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Wiedmeier-Nutor JE, McCabe CE, O'Brien DR, Jessen E, Bonolo de Campos C, Boddicker NJ, Griffin R, Allmer C, Rabe KG, Cerhan JR, Parikh SA, Kay NE, Yan H, Van Dyke DL, Slager SL, Braggio E. Utility of Targeted Sequencing Compared to FISH for Detection of Chronic Lymphocytic Leukemia Copy Number Alterations. Cancers (Basel) 2024; 16:2450. [PMID: 39001512 PMCID: PMC11240685 DOI: 10.3390/cancers16132450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by multiple copy number alterations (CNAs) and somatic mutations that are central to disease prognosis, risk stratification, and mechanisms of therapy resistance. Fluorescence in situ hybridization (FISH) panels are widely used in clinical applications as the gold standard for screening prognostic chromosomal abnormalities in CLL. DNA sequencing is an alternative approach to identifying CNAs but is not an established method for clinical CNA screening. We sequenced DNA from 509 individuals with CLL or monoclonal B-cell lymphocytosis (MBL), the precursor to CLL, using a targeted sequencing panel of 59 recurrently mutated genes in CLL and additional amplicons across regions affected by clinically relevant CNAs [i.e., del(17p), del(11q), del(13q), and trisomy 12]. We used the PatternCNV algorithm to call CNA and compared the concordance of calling clinically relevant CNAs by targeted sequencing to that of FISH. We found a high accuracy of calling CNAs via sequencing compared to FISH. With FISH as the gold standard, the specificity of targeted sequencing was >95%, sensitivity was >86%, positive predictive value was >90%, and negative predictive value was >84% across the clinically relevant CNAs. Using targeted sequencing, we were also able to identify other common CLL-associated CNAs, including del(6q), del(14q), and gain 8q, as well as complex karyotype, defined as the presence of 3 or more chromosomal abnormalities, in 26 patients. In a single and cost-effective assay that can be performed on stored DNA samples, targeted sequencing can simultaneously detect CNAs, somatic mutations, and complex karyotypes, which are all important prognostic features in CLL.
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Affiliation(s)
- J Erin Wiedmeier-Nutor
- Division of Hematology and Oncology, Department of Medicine, Mayo Clinic, Phoenix, AZ 85054, USA
| | - Chantal E McCabe
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel R O'Brien
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Erik Jessen
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Cecilia Bonolo de Campos
- Division of Hematology and Oncology, Department of Medicine, Mayo Clinic, Phoenix, AZ 85054, USA
| | - Nicholas J Boddicker
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Rosalie Griffin
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Cristine Allmer
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Kari G Rabe
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - James R Cerhan
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Sameer A Parikh
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Neil E Kay
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Huihuang Yan
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel L Van Dyke
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Susan L Slager
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Esteban Braggio
- Division of Hematology and Oncology, Department of Medicine, Mayo Clinic, Phoenix, AZ 85054, USA
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2
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Nasr AA, Fund X, Barreau S, Desterke C, Borie C, Oudrhiri N, Faivre J, Bennaceur-Griscelli A, Turhan AG. BIRC-3 mutated monoclonal B lymphocytosis without evolution to chronic lymphocytic leukemia (CLL). Leuk Lymphoma 2024; 65:692-695. [PMID: 38293748 DOI: 10.1080/10428194.2024.2308665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/17/2024] [Indexed: 02/01/2024]
Affiliation(s)
- Amen Allah Nasr
- APHP-Paris Saclay, Service d'Hématologie-Bicêtre, Kremlin-Bicêtre, France
- Faculté de Médecine Paris-Saclay, Université Paris-Saclay, Kremlin-Bicêtre, France
