Azienda Ospedaliera (AO) of Cosenza; Cosenza Italy
| | - M. Doubek
- Hematology and Oncology; University Hospital of Brno; Brno Czech Republic
| | - F.R. Mauro
- Hematology; Sapienza University; Rome Italy
| | - G. Chiodin
- Hematology; Southampton University; Southampton United Kingdom
| | - M. Mattsson
- Immunology; Genetics and Pathology, Uppsala University; Uppsala Sweden
| | - J. Bahlo
- University of Cologne; Center of Integrated Oncology Cologne-Bonn, German CLL Study Group; Köln Germany
| | - G. Cutrona
- Hematology; IRCCS Ospedale Policlinico San Martino; Genoa Italy
| | - J. Kotaskova
- Hematology and Oncology; University Hospital of Brno; Brno Czech Republic
| | - C. Deambrogi
- Translational Medicine; University of Eastern Piedmont; Novara Italy
| | - R. Moia
- Translational Medicine; University of Eastern Piedmont; Novara Italy
| | - B. Gerber
- Onco-hematology; Oncology Institute of Southern Switzerland; Bellinzona Switzerland
| | - E. Zucca
- Onco-hematology; Oncology Institute of Southern Switzerland; Bellinzona Switzerland
| | - M. Ghielmini
- Onco-hematology; Oncology Institute of Southern Switzerland; Bellinzona Switzerland
| | - F. Cavalli
- Onco-hematology; Oncology Institute of Southern Switzerland; Bellinzona Switzerland
| | - G. Stüssi
- Onco-hematology; Oncology Institute of Southern Switzerland; Bellinzona Switzerland
| | - A. Neri
- Hematology; University of Milan; Milan Italy
| | | | - R. Rosenquist
- Immunology; Genetics and Pathology, Uppsala University; Uppsala Sweden
| | - F. Forconi
- Hematology; Southampton University; Southampton United Kingdom
| | - R. Foà
- Hematology; Sapienza University; Rome Italy
| | - S. Pospisilova
- Hematology and Oncology; University Hospital of Brno; Brno Czech Republic
| | - F. Morabito
- Hematology; Augusta Victoria Hospital; Jerusalem Israel
| | - W.G. Wierda
- MD Anderson Cancer Center; University of Texas; Houston United States
| | - E. Montserrat
- Hematology; Hospital Clínic de Barcelona; Barcelona Spain
| | - G. Gaidano
- Translational Medicine; University of Eastern Piedmont; Novara Italy
| | - M. Hallek
- University of Cologne; Center of Integrated Oncology Cologne-Bonn, German CLL Study Group; Köln Germany
| | - D. Rossi
- Experimental Hematology; Institute of Oncology Research; Oncology Institute of Southern Switzerland; Bellinzona Switzerland
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42
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Spunarova M, Tom N, Pavlova S, Mraz M, Brychtova Y, Doubek M, Panovska A, Skuhrova Francova H, Brzobohata A, Pospisilova S, Mayer J, Trbusek M. Impact of gene mutations and chromosomal aberrations on progression-free survival in chronic lymphocytic leukemia patients treated with front-line chemoimmunotherapy: Clinical practice experience. Leuk Res 2019; 81:75-81. [DOI: 10.1016/j.leukres.2019.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/16/2019] [Accepted: 04/24/2019] [Indexed: 02/03/2023]
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43
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Mraz M, Pospisilova S. Detection of a deletion at 22q11 locus involving ZNF280A/ZNF280B/PRAME/GGTLC2 in B-cell malignancies: simply a consequence of an immunoglobulin lambda light chain rearrangement. Br J Haematol 2019; 186:e91-e94. [PMID: 30989644 DOI: 10.1111/bjh.15922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Marek Mraz
- Molecular Medicine, CEITEC Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Haematology and Oncology, University Hospital Brno and Faculty of Medicine MU, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine, Haematology and Oncology, University Hospital Brno and Faculty of Medicine MU, Brno, Czech Republic
