DOCSLIB.ORG

Germline and Somatic DNA Damage Repair Gene Mutations and Overall Survival in Metastatic Pancreatic Adenocarcinoma Patients Trea

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Germline and Somatic DNA Damage Repair Gene Mutations and Overall Survival in Metastatic Pancreatic Adenocarcinoma Patients Trea Published OnlineFirst August 21, 2018; DOI: 10.1158/1078-0432.CCR-18-1472 Precision Medicine and Imaging Clinical Cancer Research Germline and Somatic DNA Damage Repair Gene Mutations and Overall Survival in Metastatic Pancreatic Adenocarcinoma Patients Treated with FOLFIRINOX Amikar Sehdev1,2,3, Olumide Gbolahan1, Brad A. Hancock4, Melissa Stanley1, Safi Shahda1, Jun Wan5, Howard H. Wu4, Milan Radovich6, and Bert H. O'Neil1 Abstract Purpose: Pancreatic ductal adenocarcinoma (PDAC) is a Results: Overall, 36 patients were sequenced. DDR gene lethal cancer with lack of predictive biomarkers. We con- mutations were found in 12 patients. Mutations were seen ducted a study to assess DNA damage repair (DDR) gene in BRCA1 (N ¼ 7), BRCA2 (N ¼ 5), PALB2 (N ¼ 3), MSH2 mutations as a predictive biomarker in PDAC patients (N ¼ 1), and FANCF (N ¼ 1) of all the DDR genes treated with FOLFIRINOX. sequenced. Median age was 65.5 years, 58% were male, Experimental Design: Indiana University Simon Cancer 97.2% were Caucasian and 51.4% had any family history Center pancreatic cancer database was used to identify of cancer. The median OS was near significantly superior patients with metastatic PDAC, treated with FOLFIRINOX in those with DDR gene mutations present vs. absent and had tissue available for DNA sequencing. Baseline [14 vs. 5 months; HR, 0.58; 95% confidence interval (CI), demographic, clinical, and pathologic information was 0.29–1.14; log-rank P ¼ 0.08]. Multivariate logistic (OR, gathered. DNA isolation and targeted sequencing was 1.47; 95% CI, 1.04–2.06; P ¼ 0.04) and Cox regression (HR, performed using the Ion AmpliSeq protocol. Overall sur- 0.37; 95% CI, 0.15–0.94; P ¼ 0.04) showed presence of vival (OS) analysis was conducted using Kaplan–Meier, DDR gene mutations was associated with improved OS. logistic regression and Cox proportional hazard methods. Conclusions: In a single institution, retrospective study, Multivariate models were adjusted for age, gender, margin we found that the presence of DDR gene mutations are status, CA 19-9, adjuvant chemotherapy, tumor and nodal associated with improved OS in PDAC patients treated with stage. FOLFIRINOX. Clin Cancer Res; 24(24); 6204–11. Ó2018 AACR. Introduction alterations, makes each PDAC rather distinctive. These altera- tions can be divided into required (nearly universally seen; Pancreatic ductal adenocarcinoma (PDAC) remains a lethal such as, KRAS, and CDKN2A), frequently mutated (occurring cancer with a 5-year survival rate of less than 5% overall (1) and in more than 25% of tumors; such as, SMAD4, TP53, and 15% to 20% for early-stage resectable disease (2). Moreover, NCOA3) and low frequency mutations (occurring in less than PDAC is projected to become the second leading cause of 25% of tumors; such as RB1, BRCA2 and ERBB2; refs. 5, 6). cancer-related mortality in the United States within a decade Low-frequency mutations, including mutations in DNA dam- (3). Genome stability is compromised in all cancers, including age repair (DDR) pathways, provide a very heterogeneous PDAC and can be broadly categorized into chromosomal mutational background that gives each PDAC a unique molec- instability (CIN) and microsatellite instability (MIN; refs. 4, ular signature. 5). The spectrum of altered genes, as well as the types of DDR pathways play an important role in the cellular response to platinum chemotherapy. FOLFIRINOX (5-Fluorouracil, 1 leucovorin, irinotecan and oxaliplatin) is a platinum based Department of Medicine, Indiana University School of Medicine, Indianapolis, chemotherapeutic regimen that has shown an unprecedented Indiana. 