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Keskus A, Bryant A, Ahmad T, Yoo B, Aganezov S, Goretsky A, Donmez A, Lansdon LA, Rodriguez I, Park J, Liu Y, Cui X, Gardner J, McNulty B, Sacco S, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Cook DE, Chang PC, Kolesnikov A, Carroll A, Molloy EK, Pushel I, Guest E, Pastinen T, Shafin K, Miga KH, Malikic S, Day CP, Robine N, Sahinalp C, Dean M, Farooqi MS, Paten B, Kolmogorov M. Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads. medRxiv 2024:2024.03.22.24304756. [PMID: 38585974 PMCID: PMC10996739 DOI: 10.1101/2024.03.22.24304756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing, which results in substantial improvements in germline SV detection. However, current long-read SV detection methods do not generalize well to the analysis of somatic SVs in tumor genomes with complex rearrangements, heterogeneity, and aneuploidy. Here, we present Severus: a method for the accurate detection of different types of somatic SVs using a phased breakpoint graph approach. To benchmark various short- and long-read SV detection methods, we sequenced five tumor/normal cell line pairs with Illumina, Nanopore, and PacBio sequencing platforms; on this benchmark Severus showed the highest F1 scores (harmonic mean of the precision and recall) as compared to long-read and short-read methods. We then applied Severus to three clinical cases of pediatric cancer, demonstrating concordance with known genetic findings as well as revealing clinically relevant cryptic rearrangements missed by standard genomic panels.
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Affiliation(s)
- Ayse Keskus
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Byunggil Yoo
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | | | - Anton Goretsky
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Ataberk Donmez
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Lisa A. Lansdon
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Jimin Park
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Yuelin Liu
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Xiwen Cui
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | - Samuel Sacco
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Jyoti Shetty
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yongmei Zhao
- Sequencing Facility Bioinformatics Group, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bao Tran
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | | | | | | | | | - Erin K. Molloy
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Irina Pushel
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Erin Guest
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Tomi Pastinen
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Kishwar Shafin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Salem Malikic
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Chi-Ping Day
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Cenk Sahinalp
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Midhat S. Farooqi
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | | | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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Godinez Paredes JM, Rodriguez I, Ren M, Orozco A, Ortiz J, Albanez A, Jones C, Nahleh Z, Barreda L, Garland L, Torres-Gonzalez E, Wu D, Luo W, Liu J, Argueta V, Orozco R, Gharzouzi E, Dean M. Germline pathogenic variants associated with triple-negative breast cancer in US Hispanic and Guatemalan women using hospital and community-based recruitment strategies. Breast Cancer Res Treat 2024:10.1007/s10549-024-07300-2. [PMID: 38520597 DOI: 10.1007/s10549-024-07300-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/21/2024] [Indexed: 03/25/2024]
Abstract
PURPOSE Recruit and sequence breast cancer subjects in Guatemalan and US Hispanic populations. Identify optimum strategies to recruit Latin American and Hispanic women into genetic studies of breast cancer. METHODS We used targeted gene sequencing to identify pathogenic variants in 19 familial breast cancer susceptibility genes in DNA from unselected Hispanic breast cancer cases in the US and Guatemala. Recruitment across the US was achieved through community-based strategies. In addition, we obtained patients receiving cancer treatment at major hospitals in Texas and Guatemala. RESULTS We recruited 287 Hispanic US women, 38 (13%) from community-based and 249 (87%) from hospital-based strategies. In addition, we ascertained 801 Guatemalan women using hospital-based recruitment. In our experience, a hospital-based approach was more efficient than community-based recruitment. In this study, we sequenced 103 US and 137 Guatemalan women and found 11 and 10 pathogenic variants, respectively. The most frequently mutated genes were BRCA1, BRCA2, CHEK2, and ATM. In addition, an analysis of 287 US Hispanic patients with pathology reports showed a significantly higher percentage of triple-negative disease in patients with pathogenic variants (41% vs. 15%). Finally, an analysis of mammography usage in 801 Guatemalan patients found reduced screening in women with a lower socioeconomic status (p < 0.001). CONCLUSION Guatemalan and US Hispanic women have rates of hereditary breast cancer pathogenic variants similar to other populations and are more likely to have early age at diagnosis, a family history, and a more aggressive disease. Patient recruitment was higher using hospital-based versus community enrollment. This data supports genetic testing in breast cancer patients to reduce breast cancer mortality in Hispanic women.
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Affiliation(s)
- Jesica M Godinez Paredes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, USA
| | - Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, USA
| | - Megan Ren
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, USA
| | - Anali Orozco
- Instituto Cancerologia, Guatemala City, Guatemala
| | - Jeremy Ortiz
- Instituto Cancerologia, Guatemala City, Guatemala
| | | | - Catherine Jones
- Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | | | - Lilian Barreda
- Hospital General San Juan de Dios, Guatemala City, Guatemala
| | - Lisa Garland
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Gaithersburg, MD, USA
| | - Edmundo Torres-Gonzalez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, USA
| | - Dongjing Wu
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Gaithersburg, MD, USA
| | - Wen Luo
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Gaithersburg, MD, USA
| | - Jia Liu
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Gaithersburg, MD, USA
| | - Victor Argueta
- Hospital General San Juan de Dios, Guatemala City, Guatemala
| | - Roberto Orozco
- Hospital General San Juan de Dios, Guatemala City, Guatemala
| | | | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, USA.
- National Cancer Institute, 9615 Medical Center Drive, Rm 3130, Rockville, MD, 20850, USA.
