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Toma MM, Skorski T. Star wars against leukemia: attacking the clones. Leukemia 2024:10.1038/s41375-024-02369-6. [PMID: 39223295 DOI: 10.1038/s41375-024-02369-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
Leukemia, although most likely starts as a monoclonal genetic/epigenetic anomaly, is a polyclonal disease at manifestation. This polyclonal nature results from ongoing evolutionary changes in the genome/epigenome of leukemia cells to promote their survival and proliferation advantages. We discuss here how genetic and/or epigenetic aberrations alter intracellular microenvironment in individual leukemia clones and how extracellular microenvironment selects the best fitted clones. This dynamic polyclonal composition of leukemia makes designing an effective therapy a challenging task especially because individual leukemia clones often display substantial differences in response to treatment. Here, we discuss novel therapeutic approach employing single cell multiomics to identify and eradicate all individual clones in a patient.
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Affiliation(s)
- Monika M Toma
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA.
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
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2
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Chan-Pak-Choon F, Foulkes WD. On the Hunt for the Missed Genetic Causes of Multiple Primary Tumors. Cancer Prev Res (Phila) 2024; 17:193-195. [PMID: 38693900 DOI: 10.1158/1940-6207.capr-24-0115] [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: 03/15/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 05/03/2024]
Abstract
Improved cancer screening and treatment programs have led to an increased survivorship of patients with cancer, but consequently also to the rise in number of individuals with multiple primary tumors (MPT). Germline testing is the first approach investigating the cause of MPT, as a positive result provides a diagnosis and proper clinical management to the affected individual and their family. Negative or inconclusive genetic results could suggest non-genetic causes, but are negative genetic results truly negative? Herein, we discuss the potential sources of missed genetic causes and highlight the trove of knowledge MPT can provide. See related article by Borja et al., p. 209.
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Affiliation(s)
- Fiona Chan-Pak-Choon
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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3
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Al Assaad M, Michaud O, Semaan A, Sigouros M, Tranquille M, Phan A, Levine MF, Gundem G, Medina-Martínez JS, Papaemmanuil E, Manohar J, Wilkes D, Sboner A, Hoda SAF, Elemento O, Mosquera JM. Whole-Genome Sequencing Analysis of Male Breast Cancer Unveils Novel Structural Events and Potential Therapeutic Targets. Mod Pathol 2024; 37:100452. [PMID: 38369186 DOI: 10.1016/j.modpat.2024.100452] [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: 11/30/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 02/20/2024]
Abstract
The molecular characterization of male breast cancer (MaBC) has received limited attention in research, mostly because of its low incidence rate, accounting for only 0.5% to 1% of all reported cases of breast cancer each year. Managing MaBC presents significant challenges, with most treatment protocols being adapted from those developed for female breast cancer. Utilizing whole-genome sequencing (WGS) and state-of-the-art analyses, the genomic features of 10 MaBC cases (n = 10) were delineated and correlated with clinical and histopathologic characteristics. Using fluorescence in situ hybridization, an additional cohort of 18 patients was interrogated to supplement WGS findings. The genomic landscape of MaBC uncovered significant genetic alterations that could influence diagnosis and treatment. We found common somatic mutations in key driver genes, such as FAT1, GATA3, SMARCA4, and ARID2. Our study also mapped out structural variants that impact cancer-associated genes, such as ARID1A, ESR1, GATA3, NTRK1, and NF1. Using a WGS-based classifier, homologous recombination deficiency (HRD) was identified in 2 cases, both presenting with deleterious variants in BRCA2. Noteworthy was the observation of FGFR1 amplification in 21% of cases. Altogether, we identified at least 1 potential therapeutic target in 8 of the 10 cases, including high tumor mutational burden, FGFR1 amplification, and HRD. Our study is the first WGS characterization of MaBC, which uncovered potentially relevant variants, including structural events in cancer genes, HRD signatures, and germline pathogenic mutations. Our results demonstrate unique genetic markers and potential treatment targets in MaBC, thereby underlining the necessity of tailoring treatment strategies for this understudied patient population. These WGS-based findings add to the growing knowledge of MaBC genomics and highlight the need to expand research on this type of cancer.
