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Pérez Carretero C, González T, Quijada Álamo M, Rigolin GM, Dubuc A, Villaverde Ramiro Á, Rodríguez-Sánchez A, Rubio A, Dávila J, Vidal MJ, González Gascón Y Marín I, Hernández-Rivas JÁ, Benito R, Volpe V, Davids MS, Abramson JS, Cuneo A, Dal Cin P, Rodríguez-Vicente AE, Hernández-Rivas JM. Chronic lymphocytic leukemia patients with chromosome 6q deletion as the sole cytogenetic abnormality display a high frequency of RPS15 mutations and have a poor prognosis. Am J Hematol 2024; 99:1845-1848. [PMID: 38949404 DOI: 10.1002/ajh.27421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/10/2024] [Accepted: 06/03/2024] [Indexed: 07/02/2024]
Affiliation(s)
- Claudia Pérez Carretero
- University of Salamanca, IBSAL, IBMCC, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Teresa González
- University of Salamanca, IBSAL, IBMCC, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Miguel Quijada Álamo
- University of Salamanca, IBSAL, IBMCC, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | | | - Adrian Dubuc
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ángela Villaverde Ramiro
- University of Salamanca, IBSAL, IBMCC, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Alberto Rodríguez-Sánchez
- University of Salamanca, IBSAL, IBMCC, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Araceli Rubio
- Department of Hematology, Hospital Miguel Servet, Zaragoza, Spain
| | - Julio Dávila
- Department of Hematology, Hospital Nuestra Señora de Sonsoles, Ávila, Spain
| | - Mª Jesús Vidal
- Department of Hematology, Hospital Universitario, León, Spain
| | | | | | - Rocío Benito
- University of Salamanca, IBSAL, IBMCC, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Virginia Volpe
- Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | | | | | - Antonio Cuneo
- Hematology Section, St. Anna University Hospital, Ferrara, Italy
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ana-Eugenia Rodríguez-Vicente
- University of Salamanca, IBSAL, IBMCC, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
- Department of Human Anatomy and Histology, Faculty of Medicine, University of Salamanca, Salamanca, Spain
| | - Jesús-María Hernández-Rivas
- University of Salamanca, IBSAL, IBMCC, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
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Turk A, Čeh E, Calin GA, Kunej T. Multiple omics levels of chronic lymphocytic leukemia. Cell Death Discov 2024; 10:293. [PMID: 38906881 PMCID: PMC11192936 DOI: 10.1038/s41420-024-02068-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a lymphoproliferative malignancy characterized by the proliferation of functionally mature but incompetent B cells. It is the most prevalent type of leukemia in Western populations, accounting for approximately 25% of new leukemia cases. While recent advances, such as ibrutinib and venetoclax treatment have improved patient outlook, aggressive forms of CLL such as Richter transformation still pose a significant challenge. This discrepancy may be due to the heterogeneity of factors contributing to CLL development at multiple -omics levels. However, information on the omics of CLL is fragmented, hindering multi-omics-based research into potential treatment options. To address this, we aggregated and presented a selection of important aspects of various omics levels of the disease in this review. The purpose of the present literature analysis is to portray examples of CLL studies from different omics levels, including genomics, epigenomics, transcriptomics, epitranscriptomics, proteomics, epiproteomics, metabolomics, glycomics and lipidomics, as well as those identified by multi-omics approaches. The review includes the list of 102 CLL-associated genes with relevant genomics information. While single-omics studies yield substantial and useful data, they omit a significant level of complex biological interplay present in the disease. As multi-omics studies integrate several different layers of data, they may be better suited for complex diseases such as CLL and have thus far yielded promising results. Future multi-omics studies may assist clinicians in improved treatment choices based on CLL subtypes as well as allow the identification of novel biomarkers and targets for treatments.
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Grants
- P4-0220 Javna Agencija za Raziskovalno Dejavnost RS (Slovenian Research Agency)
- Dr. Calin is the Felix L. Haas Endowed Professor in Basic Science. Work in G.A.C.’s laboratory is supported by NCI grants 1R01 CA182905-01 and 1R01CA222007-01A1, NIGMS grant 1R01GM122775-01, DoD Idea Award W81XWH-21-1-0030, a Team DOD grant in Gastric Cancer W81XWH-21-1-0715, a Chronic Lymphocytic Leukemia Moonshot Flagship project, a CLL Global Research Foundation 2019 grant, a CLL Global Research Foundation 2020 grant, a CLL Global Research Foundation 2022 grant, The G. Harold & Leila Y. Mathers Foundation, two grants from Torrey Coast Foundation, an Institutional Research Grant and Development Grant associated with the Brain SPORE 2P50CA127001.
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Affiliation(s)
- Aleksander Turk
- Clinical Institute of Genomic Medicine, University Clinical Centre Ljubljana, Ljubljana, Slovenia
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Eva Čeh
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - George A Calin
- Department of Translational Molecular Pathology, Division of Pathology, MD Anderson Cancer Center, University of Texas, Houston, TX, 77030, USA.
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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3
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Sud A, Parry EM, Wu CJ. The molecular map of CLL and Richter's syndrome. Semin Hematol 2024; 61:73-82. [PMID: 38368146 DOI: 10.1053/j.seminhematol.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 02/19/2024]
Abstract
Clonal expansion of B-cells, from the early stages of monoclonal B-cell lymphocytosis through to chronic lymphocytic leukemia (CLL), and then in some cases to Richter's syndrome (RS) provides a comprehensive model of cancer evolution, notable for the marked morphological transformation and distinct clinical phenotypes. High-throughput sequencing of large cohorts of patients and single-cell studies have generated a molecular map of CLL and more recently, of RS, yielding fundamental insights into these diseases and of clonal evolution. A selection of CLL driver genes have been functionally interrogated to yield novel insights into the biology of CLL. Such findings have the potential to impact patient care through risk stratification, treatment selection and drug discovery. However, this molecular map remains incomplete, with extant questions concerning the origin of the B-cell clone, the role of the TME, inter- and intra-compartmental heterogeneity and of therapeutic resistance mechanisms. Through the application of multi-modal single-cell technologies across tissues, disease states and clinical contexts, these questions can now be addressed with the answers holding great promise of generating translatable knowledge to improve patient care.
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Affiliation(s)
- Amit Sud
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Department of Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Erin M Parry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA.
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Department of Medicine, Brigham and Women's Hospital, Boston, MA
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4
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Ong SY, Wang L. Leveraging genomics, transcriptomics and epigenomics to understand chemoimmunotherapy resistance in chronic lymphocytic leukemia. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2024; 7:7. [PMID: 38434768 PMCID: PMC10905154 DOI: 10.20517/cdr.2023.98] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Patients with chronic lymphocytic leukemia (CLL) have differing clinical outcomes. Recent advances integrating multi-omic data have uncovered molecular subtypes in CLL with different prognostic implications and may allow better prediction of therapy response. While finite-duration chemoimmunotherapy (CIT) has enabled deep responses and prolonged duration of responses in the past, the advent of novel targeted therapy for the treatment of CLL has dramatically changed the therapeutic landscape. In this review, we discuss the latest genomic, transcriptomic, and epigenetic alterations regarded as major drivers of resistance to CIT in CLL. Further advances in genomic medicine will allow for better prediction of response to therapy and provide the basis for rational selection of therapy for long-term remissions with minimal toxicity.
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Affiliation(s)
- Shin Yeu Ong
- Department of Hematology/Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010, USA
- Department of Hematology, Singapore General Hospital, Singapore 169608, Singapore
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
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Cooper A, Tumuluru S, Kissick K, Venkataraman G, Song JY, Lytle A, Duns G, Yu J, Kotlov N, Bagaev A, Hodkinson B, Srinivasan S, Smith SM, Scott DW, Steidl C, Godfrey JK, Kline J. CD5 Gene Signature Identifies Diffuse Large B-Cell Lymphomas Sensitive to Bruton's Tyrosine Kinase Inhibition. J Clin Oncol 2024; 42:467-480. [PMID: 38079587 DOI: 10.1200/jco.23.01574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/29/2023] [Accepted: 09/13/2023] [Indexed: 01/31/2024] Open
Abstract
PURPOSE A genetic classifier termed LymphGen accurately identifies diffuse large B-cell lymphoma (DLBCL) subtypes vulnerable to Bruton's tyrosine kinase inhibitors (BTKis), but is challenging to implement in the clinic and fails to capture all DLBCLs that benefit from BTKi-based therapy. Here, we developed a novel CD5 gene expression signature as a biomarker of response to BTKi-based therapy in DLBCL. METHODS CD5 immunohistochemistry (IHC) was performed on 404 DLBCLs to identify CD5 IHC+ and CD5 IHC- cases, which were subsequently characterized at the molecular level through mutational and transcriptional analyses. A 60-gene CD5 gene expression signature (CD5sig) was constructed using genes differentially expressed between CD5 IHC+ and CD5 IHC- non-germinal center B-cell-like (non-GCB DLBCL) DLBCLs. This CD5sig was applied to external DLBCL data sets, including pretreatment biopsies from patients enrolled in the PHOENIX study (n = 584) to define the extent to which the CD5sig could identify non-GCB DLBCLs that benefited from the addition of ibrutinib to rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). RESULTS CD5 expression was observed in 12% of non-GCB DLBCLs. CD5+ DLBCLs displayed transcriptional features of B-cell receptor (BCR) activation and were enriched for BCR-activating mutations known to correlate with BTKi sensitivity. However, most CD5+ DLBCLs lacked canonical BCR-activating mutations or were LymphGen-unclassifiable (LymphGen-Other). The CD5sig recapitulated these findings in multiple independent data sets, indicating its utility in identifying DLBCLs with genetic and nongenetic bases for BCR dependence. Supporting this notion, CD5sig+ DLBCLs derived a selective survival advantage from the addition of ibrutinib to R-CHOP in the PHOENIX study, independent of LymphGen classification. CONCLUSION CD5sig is a useful biomarker to identify DLBCLs vulnerable to BTKi-based therapies and complements current biomarker approaches by identifying DLBCLs with genetic and nongenetic bases for BTKi sensitivity.