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Rodriguez I, Rossi NM, Keskus AG, Xie Y, Ahmad T, Bryant A, Lou H, Paredes JG, Milano R, Rao N, Tulsyan S, Boland JF, Luo W, Liu J, O'Hanlon T, Bess J, Mukhina V, Gaykalova D, Yuki Y, Malik L, Billingsley KJ, Blauwendraat C, Carrington M, Yeager M, Mirabello L, Kolmogorov M, Dean M. Insights into the mechanisms and structure of breakage-fusion-bridge cycles in cervical cancer using long-read sequencing. Am J Hum Genet 2024; 111:544-561. [PMID: 38307027 PMCID: PMC10940022 DOI: 10.1016/j.ajhg.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 02/04/2024] Open
Abstract
Cervical cancer is caused by human papillomavirus (HPV) infection, has few approved targeted therapeutics, and is the most common cause of cancer death in low-resource countries. We characterized 19 cervical and four head and neck cancer cell lines using long-read DNA and RNA sequencing and identified the HPV types, HPV integration sites, chromosomal alterations, and cancer driver mutations. Structural variation analysis revealed telomeric deletions associated with DNA inversions resulting from breakage-fusion-bridge (BFB) cycles. BFB is a common mechanism of chromosomal alterations in cancer, and our study applies long-read sequencing to this important chromosomal rearrangement type. Analysis of the inversion sites revealed staggered ends consistent with exonuclease digestion of the DNA after breakage. Some BFB events are complex, involving inter- or intra-chromosomal insertions or rearrangements. None of the BFB breakpoints had telomere sequences added to resolve the dicentric chromosomes, and only one BFB breakpoint showed chromothripsis. Five cell lines have a chromosomal region 11q BFB event, with YAP1-BIRC3-BIRC2 amplification. Indeed, YAP1 amplification is associated with a 10-year-earlier age of diagnosis of cervical cancer and is three times more common in African American women. This suggests that individuals with cervical cancer and YAP1-BIRC3-BIRC2 amplification, especially those of African ancestry, might benefit from targeted therapy. In summary, we uncovered valuable insights into the mechanisms and consequences of BFB cycles in cervical cancer using long-read sequencing.
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Affiliation(s)
- Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nicole M Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Ayse G Keskus
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Hong Lou
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jesica Godinez Paredes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Rose Milano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nina Rao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sonam Tulsyan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Joseph F Boland
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Wen Luo
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jia Liu
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Tim O'Hanlon
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jazmyn Bess
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vera Mukhina
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medical Center, Baltimore, MD, USA
| | - Daria Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical System, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Yuko Yuki
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | | | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Mary Carrington
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Meredith Yeager
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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Mishra SK, Nelson CW, Zhu B, Pinheiro M, Lee HJ, Dean M, Burdett L, Yeager M, Mirabello L. Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus. Virus Evol 2024; 10:veae013. [PMID: 38455683 PMCID: PMC10919477 DOI: 10.1093/ve/veae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 03/09/2024] Open
Abstract
High-coverage sequencing allows the study of variants occurring at low frequencies within samples, but is susceptible to false-positives caused by sequencing error. Ion Torrent has a very low single nucleotide variant (SNV) error rate and has been employed for the majority of human papillomavirus (HPV) whole genome sequences. However, benchmarking of intrahost SNVs (iSNVs) has been challenging, partly due to limitations imposed by the HPV life cycle. We address this problem by deep sequencing three replicates for each of 31 samples of HPV type 18 (HPV18). Errors, defined as iSNVs observed in only one of three replicates, are dominated by C→T (G→A) changes, independently of trinucleotide context. True iSNVs, defined as those observed in all three replicates, instead show a more diverse SNV type distribution, with particularly elevated C→T rates in CCG context (CCG→CTG; CGG→CAG) and C→A rates in ACG context (ACG→AAG; CGT→CTT). Characterization of true iSNVs allowed us to develop two methods for detecting true variants: (1) VCFgenie, a dynamic binomial filtering tool which uses each variant's allele count and coverage instead of fixed frequency cut-offs; and (2) a machine learning binary classifier which trains eXtreme Gradient Boosting models on variant features such as quality and trinucleotide context. Each approach outperforms fixed-cut-off filtering of iSNVs, and performance is enhanced when both are used together. Our results provide improved methods for identifying true iSNVs in within-host applications across sequencing platforms, specifically using HPV18 as a case study.
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Affiliation(s)
- Sambit K Mishra
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Hyo Jung Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
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5
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Van den Dop LM, Van Rooijen MMJ, Tollens T, Jørgensen LN, De Vries-Reilingh TS, Piessen G, Köckerling F, Miserez M, Dean M, Berrevoet F, Dousset B, Van Westreenen HL, Gossetti F, Tetteroo GWM, Koch A, Boomsma MF, Lange JF, Jeekel J. Five-Year Follow-Up of a Slowly Resorbable Biosynthetic P4HB Mesh (Phasix) in VHWG Grade 3 Incisional Hernia Repair. Ann Surg Open 2023; 4:e366. [PMID: 38144487 PMCID: PMC10735126 DOI: 10.1097/as9.0000000000000366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/02/2023] [Indexed: 12/26/2023] Open
Abstract
Objective To assess the 5-year recurrence rate of incisional hernia repair in Ventral Hernia Working Group (VHWG) 3 hernia with a slowly resorbable mesh. Summary Background Data Incisional hernia recurs frequently after initial repair. In potentially contaminated hernia, recurrences rise to 40%. Recently, the biosynthetic Phasix mesh has been developed that is resorbed in 12-18 months. Resorbable meshes might be a solution for incisional hernia repair to decrease short- and long-term (mesh) complications. However, long-term outcomes after resorption are scarce. Methods Patients with VHWG grade 3 incisional midline hernia, who participated in the Phasix trial (Clinilcaltrials.gov: NCT02720042) were included by means of physical examination and computed tomography (CT). Primary outcome was hernia recurrence; secondary outcomes comprised of long-term mesh complications, reoperations, and abdominal wall pain [visual analogue score (VAS): 0-10]. Results In total, 61/84 (72.6%) patients were seen. Median follow-up time was 60.0 [interquartile range (IQR): 55-64] months. CT scan was made in 39 patients (68.4%). A recurrence rate of 15.9% (95% confidence interval: 6.9-24.8) was calculated after 5 years. Four new recurrences (6.6%) were found between 2 and 5 years. Two were asymptomatic. In total, 13/84 recurrences were found. No long-term mesh complications and/or interventions occurred. VAS scores were 0 (IQR: 0-2). Conclusions Hernia repair with Phasix mesh in high-risk patients (VHWG 3, body mass index >28) demonstrated a recurrence rate of 15.9%, low pain scores, no mesh-related complications or reoperations for chronic pain between the 2- and 5-year follow-up. Four new recurrences occurred, 2 were asymptomatic. The poly-4-hydroxybutyrate mesh is a safe mesh for hernia repair in VHWG 3 patients, which avoids long-term mesh complications like pain and mesh infection.