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Affiliation(s)
- Majd Al Assaad
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Olivier Michaud
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Département de Pathologie, Université Laval, Quebec City, Quebec, Canada
| | - Alissa Semaan
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Michael Sigouros
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Marvel Tranquille
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Andy Phan
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | | | | | | | | | - Jyothi Manohar
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - David Wilkes
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Syed A F Hoda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York; New York Genome Center, New York, New York.
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4
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Kahn RM, Selenica P, Boerner T, Roche KL, Xiao Y, Sia TY, Maio A, Kemel Y, Sheehan M, Salo-Mullen E, Breen KE, Zhou Q, Iasonos A, Grisham RN, O'Cearbhaill RE, Chi DS, Berger MF, Kundra R, Schultz N, Ellenson LH, Stadler ZK, Offit K, Mandelker D, Aghajanian C, Zamarin D, Sabbatini P, Weigelt B, Liu YL. Pathogenic germline variants in non-BRCA1/2 homologous recombination genes in ovarian cancer: Analysis of tumor phenotype and survival. Gynecol Oncol 2024; 180:35-43. [PMID: 38041901 PMCID: PMC10922242 DOI: 10.1016/j.ygyno.2023.11.019] [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: 10/06/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/04/2023]
Abstract
OBJECTIVE To define molecular features of ovarian cancer (OC) with germline pathogenic variants (PVs) in non-BRCA homologous recombination (HR) genes and analyze survival compared to BRCA1/2 and wildtype (WT) OC. METHODS We included patients with OC undergoing tumor-normal sequencing (MSK-IMPACT) from 07/01/2015-12/31/2020, including germline assessment of BRCA1/2 and other HR genes ATM, BARD1, BRIP1, FANCA, FANCC, NBN, PALB2, RAD50, RAD51B, RAD51C, and RAD51D. Biallelic inactivation was assessed within tumors. Progression-free (PFS) and overall survival (OS) were calculated from pathologic diagnosis using the Kaplan-Meier method with left truncation. Whole-exome sequencing (WES) was performed in a subset. RESULTS Of 882 patients with OC, 56 (6.3%) had germline PVs in non-BRCA HR genes; 95 (11%) had BRCA1-associated OC (58 germline, 37 somatic); and 59 (6.7%) had BRCA2-associated OC (40 germline, 19 somatic). High rates of biallelic alterations were observed among germline PVs in BRIP1 (11/13), PALB2 (3/4), RAD51B (3/4), RAD51C (3/4), and RAD51D (8/10). In cases with WES (27/35), there was higher tumor mutational burden (TMB; median 2.5 [1.1-6.0] vs. 1.2 mut/Mb [0.6-2.6]) and enrichment of HR-deficient (HRD) mutational signatures in tumors associated with germline PALB2 and RAD51B/C/D compared with BRIP1 PVs (p < 0.01). Other features of HRD, including telomeric-allelic imbalance (TAI) and large-scale state transitions (LSTs), were similar. Although there was heterogeneity in PFS/OS by gene group, only BRCA1/2-associated OC had improved survival compared to WT OC (p < 0.01). CONCLUSIONS OCs associated with germline PVs in non-BRCA HR genes represent a heterogenous group, with PALB2 and RAD51B/C/D associated with an HRD phenotype.
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Affiliation(s)
- Ryan M Kahn
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thomas Boerner
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kara Long Roche
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Yonghong Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tiffany Y Sia
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Maio
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Kemel
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Margaret Sheehan
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erin Salo-Mullen
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kelsey E Breen
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Qin Zhou
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexia Iasonos
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rachel N Grisham
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Roisin E O'Cearbhaill
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Dennis S Chi
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Michael F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ritika Kundra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lora H Ellenson
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia K Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carol Aghajanian
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Dmitriy Zamarin
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Paul Sabbatini
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying L Liu
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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5
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Gozzellino L, Nannini M, Urbini M, Pizzi C, Leone O, Corti B, Baldovini C, Angeli F, Foà A, Pacini D, Folesani G, Costa A, Palumbo T, Nigro MC, Pasquinelli G, Astolfi A, Pantaleo MA. Genomic Landscape Comparison of Cardiac versus Extra-Cardiac Angiosarcomas. Biomedicines 2023; 11:3290. [PMID: 38137511 PMCID: PMC10741871 DOI: 10.3390/biomedicines11123290] [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: 03/15/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Angiosarcomas (ASs) are rare malignant vascular entities that can affect several regions in our body, including the heart. Cardiac ASs comprise 25-40% of cardiac sarcomas and can cause death within months of diagnosis. Thus, our aim was to identify potential differences and/or similarities between cardiac and extra-cardiac ASs to enhance targeted therapies and, consequently, patients' prognosis. Whole-transcriptome analysis of three cardiac and eleven extra-cardiac non-cutaneous samples was performed to investigate differential gene expression and mutational events between the two groups. The gene signature of cardiac and extra-cardiac non-cutaneous ASs was also compared to that of cutaneous angiosarcomas (n = 9). H/N/K-RAS and TP53 alterations were more recurrent in extra-cardiac ASs, while POTE-gene family overexpression was peculiar to cardiac ASs. Additionally, in vitro functional analyses showed that POTEH upregulation conferred a growth advantage to recipient cells, partly supporting the cardiac AS aggressive phenotype and patients' scarce survival rate. These features should be considered when investigating alternative treatments.