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Affiliation(s)
- Alan Cooper
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL
| | - Sravya Tumuluru
- Committee on Cancer Biology, University of Chicago, Chicago, IL
| | - Kyle Kissick
- Department of Pathology, University of Chicago, Chicago, IL
| | | | - Joo Y Song
- Department of Pathology, City of Hope, Duarte, CA
| | - Andrew Lytle
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC
| | - Gerben Duns
- Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Jovian Yu
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL
| | | | | | - Brendan Hodkinson
- Oncology Translational Research, Janssen Research & Development, Spring House, PA
| | - Srimathi Srinivasan
- Oncology Translational Research, Janssen Research & Development, Lower Gwynedd Township, PA
| | - Sonali M Smith
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL
| | - David W Scott
- Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Christian Steidl
- Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - James K Godfrey
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope, Duarte, CA
| | - Justin Kline
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL
- Committee on Cancer Biology, University of Chicago, Chicago, IL
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Largeot A, Klapp V, Viry E, Gonder S, Fernandez Botana I, Blomme A, Benzarti M, Pierson S, Duculty C, Marttila P, Wierz M, Gargiulo E, Pagano G, An N, El Hachem N, Perez Hernandez D, Chakraborty S, Ysebaert L, François JH, Cortez Clemente S, Berchem G, Efremov DG, Dittmar G, Szpakowska M, Chevigné A, Nazarov PV, Helleday T, Close P, Meiser J, Stamatopoulos B, Désaubry L, Paggetti J, Moussay E. Inhibition of MYC translation through targeting of the newly identified PHB-eIF4F complex as a therapeutic strategy in CLL. Blood 2023; 141:3166-3183. [PMID: 37084385 PMCID: PMC10646824 DOI: 10.1182/blood.2022017839] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/08/2023] [Accepted: 03/05/2023] [Indexed: 04/23/2023] Open
Abstract
Dysregulation of messenger RNA (mRNA) translation, including preferential translation of mRNA with complex 5' untranslated regions such as the MYC oncogene, is recognized as an important mechanism in cancer. Here, we show that both human and murine chronic lymphocytic leukemia (CLL) cells display a high translation rate, which is inhibited by the synthetic flavagline FL3, a prohibitin (PHB)-binding drug. A multiomics analysis performed in samples from patients with CLL and cell lines treated with FL3 revealed the decreased translation of the MYC oncogene and of proteins involved in cell cycle and metabolism. Furthermore, inhibiting translation induced a proliferation arrest and a rewiring of MYC-driven metabolism. Interestingly, contrary to other models, the RAS-RAF-(PHBs)-MAPK pathway is neither impaired by FL3 nor implicated in translation regulation in CLL cells. Here, we rather show that PHBs are directly associated with the eukaryotic initiation factor (eIF)4F translation complex and are targeted by FL3. Knockdown of PHBs resembled FL3 treatment. Importantly, inhibition of translation controlled CLL development in vivo, either alone or combined with immunotherapy. Finally, high expression of translation initiation-related genes and PHBs genes correlated with poor survival and unfavorable clinical parameters in patients with CLL. Overall, we demonstrated that translation inhibition is a valuable strategy to control CLL development by blocking the translation of several oncogenic pathways including MYC. We also unraveled a new and direct role of PHBs in translation initiation, thus creating new therapeutic opportunities for patients with CLL.
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MESH Headings
- Humans
- Mice
- Animals
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Eukaryotic Initiation Factor-4F/genetics
- Prohibitins
- Genes, myc
- RNA, Messenger/genetics
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Affiliation(s)
- Anne Largeot
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Vanessa Klapp
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Elodie Viry
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Susanne Gonder
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Iria Fernandez Botana
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Arnaud Blomme
- Laboratory of Cancer Signaling, GIGA Stem Cells, University of Liège, Liège, Belgium
| | - Mohaned Benzarti
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Cancer Research, Cancer Metabolism Group, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Sandrine Pierson
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Chloé Duculty
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Petra Marttila
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Marina Wierz
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Ernesto Gargiulo
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Giulia Pagano
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ning An
- Laboratory of Cancer Signaling, GIGA Stem Cells, University of Liège, Liège, Belgium
| | - Najla El Hachem
- Laboratory of Cancer Signaling, GIGA Stem Cells, University of Liège, Liège, Belgium
| | - Daniel Perez Hernandez
- Department of Infection and Immunity, Proteomics of Cellular Signaling, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Supriya Chakraborty
- Molecular Hematology, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Loïc Ysebaert
- Haematology Department, Institut Universitaire du Cancer Toulouse Oncopole, Toulouse, France
| | - Jean-Hugues François
- Laboratoire d’hématologie, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - Susan Cortez Clemente
- Département d’hémato-oncologie, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - Guy Berchem
- Département d’hémato-oncologie, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
- Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Dimitar G. Efremov
- Molecular Hematology, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Gunnar Dittmar
- Department of Infection and Immunity, Proteomics of Cellular Signaling, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Martyna Szpakowska
- Department of Infection and Immunity, Immuno-Pharmacology and Interactomics, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Andy Chevigné
- Department of Infection and Immunity, Immuno-Pharmacology and Interactomics, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Petr V. Nazarov
- Department of Cancer Research, Multiomics Data Science, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Thomas Helleday
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
- Department of Oncology and Metabolism, Weston Park Cancer Centre, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Pierre Close
- Laboratory of Cancer Signaling, GIGA Stem Cells, University of Liège, Liège, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Johannes Meiser
- Department of Cancer Research, Cancer Metabolism Group, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Basile Stamatopoulos
- Laboratory of Clinical Cell Therapy, ULB-Research Cancer Center, Jules Bordet Institute, Université Libre de Bruxelles, Brussels, Belgium
| | - Laurent Désaubry
- Regenerative Nanomedicine Laboratory (UMR1260), Faculty of Medicine, Fédération de Médecine Translationnelle de Strasbourg, INSERM-University of Strasbourg, Strasbourg, France
| | - Jérôme Paggetti
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Etienne Moussay
- Department of Cancer Research, Tumor Stroma Interactions, Luxembourg Institute of Health, Luxembourg, Luxembourg
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Maher N, Mouhssine S, Matti BF, Alwan AF, Gaidano G. Treatment Refractoriness in Chronic Lymphocytic Leukemia: Old and New Molecular Biomarkers. Int J Mol Sci 2023; 24:10374. [PMID: 37373521 DOI: 10.3390/ijms241210374] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults. Despite its indolent clinical course, therapy refractoriness and disease progression still represent an unmet clinical need. Before the advent of pathway inhibitors, chemoimmunotherapy (CIT) was the commonest option for CLL treatment and is still widely used in areas with limited access to pathway inhibitors. Several biomarkers of refractoriness to CIT have been highlighted, including the unmutated status of immunoglobulin heavy chain variable genes and genetic lesions of TP53, BIRC3 and NOTCH1. In order to overcome resistance to CIT, targeted pathway inhibitors have become the standard of care for the treatment of CLL, with practice-changing results obtained through the inhibitors of Bruton tyrosine kinase (BTK) and BCL2. However, several acquired genetic lesions causing resistance to covalent and noncovalent BTK inhibitors have been reported, including point mutations of both BTK (e.g., C481S and L528W) and PLCG2 (e.g., R665W). Multiple mechanisms are involved in resistance to the BCL2 inhibitor venetoclax, including point mutations that impair drug binding, the upregulation of BCL2-related anti-apoptotic family members, and microenvironmental alterations. Recently, immune checkpoint inhibitors and CAR-T cells have been tested for CLL treatment, obtaining conflicting results. Potential refractoriness biomarkers to immunotherapy were identified, including abnormal levels of circulating IL-10 and IL-6 and the reduced presence of CD27+CD45RO- CD8+ T cells.
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Affiliation(s)
- Nawar Maher
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, 28100 Novara, Italy
| | - Samir Mouhssine
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, 28100 Novara, Italy
| | - Bassam Francis Matti
- Department of Hematology and Bone Marrow Transplant, Hematology and Bone Marrow Transplant Center, Baghdad 00964, Iraq
| | - Alaa Fadhil Alwan
- Department of Clinical Hematology, The National Center of Hematology, Mustansiriyah University, Baghdad 10015, Iraq
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, 28100 Novara, Italy
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8
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Zhao Y, Li Y, Zhu R, Feng R, Cui H, Yu X, Huang F, Zhang R, Chen X, Li L, Chen Y, Liu Y, Wang J, Du G, Liu Z. RPS15 interacted with IGF2BP1 to promote esophageal squamous cell carcinoma development via recognizing m 6A modification. Signal Transduct Target Ther 2023; 8:224. [PMID: 37264021 DOI: 10.1038/s41392-023-01428-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 02/23/2023] [Accepted: 03/24/2023] [Indexed: 06/03/2023] Open
Abstract
Increased rates of ribosome biogenesis have been recognized as hallmarks of many cancers and are associated with poor prognosis. Using a CRISPR synergistic activation mediator (SAM) system library targeting 89 ribosomal proteins (RPs) to screen for the most oncogenic functional RPs in human esophageal squamous cell carcinoma (ESCC), we found that high expression of RPS15 correlates with malignant phenotype and poor prognosis of ESCC. Gain and loss of function models revealed that RPS15 promotes ESCC cell metastasis and proliferation, both in vitro and in vivo. Mechanistic investigations demonstrated that RPS15 interacts with the K homology domain of insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), which recognizes and directly binds the 3'-UTR of MKK6 and MAPK14 mRNA in an m6A-dependent manner, and promotes translation of core p38 MAPK pathway proteins. By combining targeted drug virtual screening and functional assays, we found that folic acid showed a therapeutic effect on ESCC by targeting RPS15, which was augmented by the combination with cisplatin. Inhibition of RPS15 by folic acid, IGF2BP1 ablation, or SB203580 treatment were able to suppress ESCC metastasis and proliferation via the p38 MAPK signaling pathway. Thus, RPS15 promotes ESCC progression via the p38 MAPK pathway and RPS15 inhibitors may serve as potential anti-ESCC drugs.
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Affiliation(s)
- Yahui Zhao
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yang Li
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Rui Zhu
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Riyue Feng
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Heyang Cui
- Department of Oncology, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, 518035, China
| | - Xiao Yu
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Furong Huang
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ruixiang Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100021, China
| | - Xiankai Chen
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100021, China
| | - Lei Li
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Yinghui Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuhao Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Jinhua Wang
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Guanhua Du
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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9
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Barozzi C, Zacchini F, Corradini AG, Morara M, Serra M, De Sanctis V, Bertorelli R, Dassi E, Montanaro L. Alterations of ribosomal RNA pseudouridylation in human breast cancer. NAR Cancer 2023; 5:zcad026. [PMID: 37260601 PMCID: PMC10227372 DOI: 10.1093/narcan/zcad026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023] Open
Abstract
RNA modifications are key regulatory factors for several biological and pathological processes. They are abundantly represented on ribosomal RNA (rRNA), where they contribute to regulate ribosomal function in mRNA translation. Altered RNA modification pathways have been linked to tumorigenesis as well as to other human diseases. In this study we quantitatively evaluated the site-specific pseudouridylation pattern in rRNA in breast cancer samples exploiting the RBS-Seq technique involving RNA bisulfite treatment coupled with a new NGS approach. We found a wide variability among patients at different sites. The most dysregulated positions in tumors turned out to be hypermodified with respect to a reference RNA. As for 2'O-methylation level of rRNA modification, we detected variable and stable pseudouridine sites, with the most stable sites being the most evolutionary conserved. We also observed that pseudouridylation levels at specific sites are related to some clinical and bio-pathological tumor features and they are able to distinguish different patient clusters. This study is the first example of the contribution that newly available high-throughput approaches for site specific pseudouridine detection can provide to the understanding of the intrinsic ribosomal changes occurring in human tumors.