- Inserm UMR-S 1310, Villejuif, France
| | - Xavier Fund
- Inserm UMR-S 1310, Villejuif, France
- APHP Paris Saclay Service d'Oncohématologie moléculaire et Cytogénétique Hôpital Paul-Brousse, Villejuif, France
| | - Sylvain Barreau
- APHP-Paris Saclay, Service d'Hématologie-Bicêtre, Kremlin-Bicêtre, France
- Inserm UMR-S 1310, Villejuif, France
| | - Christophe Desterke
- Faculté de Médecine Paris-Saclay, Université Paris-Saclay, Kremlin-Bicêtre, France
- Inserm UMR-S 1310, Villejuif, France
| | - Claire Borie
- Inserm UMR-S 1310, Villejuif, France
- APHP Paris Saclay Service d'Oncohématologie moléculaire et Cytogénétique Hôpital Paul-Brousse, Villejuif, France
| | - Noufissa Oudrhiri
- APHP-Paris Saclay, Service d'Hématologie-Bicêtre, Kremlin-Bicêtre, France
- Inserm UMR-S 1310, Villejuif, France
- APHP Paris Saclay Service d'Oncohématologie moléculaire et Cytogénétique Hôpital Paul-Brousse, Villejuif, France
| | - Jamila Faivre
- APHP Paris Saclay Service d'Oncohématologie moléculaire et Cytogénétique Hôpital Paul-Brousse, Villejuif, France
| | - A Bennaceur-Griscelli
- APHP-Paris Saclay, Service d'Hématologie-Bicêtre, Kremlin-Bicêtre, France
- Faculté de Médecine Paris-Saclay, Université Paris-Saclay, Kremlin-Bicêtre, France
- Inserm UMR-S 1310, Villejuif, France
- APHP Paris Saclay Service d'Oncohématologie moléculaire et Cytogénétique Hôpital Paul-Brousse, Villejuif, France
- Centre for iPSC Therapies (CITHERA) INSERM UMS 45, GenopoleEvry, France
| | - A G Turhan
- APHP-Paris Saclay, Service d'Hématologie-Bicêtre, Kremlin-Bicêtre, France
- Faculté de Médecine Paris-Saclay, Université Paris-Saclay, Kremlin-Bicêtre, France
- Inserm UMR-S 1310, Villejuif, France
- APHP Paris Saclay Service d'Oncohématologie moléculaire et Cytogénétique Hôpital Paul-Brousse, Villejuif, France
- Centre for iPSC Therapies (CITHERA) INSERM UMS 45, GenopoleEvry, France
- Department of Hematology, American Hospital of Paris, Neuilly Sur Seine, France
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3
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Brunner A, Thalhammer-Thurner GC, Willenbacher W, Haun M, Zelger BG, Willenbacher E. In-depth molecular analysis of lymphomas with lymphoplasmacytic differentiation may provide more precise diagnosis and rational treatment allocation. Ann Hematol 2024; 103:553-563. [PMID: 37951851 PMCID: PMC10798918 DOI: 10.1007/s00277-023-05531-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023]
Abstract
We performed a molecular analysis of formalin-fixed paraffin embedded and decalcified bone marrow trephine biopsies of 41 patients with a B-cell disorder with lymphoplasmacytic differentiation to enable a more precise diagnosis and to describe potentially prognostic and therapeutic relevant mutations. Analysis was performed with a commercially available next-generation sequencing (NGS) lymphoma panel (Lymphoma Solution, SophiaGenetics). Results were correlated with clinical and pathological parameters. Our group covered a spectrum of B-cell disorders with plasmacytic differentiation ranging from Waldenstroem's macroglobulinemia (WM), to small-B-cell lymphomas with plasmacytic differentiation (SBCL-PC) to IgM myeloma (MM). The most helpful diagnostic criteria included morphology and immuno-phenotype as a prerequisite for the interpretation of molecular analysis. MYD88 mutation was present in nearly all WM, but also in 50% of SBCL-PCs, while MM were consistently negative. Driver mutations, such as TP53, were already detectable early in the course of the respective diseases indicating a higher risk of progression, transformation, and reduced progression-free survival. In addition, we report on a novel BIRC3 frameshift mutation in one case of a progressive WM. Our data indicate that patients with LPL/WM might benefit from thorough pathological work-up and detailed molecular analysis in terms of precise diagnosis and targeted treatment allocation.
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Affiliation(s)
- Andrea Brunner
- Department of Pathology, Neuropathology and Molecular Pathology, Innsbruck Medical University, Innsbruck, Austria.