2Center for Health Services Research, Regenstrief Institute, Indianapolis, Indiana. 3Richard M. Fairbanks School of Public Health, Indiana University, improvement in median overall survival (OS) of PDAC to 11.1 Indianapolis, Indiana. 4Department of Pathology and Laboratory Medicine, months (7). However, not all PDAC patients respond to FOL- Indiana University School of Medicine, Indianapolis, Indiana. 5Department of FIRINOX chemotherapy; objective response rate is around 32% Medical and Molecular Genetics, Indiana University School of Medicine, India- (7). Chemotherapy resistance mechanisms are multifactorial, 6 napolis, Indiana. Department of Surgery, Division of General Surgery, Indiana but alterations in DDR pathways such as nucleotide excision University School of Medicine, Indianapolis, Indiana. repair (NER), mismatch repair (MMR), and BRCA pathways (8) Corresponding Author: Amikar Sehdev, Indiana University—Purdue University likely contribute significantly. For example, the excision repair Indianapolis, 535 Barnhill Drive, RT 130B, Indianapolis, IN 46202. Phone: 317-274- cross-complementation group 1 (ERCC1) protein is a key com- 0320; Fax: 317-948-9954; E-mail: [email protected] ponent of nucleotide excision repair pathway. High expression doi: 10.1158/1078-0432.CCR-18-1472 of ERCC1 has been associated in multiple studies with acquired Ó2018 American Association for Cancer Research. or intrinsic resistance to platinum drugs (8, 9). Similarly, loss of 6204 Clin Cancer Res; 24(24) December 15, 2018 Downloaded from clincancerres.aacrjournals.org on October 2, 2021. © 2018 American Association for Cancer Research. Published OnlineFirst August 21, 2018; DOI: 10.1158/1078-0432.CCR-18-1472 DNA Repair Gene Mutations and Survival in Pancreatic Cancer baseline carbohydrate antigen 19-9 (CA 19-9), history of surgical Translational Relevance resection, type of surgical resection (R0 or R1), adjuvant chemo- Emerging data suggest that DNA damage repair (DDR) gene therapy, pathological tumor and nodal stage were collected. mutations may be predictive of response to platinum-based The start date of FOLFIRINOX and date of death were collected chemotherapy in some cancers; however, the role of these for OS calculation. mutations in pancreatic adenocarcinoma (PDAC) is unknown. FOLFIRINOX (5-Fluorouracil, leucovorin, irinote- DNA-extraction can and oxaliplatin) is a platinum-based chemotherapeutic Matched tumor-normal paired tissue sections with 20% regimen that is commonly used as first-line treatment tumor cellularity were selected for DNA isolation. The sections of patients with advanced PDAC. However, the efficacy of were scraped from glass slides using microtome blades and the FOLFIRINOX is limited by its high toxicities and low objective QIAamp DNA FFPE Tissue Kit (56404, Qiagen) was used for DNA response rate. Currently, there is no predictive biomarker isolation. to select patients for treatment with FOLFIRINOX. In this Next-generation sequencing for germline and somatic study, we report that the presence of DDR gene mutations is mutations associated with improved OS in metastatic PDAC patients Germline mutation testing was done using adjacent normal treated with FOLFIRINOX. These results will need to be further tissue whereas somatic mutation testing was done using tumor tested in a larger study and may serve to select PDAC patients tissue. Sequencing libraries were constructed using the Ion for treatment with FOLFIRINOX. AmpliSeq Kit for Chef DL8 (A29024, Thermo Scientific) in conjunction with the Ion Comprehensive Cancer Panel Primer Pool (4477685, Thermo Scientific). Templates were prepared on the Ion Chef using the Ion P1 Hi-Q Chef Kit (A27198, function of MMR genes (mainly MLH1 and MSH2) has been Thermo Scientific). Templates were sequenced to at least associated with resistance to platinum compounds (10). Finally, 