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Affiliation(s)
- Chiara Barozzi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Centre for Applied Biomedical Research – CRBA, University of Bologna, Sant’Orsola Hospital, Bologna I-40138, Italy
| | - Federico Zacchini
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Centre for Applied Biomedical Research – CRBA, University of Bologna, Sant’Orsola Hospital, Bologna I-40138, Italy
| | - Angelo Gianluca Corradini
- Unit of Pathology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Monica Morara
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Margherita Serra
- Unit of Breast Surgery, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Veronica De Sanctis
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Povo (TN) I-38123, Italy
| | - Roberto Bertorelli
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Povo (TN) I-38123, Italy
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Povo (TN) I-38123, Italy
| | - Lorenzo Montanaro
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
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10
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Robbe P, Schuh A. Genomic Stratification of Hematological Malignancies. Hemasphere 2023; 7:e902. [PMID: 37251914 PMCID: PMC10219718 DOI: 10.1097/hs9.0000000000000902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Affiliation(s)
- Pauline Robbe
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Anna Schuh
- Department of Oncology, University of Oxford, United Kingdom
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11
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Parker MD, Karbstein K. Quality control ensures fidelity in ribosome assembly and cellular health. J Cell Biol 2023; 222:e202209115. [PMID: 36790396 PMCID: PMC9960125 DOI: 10.1083/jcb.202209115] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/09/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
The coordinated integration of ribosomal RNA and protein into two functional ribosomal subunits is safeguarded by quality control checkpoints that ensure ribosomes are correctly assembled and functional before they engage in translation. Quality control is critical in maintaining the integrity of ribosomes and necessary to support healthy cell growth and prevent diseases associated with mistakes in ribosome assembly. Its importance is demonstrated by the finding that bypassing quality control leads to misassembled, malfunctioning ribosomes with altered translation fidelity, which change gene expression and disrupt protein homeostasis. In this review, we outline our understanding of quality control within ribosome synthesis and how failure to enforce quality control contributes to human disease. We first provide a definition of quality control to guide our investigation, briefly present the main assembly steps, and then examine stages of assembly that test ribosome function, establish a pass-fail system to evaluate these functions, and contribute to altered ribosome performance when bypassed, and are thus considered "quality control."
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Affiliation(s)
- Melissa D. Parker
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA
- University of Florida—Scripps Biomedical Research, Jupiter, FL, USA
| | - Katrin Karbstein
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA
- University of Florida—Scripps Biomedical Research, Jupiter, FL, USA
- Howard Hughes Medical Institute Faculty Scholar, Howard Hughes Medical Institute, Chevy Chase, MD, USA
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12
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Mollstedt J, Mansouri L, Rosenquist R. Precision diagnostics in chronic lymphocytic leukemia: Past, present and future. Front Oncol 2023; 13:1146486. [PMID: 37035166 PMCID: PMC10080996 DOI: 10.3389/fonc.2023.1146486] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/10/2023] [Indexed: 04/11/2023] Open
Abstract
Genetic diagnostics of hematological malignancies has evolved dramatically over the years, from chromosomal banding analysis to next-generation sequencing, with a corresponding increased capacity to detect clinically relevant prognostic and predictive biomarkers. In diagnostics of patients with chronic lymphocytic leukemia (CLL), we currently apply fluorescence in situ hybridization (FISH)-based analysis to detect recurrent chromosomal aberrations (del(11q), del(13q), del(17p) and trisomy 12) as well as targeted sequencing (IGHV and TP53 mutational status) for risk-stratifying purposes. These analyses are performed before start of any line of treatment and assist in clinical decision-making including selection of targeted therapy (BTK and BCL2 inhibitors). Here, we present the current view on the genomic landscape of CLL, including an update on recent advances with potential for clinical translation. We discuss different state-of-the-art technologies that are applied to enable precision diagnostics in CLL and highlight important genomic markers with current prognostic and/or predictive impact as well as those of prospective clinical relevance. In the coming years, it will be important to develop more comprehensive genomic analyses that can capture all types of relevant genetic aberrations, but also to develop highly sensitive assays to detect minor mutations that affect therapy response or confer resistance to targeted therapies. Finally, we will bring up the potential of new technologies and multi-omics analysis to further subclassify the disease and facilitate implementation of precision medicine approaches in this still incurable disease.
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Affiliation(s)
- John Mollstedt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Larry Mansouri
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
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13
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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] [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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14
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Five Percent Variant Allele Frequency Is a Reliable Reporting Threshold for TP53 Variants Detected by Next Generation Sequencing in Chronic Lymphocytic Leukemia in the Clinical Setting. Hemasphere 2022; 6:e761. [PMID: 35935605 PMCID: PMC9348859 DOI: 10.1097/hs9.0000000000000761] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 07/06/2022] [Indexed: 11/28/2022] Open
Abstract
The clinical significance of small TP53 clones detected with next generation sequencing (NGS) in chronic lymphocytic leukemia is an issue of active debate. According to the official guidelines, treatment decisions should be guided only by variants with variant allele frequency (VAF) ≥10%. We present data on 325 consecutive patients with chronic lymphocytic leukemia analyzed with NGS. In total 47 pathogenic/likely pathogenic (P/LP), TP53 variants were detected in 26 patients (8%). Eleven of these (23%) were in the 5% to 10% VAF range and reported according to our institutional policy. All TP53 variants in the 5% to 10% VAF range were confirmed (100% concordance) with a second NGS panel. Our results where further validated with the performance of Sanger sequencing and digital droplet PCR (ddPCR). In 12 patients with available fluorescence in situ hybridization data and TP53 mutations within 5% to 10% VAF, deletion of chromosome 17p (del(17p)) was detectable in only 1 patient. We propose a robust diagnostic algorithm, which allows the safe detection and reporting of TP53 variants with VAF down to 5% in the clinical setting. Our study provides evidence that NGS is equally potent to detect variants with VAF 5% to 10% compared to those with VAF 10% to 15%, highlighting the urgent need for harmonization of NGS methodologies across diagnostic laboratories.
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15
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Elhamamsy AR, Metge BJ, Alsheikh HA, Shevde LA, Samant RS. Ribosome Biogenesis: A Central Player in Cancer Metastasis and Therapeutic Resistance. Cancer Res 2022; 82:2344-2353. [PMID: 35303060 PMCID: PMC9256764 DOI: 10.1158/0008-5472.can-21-4087] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/01/2022] [Accepted: 03/16/2022] [Indexed: 01/07/2023]
Abstract
Ribosomes are a complex ensemble of rRNA and ribosomal proteins that function as mRNA translation machines. Ribosome biogenesis is a multistep process that begins in the nucleolus and concludes in the cytoplasm. The process is tightly controlled by multiple checkpoint and surveillance pathways. Perturbations in these checkpoints and pathways can lead to hyperactivation of ribosome biogenesis. Emerging evidence suggests that cancer cells harbor a specialized class of ribosomes (onco-ribosomes) that facilitates the oncogenic translation program, modulates cellular functions, and promotes metabolic rewiring. Mutations in ribosomal proteins, rRNA processing, and ribosome assembly factors result in ribosomopathies that are associated with an increased risk of developing malignancies. Recent studies have linked mutations in ribosomal proteins and aberrant ribosomes with poor prognosis, highlighting ribosome-targeted therapy as a promising approach for treating patients with cancer. Here, we summarize various aspects of dysregulation of ribosome biogenesis and the impact of resultant onco-ribosomes on malignant tumor behavior, therapeutic resistance, and clinical outcome. Ribosome biogenesis is a promising therapeutic target, and understanding the important determinants of this process will allow for improved and perhaps selective therapeutic strategies to target ribosome biosynthesis.
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Affiliation(s)
- Amr R. Elhamamsy
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Brandon J. Metge
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Heba A. Alsheikh
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Lalita A. Shevde
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama.,O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Rajeev S. Samant
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama.,O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama.,Birmingham VA Medical Center, Birmingham, Alabama.,Corresponding Author: Rajeev S. Samant, The University of Alabama at Birmingham, WTI 320E, 1824 6th Avenue South, Birmingham, AL 35233. Phone: 205-975-6262; E-mail:
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16
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He H, Huang T, Yu F, Chen K, Guo S, Zhang L, Tang X, Yuan X, Liu J, Zhou Y. KIF2C affects sperm cell differentiation in patients with Klinefelter syndrome, as revealed by RNA-Seq and scRNA-Seq data. FEBS Open Bio 2022; 12:1465-1474. [PMID: 35622500 PMCID: PMC9340869 DOI: 10.1002/2211-5463.13446] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/14/2022] [Accepted: 05/25/2022] [Indexed: 11/06/2022] Open
Abstract
Klinefelter syndrome (KS) is a leading contributor to male infertility and is characterised by complex and diverse clinical features; however, genetic changes in the KS transcriptome remain largely unknown. We therefore used transcriptomic and single‐cell RNA sequencing (scRNA‐seq) datasets from KS versus normal populations through the Gene Expression Omnibus (GEO) database to identify gene biomarkers associated with the occurrence of KS. We identified a total of 700 differentially expressed genes (DEGs) and completed Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), enrichment pathway analysis and protein‐protein interaction (PPI) network analysis. A total of four unreported KS‐related hub genes (KIF2C, MRPS2, RPS15 and TSFM) were identified. Validation of the single‐cell sequencing dataset showed that only KIF2C and RPS15 were expressed in spermatocytes and that they were differentially expressed in sperm cells. Further construction of the developmental trajectories of these two genes in sperm cells showed that the KIF2C gene showed an upward trend throughout the differentiation and development of sperm cells. In conclusion, we report here that KIF2C may be closely related to the differentiation and development of sperm cells in KS patients, which is important for revealing the molecular mechanism of KS and conducting further studies.