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Affiliation(s)
- Livia Gozzellino
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (L.G.); (M.N.); (F.A.); (M.C.N.); (M.A.P.)
| | - Margherita Nannini
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (L.G.); (M.N.); (F.A.); (M.C.N.); (M.A.P.)
- Division of Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Milena Urbini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy;
| | - Carmine Pizzi
- Unit of Cardiology, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy; (C.P.); (A.F.)
| | - Ornella Leone
- Division of Pathology, Cardiovascular and Cardiac Transplant Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (O.L.); (B.C.); (C.B.)
| | - Barbara Corti
- Division of Pathology, Cardiovascular and Cardiac Transplant Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (O.L.); (B.C.); (C.B.)
| | - Chiara Baldovini
- Division of Pathology, Cardiovascular and Cardiac Transplant Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (O.L.); (B.C.); (C.B.)
| | - Francesco Angeli
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (L.G.); (M.N.); (F.A.); (M.C.N.); (M.A.P.)
| | - Alberto Foà
- Unit of Cardiology, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy; (C.P.); (A.F.)
| | - Davide Pacini
- Cardiac Surgery Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (D.P.); (G.F.)
| | - Gianluca Folesani
- Cardiac Surgery Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (D.P.); (G.F.)
| | - Alice Costa
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Teresa Palumbo
- Interdepartmental Center Alma Mater Institute on Healthy Planet, Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy;
| | - Maria Concetta Nigro
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (L.G.); (M.N.); (F.A.); (M.C.N.); (M.A.P.)
| | - Gianandrea Pasquinelli
- Division of Pathology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Annalisa Astolfi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (L.G.); (M.N.); (F.A.); (M.C.N.); (M.A.P.)
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Maria Abbondanza Pantaleo
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (L.G.); (M.N.); (F.A.); (M.C.N.); (M.A.P.)
- Division of Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
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6
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Islam KN, Ajao A, Venkataramani K, Rivera J, Pathania S, Henke K, Siegfried KR. The RNA-binding protein Adad1 is necessary for germ cell maintenance and meiosis in zebrafish. PLoS Genet 2023; 19:e1010589. [PMID: 37552671 PMCID: PMC10437952 DOI: 10.1371/journal.pgen.1010589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 08/18/2023] [Accepted: 07/06/2023] [Indexed: 08/10/2023] Open
Abstract
The double stranded RNA binding protein Adad1 (adenosine deaminase domain containing 1) is a member of the adenosine deaminase acting on RNAs (Adar) protein family with germ cell-specific expression. In mice, Adad1 is necessary for sperm differentiation, however its function outside of mammals has not been investigated. Here, through an N-ethyl-N-nitrosourea (ENU) based forward genetic screen, we identified an adad1 mutant zebrafish line that develops as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish, however germ cells populated the gonad, proliferated, and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes, the spermatocytes failed to progress beyond the zygotene stage. Thus, Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell (LRC) assay, and found that the mutant testes had fewer LRCs and nanos2-expressing cells compared to wild-type siblings, suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by adulthood. To identify potential molecular processes regulated by Adad1, we sequenced bulk mRNA from mutants and wild-type testes and found mis-regulation of genes involved in RNA stability and modification, pointing to a potential broader role in post-transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.