500XmeancoverageontheIonProtonsequencerusingaP1 BRCA1 and BRCA2 genes have established roles in DNA repair Chip v3 (A26771, Thermo Scientific). Genomic data (BAM and chemotherapy sensitivity (11, 12). However, these data files) were uploaded to Ion Reporter (Thermo Scientific) for come from either preclinical studies or clinical studies done in somatic variant and copy-number calling. Ingenuity Variant other cancer types and the role of DDR pathway gene alterations Analysis (Qiagen) was also used for second-level annotation. on the efficacy of FOLFIRINOX in PDAC is not well known. The primary objective of this study was to assess the effect of Statistical analyses mutations in DDR genes (BRCA1, BRCA2, PALB2, CHEK1, Descriptive statistics were used to summarize the baseline CHEK2, RAD51, MLH1, MSH2, ERCC1, ERCC4, PARP1, FANCF, characteristics and mutations in DDR genes (BRCA1, BRCA2, PALB2, CHEK1, CHEK2, RAD51, MLH1, MSH2, ERCC1, ERCC4, ATR and MDC1) on the OS of patients with metastatic PDAC PARP1, FANCF, ATR and MDC1 treated with FOLFIRINOX. ). The study cohort was then divided in to those with and without germline and somatic mutations in DDR genes. Baseline characteristics were compared Materials and Methods between the two groups (DDR gene mutations present vs. absent) Study population and patient selection using x2 test for categorical variables and Student t test for Patients were selected from the Indiana University Simon continuous variables. Cancer Center pancreatic cancer database, which is a large Two statistical approaches were used for data analyses. First, Institutional review board (IRB) approved high quality pro- we analyzed the data using logistic regression analysis as in a spective and retrospective data collection repository (13). The case–control study to investigate the association between main inclusion criterion (to allow for adequate available DDR gene mutations and OS (categorized as above and below tissue) for the study was histologic diagnosis of recurrent 3rd quartile). Our goal here was to see whether PDAC patients
Load more

Recommended publications
  • Structure and Function of the Human Recq DNA Helicases
    Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2005 Structure and function of the human RecQ DNA helicases Garcia, P L Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-34420 Dissertation Published Version Originally published at: Garcia, P L. Structure and function of the human RecQ DNA helicases. 2005, University of Zurich, Faculty of Science. Structure and Function of the Human RecQ DNA Helicases Dissertation zur Erlangung der naturwissenschaftlichen Doktorw¨urde (Dr. sc. nat.) vorgelegt der Mathematisch-naturwissenschaftlichen Fakultat¨ der Universitat¨ Z ¨urich von Patrick L. Garcia aus Unterseen BE Promotionskomitee Prof. Dr. Josef Jiricny (Vorsitz) Prof. Dr. Ulrich H ¨ubscher Dr. Pavel Janscak (Leitung der Dissertation) Z ¨urich, 2005 For my parents ii Summary The RecQ DNA helicases are highly conserved from bacteria to man and are required for the maintenance of genomic stability. All unicellular organisms contain a single RecQ helicase, whereas the number of RecQ homologues in higher organisms can vary. Mu- tations in the genes encoding three of the five human members of the RecQ family give rise to autosomal recessive disorders called Bloom syndrome, Werner syndrome and Rothmund-Thomson syndrome. These diseases manifest commonly with genomic in- stability and a high predisposition to cancer. However, the genetic alterations vary as well as the types of tumours in these syndromes. Furthermore, distinct clinical features are observed, like short stature and immunodeficiency in Bloom syndrome patients or premature ageing in Werner Syndrome patients. Also, the biochemical features of the human RecQ-like DNA helicases are diverse, pointing to different roles in the mainte- nance of genomic stability.