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Affiliation(s)
- Haihong He
- Clinical Laboratory Medicine Centre, Shenzhen Hospital, Southern Medical University, Shenzhen, 518108, China
| | - Tingting Huang
- Clinical Laboratory Medicine Centre, Shenzhen Hospital, Southern Medical University, Shenzhen, 518108, China
| | - Fan Yu
- Clinical Laboratory Medicine Centre, Shenzhen Hospital, Southern Medical University, Shenzhen, 518108, China
| | - Keyan Chen
- Clinical Laboratory Medicine Centre, Shenzhen Hospital, Southern Medical University, Shenzhen, 518108, China
| | - Shixing Guo
- Clinical Laboratory Medicine Centre, Shenzhen Hospital, Southern Medical University, Shenzhen, 518108, China
| | - Lijun Zhang
- Clinical Laboratory Medicine Centre, Shenzhen Hospital, Southern Medical University, Shenzhen, 518108, China
| | - Xi Tang
- Clinical Laboratory Medicine Centre, Shenzhen Hospital, Southern Medical University, Shenzhen, 518108, China
| | - Xinhua Yuan
- Clinical Laboratory Medicine Centre, Shenzhen Hospital, Southern Medical University, Shenzhen, 518108, China
| | - Jiao Liu
- Clinical Laboratory Medicine Centre, Shenzhen Hospital, Southern Medical University, Shenzhen, 518108, China
| | - Yiwen Zhou
- Clinical Laboratory Medicine Centre, Shenzhen Hospital, Southern Medical University, Shenzhen, 518108, China
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17
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Youssef ASED, Abdel-Fattah MA, Lotfy MM, Nassar A, Abouelhoda M, Touny AO, Hassan ZK, Mohey Eldin M, Bahnassy AA, Khaled H, Zekri ARN. Multigene Panel Sequencing Reveals Cancer-Specific and Common Somatic Mutations in Colorectal Cancer Patients: An Egyptian Experience. Curr Issues Mol Biol 2022; 44:1332-1352. [PMID: 35723313 PMCID: PMC8947625 DOI: 10.3390/cimb44030090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 12/11/2022] Open
Abstract
This study aims at identifying common pathogenic somatic mutations at different stages of colorectal carcinogenesis in Egyptian patients. Our cohort included colonoscopic biopsies collected from 120 patients: 20 biopsies from patients with inflammatory bowel disease, 38 from colonic polyp patients, and 62 from patients with colorectal cancer. On top of this, the cohort included 20 biopsies from patients with non-specific mild to moderated colitis. Targeted DNA sequencing using a customized gene panel of 96 colorectal related genes running on the Ion Torrent NGS technology was used to process the samples. Our results revealed that 69% of all cases harbored at least one somatic mutation. Fifty-seven genes were found to carry 232 somatic non-synonymous variants. The most frequently pathogenic somatic mutations were localized in TP53, APC, KRAS, and PIK3CA. In total, 16 somatic mutations were detected in the CRC group and in either the IBD or CP group. In addition, our data showed that 51% of total somatic variants were CRC-specific variants. The average number of CRC-specific variants per sample is 2.4. The top genes carrying CRC-specific mutations are APC, TP53, PIK3CA, FBXW7, ATM, and SMAD4. It seems obvious that TP53 and APC genes were the most affected genes with somatic mutations in all groups. Of interest, 85% and 28% of the APC and TP53 deleterious somatic mutations were located in Exon 14 and Exon 3, respectively. Besides, 37% and 28% of the total somatic mutations identified in APC and TP53 were CRC-specific variants, respectively. Moreover, we identified that, in 29 somatic mutations in 21 genes, their association with CRC patients was unprecedented. Ten detected variants were likely to be novel: six in PIK3CA and four variants in FBXW7. The detected P53, Wnt/βcatenin, Angiogenesis, EGFR, TGF-β and Interleukin signaling pathways were the most altered pathways in 22%, 16%, 12%, 10%, 9% and 9% of the CRC patients, respectively. These results would contribute to a better understanding of the colorectal cancer and in introducing personalized therapies for Egyptian CRC patients.
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Affiliation(s)
- Amira Salah El-Din Youssef
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11796, Egypt; (M.M.L.); (A.N.); (Z.K.H.)
| | | | - Mai M. Lotfy
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11796, Egypt; (M.M.L.); (A.N.); (Z.K.H.)
| | - Auhood Nassar
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11796, Egypt; (M.M.L.); (A.N.); (Z.K.H.)
| | | | - Ahmed O. Touny
- Surgical Oncology Department, National Cancer Institute, Cairo University, Cairo 11796, Egypt;
| | - Zeinab K. Hassan
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11796, Egypt; (M.M.L.); (A.N.); (Z.K.H.)
| | - Mohammed Mohey Eldin
- Tropical Medicine Department, El Kasr Al-Aini, Cairo University, Cairo 11562, Egypt;
| | - Abeer A. Bahnassy
- Molecular Pathology Department, National Cancer Institute, Cairo University, Cairo 11796, Egypt;
| | - Hussein Khaled
- Medical Oncology Department, National Cancer Institute, Cairo University, Cairo 11796, Egypt;
| | - Abdel Rahman N. Zekri
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11796, Egypt; (M.M.L.); (A.N.); (Z.K.H.)
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18
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Soussi T, Baliakas P. Landscape of TP53 Alterations in Chronic Lymphocytic Leukemia via Data Mining Mutation Databases. Front Oncol 2022; 12:808886. [PMID: 35251978 PMCID: PMC8890000 DOI: 10.3389/fonc.2022.808886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/20/2022] [Indexed: 11/16/2022] Open
Abstract
Locus-specific databases are invaluable tools for both basic and clinical research. The extensive information they contain is gathered from the literature and manually curated by experts. Cancer genome sequencing projects generate an immense amount of data, which are stored directly in large repositories (cancer genome databases). The presence of a TP53 defect (17p deletion and/or TP53 mutations) is an independent prognostic factor in chronic lymphocytic leukemia (CLL) and TP53 status analysis has been adopted in routine clinical practice. For that reason, TP53 mutation databases have become essential for the validation of the plethora of TP53 variants detected in tumor samples. TP53 profiles in CLL are characterized by a great number of subclonal TP53 mutations with low variant allelic frequencies and the presence of multiple minor subclones harboring different TP53 mutations. In this review, we describe the various characteristics of the multiple levels of heterogeneity of TP53 variants in CLL through the analysis of TP53 mutation databases and the utility of their diagnosis in the clinic.
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Affiliation(s)
- Thierry Soussi
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.,Sorbonne Université, UPMC Univ Paris 06, Paris, France
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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19
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Nicolò A, Linder AT, Jumaa H, Maity PC. The Determinants of B Cell Receptor Signaling as Prototype Molecular Biomarkers of Leukemia. Front Oncol 2022; 11:771669. [PMID: 34993136 PMCID: PMC8724047 DOI: 10.3389/fonc.2021.771669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/02/2021] [Indexed: 12/20/2022] Open
Abstract
Advanced genome-wide association studies (GWAS) identified several transforming mutations in susceptible loci which are recognized as valuable prognostic markers in chronic lymphocytic leukemia (CLL) and B cell lymphoma (BCL). Alongside, robust genetic manipulations facilitated the generation of preclinical mouse models to validate mutations associated with poor prognosis and refractory B cell malignancies. Taken together, these studies identified new prognostic markers that could achieve characteristics of precision biomarkers for molecular diagnosis. On the contrary, the idea of augmented B cell antigen receptor (BCR) signaling as a transforming cue has somewhat receded despite the efficacy of Btk and Syk inhibitors. Recent studies from several research groups pointed out that acquired mutations in BCR components serve as faithful biomarkers, which become important for precision diagnostics and therapy, due to their relevant role in augmented BCR signaling and CLL pathogenesis. For example, we showed that expression of a single point mutated immunoglobulin light chain (LC) recombined through the variable gene segment IGLV3-21, named IGLV3-21R110, marks severe CLL cases. In this perspective, we summarize the molecular mechanisms fine-tuning B cell transformation, focusing on immunoglobulin point mutations and recurrent mutations in tumor suppressors. We present a stochastic model for gain-of-autonomous BCR signaling and subsequent neoplastic transformation. Of note, additional mutational analyses on immunoglobulin heavy chain (HC) derived from non-subset #2 CLL IGLV3-21R110 cases endorses our perspective. Altogether, we propose a model of malignant transformation in which the augmented BCR signaling creates a conducive platform for the appearance of transforming mutations.
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Affiliation(s)
| | | | - Hassan Jumaa
- Institute of Immunology, Ulm University, Ulm, Germany
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20
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Are we finally getting personal? Moving towards a personalized approach in chronic lymphocytic leukemia. Semin Cancer Biol 2022; 84:329-338. [DOI: 10.1016/j.semcancer.2022.01.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/21/2022]
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21
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Rössler I, Weigl S, Fernández-Fernández J, Martín-Villanueva S, Strauss D, Hurt E, de la Cruz J, Pertschy B. The C-terminal tail of ribosomal protein Rps15 is engaged in cytoplasmic pre-40S maturation. RNA Biol 2021; 19:560-574. [PMID: 35438042 PMCID: PMC9037480 DOI: 10.1080/15476286.2022.2064073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 04/04/2022] [Indexed: 11/22/2022] Open
Abstract
The small ribosomal subunit protein Rps15/uS19 is involved in early nucleolar ribosome biogenesis and subsequent nuclear export of pre-40S particles to the cytoplasm. In addition, the C-terminal tail of Rps15 was suggested to play a role in mature ribosomes, namely during translation elongation. Here, we show that Rps15 not only functions in nucleolar ribosome assembly but also in cytoplasmic pre-40S maturation, which is indicated by a strong genetic interaction between Rps15 and the 40S assembly factor Ltv1. Specifically, mutations either in the globular or C-terminal domain of Rps15 when combined with the non-essential ltv1 null allele are lethal or display a strong growth defect. However, not only rps15 ltv1 double mutants but also single rps15 C-terminal deletion mutants exhibit an accumulation of the 20S pre-rRNA in the cytoplasm, indicative of a cytoplasmic pre-40S maturation defect. Since in pre-40S particles, the C-terminal tail of Rps15 is positioned between assembly factors Rio2 and Tsr1, we further tested whether Tsr1 is genetically linked to Rps15, which indeed could be demonstrated. Thus, the integrity of the Rps15 C-terminal tail plays an important role during late pre-40S maturation, perhaps in a quality control step to ensure that only 40S ribosomal subunits with functional Rps15 C-terminal tail can efficiently enter translation. As mutations in the C-terminal tail of human RPS15 have been observed in connection with chronic lymphocytic leukaemia, it is possible that apart from defects in translation, an impaired late pre-40S maturation step in the cytoplasm could also be a reason for this disease.
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Affiliation(s)
- Ingrid Rössler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Sarah Weigl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - José Fernández-Fernández
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Sara Martín-Villanueva
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Daniela Strauss
- Biochemistry Center BZH, Heidelberg University, Heidelberg, Germany
| | - Ed Hurt
- Biochemistry Center BZH, Heidelberg University, Heidelberg, Germany
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Brigitte Pertschy
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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22
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Ten Hacken E, Wu CJ. Understanding CLL biology through mouse models of human genetics. Blood 2021; 138:2621-2631. [PMID: 34940815 PMCID: PMC8703365 DOI: 10.1182/blood.2021011993] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/04/2021] [Indexed: 12/25/2022] Open
Abstract
Rapid advances in large-scale next-generation sequencing studies of human samples have progressively defined the highly heterogeneous genetic landscape of chronic lymphocytic leukemia (CLL). At the same time, the numerous challenges posed by the difficulties in rapid manipulation of primary B cells and the paucity of CLL cell lines have limited the ability to interrogate the function of the discovered putative disease "drivers," defined in human sequencing studies through statistical inference. Mouse models represent a powerful tool to study mechanisms of normal and malignant B-cell biology and for preclinical testing of novel therapeutics. Advances in genetic engineering technologies, including the introduction of conditional knockin/knockout strategies, have opened new opportunities to model genetic lesions in a B-cell-restricted context. These new studies build on the experience of generating the MDR mice, the first example of a genetically faithful CLL model, which recapitulates the most common genomic aberration of human CLL: del(13q). In this review, we describe the application of mouse models to the studies of CLL pathogenesis and disease transformation from an indolent to a high-grade malignancy (ie, Richter syndrome [RS]) and treatment, with a focus on newly developed genetically inspired mouse lines modeling recurrent CLL genetic events. We discuss how these novel mouse models, analyzed using new genomic technologies, allow the dissection of mechanisms of disease evolution and response to therapy with greater depth than previously possible and provide important insight into human CLL and RS pathogenesis and therapeutic vulnerabilities. These models thereby provide valuable platforms for functional genomic analyses and treatment studies.