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Affiliation(s)
- Kazi Nazrul Islam
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Anuoluwapo Ajao
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Kavita Venkataramani
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Joshua Rivera
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Shailja Pathania
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Katrin Henke
- Department of Orthopaedics, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Kellee Renee Siegfried
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
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7
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Imyanitov EN, Kuligina ES, Sokolenko AP, Suspitsin EN, Yanus GA, Iyevleva AG, Ivantsov AO, Aleksakhina SN. Hereditary cancer syndromes. World J Clin Oncol 2023; 14:40-68. [PMID: 36908677 PMCID: PMC9993141 DOI: 10.5306/wjco.v14.i2.40] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/09/2022] [Accepted: 02/14/2023] [Indexed: 02/21/2023] Open
Abstract
Hereditary cancer syndromes (HCSs) are arguably the most frequent category of Mendelian genetic diseases, as at least 2% of presumably healthy subjects carry highly-penetrant tumor-predisposing pathogenic variants (PVs). Hereditary breast-ovarian cancer and Lynch syndrome make the highest contribution to cancer morbidity; in addition, there are several dozen less frequent types of familial tumors. The development of the majority albeit not all hereditary malignancies involves two-hit mechanism, i.e. the somatic inactivation of the remaining copy of the affected gene. Earlier studies on cancer families suggested nearly fatal penetrance for the majority of HCS genes; however, population-based investigations and especially large-scale next-generation sequencing data sets demonstrate that the presence of some highly-penetrant PVs is often compatible with healthy status. Hereditary cancer research initially focused mainly on cancer detection and prevention. Recent studies identified multiple HCS-specific drug vulnerabilities, which translated into the development of highly efficient therapeutic options.
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Affiliation(s)
- Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Ekaterina S Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Anna P Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Evgeny N Suspitsin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Grigoriy A Yanus
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Aglaya G Iyevleva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Alexandr O Ivantsov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Svetlana N Aleksakhina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
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8
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Nunziato M, Scaglione GL, Di Maggio F, Nardelli C, Capoluongo E, Salvatore F. The performance of multi-gene panels for breast/ovarian cancer predisposition. Clin Chim Acta 2023; 539:151-161. [PMID: 36521553 DOI: 10.1016/j.cca.2022.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
BRCA1 and BRCA2 are the most mutated genes in breast cancer. We analyzed 48 breast cancer subjects using two methods that differ in terms of number of genes investigated and strategy used (primers: Panel A - 12 genes - vs probes: Panel B - 48 genes). Both the panels and procedures identified "pathogenic" or "likely pathogenic" variants in TP53, ATM, CHEK2 and BARD1 besides BRCA1 and BRCA2. Panel B identified two other putatively pathogenic variants in RNASEL and in RAD50. Identification of variants other than the BRCA genes can be useful in patient management. A total of 121 variants were distributed within the 12 genes and were correctly detected by both panels. However, the number of calls without divergence, namely ± 0.10 difference of allelic frequency, was 78.3%, while calls with a divergence below 0.10 was 16.7%, thus indicating that only 5% (n = 275) of 5,412 calls had a divergence above 0.10. Although these panels differ from each other, both are useful in different situations, particularly when patients should be tested for genes other than BRCA1/2 (as occurs in patients affected by a so called hereditary syndrome) or for therapeutic purposes.
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Affiliation(s)
- Marcella Nunziato
- CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini, 5, 80131 Naples, Italy
| | - Giovanni Luca Scaglione
- CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini, 5, 80131 Naples, Italy; Istituto Dermopatico dell'Immacolata IDI-IRCCS, Via dei Monti di Creta, 104, 00167 Rome, Italy
| | - Federica Di Maggio
- CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini, 5, 80131 Naples, Italy
| | - Carmela Nardelli
- CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini, 5, 80131 Naples, Italy
| | - Ettore Capoluongo
- CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini, 5, 80131 Naples, Italy; Department of Clinical Pathology and Genomics, Ospedale Cannizzaro, Via Messina, 829, 95126 Catania, Italy.
| | - Francesco Salvatore
- CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini, 5, 80131 Naples, Italy.