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Xochelli A, Bikos V, Polychronidou E, Galigalidou C, Agathangelidis A, Charlotte F, Moschonas P, Davis Z, Colombo M, Roumelioti M, Sutton LA, Groenen P, van den Brand M, Boudjoghra M, Algara P, Traverse-Glehen A, Ferrer A, Stalika E, Karypidou M, Kanellis G, Kalpadakis C, Mollejo M, Pangalis G, Vlamos P, Amini RM, Pospisilova S, Gonzalez D, Ponzoni M, Anagnostopoulos A, Giudicelli V, Lefranc MP, Espinet B, Panagiotidis P, Piris MA, Du MQ, Rosenquist R, Papadaki T, Belessi C, Ferrarini M, Oscier D, Tzovaras D, Ghia P, Davi F, Hadzidimitriou A, Stamatopoulos K. Disease-biased and shared characteristics of the immunoglobulin gene repertoires in marginal zone B cell lymphoproliferations. J Pathol 2019; 247:416-421. [PMID: 30484876 DOI: 10.1002/path.5209] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 11/12/2018] [Accepted: 11/21/2018] [Indexed: 01/14/2023]
Abstract
The B cell receptor immunoglobulin (Ig) gene repertoires of marginal zone (MZ) lymphoproliferations were analyzed in order to obtain insight into their ontogenetic relationships. Our cohort included cases with MZ lymphomas (n = 488), i.e. splenic (SMZL), nodal (NMZL) and extranodal (ENMZL), as well as provisional entities (n = 76), according to the WHO classification. The most striking Ig gene repertoire skewing was observed in SMZL. However, restrictions were also identified in all other MZ lymphomas studied, particularly ENMZL, with significantly different Ig gene distributions depending on the primary site of involvement. Cross-entity comparisons of the MZ Ig sequence dataset with a large dataset of Ig sequences (MZ-related or not; n = 65 837) revealed four major clusters of cases sharing homologous ('public') heavy variable complementarity-determining region 3. These clusters included rearrangements from SMZL, ENMZL (gastric, salivary gland, ocular adnexa), chronic lymphocytic leukemia, but also rheumatoid factors and non-malignant splenic MZ cells. In conclusion, different MZ lymphomas display biased immunogenetic signatures indicating distinct antigen exposure histories. The existence of rare public stereotypes raises the intriguing possibility that common, pathogen-triggered, immune-mediated mechanisms may result in diverse B lymphoproliferations due to targeting versatile progenitor B cells and/or operating in particular microenvironments. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Aliki Xochelli
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Vasilis Bikos
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Eleftheria Polychronidou
- Information Technologies Institute, CERTH, Thessaloniki, Greece
- Department of Informatics, Ionian University, Corfu, Greece
| | | | - Andreas Agathangelidis
- Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy
| | - Frédéric Charlotte
- Department of Pathology, Hopital Pitie-Salpetriere and Sorbonne University, Paris, France
| | | | - Zadie Davis
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Monica Colombo
- Molecular Pathology, Ospedale Policlinico SanMartino, Genoa, Italy
| | - Maria Roumelioti
- First Department of Propaedeutic Medicine, University of Athens, Athens, Greece
| | - Lesley-Ann Sutton
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Patricia Groenen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michiel van den Brand
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Myriam Boudjoghra
- Department of Hematology, Hopital Pitie-Salpetriere and Sorbonne University, Paris, France
| | | | | | - Ana Ferrer
- Laboratori de Citologia Hematològica i Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | | | - Maria Karypidou
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - George Kanellis
- Hematopathology Department, Evangelismos Hospital, Athens, Greece
| | | | | | | | | | - Rose-Marie Amini
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - David Gonzalez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | | | | | - Véronique Giudicelli
- IMGT®, the international ImMunoGeneTics Information System®, Université de Montpellier, LIGM, Institut de Génétique Humaine IGH, UMR CNRS UM, Montpellier, France
| | - Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics Information System®, Université de Montpellier, LIGM, Institut de Génétique Humaine IGH, UMR CNRS UM, Montpellier, France
| | - Blanca Espinet
- Laboratori de Citologia Hematològica i Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | | | | | - Ming-Qing Du
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Manlio Ferrarini