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Affiliation(s)
- Elisa Ten Hacken
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA; and
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
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23
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Chatzikonstantinou T, Demosthenous C, Baliakas P. Biology and Treatment of High-Risk CLL: Significance of Complex Karyotype. Front Oncol 2021; 11:788761. [PMID: 34912723 PMCID: PMC8667220 DOI: 10.3389/fonc.2021.788761] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/04/2021] [Indexed: 12/23/2022] Open
Abstract
Several reports highlight the clinical significance of cytogenetic complexity, namely, complex karyotype (CK) identified though the performance of chromosome banding analysis (CBA) in chronic lymphocytic leukemia. Indeed, apart from a number of studies underscoring the prognostic and predictive value of CK in the chemo(immune)therapy era, mounting evidence suggests that CK could serve as an independent prognosticator and predictor even in patients treated with novel agents. In the present review, we provide an overview of the current knowledge regarding the clinical impact of CK in CLL, touching upon open issues related to the incorporation of CK in the clinical setting.
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Affiliation(s)
- Thomas Chatzikonstantinou
- Hematology Department-Bone Marrow Transplantation (BMT) Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Christos Demosthenous
- Hematology Department-Bone Marrow Transplantation (BMT) Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
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24
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Galigalidou C, Zaragoza-Infante L, Iatrou A, Chatzidimitriou A, Stamatopoulos K, Agathangelidis A. Understanding Monoclonal B Cell Lymphocytosis: An Interplay of Genetic and Microenvironmental Factors. Front Oncol 2021; 11:769612. [PMID: 34858849 PMCID: PMC8631769 DOI: 10.3389/fonc.2021.769612] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
The term monoclonal B-cell lymphocytosis (MBL) describes the presence of a clonal B cell population with a count of less than 5 × 109/L and no symptoms or signs of disease. Based on the B cell count, MBL is further classified into 2 distinct subtypes: 'low-count' and 'high-count' MBL. High-count MBL shares a series of biological and clinical features with chronic lymphocytic leukemia (CLL), at least of the indolent type, and evolves to CLL requiring treatment at a rate of 1-2% per year, whereas 'low-count' MBL seems to be distinct, likely representing an immunological rather than a pre-malignant condition. That notwithstanding, both subtypes of MBL can carry 'CLL-specific' genomic aberrations such as cytogenetic abnormalities and gene mutations, yet to a much lesser extent compared to CLL. These findings suggest that such aberrations are mostly relevant for disease progression rather than disease onset, indirectly pointing to microenvironmental drive as a key contributor to the emergence of MBL. Understanding microenvironmental interactions is therefore anticipated to elucidate MBL ontogeny and, most importantly, the relationship between MBL and CLL.
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Affiliation(s)
- Chrysi Galigalidou
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.,Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Laura Zaragoza-Infante
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.,Hematology Department, University General Hospital of Thessaloniki AHEPA, Thessaloniki, Greece
| | - Anastasia Iatrou
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece
| | - Anastasia Chatzidimitriou
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Agathangelidis
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.,Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
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25
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Zhang T, Ma C, Zhang Z, Zhang H, Hu H. NF-κB signaling in inflammation and cancer. MedComm (Beijing) 2021; 2:618-653. [PMID: 34977871 PMCID: PMC8706767 DOI: 10.1002/mco2.104] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
Since nuclear factor of κ-light chain of enhancer-activated B cells (NF-κB) was discovered in 1986, extraordinary efforts have been made to understand the function and regulating mechanism of NF-κB for 35 years, which lead to significant progress. Meanwhile, the molecular mechanisms regulating NF-κB activation have also been illuminated, the cascades of signaling events leading to NF-κB activity and key components of the NF-κB pathway are also identified. It has been suggested NF-κB plays an important role in human diseases, especially inflammation-related diseases. These studies make the NF-κB an attractive target for disease treatment. This review aims to summarize the knowledge of the family members of NF-κB, as well as the basic mechanisms of NF-κB signaling pathway activation. We will also review the effects of dysregulated NF-κB on inflammation, tumorigenesis, and tumor microenvironment. The progression of the translational study and drug development targeting NF-κB for inflammatory diseases and cancer treatment and the potential obstacles will be discussed. Further investigations on the precise functions of NF-κB in the physiological and pathological settings and underlying mechanisms are in the urgent need to develop drugs targeting NF-κB for inflammatory diseases and cancer treatment, with minimal side effects.
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Affiliation(s)
- Tao Zhang
- Cancer Center and Center for Immunology and HematologyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Chao Ma
- Cancer Center and Center for Immunology and HematologyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Zhiqiang Zhang
- Immunobiology and Transplant Science CenterHouston Methodist HospitalHoustonTexasUSA
| | - Huiyuan Zhang
- Cancer Center and Center for Immunology and HematologyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Hongbo Hu
- Cancer Center and Center for Immunology and HematologyWest China HospitalSichuan UniversityChengduSichuanChina
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26
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Mansouri L, Thorvaldsdottir B, Laidou S, Stamatopoulos K, Rosenquist R. Precision diagnostics in lymphomas - Recent developments and future directions. Semin Cancer Biol 2021; 84:170-183. [PMID: 34699973 DOI: 10.1016/j.semcancer.2021.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 01/03/2023]
Abstract
Genetics is an integral part of the clinical diagnostics of lymphomas that improves disease subclassification and patient risk-stratification. With the introduction of high-throughput sequencing technologies, a rapid, in-depth portrayal of the genomic landscape in major lymphoma entities was achieved. Whilst a few lymphoma entities were characterized by a predominant gene mutation (e.g. Waldenström's macroglobulinemia and hairy cell leukemia), the vast majority demonstrated a very diverse genetic landscape with a high number of recurrent gene mutations (e.g. chronic lymphocytic leukemia and diffuse large B cell lymphoma), indeed reflecting the great clinical heterogeneity among lymphomas. These studies have allowed better understanding of the ontogeny and evolution of different lymphomas, while also identifying new genetic markers that can complement lymphoma diagnostics and improve prognostication. However, despite these efforts, there is still a limited number of gene mutations with predictive impact that can guide treatment selection. In this review, we will highlight clinically relevant diagnostic, prognostic and predictive markers in lymphomas that are used today in routine diagnostics. We will also discuss how comprehensive genomic characterization using broad sequencing panels, allowing for the simultaneous detection of different types of genetic aberrations, may aid future development of precision diagnostics in lymphomas. This may in turn pave the way for the implementation of tailored precision therapy strategies at the individual patient level.
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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
| | - Stamatia Laidou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Kostas Stamatopoulos
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden.
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27
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Kwok M, Agathanggelou A, Davies N, Stankovic T. Targeting the p53 Pathway in CLL: State of the Art and Future Perspectives. Cancers (Basel) 2021; 13:4681. [PMID: 34572908 PMCID: PMC8468925 DOI: 10.3390/cancers13184681] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 12/20/2022] Open
Abstract
The p53 pathway is a desirable therapeutic target, owing to its critical role in the maintenance of genome integrity. This is exemplified in chronic lymphocytic leukemia (CLL), one of the most common adult hematologic malignancies, in which functional loss of p53 arising from genomic aberrations are frequently associated with clonal evolution, disease progression, and therapeutic resistance, even in the contemporary era of CLL targeted therapy and immunotherapy. Targeting the 'undruggable' p53 pathway therefore arguably represents the holy grail of cancer research. In recent years, several strategies have been proposed to exploit p53 pathway defects for cancer treatment. Such strategies include upregulating wild-type p53, restoring tumor suppressive function in mutant p53, inducing synthetic lethality by targeting collateral genome maintenance pathways, and harnessing the immunogenicity of p53 pathway aberrations. In this review, we will examine the biological and clinical implications of p53 pathway defects, as well as our progress towards development of therapeutic approaches targeting the p53 pathway, specifically within the context of CLL. We will appraise the opportunities and pitfalls associated with these therapeutic strategies, and evaluate their place amongst the array of new biological therapies for CLL.
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Affiliation(s)
- Marwan Kwok
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, UK; (A.A.); (N.D.)
- Centre for Clinical Haematology, Queen Elizabeth Hospital Birmingham, Birmingham B15 2SY, UK
| | - Angelo Agathanggelou
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, UK; (A.A.); (N.D.)
| | - Nicholas Davies
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, UK; (A.A.); (N.D.)
| | - Tatjana Stankovic
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, UK; (A.A.); (N.D.)
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28
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Kolijn PM, Muggen AF, Ljungström V, Agathangelidis A, Wolvers-Tettero ILM, Beverloo HB, Pál K, Hengeveld PJ, Darzentas N, Hendriks RW, van Dongen JJM, Rosenquist R, Langerak AW. Consistent B Cell Receptor Immunoglobulin Features Between Siblings in Familial Chronic Lymphocytic Leukemia. Front Oncol 2021; 11:740083. [PMID: 34513715 PMCID: PMC8427434 DOI: 10.3389/fonc.2021.740083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
Key processes in the onset and evolution of chronic lymphocytic leukemia (CLL) are thought to include chronic (antigenic) activation of mature B cells through the B cell receptor (BcR), signals from the microenvironment, and acquisition of genetic alterations. Here we describe three families in which two or more siblings were affected by CLL. We investigated whether there are immunogenetic similarities in the leukemia-specific immunoglobulin heavy (IGH) and light (IGL/IGK) chain gene rearrangements of the siblings in each family. Furthermore, we performed array analysis to study if similarities in CLL-associated chromosomal aberrations are present within each family and screened for somatic mutations using paired tumor/normal whole-genome sequencing (WGS). In two families a consistent IGHV gene mutational status (one IGHV-unmutated, one IGHV-mutated) was observed. Intriguingly, the third family with four affected siblings was characterized by usage of the lambda IGLV3-21 gene, with the hallmark R110 mutation of the recently described clinically aggressive IGLV3-21R110 subset. In this family, the CLL-specific rearrangements in two siblings could be assigned to either stereotyped subset #2 or the immunogenetically related subset #169, both of which belong to the broader IGLV3-21R110 subgroup. Consistent patterns of cytogenetic aberrations were encountered in all three families. Furthermore, the CLL clones carried somatic mutations previously associated with IGHV mutational status, cytogenetic aberrations and stereotyped subsets, respectively. From these findings, we conclude that similarities in immunogenetic characteristics in familial CLL, in combination with genetic aberrations acquired, point towards shared underlying mechanisms behind CLL development within each family.
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Affiliation(s)
- P Martijn Kolijn
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Alice F Muggen
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Ingrid L M Wolvers-Tettero
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - H Berna Beverloo
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Karol Pál
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Paul J Hengeveld
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Nikos Darzentas
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | | | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden
| | - Anton W Langerak
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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29
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González-Rincón J, Garcia-Vela JA, Gómez S, Fernández-Cuevas B, Nova-Gurumeta S, Pérez-Sanz N, Alcoceba M, González M, Anguita E, López-Jiménez J, González-Barca E, Yáñez L, Pérez-Persona E, de la Serna J, Fernández-Zarzoso M, Deben G, Peñalver FJ, Fernández MC, de Oteyza JP, Andreu MÁ, Ruíz-Guinaldo MÁ, Paz-Arias R, García-Malo MD, Recasens V, Collado R, Córdoba R, Navarro-Matilla B, Sánchez-Beato M, García-Marco JA. Genomic mutation profile in progressive chronic lymphocytic leukemia patients prior to first-line chemoimmunotherapy with FCR and rituximab maintenance (REM). PLoS One 2021; 16:e0257353. [PMID: 34506616 PMCID: PMC8432772 DOI: 10.1371/journal.pone.0257353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/24/2021] [Indexed: 11/18/2022] Open
Abstract
Chronic Lymphocytic Leukemia (CLL) is the most prevalent leukemia in Western countries and is notable for its variable clinical course. This variability is partly reflected by the mutational status of IGHV genes. Many CLL samples have been studied in recent years by next-generation sequencing. These studies have identified recurrent somatic mutations in NOTCH1, SF3B1, ATM, TP53, BIRC3 and others genes that play roles in cell cycle, DNA repair, RNA metabolism and splicing. In this study, we have taken a deep-targeted massive sequencing approach to analyze the impact of mutations in the most frequently mutated genes in patients with CLL enrolled in the REM (rituximab en mantenimiento) clinical trial. The mutational status of our patients with CLL, except for the TP53 gene, does not seem to affect the good results obtained with maintenance therapy with rituximab after front-line FCR treatment.