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9
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Chatila WK, Walch H, Hechtman JF, Moyer SM, Sgambati V, Faleck DM, Srivastava A, Tang L, Benhamida J, Ismailgeci D, Campos C, Wu F, Chang Q, Vakiani E, de Stanchina E, Weiser MR, Widmar M, Yantiss RK, Shah MA, Bass AJ, Stadler ZK, Katz LH, Mellinghoff IK, Sethi NS, Schultz N, Ganesh K, Kelsen D, Yaeger R. Integrated clinical and genomic analysis identifies driver events and molecular evolution of colitis-associated cancers. Nat Commun 2023; 14:110. [PMID: 36611031 PMCID: PMC9825391 DOI: 10.1038/s41467-022-35592-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/13/2022] [Indexed: 01/08/2023] Open
Abstract
Inflammation has long been recognized to contribute to cancer development, particularly across the gastrointestinal tract. Patients with inflammatory bowel disease have an increased risk for bowel cancers, and it has been posited that a field of genetic changes may underlie this risk. Here, we define the clinical features, genomic landscape, and germline alterations in 174 patients with colitis-associated cancers and sequenced 29 synchronous or isolated dysplasia. TP53 alterations, an early and highly recurrent event in colitis-associated cancers, occur in half of dysplasia, largely as convergent evolution of independent events. Wnt pathway alterations are infrequent, and our data suggest transcriptional rewiring away from Wnt. Sequencing of multiple dysplasia/cancer lesions from mouse models and patients demonstrates rare shared alterations between lesions. These findings suggest neoplastic bowel lesions developing in a background of inflammation experience lineage plasticity away from Wnt activation early during tumorigenesis and largely occur as genetically independent events.
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Affiliation(s)
- Walid K Chatila
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Henry Walch
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sydney M Moyer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Valeria Sgambati
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Faleck
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amitabh Srivastava
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamal Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dorina Ismailgeci
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carl Campos
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fan Wu
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Qing Chang
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin R Weiser
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Widmar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rhonda K Yantiss
- Department of Pathology, Weill Cornell Medicine, New York, NY, USA
| | - Manish A Shah
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Adam J Bass
- Herbert Irving Comprehensive Cancer Research Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lior H Katz
- Gastroenterology Institute, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Ingo K Mellinghoff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nilay S Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karuna Ganesh
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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10
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Moore G, Majumdar R, Powell SN, Khan AJ, Weinhold N, Yin S, Higginson DS. Templated Insertions Are Associated Specifically with BRCA2 Deficiency and Overall Survival in Advanced Ovarian Cancer. Mol Cancer Res 2022; 20:1061-1070. [PMID: 35385581 PMCID: PMC9372910 DOI: 10.1158/1541-7786.mcr-21-1012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/14/2022] [Accepted: 04/01/2022] [Indexed: 01/09/2023]
Abstract
Cancer cells defective in homologous recombination (HR) are responsive to DNA-crosslinking chemotherapies, PARP inhibitors, and inhibitors of polymerase theta (Pol θ), a key mediator of the backup pathway alternative end-joining. Such cancers include those with pathogenic biallelic alterations in core HR genes and another cohort of cases that exhibit sensitivity to the same agents and harbor genomic hallmarks of HR deficiency (HRD). These HRD signatures include a single-base substitution pattern, large rearrangements, characteristic tandem duplications, and small deletions. Here, we used what is now known about the backup pathway alternative end-joining (Alt-EJ) through the key factor Pol θ to design and test novel signatures of polymerase theta-mediated (TMEJ) repair. We generated two novel signatures; a signature composed of small deletions with microhomology and another consisting of small, templated insertions (TINS). We find that TINS consistent with TMEJ repair are highly specific to tumors with pathogenic biallelic mutations in BRCA2 and that high TINS genomic signature content in advanced ovarian cancers associate with overall survival following treatment with platinum agents. In addition, the combination of TINS with other HRD metrics significantly improves the association of platinum sensitivity with survival compared with current state-of-the-art signatures. IMPLICATIONS Small, templated insertions indicative of theta-mediated end-joining likely can be used in conjunction with other HRD mutational signatures as a prognostic tool for patient response to therapies targeting HR deficiency.
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Affiliation(s)
- Grace Moore
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Rahul Majumdar
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Simon N. Powell
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Atif J. Khan
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Nils Weinhold
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Shen Yin
- Epidemiology & Biostatistics, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Daniel S. Higginson
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065.,Corresponding author: Daniel S.
Higginson, Department of Radiation Oncology, Memorial Sloan Kettering Cancer
Center, 1275 York Ave Box #22, New York, NY 10065; Phone: (646) 888-3567;
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