    [Show full text]
  • Open Full Page
    CCR PEDIATRIC ONCOLOGY SERIES CCR Pediatric Oncology Series Recommendations for Childhood Cancer Screening and Surveillance in DNA Repair Disorders Michael F. Walsh1, Vivian Y. Chang2, Wendy K. Kohlmann3, Hamish S. Scott4, Christopher Cunniff5, Franck Bourdeaut6, Jan J. Molenaar7, Christopher C. Porter8, John T. Sandlund9, Sharon E. Plon10, Lisa L. Wang10, and Sharon A. Savage11 Abstract DNA repair syndromes are heterogeneous disorders caused by around the world to discuss and develop cancer surveillance pathogenic variants in genes encoding proteins key in DNA guidelines for children with cancer-prone disorders. Herein, replication and/or the cellular response to DNA damage. The we focus on the more common of the rare DNA repair dis- majority of these syndromes are inherited in an autosomal- orders: ataxia telangiectasia, Bloom syndrome, Fanconi ane- recessive manner, but autosomal-dominant and X-linked reces- mia, dyskeratosis congenita, Nijmegen breakage syndrome, sive disorders also exist. The clinical features of patients with DNA Rothmund–Thomson syndrome, and Xeroderma pigmento- repair syndromes are highly varied and dependent on the under- sum. Dedicated syndrome registries and a combination of lying genetic cause. Notably, all patients have elevated risks of basic science and clinical research have led to important in- syndrome-associated cancers, and many of these cancers present sights into the underlying biology of these disorders. Given the in childhood. Although it is clear that the risk of cancer is rarity of these disorders, it is recommended that centralized increased, there are limited data defining the true incidence of centers of excellence be involved directly or through consulta- cancer and almost no evidence-based approaches to cancer tion in caring for patients with heritable DNA repair syn- surveillance in patients with DNA repair disorders.
    [Show full text]
  • Identification of Novel Pathogenic MSH2 Mutation and New DNA Repair Genes Variants: Investigation of a Tunisian Lynch Syndrome F
    Jaballah‑Gabteni et al. J Transl Med (2019) 17:212 https://doi.org/10.1186/s12967‑019‑1961‑9 Journal of Translational Medicine RESEARCH Open Access Identifcation of novel pathogenic MSH2 mutation and new DNA repair genes variants: investigation of a Tunisian Lynch syndrome family with discordant twins Amira Jaballah‑Gabteni1,3* , Haifa Tounsi1,3, Maria Kabbage1,3, Yosr Hamdi3, Sahar Elouej3,4, Ines Ben Ayed1,3, Mouna Medhioub2, Moufda Mahmoudi2, Hamza Dallali3, Hamza Yaiche1,3, Nadia Ben Jemii1,3, Affa Maaloul1, Najla Mezghani1,3, Sonia Abdelhak3, Lamine Hamzaoui2, Mousaddak Azzouz2 and Samir Boubaker1,3 Abstract Background: Lynch syndrome (LS) is a highly penetrant inherited cancer predisposition syndrome, characterized by autosomal dominant inheritance and germline mutations in DNA mismatch repair genes. Despite several genetic variations that have been identifed in various populations, the penetrance is highly variable and the reasons for this have not been fully elucidated. This study investigates whether, besides pathogenic mutations, environment and low penetrance genetic risk factors may result in phenotype modifcation in a Tunisian LS family. Patients and methods: A Tunisian family with strong colorectal cancer (CRC) history that fulfll the Amsterdam I criteria for the diagnosis of Lynch syndrome was proposed for oncogenetic counseling. The index case was a man, diagnosed at the age of 33 years with CRC. He has a monozygotic twin diagnosed at the age of 35 years with crohn disease. Forty‑seven years‑old was the onset age of his paternal uncle withCRC. An immunohistochemical (IHC) labe‑ ling for the four proteins (MLH1, MSH2, MSH6 and PMS2) of the MisMatchRepair (MMR) system was performed for the index case.