- Direzione Scientifica, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria (AOU) San Martino-IST, Genoa, Italy
| | - David Oscier
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | | | - Paolo Ghia
- Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy
| | - Frederic Davi
- Department of Hematology, Hopital Pitie-Salpetriere and Sorbonne University, Paris, France
| | - Anastasia Hadzidimitriou
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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45
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Baliakas P, Moysiadis T, Hadzidimitriou A, Xochelli A, Jeromin S, Agathangelidis A, Mattsson M, Sutton LA, Minga E, Scarfò L, Rossi D, Davis Z, Villamor N, Parker H, Kotaskova J, Stalika E, Plevova K, Mansouri L, Cortese D, Navarro A, Delgado J, Larrayoz M, Young E, Anagnostopoulos A, Smedby KE, Juliusson G, Sheehy O, Catherwood M, Strefford JC, Stavroyianni N, Belessi C, Pospisilova S, Oscier D, Gaidano G, Campo E, Haferlach C, Ghia P, Rosenquist R, Stamatopoulos K. Tailored approaches grounded on immunogenetic features for refined prognostication in chronic lymphocytic leukemia. Haematologica 2019; 104:360-369. [PMID: 30262567 PMCID: PMC6355487 DOI: 10.3324/haematol.2018.195032] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 09/25/2018] [Indexed: 12/21/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) patients with differential somatic hypermutation status of the immunoglobulin heavy variable genes, namely mutated or unmutated, display fundamental clinico-biological differences. Considering this, we assessed prognosis separately within mutated (M-CLL) and unmutated (U-CLL) CLL in 3015 patients, hypothesizing that the relative significance of relevant indicators may differ between these two categories. Within Binet A M-CLL patients, besides TP53 abnormalities, trisomy 12 and stereotyped subset #2 membership were equivalently associated with the shortest time-to-first-treatment and a treatment probability at five and ten years after diagnosis of 40% and 55%, respectively; the remaining cases exhibited 5-year and 10-year treatment probability of 12% and 25%, respectively. Within Binet A U-CLL patients, besides TP53 abnormalities, del(11q) and/or SF3B1 mutations were associated with the shortest time-to-first-treatment (5- and 10-year treatment probability: 78% and 98%, respectively); in the remaining cases, males had a significantly worse prognosis than females. In conclusion, the relative weight of indicators that can accurately risk stratify early-stage CLL patients differs depending on the somatic hypermutation status of the immunoglobulin heavy variable genes of each patient. This finding highlights the fact that compartmentalized approaches based on immunogenetic features are necessary to refine and tailor prognostication in CLL.
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MESH Headings
- Aged
- Aged, 80 and over
- Biomarkers, Tumor
- Chromosome Aberrations
- Disease Susceptibility
- Female
- Humans
- Immunogenetics
- Kaplan-Meier Estimate
- Leukemia, Lymphocytic, Chronic, B-Cell/etiology
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Male
- Mutation
- Neoplasm Staging
- Prognosis
- Time-to-Treatment
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Affiliation(s)
- Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Theodoros Moysiadis
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Anastasia Hadzidimitriou
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Aliki Xochelli
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | | | - Andreas Agathangelidis
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Mattias Mattsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Eva Minga
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Lydia Scarfò
- Division of Experimental Oncology, IRCCS Istituto Scientifico San Raffaele and Università Vita-Salute San Raffaele, Milan, Italy
| | - Davide Rossi
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Zadie Davis
- Department of Haematology, Royal Bournemouth Hospital, UK
| | - Neus Villamor
- Hemopathology Unit, Hospital Clinic, Barcelona, Spain
| | - Helen Parker