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Affiliation(s)
- L M Van den Dop
- From the Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - M M J Van Rooijen
- From the Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - T Tollens
- Department of Surgery, Imelda Hospital, Bonheiden, Belgium
| | - L N Jørgensen
- Department of Surgery, Bispebjerg Hospital, Copenhagen, Denmark
| | | | - G Piessen
- Department of Surgery, University Hospital Lille, Lille, France
| | - F Köckerling
- Department of Surgery, Vivantes Klinikum Spandau, Berlin, Germany
| | - M Miserez
- Department of Abdominal Surgery, University Hospital Leuven, Leuven, Belgium
| | - M Dean
- Department of Surgery, University College London Hospital, London, United Kingdom
| | - F Berrevoet
- Department of Surgery, University Hospital Gent, Gent, Belgium
| | - B Dousset
- Department of Surgery, Hôpital Cochin, Paris, France
| | | | - F Gossetti
- Department of Surgery, Università di Roma Sapienza, Rome, Italy
| | - G W M Tetteroo
- Department of Surgery, IJsselland Hospital, Capelle aan den IJssel, the Netherlands
| | - A Koch
- Department of Surgery, Chirurgische Praxis Ärztehaus, Cottbus, Germany
| | - M F Boomsma
- Department of Radiology, Isala hospital, Zwolle, the Netherlands
| | - J F Lange
- From the Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - J Jeekel
- From the Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands
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6
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Rao N, Starrett GJ, Piaskowski ML, Butler KE, Golubeva Y, Yan W, Lawrence SM, Dean M, Garcia-Closas M, Baris D, Johnson A, Schwenn M, Malats N, Real FX, Kogevinas M, Rothman N, Silverman DT, Dyrskjøt L, Buck CB, Koutros S, Prokunina-Olsson L. Analysis of Several Common APOBEC-type Mutations in Bladder Tumors Suggests Links to Viral Infection. Cancer Prev Res (Phila) 2023; 16:561-570. [PMID: 37477495 PMCID: PMC10592262 DOI: 10.1158/1940-6207.capr-23-0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/16/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
FGFR3 and PIK3CA are among the most frequently mutated genes in bladder tumors. We hypothesized that recurrent mutations in these genes might be caused by common carcinogenic exposures such as smoking and other factors. We analyzed 2,816 bladder tumors with available data on FGFR3 and/or PIK3CA mutations, focusing on the most recurrent mutations detected in ≥10% of tumors. Compared to tumors with other FGFR3/PIK3CA mutations, FGFR3-Y375C was more common in tumors from smokers than never-smokers (P = 0.009), while several APOBEC-type driver mutations were enriched in never-smokers: FGFR3-S249C (P = 0.013) and PIK3CA-E542K/PIK3CA-E545K (P = 0.009). To explore possible causes of these APOBEC-type mutations, we analyzed RNA sequencing (RNA-seq) data from 798 bladder tumors and detected several viruses, with BK polyomavirus (BKPyV) being the most common. We then performed IHC staining for polyomavirus (PyV) Large T-antigen (LTAg) in an independent set of 211 bladder tumors. Overall, by RNA-seq or IHC-LTAg, we detected PyV in 26 out of 1,010 bladder tumors with significantly higher detection (P = 4.4 × 10-5), 25 of 554 (4.5%) in non-muscle-invasive bladder cancers (NMIBC) versus 1 of 456 (0.2%) of muscle-invasive bladder cancers (MIBC). In the NMIBC subset, the FGFR3/PIK3CA APOBEC-type driver mutations were detected in 94.7% (18/19) of PyV-positive versus 68.3% (259/379) of PyV-negative tumors (P = 0.011). BKPyV tumor positivity in the NMIBC subset with FGFR3- or PIK3CA-mutated tumors was also associated with a higher risk of progression to MIBC (P = 0.019). In conclusion, our results support smoking and BKPyV infection as risk factors contributing to bladder tumorigenesis in the general patient population through distinct molecular mechanisms. PREVENTION RELEVANCE Tobacco smoking likely causes one of the most common mutations in bladder tumors (FGFR3-Y375C), while viral infections might contribute to three others (FGFR3-S249C, PIK3CA-E542K, and PIK3CA-E545K). Understanding the causes of these mutations may lead to new prevention and treatment strategies, such as viral screening and vaccination.
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Affiliation(s)
- Nina Rao
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Gabriel J Starrett
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Mary L Piaskowski
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Kelly E Butler
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yelena Golubeva
- Molecular Digital Pathology Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Wusheng Yan
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Scott M Lawrence
- Molecular Digital Pathology Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Dalsu Baris
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | | | - Francisco X Real
- CNIO, Madrid, Spain
- CIBERONC, Madrid, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Debra T Silverman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Christopher B Buck
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
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7
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Rodriguez I, Rossi NM, Keskus A, Xie Y, Ahmad T, Bryant A, Lou H, Paredes JG, Milano R, Rao N, Tulsyan S, Boland JF, Luo W, Liu J, O’Hanlon T, Bess J, Mukhina V, Gaykalova D, Yuki Y, Malik L, Billingsley K, Blauwendraat C, Carrington M, Yeager M, Mirabello L, Kolmogorov M, Dean M. Insights into the Mechanisms and Structure of Breakage-Fusion-Bridge Cycles in Cervical Cancer using Long-Read Sequencing. medRxiv 2023:2023.08.21.23294276. [PMID: 37662332 PMCID: PMC10473792 DOI: 10.1101/2023.08.21.23294276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Cervical cancer is caused by human papillomavirus (HPV) infection, has few approved targeted therapeutics, and is the most common cause of cancer death in low-resource countries. We characterized 19 cervical and four head and neck cell lines using long-read DNA and RNA sequencing and identified the HPV types, HPV integration sites, chromosomal alterations, and cancer driver mutations. Structural variation analysis revealed telomeric deletions associated with DNA inversions resulting from breakage-fusion-bridge (BFB) cycles. BFB is a common mechanism of chromosomal alterations in cancer, and this is one of the first analyses of these events using long-read sequencing. Analysis of the inversion sites revealed staggered ends consistent with exonuclease digestion of the DNA after breakage. Some BFB events are complex, involving inter- or intra-chromosomal insertions or rearrangements. None of the BFB breakpoints had telomere sequences added to resolve the dicentric chromosomes and only one BFB breakpoint showed chromothripsis. Five cell lines have a Chr11q BFB event, with YAP1/BIRC2/BIRC3 gene amplification. Indeed, YAP1 amplification is associated with a 10-year earlier age of diagnosis of cervical cancer and is three times more common in African American women. This suggests that cervical cancer patients with YAP1/BIRC2/BIRC3-amplification, especially those of African American ancestry, might benefit from targeted therapy. In summary, we uncovered new insights into the mechanisms and consequences of BFB cycles in cervical cancer using long-read sequencing.