    [Show full text]
  • A Dissertation Entitled the Role of Base Excision Repair And
    A Dissertation Entitled The Role of Base Excision Repair and Mismatch Repair Proteins in the Processing of Cisplatin Interstrand Cross-Links. by Akshada Sawant Submitted to the Graduate Faculty as partial fulfillment of the requirements for the Doctor of Philosophy Degree in Biomedical Science Dr. Stephan M. Patrick, Committee Chair Dr. Kandace Williams, Committee Member Dr. William Maltese, Committee Member Dr. Manohar Ratnam, Committee Member Dr. David Giovannucci, Committee Member Dr. Patricia R. Komuniecki, Dean College of Graduate Studies The University of Toledo August 2014 Copyright 2014, Akshada Sawant This document is copyrighted material. Under copyright law, no parts of this document may be reproduced without the expressed permission of the author. An Abstract of The Role of Base Excision Repair and Mismatch Repair Proteins in the Processing of Cisplatin Interstrand Cross-Links By Akshada Sawant Submitted to the Graduate Faculty as partial fulfillment of the requirements for the Doctor of Philosophy Degree in Biomedical Science The University of Toledo August 2014 Cisplatin is a well-known anticancer agent that forms a part of many combination chemotherapeutic treatments used against a variety of human cancers. Despite successful treatment, the development of resistance is the major limitation of the cisplatin based therapy. Base excision repair modulates cisplatin cytotoxicity. Moreover, mismatch repair deficiency gives rise to cisplatin resistance and leads to poor prognosis of the disease. Various models have been proposed to explain this low level of resistance caused due to loss of MMR proteins. In our previous studies, we have shown that BER processing of the cisplatin ICLs is mutagenic. Our studies showed that these mismatches lead to the activation and the recruitment of mismatch repair proteins.
    [Show full text]
  • Fanconi Anemia, Bloom Syndrome and Breast Cancer
    A multiprotein complex in DNA damage response network of Fanconi anemia, Bloom syndrome and Breast cancer Weidong Wang Lab of Genetics, NIA A Multi-protein Complex Connects Two Genomic Instability Diseases: Bloom Syndrome and Fanconi Anemia Bloom Syndrome . Genomic Instability: -sister-chromatid exchange . Cancer predisposition . Mutation in BLM, a RecQ DNA Helicase . BLM participates in: HR-dependent DSB repair Recovery of stalled replication forks . BLM works with Topo IIIa and RMI to Suppress crossover recombination Courtesy of Dr. Ian Hickson A Multi-protein Complex Connects Two Genomic Instability Diseases: Bloom Syndrome and Fanconi Anemia P I l o r t n o BLM IP kDa C HeLa BLAP 250 Nuclear Extract 200- BLM* FANCA* 116- TOPO IIIα* 97- BLAP 100 MLH1* BLM IP BLAP 75 * 66- RPA 70 IgG H 45- * 30- RPA32 IgG L 20- * 12- RPA14 Meetei et al. MCB 2003 A Multi-protein Complex Connects Two Genomic Instability Diseases: Bloom Syndrome and Fanconi Anemia P I A C N A F BLM IP HeLa FANCM= FAAP 250 BLAP 250 Nuclear Extract BLM* BLM* * FANCA* FANCA TOPO IIIα* TOPO IIIα* FAAP 100 BLAP 100 FANCB= FAAP 95 MLH1 FANCA IP BLM IP BLAP 75 BLAP 75 RPA70*/FANCG* RPA 70* FANCC*/FANCE* IgG H FANCL= FAAP 43 FANCF* RPA32* IgG L Meetei et al. MCB 2003 Meetei et al. Nat Genet. 2003, 2004, 2005 BRAFT-a Multisubunit Machine that Maintains Genome Stability and is defective in Fanconi anemia and Bloom syndrome BRAFT Super-complex Fanconi Anemia Bloom Syndrome Core Complex Complex 12 polypeptides 7 polypeptides FANCA BLM Helicase (HJ, fork, D-loop), fork FANCC regression, dHJ dissolution Topo IIIα Topoisomerase, FANCE dHJ dissolution FANCF BLAP75 RMI1 FANCG Stimulates dHJ dissolution.