- Cancer Genomics, Academic Unit of Cancer Sciences, Cancer Research UK Centre and Experimental Cancer Medicine Centre, Faculty of Medicine, University of Southampton, UK
| | - Jana Kotaskova
- Central European Institute of Technology, Masaryk University and University Hospital Brno, Czech Republic
| | - Evangelia Stalika
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University and University Hospital Brno, Czech Republic
| | - Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Diego Cortese
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Alba Navarro
- Hemopathology Unit, Hospital Clinic, Barcelona, Spain
| | - Julio Delgado
- Hematology Department, Hospital Clinic, Barcelona, Spain
| | - Marta Larrayoz
- Cancer Genomics, Academic Unit of Cancer Sciences, Cancer Research UK Centre and Experimental Cancer Medicine Centre, Faculty of Medicine, University of Southampton, UK
| | - Emma Young
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | | | - Karin E Smedby
- Department of Medicine, Solna, Clinical Epidemiology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Gunnar Juliusson
- Lund University and Hospital Department of Hematology, Lund Stem Cell Center, Sweden
| | - Oonagh Sheehy
- Department of Hemato-Oncology, Belfast City Hospital, UK
| | | | - Jonathan C Strefford
- Cancer Genomics, Academic Unit of Cancer Sciences, Cancer Research UK Centre and Experimental Cancer Medicine Centre, Faculty of Medicine, University of Southampton, UK
| | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | | | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University and University Hospital Brno, Czech Republic
| | - David Oscier
- Department of Haematology, Royal Bournemouth Hospital, UK
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Elias Campo
- Hemopathology Unit, Hospital Clinic, Barcelona, Spain
- Department of Pathology, University of Barcelona, Spain
| | | | - Paolo Ghia
- Division of Experimental Oncology, IRCCS Istituto Scientifico San Raffaele and Università Vita-Salute San Raffaele, Milan, Italy
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
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Pospisilova S, Pazourkova E, Horinek A, Brisuda A, Svobodova I, Soukup V, Hrbacek J, Capoun O, Hanus T, Mares J, Korabecna M, Babjuk M. MicroRNAs in urine supernatant as potential non-invasive markers for bladder cancer detection. Neoplasma 2019; 63:799-808. [PMID: 27468885 DOI: 10.4149/neo_2016_518] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Urinary bladder carcinoma contributes to 4% of newly diagnosed oncological diseases in the Czech Republic. Biomarkers for its early non-invasive detection are therefore highly desirable. Urine seems to be an ideal source of such biomarkers due to the content of cell-free nucleic acids, especially microRNAs (miRNAs).To find potential biomarkers among miRNAs in urine supernatant, we examined in total 109 individuals (36 controls and 73 bladder cancer patients) in three phases. In the first - discovery - phase, microarray cards with 381 miRNAs were used for miRNA analysis of 13 controls and 46 bladder cancer patients. In the second - verification - phase, the results of this first phase were verified on the same groups of subjects by single-target qPCR assays for the selected miRNAs. For the third - validation - phase, new independent samples of urine supernatant (23 controls and 27 bladder cancer patients) were analyzed using single-target qPCR assays for 13 verified in the previous phase. The results of all phases were normalized to miR-191, miR-28-3p, and miR-200b, which were selected as suitable for our study by the qBase+®.We found that miR-125b, miR-30b, miR-204, miR-99a, and miR-532-3p are significantly down-regulated in patients' urine supernatant. In our experiments, the analysis of miR-125 levels provided the highest AUC (0.801) with 95.65% specificity and 59.26% sensitivity, the analysis of miR-99a lead to AUC (0.738) with 82.61% specificity and 74.07% sensitivity. We demonstrate that levels of these miRNAs could potentially serve as promising diagnostic markers for the non-invasive diagnostics of bladder cancer.