| | | | - Wolfgang Willenbacher
- Internal Medicine V, Haematology & Oncology, Innsbruck Medical University, Innsbruck, Austria
- Syndena GmbH, Connect to Cure, Innsbruck, Austria
| | - Margot Haun
- Department of Pathology, Neuropathology and Molecular Pathology, Innsbruck Medical University, Innsbruck, Austria
- Institute of Pathophysiology, Innsbruck Medical University, Innsbruck, Austria
| | - Bettina Gudrun Zelger
- Department of Pathology, Neuropathology and Molecular Pathology, Innsbruck Medical University, Innsbruck, Austria
| | - Ella Willenbacher
- Internal Medicine V, Haematology & Oncology, Innsbruck Medical University, Innsbruck, Austria
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Wang H, Yang L, Li Q, Song H, Ji H. Case report: Composite mantle cell lymphoma and classical Hodgkin lymphoma. Pathol Oncol Res 2023; 29:1611051. [PMID: 37006439 PMCID: PMC10064289 DOI: 10.3389/pore.2023.1611051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/01/2023] [Indexed: 03/19/2023]
Abstract
Composite mantle cell lymphoma and classical Hodgkin lymphoma is very rare and the actual origin of it is still unclear. Here we reported a new case of composite mantle cell lymphoma and classical Hodgkin lymphoma and analyzed its molecular changes. Eight mutations were identified in its Hodgkin component through next-generation sequencing. In addition, we reviewed the published cases of composite mantle cell lymphoma and classical Hodgkin lymphoma and summarized the molecular changes of reported cases as well as the current case to explore the possible pathway of histogenesis.
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Affiliation(s)
- Hongyu Wang
- Department of Pathology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Liqun Yang
- Huayin Health Hematopathology Comprehensive Diagnostic Center, Chengdu Huayin Medical Laboratory Center, Chengdu, China
| | - Qiuyao Li
- Department of Pathology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Haiyun Song
- Department of Pathology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Hong Ji
- Department of Pathology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
- *Correspondence: Hong Ji,
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Invernizzi R. Images from the Haematologica Atlas of Hematologic Cytology: Gaucher disease. Haematologica 2022; 107:2527. [PMID: 36321399 PMCID: PMC9614540 DOI: 10.3324/haematol.2022.281777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Indexed: 12/12/2022] Open
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6
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Expression Analysis of BIRC3 as One Target Gene of Transcription Factor NF-κB for Esophageal Cancer. Processes (Basel) 2022. [DOI: 10.3390/pr10091673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Esophageal cancer (ESCA) is one of the highest lethal malignancy tumors worldwide. Baculoviral IAP repeat-containing protein 3 (BIRC3) is the main inhibitor of apoptosis in many malignancies. The aim of this study was to clarify how BIRC3 acts in ESCA cells. Through TNMplot and GEPIA2 analysis, BIRC3 was found abundantly expressed in ESCA cells. The quantitative RT-PCR assay confirmed BIRC3 was pronouncedly induced in all used ESCA cell lines. In addition, proinflammatory cytokines TNFα and IL-1β were shown to have promotion effects on BIRC3 expression in ESCA cells. These promotive effects were blocked when the function of NF-κB was inhibited by bay 11-7082, which indicates the expression of the BIRC3 gene was regulated via the NF-κB transcription pathway in ESCA. Moreover, bioinformatics analysis showed that the BIRC3 gene had many NF-κB binding cis-elements. Chromatin immunoprecipitation was then performed and it was found that NF-κB directly interacts with cis-elements of the BIRC3 gene. In conclusion, our data proved that the high expression level of BIRC3 maintained the survival of ESCA cells. BIRC3 was up-regulated by proinflammatory cytokine TNFα and IL-1β through the NF-κB signaling pathway, and this may be helpful for esophageal cancer prevention and therapy.
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Öztürk S, Paul Y, Afzal S, Gil-Farina I, Jauch A, Bruch PM, Kalter V, Hanna B, Arseni L, Roessner PM, Schmidt M, Stilgenbauer S, Dietrich S, Lichter P, Zapatka M, Seiffert M. Longitudinal analyses of CLL in mice identify leukemia-related clonal changes including a Myc gain predicting poor outcome in patients. Leukemia 2022; 36:464-475. [PMID: 34417556 PMCID: PMC8807396 DOI: 10.1038/s41375-021-01381-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 02/07/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is a B-cell malignancy mainly occurring at an advanced age with no single major genetic driver. Transgenic expression of TCL1 in B cells leads after a long latency to a CLL-like disease in aged Eµ-TCL1 mice suggesting that TCL1 overexpression is not sufficient for full leukemic transformation. In search for secondary genetic events and to elucidate the clonal evolution of CLL, we performed whole exome and B-cell receptor sequencing of longitudinal leukemia samples of Eµ-TCL1 mice. We observed a B-cell receptor stereotypy, as described in patients, confirming that CLL is an antigen-driven disease. Deep sequencing showed that leukemia in Eµ-TCL1 mice is mostly monoclonal. Rare oligoclonality was associated with inability of tumors to develop disease upon adoptive transfer in mice. In addition, we identified clonal changes and a sequential acquisition of mutations with known relevance in CLL, which highlights the genetic similarities and therefore, suitability of the Eµ-TCL1 mouse model for progressive CLL. Among them, a recurrent gain of chromosome 15, where Myc is located, was identified in almost all tumors in Eµ-TCL1 mice. Interestingly, amplification of 8q24, the chromosomal region containing MYC in humans, was associated with worse outcome of patients with CLL.