    [Show full text]
  • HEREDITARY CANCER PANELS Part I
    Pathology and Laboratory Medicine Clinic Building, K6, Core Lab, E-655 2799 W. Grand Blvd. HEREDITARY CANCER PANELS Detroit, MI 48202 855.916.4DNA (4362) Part I- REQUISITION Required Patient Information Ordering Physician Information Name: _________________________________________________ Gender: M F Name: _____________________________________________________________ MRN: _________________________ DOB: _______MM / _______DD / _______YYYY Address: ___________________________________________________________ ICD10 Code(s): _________________/_________________/_________________ City: _______________________________ State: ________ Zip: __________ ICD-10 Codes are required for billing. When ordering tests for which reimbursement will be sought, order only those tests that are medically necessary for the diagnosis and treatment of the patient. Phone: _________________________ Fax: ___________________________ Billing & Collection Information NPI: _____________________________________ Patient Demographic/Billing/Insurance Form is required to be submitted with this form. Most genetic testing requires insurance prior authorization. Due to high insurance deductibles and member policy benefits, patients may elect to self-pay. Call for more information (855.916.4362) Bill Client or Institution Client Name: ______________________________________________________ Client Code/Number: _____________ Bill Insurance Prior authorization or reference number: __________________________________________ Patient Self-Pay Call for pricing and payment options Toll
    [Show full text]
  • An ERCC4 Regulatory Variant Predicts Grade‐
    IJC International Journal of Cancer An ERCC4 regulatory variant predicts grade-3 or -4 toxicities in patients with advanced non-small cell lung cancer treated by platinum-based therapy Ruoxin Zhang1, Ming Jia1,2, Yuan Xu1,2, Danwen Qian1,2, Mengyun Wang1, Meiling Zhu3, Menghong Sun1,4, Jianhua Chang1,5 and Qingyi Wei 1,2,6 1 Cancer Institute, Collaborative Innovative Center for Cancer Medicine, Fudan University Shanghai Cancer Center, 270 Dong An Road, Xuhui District, Shanghai, 200032, People’s Republic of China 2 Department of Oncology, Shanghai Medical College, Fudan University Shanghai Cancer Center, 270 Dong An Road, Shanghai, 200032, People’s Republic of China 3 Department of Oncology, Xinhua Hospital affiliated to Shanghai Jiaotong University, No. 1665 Kong Jiang Road, Shanghai, 200092, People’s Republic of China 4 Department of Pathology, Fudan University Shanghai Cancer Center, 270 Dong An Road, Shanghai, 200032, People’s Republic of China 5 Department of Medical Oncology, Fudan University Shanghai Cancer Center, 270 Dong An Road, Shanghai, 200032, People’s Republic of China 6 Duke Cancer Institute, Duke University Medical Center, 10 Bryn Searle Dr., Durham, NC 27710, USA Platinum-based chemotherapy (PBC) in combination with the 3rd generation drugs is the first-line treatment for patients with advanced non-small cell lung cancer (NSCLC); however, the efficacy is severely hampered by grade 3–4 toxicities. Nucleotide excision repair (NER) pathway is the main mechanism of removing platinum-induced DNA adducts that contribute to the toxic- Cancer Epidemiology ity and outcome of PBC. We analyzed data from 710 Chinese NSCLC patients treated with PBC and assessed the associations of 25 potentially functional single nucleotide polymorphisms (SNPs) in nine NER core genes with overall, gastrointestinal and hematologic toxicities.