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Affiliation(s)
- Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nicole M. Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Ayse Keskus
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Hong Lou
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jesica Godinez Paredes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Rose Milano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nina Rao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sonam Tulsyan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Joseph F. Boland
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Wen Luo
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jia Liu
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Tim O’Hanlon
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jazmyn Bess
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vera Mukhina
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medical Center, Baltimore, MD, USA
| | - Daria Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical System, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Laksh Malik
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Kimberley Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Meredith Yeager
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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Rossi NM, Dai J, Xie Y, Wangsa D, Heselmeyer-Haddad K, Lou H, Boland JF, Yeager M, Orozco R, Freites EA, Mirabello L, Gharzouzi E, Dean M. Extrachromosomal Amplification of Human Papillomavirus Episomes Is a Mechanism of Cervical Carcinogenesis. Cancer Res 2023; 83:1768-1781. [PMID: 36971511 PMCID: PMC10239328 DOI: 10.1158/0008-5472.can-22-3030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/18/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
SIGNIFICANCE Multimers of the HPV genome are generated in cervical tumors replicating as extrachromosomal episomes, which is associated with deletion and rearrangement of the HPV genome and provides a mechanism for oncogenesis without integration.
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Affiliation(s)
- Nicole M. Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jieqiong Dai
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Darawalee Wangsa
- Center for Cancer Research, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kerstin Heselmeyer-Haddad
- Center for Cancer Research, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hong Lou
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph F. Boland
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | - Meredith Yeager
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Enrique Alvirez Freites
- Hospital Central Universitario “Dr. Antonio M Pineda,” Barquisimeto, Lara State, Venezuela, and Universidad Andino de Cusco, Cusco, Perú
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | | | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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Gonzalez N, Rao N, Dean M, Lee D, Hurson AN, Baris D, Schwenn M, Johnson A, Prokunina-Olsson L, Friesen MC, Zhu B, Rothman N, Silverman DT, Koutros S. Nitrated Polycyclic Aromatic Hydrocarbon (Nitro-PAH) Signatures and Somatic Mutations in Diesel Exhaust-Exposed Bladder Tumors. Cancer Epidemiol Biomarkers Prev 2023; 32:840-847. [PMID: 36996403 PMCID: PMC10239365 DOI: 10.1158/1055-9965.epi-22-1208] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/01/2023] [Accepted: 03/24/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Diesel exhaust is a complex mixture, including polycyclic aromatic hydrocarbons (PAH) and nitrated PAHs (nitro-PAH), many of which are potent mutagens and possible bladder carcinogens. To explore the association between diesel exposure and bladder carcinogenesis, we examined the relationship between exposure and somatic mutations and mutational signatures in bladder tumors. METHODS Targeted sequencing was conducted in bladder tumors from the New England Bladder Cancer Study. Using data on 797 cases and 1,418 controls, two-stage polytomous logistic regression was used to evaluate etiologic heterogeneity between bladder cancer subtypes and quantitative, lifetime estimates of respirable elemental carbon (REC), a surrogate for diesel exposure. Poisson regression was used to evaluate associations between REC and mutational signatures. RESULTS We observed significant heterogeneity in the diesel-bladder cancer risk relationship, with a strong positive association among cases with high-grade, nonmuscle invasive TP53-mutated tumors compared with controls [ORTop Tertile vs.Unexposed, 4.8; 95% confidence interval (CI), 2.2-10.5; Ptrend < 0.001; Pheterogeneity = 0.002]. In muscle-invasive tumors, we observed a positive association between diesel exposure and the nitro-PAH signatures of 1,6-dintropyrene (RR, 1.93; 95% CI, 1.28-2.92) and 3-nitrobenzoic acid (RR, 1.97; 95% CI, 1.33-2.92). CONCLUSIONS The relationship between diesel exhaust and bladder cancer was heterogeneous based on the presence of TP53 mutations in tumors, further supporting the link between PAH exposure and TP53 mutations in carcinogenesis. Future studies that can identify nitro-PAH signatures in exposed tumors are warranted to add human data supporting the link between diesel and bladder cancer. IMPACT This study provides additional insight into the etiology and possible mechanisms related to diesel exhaust-induced bladder cancer.
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Affiliation(s)
- Nicole Gonzalez
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Nina Rao
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Donghyuk Lee
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Statistics, Pusan National University, Busan, Korea
| | - Amber N. Hurson
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Dalsu Baris
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | | | | | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Melissa C. Friesen
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Bin Zhu
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Debra T. Silverman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
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Paredes JG, Rodriguez I, Ren M, Orozco A, Ortiz J, Albanez A, Jones C, Nahleh Z, Barreda L, Garland L, Wu D, Wang J, Argueta V, Orozco R, Gharzouzi E, Dean M. Abstract 1938: Germline mutations in breast cancer genes are associated with early age of diagnosis and triple negative disease in Guatemalan and US Hispanic women. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-1938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Abstract Background: Mutations in hereditary breast cancer genes play an essential role in cancer risk. Little is known of the type and frequency of mutations in Hispanic populations in the United States and Central American countries, including Guatemala.
Methods: We used exome sequencing to identify mutations in blood DNA from unselected Hispanic breast cancer cases from community recruitment and from two hospitals each in Texas and Guatemala. Data from a structured questionnaire was used to compare mutation carriers of medium and high penetrance genes. Variants were annotated with ClinVar and VarSome.