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Papakonstantinou N, Ntoufa S, Tsagiopoulou M, Moysiadis T, Bhoi S, Malousi A, Psomopoulos F, Mansouri L, Laidou S, Papazoglou D, Gounari M, Pasentsis K, Plevova K, Kuci-Emruli V, Duran-Ferrer M, Davis Z, Ek S, Rossi D, Gaidano G, Ritgen M, Oscier D, Stavroyianni N, Pospisilova S, Davi F, Ghia P, Hadzidimitriou A, Belessi C, Martin-Subero JI, Pott C, Rosenquist R, Stamatopoulos K. Integrated epigenomic and transcriptomic analysis reveals TP63 as a novel player in clinically aggressive chronic lymphocytic leukemia. Int J Cancer 2019; 144:2695-2706. [PMID: 30447004 DOI: 10.1002/ijc.31999] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 10/01/2018] [Accepted: 10/29/2018] [Indexed: 01/19/2023]
Abstract
Chronic lymphocytic leukemia (CLL) stereotyped subsets #6 and #8 include cases expressing unmutated B cell receptor immunoglobulin (BcR IG) (U-CLL). Subset #6 (IGHV1-69/IGKV3-20) is less aggressive compared to subset #8 (IGHV4-39/IGKV1(D)-39) which has the highest risk for Richter's transformation among all CLL. The underlying reasons for this divergent clinical behavior are not fully elucidated. To gain insight into this issue, here we focused on epigenomic signatures and their links with gene expression, particularly investigating genome-wide DNA methylation profiles in subsets #6 and #8 as well as other U-CLL cases not expressing stereotyped BcR IG. We found that subset #8 showed a distinctive DNA methylation profile compared to all other U-CLL cases, including subset #6. Integrated analysis of DNA methylation and gene expression revealed significant correlation for several genes, particularly highlighting a relevant role for the TP63 gene which was hypomethylated and overexpressed in subset #8. This observation was validated by quantitative PCR, which also revealed TP63 mRNA overexpression in additional nonsubset U-CLL cases. BcR stimulation had distinct effects on p63 protein expression, particularly leading to induction in subset #8, accompanied by increased CLL cell survival. This pro-survival effect was also supported by siRNA-mediated downregulation of p63 expression resulting in increased apoptosis. In conclusion, we report that DNA methylation profiles may vary even among CLL patients with similar somatic hypermutation status, supporting a compartmentalized approach to dissecting CLL biology. Furthermore, we highlight p63 as a novel prosurvival factor in CLL, thus identifying another piece of the complex puzzle of clinical aggressiveness.
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Affiliation(s)
- Nikos Papakonstantinou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stavroula Ntoufa
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maria Tsagiopoulou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Theodoros Moysiadis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Sujata Bhoi
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andigoni Malousi
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Laboratory of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Stamatia Laidou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Despoina Papazoglou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Maria Gounari
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Konstantinos Pasentsis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Karla Plevova
- Center of Molecular Biology and Gene Therapy, Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Medical Faculty of the Masaryk University, Brno, Czech republic
| | - Venera Kuci-Emruli
- Department of Immunotechnology, Faculty of Engineering, Lund University, Sweden
| | - Marti Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain
| | - Zadie Davis
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Sara Ek
- Department of Immunotechnology, Faculty of Engineering, Lund University, Sweden
| | - Davide Rossi
- Hematology, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Matthias Ritgen
- Second Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany
| | - David Oscier
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Sarka Pospisilova
- Center of Molecular Biology and Gene Therapy, Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Medical Faculty of the Masaryk University, Brno, Czech republic
| | - Frederic Davi
- Hematology Department and University Pierre et Marie Curie, Paris, France
| | - Paolo Ghia
- Division of Experimental Oncology, Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy
| | - Anastasia Hadzidimitriou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | | | - Jose I Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain
| | - Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Olbertova H, Plevova K, Stranska K, Pospisilova S. Telomere dynamics in adult hematological malignancies. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2019; 163:1-7. [PMID: 30631211 DOI: 10.5507/bp.2018.084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/19/2018] [Indexed: 02/08/2023] Open
Abstract
Telomeres are repetitive DNA sequences protecting physical ends of linear chromosomes against degradation and end-to-end chromosomal fusion. Telomeres shorten with each cell division, which regulates the cellular lifespan in somatic cells and limits their renewal capacity. Cancer cells are often able to overcome this physiological barrier and become immortal with unlimited replicative capacity. In this review, we present current knowledge on the role of telomeres in human aging with a focus on their behavior in hematological malignancies of adults. Associations of telomere length to age-related diseases and to the prevention of telomere shortening are also discussed.