    [Show full text]
  • Epigenetic Regulation of DNA Repair Genes and Implications for Tumor Therapy ⁎ ⁎ Markus Christmann , Bernd Kaina
    Mutation Research-Reviews in Mutation Research xxx (xxxx) xxx–xxx Contents lists available at ScienceDirect Mutation Research-Reviews in Mutation Research journal homepage: www.elsevier.com/locate/mutrev Review Epigenetic regulation of DNA repair genes and implications for tumor therapy ⁎ ⁎ Markus Christmann , Bernd Kaina Department of Toxicology, University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany ARTICLE INFO ABSTRACT Keywords: DNA repair represents the first barrier against genotoxic stress causing metabolic changes, inflammation and DNA repair cancer. Besides its role in preventing cancer, DNA repair needs also to be considered during cancer treatment Genotoxic stress with radiation and DNA damaging drugs as it impacts therapy outcome. The DNA repair capacity is mainly Epigenetic silencing governed by the expression level of repair genes. Alterations in the expression of repair genes can occur due to tumor formation mutations in their coding or promoter region, changes in the expression of transcription factors activating or Cancer therapy repressing these genes, and/or epigenetic factors changing histone modifications and CpG promoter methylation MGMT Promoter methylation or demethylation levels. In this review we provide an overview on the epigenetic regulation of DNA repair genes. GADD45 We summarize the mechanisms underlying CpG methylation and demethylation, with de novo methyl- TET transferases and DNA repair involved in gain and loss of CpG methylation, respectively. We discuss the role of p53 components of the DNA damage response, p53, PARP-1 and GADD45a on the regulation of the DNA (cytosine-5)- methyltransferase DNMT1, the key enzyme responsible for gene silencing. We stress the relevance of epigenetic silencing of DNA repair genes for tumor formation and tumor therapy.
    [Show full text]
  • Challenges in Reporting Pathogenic/Potentially
    www.nature.com/scientificreports OPEN Challenges in reporting pathogenic/ potentially pathogenic variants in 94 cancer predisposing genes - in pediatric patients screened with NGS panels Adela Chirita-Emandi 1,2,6*, Nicoleta Andreescu1,2,6, Cristian G. Zimbru1,3, Paul Tutac1,2, Smaranda Arghirescu4,5, Margit Serban5 & Maria Puiu1,2 The beneft of reporting unsolicited fndings in Next Generation Sequencing (NGS) related to cancer genes in children may have implications for family members, nevertheless, could also cause distress. We aimed to retrospectively investigate germline variants in 94 genes implicated in oncogenesis, in patients referred to NGS testing for various rare genetic diseases and reevaluate the utility of reporting diferent classes of pathogenicity. We used in silico prediction software to classify variants and conducted manual review to examine unsolicited fndings frequencies in 145 children with rare diseases, that underwent sequencing - using a 4813 gene panel. The anonymized reanalysis revealed 18250 variants, of which 126 were considered after fltering. Six pathogenic variants (in BRCA1,BMPR1A,FANCA,FANCC,NBN genes) with cancer related phenotype and three unsolicited variants (in BRCA2,PALB2,RAD50 genes) were reported to patients. Additionally, three unsolicited variants in ATR, BLM (in two individuals), and FANCB genes presented potential cancer susceptibility, were not reported to patients. In retrospect, 4.8% (7/145) of individuals in our cohort had unsolicited NGS fndings related to cancer. More eforts are needed to create an updatable consensus in reporting variants in cancer predisposing genes, especially for children. Consent process is crucial to inform of both value and risk of additional genetic information. Next-Generation Sequencing (NGS) for large panels of genes or exomes are increasingly and successfully used in medical management for rare diseases and cancer.