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Affiliation(s)
- Julia González-Rincón
- Lymphoma Research Group, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDPHISA), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Sagrario Gómez
- Lymphoma Research Group, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDPHISA), Madrid, Spain
| | - Belén Fernández-Cuevas
- Hematology Department, Hospital Universitario Puerta de Hierro-Majadahonda and Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDIPHISA), Madrid, Spain
| | - Sara Nova-Gurumeta
- Hematology Department, Hospital Universitario Puerta de Hierro-Majadahonda and Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDIPHISA), Madrid, Spain
| | - Nuria Pérez-Sanz
- Hematology Department, Hospital Universitario Puerta de Hierro-Majadahonda and Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDIPHISA), Madrid, Spain
| | - Miguel Alcoceba
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Marcos González
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Eduardo Anguita
- Hematology, Hospital Clínico San Carlos, IdISSC, UCM, Madrid, Spain
| | | | - Eva González-Barca
- Hematology, Institut Català d’Oncologia, IDIBELL, L’Hospitalet de LLobregat, Spain
| | - Lucrecia Yáñez
- Hematology, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | - Rosa Collado
- Citogenetics and molecular biology laboratory, Consorcio Hospital General Universitario, Valencia, Spain
| | - Raúl Córdoba
- Hematology, Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - Belén Navarro-Matilla
- Hematology Department, Hospital Universitario Puerta de Hierro-Majadahonda and Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDIPHISA), Madrid, Spain
| | - Margarita Sánchez-Beato
- Lymphoma Research Group, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDPHISA), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- * E-mail: (MSB); (JAGM)
| | - José A. García-Marco
- Hematology Department, Hospital Universitario Puerta de Hierro-Majadahonda and Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDIPHISA), Madrid, Spain
- * E-mail: (MSB); (JAGM)
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30
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Kang J, Brajanovski N, Chan KT, Xuan J, Pearson RB, Sanij E. Ribosomal proteins and human diseases: molecular mechanisms and targeted therapy. Signal Transduct Target Ther 2021; 6:323. [PMID: 34462428 PMCID: PMC8405630 DOI: 10.1038/s41392-021-00728-8] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 07/12/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ribosome biogenesis and protein synthesis are fundamental rate-limiting steps for cell growth and proliferation. The ribosomal proteins (RPs), comprising the structural parts of the ribosome, are essential for ribosome assembly and function. In addition to their canonical ribosomal functions, multiple RPs have extra-ribosomal functions including activation of p53-dependent or p53-independent pathways in response to stress, resulting in cell cycle arrest and apoptosis. Defects in ribosome biogenesis, translation, and the functions of individual RPs, including mutations in RPs have been linked to a diverse range of human congenital disorders termed ribosomopathies. Ribosomopathies are characterized by tissue-specific phenotypic abnormalities and higher cancer risk later in life. Recent discoveries of somatic mutations in RPs in multiple tumor types reinforce the connections between ribosomal defects and cancer. In this article, we review the most recent advances in understanding the molecular consequences of RP mutations and ribosomal defects in ribosomopathies and cancer. We particularly discuss the molecular basis of the transition from hypo- to hyper-proliferation in ribosomopathies with elevated cancer risk, a paradox termed "Dameshek's riddle." Furthermore, we review the current treatments for ribosomopathies and prospective therapies targeting ribosomal defects. We also highlight recent advances in ribosome stress-based cancer therapeutics. Importantly, insights into the mechanisms of resistance to therapies targeting ribosome biogenesis bring new perspectives into the molecular basis of cancer susceptibility in ribosomopathies and new clinical implications for cancer therapy.
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Affiliation(s)
- Jian Kang
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Natalie Brajanovski
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Keefe T. Chan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Jiachen Xuan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Richard B. Pearson
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC Australia
| | - Elaine Sanij
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia ,grid.1073.50000 0004 0626 201XSt. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia
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31
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Pacholewska A, Grimm C, Herling CD, Lienhard M, Königs A, Timmermann B, Altmüller J, Mücke O, Reinhardt HC, Plass C, Herwig R, Hallek M, Schweiger MR. Altered DNA Methylation Profiles in SF3B1 Mutated CLL Patients. Int J Mol Sci 2021; 22:ijms22179337. [PMID: 34502260 PMCID: PMC8431484 DOI: 10.3390/ijms22179337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in splicing factor genes have a severe impact on the survival of cancer patients. Splicing factor 3b subunit 1 (SF3B1) is one of the most frequently mutated genes in chronic lymphocytic leukemia (CLL); patients carrying these mutations have a poor prognosis. Since the splicing machinery and the epigenome are closely interconnected, we investigated whether these alterations may affect the epigenomes of CLL patients. While an overall hypomethylation during CLL carcinogenesis has been observed, the interplay between the epigenetic stage of the originating B cells and SF3B1 mutations, and the subsequent effect of the mutations on methylation alterations in CLL, have not been investigated. We profiled the genome-wide DNA methylation patterns of 27 CLL patients with and without SF3B1 mutations and identified local decreases in methylation levels in SF3B1mut CLL patients at 67 genomic regions, mostly in proximity to telomeric regions. These differentially methylated regions (DMRs) were enriched in gene bodies of cancer-related signaling genes, e.g., NOTCH1, HTRA3, and BCL9L. In our study, SF3B1 mutations exclusively emerged in two out of three epigenetic stages of the originating B cells. However, not all the DMRs could be associated with the methylation programming of B cells during development, suggesting that mutations in SF3B1 cause additional epigenetic aberrations during carcinogenesis.
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Affiliation(s)
- Alicja Pacholewska
- Institute for Translational Epigenetics, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (A.P.); (C.G.); (A.K.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Christina Grimm
- Institute for Translational Epigenetics, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (A.P.); (C.G.); (A.K.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Carmen D. Herling
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German CLL Study Group, Department I of Internal Medicine, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (C.D.H.); (H.C.R.); (M.H.)
| | - Matthias Lienhard
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; (M.L.); (R.H.)
| | - Anja Königs
- Institute for Translational Epigenetics, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (A.P.); (C.G.); (A.K.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany;
| | - Oliver Mücke
- German Cancer Research Center, Cancer Epigenomics, 69120 Heidelberg, Germany; (O.M.); (C.P.)
| | - Hans Christian Reinhardt
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German CLL Study Group, Department I of Internal Medicine, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (C.D.H.); (H.C.R.); (M.H.)
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- West German Cancer Center Essen, Department of Hematology and Stem Cell Transplantation, University Hospital Essen, 45147 Essen, Germany
| | - Christoph Plass
- German Cancer Research Center, Cancer Epigenomics, 69120 Heidelberg, Germany; (O.M.); (C.P.)
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; (M.L.); (R.H.)
| | - Michael Hallek
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German CLL Study Group, Department I of Internal Medicine, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (C.D.H.); (H.C.R.); (M.H.)
| | - Michal R. Schweiger
- Institute for Translational Epigenetics, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (A.P.); (C.G.); (A.K.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Correspondence:
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32
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Genetics of Chronic Lymphocytic Leukemia. ACTA ACUST UNITED AC 2021; 27:259-265. [PMID: 34398552 DOI: 10.1097/ppo.0000000000000538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
ABSTRACT During the past 10 years, relevant advances have been made in the understanding of the pathogenesis of chronic lymphocytic leukemia via the integrated analysis of its genome and related epigenome, and transcriptome. These analyses also had an impact on our understanding of the initiation, as well as of the evolution of chronic lymphocytic leukemia, including resistance to chemotherapy and sensitivity and resistance to novel targeted therapies. This chapter will review the current state of the art in this field, with emphasis on the genetic heterogeneity of the disease and the biological pathways that are altered by the genetic lesions.
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RPS15 mutations rewire RNA translation in chronic lymphocytic leukemia. Blood Adv 2021; 5:2788-2792. [PMID: 34251413 DOI: 10.1182/bloodadvances.2020001717] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/29/2021] [Indexed: 11/20/2022] Open
Abstract
Recent studies of chronic lymphocytic leukemia (CLL) have reported recurrent mutations in the RPS15 gene, which encodes the ribosomal protein S15 (RPS15), a component of the 40S ribosomal subunit. Despite some evidence about the role of mutant RPS15 (mostly obtained from the analysis of cell lines), the precise impact of RPS15 mutations on the translational program in primary CLL cells remains largely unexplored. Here, using RNA sequencing and ribosome profiling, a technique that involves measuring translational efficiency, we sought to obtain global insight into changes in translation induced by RPS15 mutations in CLL cells. To this end, we evaluated primary CLL cells from patients with wild-type or mutant RPS15 as well as MEC1 CLL cells transfected with mutant or wild-type RPS15. Our data indicate that RPS15 mutations rewire the translation program of primary CLL cells by reducing their translational efficiency, an effect not seen in MEC1 cells. In detail, RPS15 mutant primary CLL cells displayed altered translation efficiency of other ribosomal proteins and regulatory elements that affect key cell processes, such as the translational machinery and immune signaling, as well as genes known to be implicated in CLL, hence highlighting a relevant role for RPS15 in the natural history of CLL.
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34
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The Biology of Chronic Lymphocytic Leukemia: Diagnostic and Prognostic Implications. ACTA ACUST UNITED AC 2021; 27:266-274. [PMID: 34398553 DOI: 10.1097/ppo.0000000000000534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
ABSTRACT The high degree of clinical heterogeneity of chronic lymphocytic leukemia (CLL) is influenced by the disease molecular complexity. Genetic studies have allowed to better understand CLL biology and to identify molecular biomarkers of clinical relevance. TP53 disruption represents the strongest prognosticator of chemorefractoriness and indicates the use of Bruton tyrosine kinase inhibitors (BTKis) and BCL2 inhibitors. Unmutated IGHV (immunoglobulin heavy variable) genes also predict refractoriness to chemoimmunotherapy; importantly, when treated with B-cell receptor inhibitors or BCL2 inhibitors, IGHV unmutated patients display an outcome similar to that of IGHV mutated CLL. Before choosing treatment, a comprehensive assessment of TP53 and IGHV status is recommended by all guidelines for CLL clinical management. In case of fixed-duration therapeutic strategies, monitoring of minimal residual disease may provide a tool to decide treatment duration. The current precision medicine management of CLL patients might be further improved by the adoption of novel biomarkers that are emerging as clinically meaningful for this disease.