Results: We recruited 262 Hispanic US women, 37 (14%) from community-based recruitment and 225 (86%) from hospitals in Texas. In addition, we ascertained 633 patients from two hospitals in Guatemala City. A total of 91 out of 895 subjects (10%) had a variant classified as pathogenic in a gene with known high or medium penetrance for inherited breast cancer. The most frequently mutated genes were the high penetrance BRCA1 (44/895, 4.9%) followed by BRCA2 (23/895, 2.6%), PALB2 (5/895, 0.6%), CHEK2 (5/895 0.6%), ATM (6/895, 0.7%) and TP53 (6/895, 0.7%). Pathogenic variants were also detected in the moderate penetrance genes BARD1 and MSH6, and rare pathogenic variants detected in the low penetrance genes AXIN2, FH, MLH1, MSH2, MUTYH, NF1, and SDHB. The high ratio of BRCA1/BRCA2 mutations is due to the presence of two potential founder mutations, BRCA1 c.212+1G>A splice mutation (18 cases) and BRCA1 c.799delT (9 cases) in Guatemala. Compared to all others, cases with pathogenic mutations had a significantly earlier age at diagnosis (45 vs. 52 years, P<0.001) and were more likely to have a diagnosis before menopause. A higher percentage of mutation carriers had a relative with any cancer (51% vs. 37%, P=0.038) or breast cancer (33% vs. 15%, P<0.001). Patients with pathogenic mutations had a significantly higher percentage of triple-negative disease (60% vs. 13%, P=0.00046). Finally, mammography usage was less frequent in women with a lower socioeconomic status, indicating that this group is less likely to be screened for breast cancer (P<0.001).
Conclusions: Guatemalan women have rates of hereditary breast cancer mutations like other populations, and these women are more likely to have early age at diagnosis, triple-negative disease, and
family history. Patient recruitment was higher using hospital-based versus community enrollment. This data supports genetic testing in breast cancer patients and those at high risk as part of a strategy to reduce breast cancer mortality in Hispanic women.
Citation Format: Jesica Godinez Paredes, Isabel Rodriguez, Megan Ren, Anali Orozco, Jeremy Ortiz, Anaseidy Albanez, Catherine Jones, Zeina Nahleh, Lilian Barreda, Lisa Garland, Dongjing Wu, Jiahui Wang, Victor Argueta, Roberto Orozco, Eduardo Gharzouzi, Michael Dean. Germline mutations in breast cancer genes are associated with early age of diagnosis and triple negative disease in Guatemalan and US Hispanic women [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1938.
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Affiliation(s)
| | | | - Megan Ren
- 1National Cancer Institute, Rockville, MD
| | - Anali Orozco
- 2Instituto Cancerologia, Guatemala City, Guatemala
| | - Jeremy Ortiz
- 2Instituto Cancerologia, Guatemala City, Guatemala
| | | | - Catherine Jones
- 3Texas Tech University Health Sciences Center Cancer Institute, Lubbock, TX
| | | | - Lilian Barreda
- 5Hospital General San Juan de Dios, Guatemala City, Guatemala
| | - Lisa Garland
- 6Frederick National Laboratory for Cancer Research, Rockville, MD
| | - Dongjing Wu
- 6Frederick National Laboratory for Cancer Research, Rockville, MD
| | - Jiahui Wang
- 6Frederick National Laboratory for Cancer Research, Rockville, MD
| | - Victor Argueta
- 5Hospital General San Juan de Dios, Guatemala City, Guatemala
| | - Roberto Orozco
- 5Hospital General San Juan de Dios, Guatemala City, Guatemala
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11
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Keskus A, Ahmad T, Donmez A, Xie Y, Rodriguez I, Milano R, Rossi N, Lou H, Malik L, Billingsley K, Blauwendraat C, Dean M, Kolmogorov M. Abstract 4289: Long-read, assembly-based characterization of rearranged cancer karyotypes. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-4289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Introduction: Recent pan-cancer whole-genome sequencing studies revealed the rich landscape of structural variants (SV), from simpler indels to complex events involving multiple breakpoints and sequence gain/loss. SVs may contribute to tumorigenesis through direct modification of coding sequence or deregulation from copy number alterations, enhancer hijacking, or topological domain modification.
A substantial part of the variation in the human genome is not accessible to short reads due to mapping ambiguities. Recent benchmarking studies reported that the best short-read methods only have 30-70% SV sensitivity. Long-read sequencing (such as PacBio or Oxford Nanopore) can overcome the limitations of short reads, however the current methods were not designed for the analysis of rearranged cancer genomes with complex copy number profiles.
Methods: We developed BGA (Breakpoint Graph Assembler), a method that combines the ideas from long-read assembly and breakpoint graph frameworks. BGA detects abnormally mapped reads and builds a breakpoint graph that characterizes the structure of derived cancer karyotypes. Complex events with multiple breakpoints form connectivity clusters and are classified based on the subgraph properties. BGA also takes advantage of phased haplotypes and can incorporate multiple related datasets (such as in tumor-normal comparison or multi-site tumor sampling). BGA is freely available at: https://github.com/KolmogorovLab/BGA.
Results: We first analyzed three cancer cell lines and corresponding matching normal DNAs (HCC1954, H2009, and COLO829). In each cell line, we identified 8-56 somatic rearrangement clusters involving more than two breakpoints and at least 1kb of sequence. In H2009, we identified a chromoplexy event involving chr13 and chr1, consistent with previous FISH experiments. COLO829 showed the lowest number of somatic rearrangement clusters (n=8), including translocation and inversion events between chr3, chr10, and chr12 within the RARB, BICC1, and TRHDE genes. Homologous recombination deficient HCC1954 has the highest number of complex events including the chr17q arm which hosts ERBB2, chromoplexy between chr8, chr5, and chromothripsis in chr21.
In addition, we analyzed three other HPV-infected cell lines (CaSki, SCC152, SNU1000). In each of them, we observed complex clusters of HPV-HPV and HPV-human breakpoints that formed cycles, suggesting extrachromosomal amplification. The HPV fragments had many interactions with chromosomal DNA in CaSki and SC152, but not in mostly episomal SNU1000 cells. We also observed karyotype-scale changes that did not involve HPV sequences, such as the simultaneous exchange of six chromosome arms of chr2, chr7, and chr17 in CaSki.