    [Show full text]
  • The Diagnostic Value of DNA Repair Gene in Breast Cancer Recurrence and Metastasis
    The Diagnostic Value of DNA Repair Gene in Breast Cancer Recurrence and Metastasis Yongxin Yang Southwest Medical University Xiabin Li Southwest Medical University Liyue Hao Southwest Medical University Deyong Jiang Centers for Disease Control and Prevention Bin Wu Southwest Medical University Tao He Southwest Medical University Yan Tang ( [email protected] ) Research Keywords: PARP1, XRCC4, ERCC1, Breast cancer Posted Date: June 25th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-36932/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/19 Abstract Background: DNA repair genes play a vital role in the treatment of many cancers, and DNA repair genes can be used in breast cancer recurrence and metastasis research. We found that the expression of DNA repair genes in breast cancer patients after recurrence and metastasis is abnormal, however, the clinical predictive signicance of DNA repair genes is still elusive. Methods: The nested case-control method was used in patients with breast cancer recurrence and metastasis after surgery (n=109) and patients without recurrence and metastasis after surgery (n=109). The proteins and mRNA of DNA repair genes were detected by immunohistochemistry and Real-time PCR respectively. Results: PARP1(OR=1.485, 95%CI:1.279~1.725, P<0.05), XRCC4(OR= 1.419, 95%CI:1.217~ 1.656, P<0.05) and ERCC1 (OR=1.181, 95%CI: 1.032~1.353, P<0.05) were risk factors for postoperative recurrence and metastasis of breast cancer. Therefore, we used the ROC
    [Show full text]
  • WRN Promoter Methylation Possibly Connects Mucinous Differentiation, Microsatellite Instability and Cpg Island Methylator Phenotype in Colorectal Cancer
    Modern Pathology (2008) 21, 150–158 & 2008 USCAP, Inc All rights reserved 0893-3952/08 $30.00 www.modernpathology.org WRN promoter methylation possibly connects mucinous differentiation, microsatellite instability and CpG island methylator phenotype in colorectal cancer Takako Kawasaki1,2, Mutsuko Ohnishi2, Yuko Suemoto2, Gregory J Kirkner3, Zhiqian Liu2, Hiroyuki Yamamoto4, Massimo Loda1,2, Charles S Fuchs2,3 and Shuji Ogino1,2 1Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA; 2Department of Medical Oncology, Dana–Farber Cancer Institute, Boston, MA, USA; 3Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA and 4First Department of Internal Medicine, Sapporo Medical University, Sapporo, Japan Werner syndrome is a premature aging syndrome characterized by early onset of cancer and abnormal cellular metabolism of glycosaminoglycan. The WRN helicase plays an important role in the maintenance of telomere function. WRN promoter methylation and gene silencing are common in colorectal cancer with the CpG island methylator phenotype (CIMP), which is associated with microsatellite instability (MSI) and mucinous tumors. However, no study has examined the relationship between mucinous differentiation, WRN methylation, CIMP and MSI in colorectal cancer. Utilizing 903 population-based colorectal cancers and real-time PCR (MethyLight), we quantified DNA methylation in WRN and eight other promoters (CACNA1G, CDKN2A, CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1) known to be specific for CIMP. Supporting WRN as a good CIMP marker, WRN methylation was correlated well with CIMP-high diagnosis (Z6/8 methylated promoters), demonstrating 89% sensitivity and 81% specificity. WRN methylation was associated with the presence of any mucinous component and Z50% mucinous component (Po0.0001).
    [Show full text]
  • Gene Expression Responses to DNA Damage Are Altered in Human Aging and in Werner Syndrome
    Oncogene (2005) 24, 5026–5042 & 2005 Nature Publishing Group All rights reserved 0950-9232/05 $30.00 www.nature.com/onc Gene expression responses to DNA damage are altered in human aging and in Werner Syndrome Kasper J Kyng1,2, Alfred May1, Tinna Stevnsner2, Kevin G Becker3, Steen Klvra˚ 4 and Vilhelm A Bohr*,1 1Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA; 2Danish Center for Molecular Gerontology, Department of Molecular Biology, University of Aarhus, DK-8000 Aarhus C, Denmark; 3Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; 4Institute for Human Genetics, University of Aarhus, Denmark The accumulation of DNA damage and mutations is syndromes, caused by heritable mutations inactivating considered a major cause of cancer and aging. While it is proteins that sense or repair DNA damage, which known that DNA damage can affect changes in gene accelerate some but not all signs of normal aging (Hasty expression, transcriptional regulation after DNA damage et al., 2003). Age is associated withan increase in is poorly understood. We characterized the expression of susceptibility to various forms of stress, and sporadic 6912 genes in human primary fibroblasts after exposure to reports suggest that an age-related decrease in DNA three different kinds of cellular stress that introduces repair may increase the susceptibility of cells to agents DNA damage: 4-nitroquinoline-1-oxide (4NQO), c-irra- causing DNA damage. Reduced base excision repair has diation, or UV-irradiation. Each type of stress elicited been demonstrated in nuclear extracts from aged human damage specific gene expression changes of up to 10-fold.
    [Show full text]