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Affiliation(s)
- Helena Olbertova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Kamila Stranska
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Vonkova B, Blahakova I, Hruban L, Janku P, Pospisilova S. MicroRNA-210 expression during childbirth and postpartum as a potential biomarker of acute fetal hypoxia. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2018; 163:259-264. [PMID: 30565568 DOI: 10.5507/bp.2018.075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE To explore whether miR-210 expression can be used as a diagnostic and prognostic marker in acute fetal hypoxia. METHODS Whole blood samples of 29 women and their fetuses without hypoxia and 24 women and their fetuses with hypoxia were analysed in this study. Reverse transcription and quantitative real-time PCR were used to measure the expression of miR-210. Expression level differences between the control and hypoxic group in labour time and postpartum change fold were analyzed by standard statistical tests. RESULTS We confirmed that miR-210 is significantly more upregulated in fetal blood with acute hypoxia when compared to maternal blood (P Conclusions: Our study confirmed miR-210 upregulation in the blood of pregnant women with acute fetal hypoxia at the time of labour compared to pregnant women without acute fetal hypoxia. Additional investigation should be done to determine miR-210 clearance and the possibility of using miR-210 as a diagnostic and prognostic marker.
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Affiliation(s)
- Barbara Vonkova
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Center of Molecular Biology and Gene Therapy, Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Czech Republic.,Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ivona Blahakova
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Center of Molecular Biology and Gene Therapy, Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Czech Republic
| | - Lukas Hruban
- Department of Gynaecology and Obstetrics, The University Hospital Brno, Czech Republic
| | - Petr Janku
- Department of Gynaecology and Obstetrics, The University Hospital Brno, Czech Republic
| | - Sarka Pospisilova
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Center of Molecular Biology and Gene Therapy, Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Czech Republic
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50
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Campo E, Cymbalista F, Ghia P, Jäger U, Pospisilova S, Rosenquist R, Schuh A, Stilgenbauer S. TP53 aberrations in chronic lymphocytic leukemia: an overview of the clinical implications of improved diagnostics. Haematologica 2018; 103:1956-1968. [PMID: 30442727 PMCID: PMC6269313 DOI: 10.3324/haematol.2018.187583] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/26/2018] [Indexed: 12/19/2022] Open
Abstract
Chronic lymphocytic leukemia is associated with a highly heterogeneous disease course in terms of clinical outcomes and responses to chemoimmunotherapy. This heterogeneity is partly due to genetic aberrations identified in chronic lymphocytic leukemia cells such as mutations of TP53 and/or deletions in chromosome 17p [del(17p)], resulting in loss of one TP53 allele. These aberrations are associated with markedly decreased survival and predict impaired response to chemoimmunotherapy thus being among the strongest predictive markers guiding treatment decisions in chronic lymphocytic leukemia. Clinical trials demonstrate the importance of accurately testing for TP53 aberrations [both del(17p) and TP53 mutations] before each line of treatment to allow for appropriate treatment decisions that can optimize patients' outcomes. The current report reviews the diagnostic methods to detect TP53 disruption better, the role of TP53 aberrations in treatment decisions and current therapies available for patients with chronic lymphocytic leukemia carrying these abnormalities. The standardization in sequencing technologies for accurate identification of TP53 mutations and the importance of continued evaluation of TP53 aberrations throughout initial and subsequent lines of therapy remain unmet clinical needs as new therapeutic alternatives become available.
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Affiliation(s)
- Elias Campo
- Hospital Clinic of Barcelona, University of Barcelona, Institute of Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona, and CIBERONC, Spain
| | - Florence Cymbalista
- Hôpital Avicenne, AP-HP, UMR INSERMU978/Paris 13 University, Bobigny, France
| | - Paolo Ghia
- Università Vita-Salute San Raffaele and IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Sarka Pospisilova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Stephan Stilgenbauer
- Internal Medicine III, Ulm University, Germany and Innere Medizin I, Universitätsklinikum des Saarlandes, Homburg, Germany
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