Citation Format: Ayse Keskus, Tanveer Ahmad, Ataberk Donmez, Yi Xie, Isabel Rodriguez, Rose Milano, Nicole Rossi, Hong Lou, Laksh Malik, Kimberley Billingsley, Cornelis Blauwendraat, Michael Dean, Mikhail Kolmogorov. Long-read, assembly-based characterization of rearranged cancer karyotypes. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4289.
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Affiliation(s)
- Ayse Keskus
- 1National Cancer Institute, NCI, Bethesda, MD
| | | | | | - Yi Xie
- 2National Cancer Institute, NCI, Rockville, MD
| | | | - Rose Milano
- 2National Cancer Institute, NCI, Rockville, MD
| | | | - Hong Lou
- 3National Laboratory for Cancer Research, Frederick, MD
| | - Laksh Malik
- 4National Institutes of Health, Bethesda, MD
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Del Valle Diaz F, Dean M, Lemoine C, Copeland L, Silverman J, Zoni C, Raines T, Ravi Y, Sai-Sudhakar C. Donor Cause of Death and Ejection Fraction in Heart Transplant Recipients. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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13
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Starrett GJ, Yu K, Golubeva Y, Lenz P, Piaskowski ML, Petersen D, Dean M, Israni A, Hernandez BY, Tucker TC, Cheng I, Gonsalves L, Morris CR, Hussain SK, Lynch CF, Harris RS, Prokunina-Olsson L, Meltzer PS, Buck CB, Engels EA. Evidence for virus-mediated oncogenesis in bladder cancers arising in solid organ transplant recipients. eLife 2023; 12:e82690. [PMID: 36961501 PMCID: PMC10446826 DOI: 10.7554/elife.82690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 03/22/2023] [Indexed: 03/25/2023] Open
Abstract
A small percentage of bladder cancers in the general population have been found to harbor DNA viruses. In contrast, up to 25% of tumors of solid organ transplant recipients, who are at an increased risk of developing bladder cancer and have an overall poorer outcomes, harbor BK polyomavirus (BKPyV). To better understand the biology of the tumors and the mechanisms of carcinogenesis from potential oncoviruses, we performed whole genome and transcriptome sequencing on bladder cancer specimens from 43 transplant patients. Nearly half of the tumors from this patient population contained viral sequences. The most common were from BKPyV (N=9, 21%), JC polyomavirus (N=7, 16%), carcinogenic human papillomaviruses (N=3, 7%), and torque teno viruses (N=5, 12%). Immunohistochemistry revealed variable Large T antigen expression in BKPyV-positive tumors ranging from 100% positive staining of tumor tissue to less than 1%. In most cases of BKPyV-positive tumors, the viral genome appeared to be clonally integrated into the host chromosome consistent with microhomology-mediated end joining and coincided with focal amplifications of the tumor genome similar to other virus-mediated cancers. Significant changes in host gene expression consistent with the functions of BKPyV Large T antigen were also observed in these tumors. Lastly, we identified four mutation signatures in our cases, with those attributable to APOBEC3 and SBS5 being the most abundant. Mutation signatures associated with an antiviral drug, ganciclovir, and aristolochic acid, a nephrotoxic compound found in some herbal medicines, were also observed. The results suggest multiple pathways to carcinogenesis in solid organ transplant recipients with a large fraction being virus-associated.
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Affiliation(s)
| | - Kelly Yu
- DCEG, NCI, NIHRockvilleUnited States
| | | | - Petra Lenz
- Leidos Biomedical Research IncFrederickUnited States
| | | | | | | | - Ajay Israni
- Department of Medicine, Nephrology Division, Hennepin Healthcare System, University of MinnesotaMinneapolisUnited States
| | | | - Thomas C Tucker
- The Kentucky Cancer Registry, University of KentuckyLexingtonUnited States
| | - Iona Cheng
- Department of Epidemiology and Biostatistics,and Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoFremontUnited States
| | - Lou Gonsalves
- Connecticut Tumor Registry, Connecticut Department of Public HealthHartfordUnited States
| | - Cyllene R Morris
- California Cancer Reporting and Epidemiologic Surveillance Program, University of California, DavisDavisUnited States
| | - Shehnaz K Hussain
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Charles F Lynch
- The Iowa Cancer Registry, University of IowaIowa CityUnited States
| | - Reuben S Harris
- Howard Hughes Medical Institute, University of MinnesotaMinneapolisUnited States
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Van Den Dop M, Tollens T, Jørgensen L, De Vries-Reilingh T, Piessen G, Köckerling F, Miserez M, Dean M, Berrevoet F, Dousset B, Van Westreenen G, Gosetti F, Lange J, Tetteroo G, Jeekel H. OC-053 LONG-TERM FOLLOW-UP OF A SLOWLY RESORBABLE BIOSYNTHETIC MESH IN VHWG GRADE 3 HERNIA REPAIR. Br J Surg 2022. [DOI: 10.1093/bjs/znac308.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Background
Incisional hernia recurrence occurs frequently after initial repair. In potentially contaminated hernia, these numbers can rise up to 50%. Recently, resorbable meshes have been used to prevent infection in complicated incisional hernia and prevent long term mesh complications. Present study focuses on the long term outcomes of a resorbable mesh.
Methods
Patients included in the priorly conducted Phasix trial with Ventral Hernia Working Group (VHWG) grade 3 hernia were invited for an abdominal CT scan and physical examination. Primary outcome was hernia recurrence, secondary outcomes comprised of abdominal wall configuration, mesh resorption and long term mesh complications.
Results
Of the 84 patients included in the 2-year follow-up, 56 were available for long term follow-up up to five years. Mean follow-up time was 4.2 years. CT scan was made in 36 (64.3%) of patients. Kaplan-Meier analysis showed a recurrence rate of 16.7% after five years. Four (7.1%) new recurrences were found between 2-year and 4.2 years follow-up of which three by CT scan. In 50% of CT scans, no signs of postoperative distortions of the abdominal wall were observed. No long term mesh complications were reported.