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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: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [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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Abstract
Chronic lymphocytic leukemia (CLL) is characterized by extreme genomic heterogeneity. Numerous recurrent genetic abnormalities are associated with dismal clinical outcome in patients treated with chemo(immuno)therapy, with aberrations of the TP53 gene being the main genomic abnormalities that dictate treatment choice. In the era of novel agents the predictive significance of the genomic aberrations is highly challenged as the results of the clinical trials performed thus far question the previously established unfavorable impact of genomic aberrations, even that of the TP53 gene. The prognostic and predictive value of the most common genomic abnormalities is discussed in the present review.
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Pérez-Carretero C, González-Gascón-y-Marín I, Rodríguez-Vicente AE, Quijada-Álamo M, Hernández-Rivas JÁ, Hernández-Sánchez M, Hernández-Rivas JM. The Evolving Landscape of Chronic Lymphocytic Leukemia on Diagnosis, Prognosis and Treatment. Diagnostics (Basel) 2021; 11:diagnostics11050853. [PMID: 34068813 PMCID: PMC8151186 DOI: 10.3390/diagnostics11050853] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/25/2021] [Accepted: 05/05/2021] [Indexed: 12/22/2022] Open
Abstract
The knowledge of chronic lymphocytic leukemia (CLL) has progressively deepened during the last forty years. Research activities and clinical studies have been remarkably fruitful in novel findings elucidating multiple aspects of the pathogenesis of the disease, improving CLL diagnosis, prognosis and treatment. Whereas the diagnostic criteria for CLL have not substantially changed over time, prognostication has experienced an expansion with the identification of new biological and genetic biomarkers. Thanks to next-generation sequencing (NGS), an unprecedented number of gene mutations were identified with potential prognostic and predictive value in the 2010s, although significant work on their validation is still required before they can be used in a routine clinical setting. In terms of treatment, there has been an impressive explosion of new approaches based on targeted therapies for CLL patients during the last decade. In this current chemotherapy-free era, BCR and BCL2 inhibitors have changed the management of CLL patients and clearly improved their prognosis and quality of life. In this review, we provide an overview of these novel advances, as well as point out questions that should be further addressed to continue improving the outcomes of patients.
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Affiliation(s)
- Claudia Pérez-Carretero
- Cancer Research Center (IBMCC) CSIC-University of Salamanca, 37007 Salamanca, Spain; (C.P.-C.); (A.E.R.-V.); (M.Q.-Á.)
- Instituto de Investigación Biomédica (IBSAL), 37007 Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, 37007 Salamanca, Spain
| | | | - Ana E. Rodríguez-Vicente
- Cancer Research Center (IBMCC) CSIC-University of Salamanca, 37007 Salamanca, Spain; (C.P.-C.); (A.E.R.-V.); (M.Q.-Á.)
- Instituto de Investigación Biomédica (IBSAL), 37007 Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, 37007 Salamanca, Spain
| | - Miguel Quijada-Álamo
- Cancer Research Center (IBMCC) CSIC-University of Salamanca, 37007 Salamanca, Spain; (C.P.-C.); (A.E.R.-V.); (M.Q.-Á.)
- Instituto de Investigación Biomédica (IBSAL), 37007 Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, 37007 Salamanca, Spain
| | - José-Ángel Hernández-Rivas
- Department of Hematology, Infanta Leonor University Hospital, 28031 Madrid, Spain; (I.G.-G.-y-M.); (J.-Á.H.-R.)
- Department of Medicine, Complutense University, 28040 Madrid, Spain
| | - María Hernández-Sánchez
- Cancer Research Center (IBMCC) CSIC-University of Salamanca, 37007 Salamanca, Spain; (C.P.-C.); (A.E.R.-V.); (M.Q.-Á.)
- Instituto de Investigación Biomédica (IBSAL), 37007 Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, 37007 Salamanca, Spain
- Correspondence: (M.H.-S.); (J.M.H.-R.); Tel.: +34-923-294-812 (M.H.-S. & J.M.H.-R.)
| | - Jesús María Hernández-Rivas
- Cancer Research Center (IBMCC) CSIC-University of Salamanca, 37007 Salamanca, Spain; (C.P.-C.); (A.E.R.-V.); (M.Q.-Á.)
- Instituto de Investigación Biomédica (IBSAL), 37007 Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, 37007 Salamanca, Spain
- Department of Medicine, University of Salamanca, 37008 Salamanca, Spain
- Correspondence: (M.H.-S.); (J.M.H.-R.); Tel.: +34-923-294-812 (M.H.-S. & J.M.H.-R.)
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Davis AR, Stone SL, Oran AR, Sussman RT, Bhattacharyya S, Morrissette JJD, Bagg A. Targeted massively parallel sequencing of mature lymphoid neoplasms: assessment of empirical application and diagnostic utility in routine clinical practice. Mod Pathol 2021; 34:904-921. [PMID: 33311649 DOI: 10.1038/s41379-020-00720-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022]
Abstract
Massively parallel sequencing (MPS) has become a viable diagnostic tool to interrogate genetic profiles of numerous tumors but has yet to be routinely adopted in the setting of lymphoma. Here, we report the empirical application of a targeted 40-gene panel developed for use in mature lymphoid neoplasms (MLNs) and report our experience on over 500 cases submitted for MPS during the first year of its clinical use. MPS was applied to both fresh and fixed specimens. The most frequent diagnoses were diffuse large B-cell lymphoma (116), chronic lymphocytic leukemia/small lymphocytic lymphoma (60), marginal zone lymphoma (52), and follicular lymphoma (43), followed by a spectrum of mature T-cell neoplasms (40). Of 534 cases submitted, 471 generated reportable results in MLNs, with disease-associated variants (DAVs) detected in 241 cases (51.2%). The most frequent DAVs affected TP53 (30%), CREBBP (14%), MYD88 (14%), TNFRSF14 (10%), TNFAIP3 (10%), B2M (7%), and NOTCH2 (7%). The bulk of our findings confirm what is reported in the scientific literature. While a substantial majority of mutations did not directly impact diagnosis, MPS results were utilized to either change, refine, or facilitate the final diagnosis in ~10.8% of cases with DAVs and 5.5% of cases overall. In addition, we identified preanalytic variables that significantly affect assay performance highlighting items for specimen triage. We demonstrate the technical viability and utility of the judicious use of a targeted MPS panel that may help to establish general guidelines for specimen selection and diagnostic application in MLNs in routine clinical practice.
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Affiliation(s)
- Adam R Davis
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Sara L Stone
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda R Oran
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Robyn T Sussman
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Siddharth Bhattacharyya
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer J D Morrissette
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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Bhaskar V, Graff-Meyer A, Schenk AD, Cavadini S, von Loeffelholz O, Natchiar SK, Artus-Revel CG, Hotz HR, Bretones G, Klaholz BP, Chao JA. Dynamics of uS19 C-Terminal Tail during the Translation Elongation Cycle in Human Ribosomes. Cell Rep 2021; 31:107473. [PMID: 32268098 DOI: 10.1016/j.celrep.2020.03.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 12/06/2019] [Accepted: 03/12/2020] [Indexed: 01/08/2023] Open
Abstract
Ribosomes undergo multiple conformational transitions during translation elongation. Here, we report the high-resolution cryoelectron microscopy (cryo-EM) structure of the human 80S ribosome in the post-decoding pre-translocation state (classical-PRE) at 3.3-Å resolution along with the rotated (hybrid-PRE) and the post-translocation states (POST). The classical-PRE state ribosome structure reveals a previously unobserved interaction between the C-terminal region of the conserved ribosomal protein uS19 and the A- and P-site tRNAs and the mRNA in the decoding site. In addition to changes in the inter-subunit bridges, analysis of different ribosomal conformations reveals the dynamic nature of this domain and suggests a role in tRNA accommodation and translocation during elongation. Furthermore, we show that disease-associated mutations in uS19 result in increased frameshifting. Together, this structure-function analysis provides mechanistic insights into the role of the uS19 C-terminal tail in the context of mammalian ribosomes.
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Affiliation(s)
- Varun Bhaskar
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | | | - Andreas D Schenk
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Ottilie von Loeffelholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, INSERM, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France; Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U964, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - S Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, INSERM, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France; Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U964, Illkirch, France; Université de Strasbourg, Illkirch, France
| | | | - Hans-Rudolf Hotz
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Gabriel Bretones
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, INSERM, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France; Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U964, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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40
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Huang H, Ghalei H, Karbstein K. Quality control of 40S ribosome head assembly ensures scanning competence. J Cell Biol 2021; 219:152152. [PMID: 33007085 PMCID: PMC7534925 DOI: 10.1083/jcb.202004161] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/25/2020] [Accepted: 08/13/2020] [Indexed: 11/22/2022] Open
Abstract
During translation initiation, 40S ribosomes scan the mRNA until they encounter the start codon, where conformational changes produce a translation-competent 80S complex. Destabilizing the scanning complex results in misinitiation at non-AUG codons, demonstrating its importance for fidelity. Here, we use a combination of biochemical and genetic analyses to demonstrate that the ability of the nascent subunit to adopt the scanning complex is tested during assembly via structural mimicry. Specifically, formation of the 80S-like assembly intermediate, which structurally resembles scanning complexes, requires the correct folding of two rRNA elements in the subunit head and the proper positioning of the universally conserved head proteins Rps3, Rps15, Rps20, and Rps29. rRNA misfolding impairs the formation of 80S-like ribosomes, and bypass of individual checkpoints using cancer-associated mutations produces ribosomes defective in accurate start-site selection. Thus, the formation of 80S-like assembly intermediates is a quality control step that ensures scanning competence of the nascent subunit.
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Affiliation(s)
- Haina Huang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL
| | - Homa Ghalei
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL
| | - Katrin Karbstein
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL.,Howard Hughes Medical Institute, Chevy Chase, MD
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41
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Eukaryotic protein uS19: a component of the decoding site of ribosomes and a player in human diseases. Biochem J 2021; 478:997-1008. [PMID: 33661277 DOI: 10.1042/bcj20200950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 11/17/2022]
Abstract
Proteins belonging to the universal ribosomal protein (rp) uS19 family are constituents of small ribosomal subunits, and their conserved globular parts are involved in the formation of the head of these subunits. The eukaryotic rp uS19 (previously known as S15) comprises a C-terminal extension that has no homology in the bacterial counterparts. This extension is directly implicated in the formation of the ribosomal decoding site and thereby affects translational fidelity in a manner that has no analogy in bacterial ribosomes. Another eukaryote-specific feature of rp uS19 is its essential participance in the 40S subunit maturation due to the interactions with the subunit assembly factors required for the nuclear exit of pre-40S particles. Beyond properties related to the translation machinery, eukaryotic rp uS19 has an extra-ribosomal function concerned with its direct involvement in the regulation of the activity of an important tumor suppressor p53 in the Mdm2/Mdmx-p53 pathway. Mutations in the RPS15 gene encoding rp uS19 are linked to diseases (Diamond Blackfan anemia, chronic lymphocytic leukemia and Parkinson's disease) caused either by defects in the ribosome biogenesis or disturbances in the functioning of ribosomes containing mutant rp uS19, likely due to the changed translational fidelity. Here, we review currently available data on the involvement of rp uS19 in the operation of the translational machinery and in the maturation of 40S subunits, on its extra-ribosomal function, and on relationships between mutations in the RPS15 gene and certain human diseases.