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Affiliation(s)
- Selcen Öztürk
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yashna Paul
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Saira Afzal
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
- GeneWerk GmbH, Heidelberg, Germany
| | - Irene Gil-Farina
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
- GeneWerk GmbH, Heidelberg, Germany
| | - Anna Jauch
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Peter-Martin Bruch
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Verena Kalter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bola Hanna
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lavinia Arseni
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp M Roessner
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manfred Schmidt
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
- GeneWerk GmbH, Heidelberg, Germany
| | | | - Sascha Dietrich
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Seiffert
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Cusenza VY, Bisagni A, Rinaldini M, Cattani C, Frazzi R. Copy Number Variation and Rearrangements Assessment in Cancer: Comparison of Droplet Digital PCR with the Current Approaches. Int J Mol Sci 2021; 22:ijms22094732. [PMID: 33946969 PMCID: PMC8124143 DOI: 10.3390/ijms22094732] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
The cytogenetic and molecular assessment of deletions, amplifications and rearrangements are key aspects in the diagnosis and therapy of cancer. Not only the initial evaluation and classification of the disease, but also the follow-up of the tumor rely on these laboratory approaches. The therapeutic choice can be guided by the results of the laboratory testing. Genetic deletions and/or amplifications directly affect the susceptibility or the resistance to specific therapies. In an era of personalized medicine, the correct and reliable molecular characterization of the disease, also during the therapeutic path, acquires a pivotal role. Molecular assays like multiplex ligation-dependent probe amplification and droplet digital PCR represent exceptional tools for a sensitive and reliable detection of genetic alterations and deserve a role in molecular oncology. In this manuscript we provide a technical comparison of these two approaches with the golden standard represented by fluorescence in situ hybridization. We also describe some relevant targets currently evaluated with these techniques in solid and hematologic tumors.
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Affiliation(s)
- Vincenza Ylenia Cusenza
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy;
| | - Alessandra Bisagni
- Pathology Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy;
| | - Monia Rinaldini
- Medical Genetics Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (M.R.); (C.C.)
| | - Chiara Cattani
- Medical Genetics Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (M.R.); (C.C.)
| | - Raffaele Frazzi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy;
- Correspondence:
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9
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Abstract
BACKGROUND The evasion from apoptosis is a common strategy adopted by most tumors, and inhibitors of apoptosis proteins (IAPs) are among the most studied molecular and therapeutic targets. BIRC3 (cellular IAP2) and BIRC5 (survivin) are two of the eight members of the human IAPs family. This family is characterized by the presence of the baculoviral IAP repeat (BIR) domains, involved in protein-protein interactions. In addition to the BIR domains, IAPs also contain other important domains like the C-terminal ubiquitin-conjugating (UBC) domain, the caspase recruitment (CARD) domain and the C-terminal Ring zinc-finger (RING) domain. MAIN BODY BIRC3 and BIRC5 have been characterized in some solid and hematological tumors and are therapeutic targets for the family of drugs called "Smac mimetics". Many evidences point to the pro-survival and antiapoptotic role of BIRC3 in cancer cells, however, not all the data are consistent and the resulting picture is heterogeneous. For instance, BIRC3 genetic inactivation due to deletions or point mutations is consistently associated to shorter progression free survival and poor prognosis in chronic lymphocytic leukemia patients. BIRC3 inactivation has also been associated to chemoimmunotherapy resistance. On the contrary, the progression from low grade gliomas to high grade gliomas is accompanied by BIRC3 expression increase, which bears relevant prognostic consequences. Due to the relationship between BIRC3, MAP3K14 and the non-canonical NF-kB pathway, BIRC3 inactivation bears consequences also on the tumor cells relying on NF-kB pathway to survive. BIRC5, on the contrary, is commonly considered an anti-apoptotic molecule, promoting cell division and tumor progression and it is widely regarded as potential therapeutic target. CONCLUSIONS The present manuscript collects and reviews the most recent literature concerning the role played by BIRC3 and BIRC5 in cancer cells, providing useful information for the choice of the best therapeutic targets.
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Affiliation(s)
- Raffaele Frazzi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Viale Risorgimento 80, Reggio Emilia, Italy.
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