Conclusion
After long term follow-up, VHWG 3 hernia repair with biosynthetic mesh demonstrated good performance with regard to hernia recurrence. Possibly, tissue reconstruction took place in the first two years after implantation by the use it or lose it principle, which led to sufficient native abdominal wall strength to prevent recurrences after resorption of the mesh.
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Affiliation(s)
- M Van Den Dop
- Surgery, Erasmus University Medical Centre , Rotterdam , Netherlands
| | - T Tollens
- Surgery, Imelda hospital , Bonheiden , Belgium
| | - L Jørgensen
- Surgery, Bispebjerg Hospital , Copenhagen , Denmark
| | | | - G Piessen
- Surgery, University Hospital Lille , Lille , France
| | - F Köckerling
- Surgery, Vivantes Klinikum Spandau , Berlin , Germany
| | - M Miserez
- Abdominal Surgery, University Hospital Leuven , Leuven , Belgium
| | - M Dean
- Surgery, University College London Hospital , London , United Kingdom
| | - F Berrevoet
- Surgery, University Hospital Gent , Gent , Belgium
| | - B Dousset
- Digsetive, hepatobiliary and Endocrine surgery , Hôpital Cochin, Paris , France
| | | | - F Gosetti
- Surgery, Università di Roma Sapienza , Rome , Italy
| | - J Lange
- Surgery, Erasmus University Medical Centre , Rotterdam , Netherlands
| | - G Tetteroo
- Surgery, IJsselland hospital , Capelle aan den IJssel , Netherlands
| | - H Jeekel
- Surgery, Erasmus University Medical Centre , Rotterdam , Netherlands
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15
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Gibson A, Dean M, Elegbede A, Pabani A, Bebb G, Cheung W. EP05.02-001 Early Treatment Failure Of Consolidation Durvalumab for Unresectable Stage III NSCLC: A Real-World Canadian Cohort. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Litt I, Gibson A, Dean M, Elegbede A, Bebb G, Cheung W, Pabani A. EP08.02-071 Brain Metastases in EGFR-mutant NSCLC: Outcome of Osimertinib +/- Radiation Therapy in a Real-World Canadian Cohort. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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17
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Gibson A, Litt I, Hao D, Dean M, Elegbede A, Bebb G, Pabani A, Cheung W. EP08.02-014 Impact of East Asian Ancestry on Response to First-Line Osimertinib: A Real-World Canadian Cohort. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Ford-Sahibzada C, Dean M, Peters C, Brenner D, Gibson A, D'Silva A, Elegbede A, Tudor R, Bebb G, Cheung W. EP04.02-001 Sex as a Potential Independent Prognostic Factor in Non-Small Cell Lung Cancer Survival. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Dean M, Moitra K, Allikmets R. The human ATP-binding cassette (ABC) transporter superfamily. Hum Mutat 2022; 43:1162-1182. [PMID: 35642569 PMCID: PMC9357071 DOI: 10.1002/humu.24418] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/12/2022]
Abstract
The ATP-binding cassette (ABC) transporter superfamily comprises membrane proteins that efflux various substrates across extra- and intracellular membranes. Mutations in ABC genes cause 21 human disorders or phenotypes with Mendelian inheritance, including cystic fibrosis, adrenoleukodystrophy, retinal degeneration, cholesterol, and bile transport defects. To provide tools to study the function of human ABC transporters we compiled data from multiple genomics databases. We analyzed ABC gene conservation within human populations and across vertebrates and surveyed phenotypes of ABC gene mutations in mice. Most mouse ABC gene disruption mutations have a phenotype that mimics human disease, indicating they are applicable models. Interestingly, several ABCA family genes, whose human function is unknown, have cholesterol level phenotypes in the mouse. Genome-wide association studies confirm and extend ABC traits and suggest several new functions to investigate. Whole-exome sequencing of tumors from diverse cancer types demonstrates that mutations in ABC genes are not common in cancer, but specific genes are overexpressed in select tumor types. Finally, an analysis of the frequency of loss-of-function mutations demonstrates that many human ABC genes are essential with a low level of variants, while others have a higher level of genetic diversity.
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Affiliation(s)
- Michael Dean
- Laboratory of Translational Genomics, National Cancer Institute, Gaithersburg, Maryland 21702
| | | | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, New York, 10032
- Department of Pathology & Cell Biology, Columbia University, New York, New York, 10032
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20
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Jiménez-Morales S, Ren X, Dean M. Editorial: The Genetic Causes Underlying Immune Mediated Disease: A Focus on Autoimmunity and Cancer. Front Genet 2022; 13:889160. [PMID: 35401679 PMCID: PMC8990264 DOI: 10.3389/fgene.2022.889160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/10/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Silvia Jiménez-Morales
- Laboratory of Cancer Genomics, Instituto Nacional de Medicina Genómica, Mexico, Mexico
- *Correspondence: Silvia Jiménez-Morales,
| | - Xianwen Ren
- Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing, China
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
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21
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Lino-Silva LS, Lajous M, Brochier M, Santiago-Ruiz L, Melchor-Ruan J, Xie Y, Wang M, Wu D, Higson H, Jones K, Romero-Martínez M, Villalpando S, Mohar A, Smith JW, Alvarez CS, McGlynn KA, Dean M, Groopman J. Aflatoxin levels and prevalence of TP53 aflatoxin-mutations in hepatocellular carcinomas in Mexico. Salud Publica Mex 2022; 64:35-40. [DOI: 10.21149/13189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/25/2021] [Indexed: 11/06/2022] Open
Abstract
Objective. To determine the exposure to aflatoxin B1 (AFB1) in southern Mexico and the presence of the aflatoxin signature mutation in hepatocellular carcinoma (HCC) tissue from patients from a cancer referral center. Materials and methods. We estimated the prevalence and distribution of AFB1 in a representative sample of 100 women and men from Chiapas using the National Health and Nutrition Survey 2018-19. We also examined the presence of the aflatoxin signature mutation in codon 249 (R249S), and other relevant mutations of the TP53 gene in HCC tissue blocks from 24 women and 26 men treated in a national cancer referral center. Results. The prevalence of AFB1 in serum samples was 85.5% (95%CI 72.1-93.1) and the median AFB1 was 0.117 pg/μL (IQR, 0.050–0.350). We detected TP53 R249S in three of the 50 HCCs (6.0%) and observed four other G>T transversions potentially induced by AFB1. Conclusion. Our analysis provides evidence that AFB1 may have a relevant role on HCC etiology in Mexico.