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42
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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] [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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43
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Prognostic and predictive impact of genetic markers in patients with CLL treated with obinutuzumab and venetoclax. Blood 2021; 135:2402-2412. [PMID: 32206772 DOI: 10.1182/blood.2019004492] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/24/2020] [Indexed: 01/01/2023] Open
Abstract
Genetic parameters are established prognostic factors in chronic lymphocytic leukemia (CLL) treated with chemoimmunotherapy, but are less well studied with novel compounds. We assessed immunoglobulin heavy variable chain (IGHV) mutation status, common genomic aberrations, and gene mutations in 421 untreated patients within the CLL14 trial (NCT02242942), comparing obinutuzumab+chlorambucil (GClb) vs obinutuzumab+venetoclax (VenG). The incidences of genomic aberrations considering the hierarchical model were del(17p) 7%, del(11q) 18%, +12 18%, and del(13q) 35%, whereas IGHV was unmutated in 60% of patients. NOTCH1 mutations were most common (23%), followed by SF3B1 (16%), ATM (13%), and TP53 (10%). Although the overall response rate (ORR) for GClb was lower in patients with del(17p), del(11q), mutated TP53, ATM, and BIRC3, none of these parameters reduced complete remission (CR) rate and ORR with VenG. At a median follow-up of 28 months, del(17p) and mutated TP53 were the only abnormalities with an effect on progression-free survival (PFS) for both treatment groups: GClb (hazard ratio [HR], 4.6 [P < .01]; HR, 2.7 [P < .01], respectively) and VenG (HR, 4.4 [P < .01]; HR, 3.1 [P < .01], respectively). No other factors affected outcome with VenG, whereas for GClb del(11q), BIRC3, NOTCH1, and unmutated IGHV were associated with shorter PFS. Multivariable analysis identified del(17p), del(11q), unmutated IGHV, and mutated TP53, BIRC3, and SF3B1 as independent prognostic factors for PFS with GClb, whereas for VenG, only del(17p) was significant. VenG was superior to GClb across most genetic subgroups. Patients with adverse genetic markers had the strongest benefit from VenG, particularly subjects with unmutated IGHV, which was identified as a predictive factor in a multivariable treatment-interaction analysis.
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Abstract
Patients with chronic lymphocytic leukemia can be divided into three categories: those who are minimally affected by the problem, often never requiring therapy; those that initially follow an indolent course but subsequently progress and require therapy; and those that from the point of diagnosis exhibit an aggressive disease necessitating treatment. Likewise, such patients pass through three phases: development of the disease, diagnosis, and need for therapy. Finally, the leukemic clones of all patients appear to require continuous input from the exterior, most often through membrane receptors, to allow them to survive and grow. This review is presented according to the temporal course that the disease follows, focusing on those external influences from the tissue microenvironment (TME) that support the time lines as well as those internal influences that are inherited or develop as genetic and epigenetic changes occurring over the time line. Regarding the former, special emphasis is placed on the input provided via the B-cell receptor for antigen and the C-X-C-motif chemokine receptor-4 and the therapeutic agents that block these inputs. Regarding the latter, prominence is laid upon inherited susceptibility genes and the genetic and epigenetic abnormalities that lead to the developmental and progression of the disease.
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MESH Headings
- Disease Progression
- Humans
- Immunotherapy
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/etiology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Mutation
- PAX5 Transcription Factor/metabolism
- Receptors, Antigen, B-Cell
- Signal Transduction
- Tumor Microenvironment
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Affiliation(s)
- Nicholas Chiorazzi
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, New York 11030, USA
| | - Shih-Shih Chen
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, New York 11030, USA
| | - Kanti R Rai
- The Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York 11549, USA
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45
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Hua X, Chen J, Ge S, Xiao H, Zhang L, Liang C. Integrated analysis of the functions of RNA binding proteins in clear cell renal cell carcinoma. Genomics 2020; 113:850-860. [PMID: 33169673 DOI: 10.1016/j.ygeno.2020.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/16/2020] [Indexed: 12/29/2022]
Abstract
RNA binding proteins (RBPs) dysregulation is involved in the processes of various tumors. However, the roles of RBPs in clear cell renal cell carcinoma (ccRCC) remain poorly understand. In present study, we first performed consensus clustering and identified two clusters, of which cluster 2 was closely correlated with the malignancy of ccRCC. Differentially expressed RBPs between normal and tumor tissues were obtained, comprising 71 up-regulated and 44 down-regulated ones. Then, ten hub genes were selected and validated using The Human Protein Atlas database and receiver operating characteristic curves, showing good diagnostic value for cancers. Besides, we identified ten RBPs with the most useful prognostic values, and were used to construct a risk score model. The model could be used to stratify patients with different prognosis and phenotype distributions. The model showed good performance and can be used as a complementation for clinical factors to guide clinical practice in the future.
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Affiliation(s)
- Xiaoliang Hua
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China
| | - Juan Chen
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, the College of Laboratory Medicine, Chongqing Medical University, 400016, Chongqing, China
| | - Shengdong Ge
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China
| | - Haibing Xiao
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China
| | - Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China.
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China.
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Venturi G, Montanaro L. How Altered Ribosome Production Can Cause or Contribute to Human Disease: The Spectrum of Ribosomopathies. Cells 2020; 9:E2300. [PMID: 33076379 PMCID: PMC7602531 DOI: 10.3390/cells9102300] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
A number of different defects in the process of ribosome production can lead to a diversified spectrum of disorders that are collectively identified as ribosomopathies. The specific factors involved may either play a role only in ribosome biogenesis or have additional extra-ribosomal functions, making it difficult to ascribe the pathogenesis of the disease specifically to an altered ribosome biogenesis, even if the latter is clearly affected. We reviewed the available literature in the field from this point of view with the aim of distinguishing, among ribosomopathies, the ones due to specific alterations in the process of ribosome production from those characterized by a multifactorial pathogenesis.
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Affiliation(s)
- Giulia Venturi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
- Center for Applied Biomedical Research, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
- Center for Applied Biomedical Research, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
- Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, 40138 Bologna, Italy
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Clonal dynamics in chronic lymphocytic leukemia. Blood Adv 2020; 3:3759-3769. [PMID: 31770443 DOI: 10.1182/bloodadvances.2019000367] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/20/2019] [Indexed: 12/28/2022] Open
Abstract
Chronic lymphocytic leukemia has a highly variable disease course across patients, thought to be driven by the vast inter- and intrapatient molecular heterogeneity described in several large-scale DNA-sequencing studies conducted over the past decade. Although the last 5 years have seen a dramatic shift in the therapeutic landscape for chronic lymphocytic leukemia, including the regulatory approval of several potent targeted agents (ie, idelalisib, ibrutinib, venetoclax), the vast majority of patients still inevitably experience disease recurrence or persistence. Recent genome-wide sequencing approaches have helped to identify subclonal populations within tumors that demonstrate a broad spectrum of somatic mutations, diverse levels of response to therapy, patterns of repopulation, and growth kinetics. Understanding the impact of genetic, epigenetic, and transcriptomic features on clonal growth dynamics and drug response will be an important step toward the selection and timing of therapy.
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Polymenis M. Ribosomal proteins: mutant phenotypes by the numbers and associated gene expression changes. Open Biol 2020; 10:200114. [PMID: 32810425 PMCID: PMC7479938 DOI: 10.1098/rsob.200114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ribosomal proteins are highly conserved, many universally so among organisms. All ribosomal proteins are structural parts of the same molecular machine, the ribosome. However, when ribosomal proteins are mutated individually, they often lead to distinct and intriguing phenotypes, including specific human pathologies. This review is an attempt to collect and analyse all the reported phenotypes of each ribosomal protein mutant in several eukaryotes (Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus, Homo sapiens). These phenotypes were processed with unbiased computational approaches to reveal associations between different phenotypes and the contributions of individual ribosomal protein genes. An overview of gene expression changes in ribosomal protein mutants, with emphasis on ribosome profiling studies, is also presented. The available data point to patterns that may account for most of the observed phenotypes. The information presented here may also inform future studies about the molecular basis of the phenotypes that arise from mutations in ribosomal proteins.
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Affiliation(s)
- Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
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Hobeika C, Rached G, Chebly A, Chouery E, Kourie HR. Whole-exome and whole-genome sequencing in chronic lymphocytic leukemia: new biomarkers to target. Pharmacogenomics 2020; 21:957-962. [PMID: 32799640 DOI: 10.2217/pgs-2020-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Many biomarkers indicate prognosis in chronic lymphocytic leukemia; such as fluorescence in situ hybridization testing: 17p or 11q deletions have a worse prognosis than trisomy 12, 13q deletion or normal result, or the mutational status of the immunoglobulin heavy chain (IGHV): unmutated IGHV have a worse prognosis than mutated IGHV. Recently, many gene mutations (TP53, NOTCH1 etc.,) have been linked to a worse prognosis. With the new era of high-throughput sequencing, it has become easier to study gene mutations and their implication in predicting prognosis. In this review, we aim to review all the studies that performed whole-exome sequencing or whole-genome sequencing on chronic lymphocytic leukemia cells and explore the implication of various genes in disease prognosis.
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Affiliation(s)
- Charbel Hobeika
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon
| | - Gaelle Rached
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon
| | - Alain Chebly
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon
| | - Eliane Chouery
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon
| | - Hampig Raphael Kourie
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon.,Department of Hematology-Oncology, Hotel Dieu de France University Hospital, Faculty of Medicine, Saint Joseph University, Beirut, BP-17 5208, Lebanon
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50
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Lee J, Wang YL. Prognostic and Predictive Molecular Biomarkers in Chronic Lymphocytic Leukemia. J Mol Diagn 2020; 22:1114-1125. [PMID: 32615167 DOI: 10.1016/j.jmoldx.2020.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 05/29/2020] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a malignancy of B cells with a variable clinical course. Prognostication is important to place patients into different risk categories for guiding decisions on clinical management, to treat or not to treat. Although several clinical, cytogenetic, and molecular parameters have been established, in the past decade, a tremendous understanding of molecular lesions has been obtained with the advent of high-throughput sequencing. Meanwhile, rapid advances in the understanding of the CLL oncogenic pathways have led to the development of small-molecule targeting signal transducers, Bruton tyrosine kinase and phosphatidylinositol 3-kinase, as well as anti-apoptotic protein BCL2 apoptosis regulator. After an initial response to these targeted therapies, some patients develop resistance and experience disease progression. Novel gene mutations have been identified that account for some of the drug resistance mechanisms. This article focuses on the prognostic and predictive molecular biomarkers in CLL relevant to the molecular pathology practice, beginning with a review of well-established prognostic markers that have already been incorporated into major clinical guidelines, which will be followed by a discussion of emerging biomarkers that are expected to impact clinical practice soon in the future. Special emphasis will be put on predictive biomarkers related to newer targeted therapies in hopes that this review will serve as a useful reference for molecular diagnostic professionals, clinicians, as well as laboratory investigators and trainees.
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Affiliation(s)
- Jimmy Lee
- Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois
| | - Y Lynn Wang
- Department of Pathology, Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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