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22
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Alvarez CS, Rivera‐Andrade A, Kroker‐Lobos MF, Florio AA, Smith JW, Egner PA, Freedman ND, Lazo M, Guallar E, Dean M, Graubard BI, Ramírez‐Zea M, McGlynn KA, Groopman JD. Associations between aflatoxin
B
1
‐albumin adduct levels with metabolic conditions in Guatemala: A cross‐sectional study. Health Sci Rep 2022; 5:e495. [PMID: 35229049 PMCID: PMC8865065 DOI: 10.1002/hsr2.495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/19/2021] [Accepted: 12/07/2021] [Indexed: 12/30/2022] Open
Abstract
Background and Aims Metabolic conditions such as obesity, type 2 diabetes, metabolic syndrome, and nonalcoholic fatty liver disease (NAFLD) are highly prevalent in Guatemala and increase the risk for a number of disorders, including hepatocellular carcinoma (HCC). Aflatoxin B1 (AFB1) levels are also notably elevated in the population and are known to be associated with HCC risk. Whether AFB1 also contributes to the high prevalence of the metabolic disorders has not been previously examined. Therefore, the purpose of this study was to assess the association between AFB1 and the metabolic conditions. Methods Four‐hundred twenty‐three individuals were included in the study, in which AFB1‐albumin adduct levels were measured in sera. Metabolic conditions included diabetes, obesity, central obesity, metabolic syndrome, and NAFLD. Crude and adjusted prevalence odds ratios (PORs) and 95% confidence intervals (95% CI) were estimated for the associations between the metabolic conditions and AFB1‐albumin adduct levels categorized into quartiles. Results The study found a significant association between AFB1‐albumin adduct levels and diabetes (Q4 vs Q1 POR = 3.74, 95%CI: 1.71‐8.19; P‐trend .003). No associations were observed between AFB1‐albumin adduct levels and the other conditions. Conclusions As diabetes is the metabolic condition most consistently linked to HCC, the possible association between AFB1 exposure and diabetes may be of public health importance. Further studies are warranted to replicate the findings and examine potential mechanisms.
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Affiliation(s)
- Christian S. Alvarez
- Division of Cancer Epidemiology and Genetics National Cancer Institute Rockville Maryland USA
| | - Alvaro Rivera‐Andrade
- INCAP Research Center for the Prevention of Chronic Diseases Institute of Nutrition of Central America and Panama Guatemala City Guatemala
| | - María F. Kroker‐Lobos
- INCAP Research Center for the Prevention of Chronic Diseases Institute of Nutrition of Central America and Panama Guatemala City Guatemala
| | - Andrea A. Florio
- Division of Cancer Epidemiology and Genetics National Cancer Institute Rockville Maryland USA
- Department of Nutrition, Harvard TH Chan School of Public Health Harvard University Boston Massachusetts USA
| | - Joshua W. Smith
- Department of Environmental Health and Engineering, Bloomberg School of Public Health Johns Hopkins University Baltimore Maryland USA
| | - Patricia A. Egner
- Department of Environmental Health and Engineering, Bloomberg School of Public Health Johns Hopkins University Baltimore Maryland USA
| | - Neal D. Freedman
- Division of Cancer Epidemiology and Genetics National Cancer Institute Rockville Maryland USA
| | - Mariana Lazo
- Division of General Internal Medicine, School of Medicine Johns Hopkins University Baltimore Maryland USA
- Urban Health Collaborative, Dornsife School of Public Health Drexel University Philadelphia Pennsylvania USA
| | - Eliseo Guallar
- Department of Epidemiology, Bloomberg School of Public Health Johns Hopkins University Baltimore Maryland USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics National Cancer Institute Rockville Maryland USA
| | - Barry I. Graubard
- Division of Cancer Epidemiology and Genetics National Cancer Institute Rockville Maryland USA
| | - Manuel Ramírez‐Zea
- INCAP Research Center for the Prevention of Chronic Diseases Institute of Nutrition of Central America and Panama Guatemala City Guatemala
| | - Katherine A. McGlynn
- Division of Cancer Epidemiology and Genetics National Cancer Institute Rockville Maryland USA
| | - John D. Groopman
- Department of Environmental Health and Engineering, Bloomberg School of Public Health Johns Hopkins University Baltimore Maryland USA
- Department of Epidemiology, Bloomberg School of Public Health Johns Hopkins University Baltimore Maryland USA
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23
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Naranbhai V, Viard M, Dean M, Groha S, Braun DA, Labaki C, Shukla SA, Yuki Y, Shah P, Chin K, Wind-Rotolo M, Mu XJ, Robbins PB, Gusev A, Choueiri TK, Gulley JL, Carrington M. HLA-A*03 and response to immune checkpoint blockade in cancer: an epidemiological biomarker study. Lancet Oncol 2022; 23:172-184. [PMID: 34895481 PMCID: PMC8742225 DOI: 10.1016/s1470-2045(21)00582-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Predictive biomarkers could allow more precise use of immune checkpoint inhibitors (ICIs) in treating advanced cancers. Given the central role of HLA molecules in immunity, variation at the HLA loci could differentially affect the response to ICIs. The aim of this epidemiological study was to determine the effect of HLA-A*03 as a biomarker for predicting response to immunotherapy. METHODS In this epidemiological study, we investigated the clinical outcomes (overall survival, progression free survival, and objective response rate) after treatment for advanced cancer in eight cohorts of patients: three observational cohorts of patients with various types of advanced tumours (the Memorial Sloan Kettering Integrated Mutation Profiling of Actionable Cancer Targets [MSK-IMPACT] cohort, the Dana-Farber Cancer Institute [DFCI] Profile cohort, and The Cancer Genome Atlas) and five clinical trials of patients with advanced bladder cancer (JAVELIN Solid Tumour) or renal cell carcinoma (CheckMate-009, CheckMate-010, CheckMate-025, and JAVELIN Renal 101). In total, these cohorts included 3335 patients treated with various ICI agents (anti-PD-1, anti-PD-L1, and anti-CTLA-4 inhibitors) and 10 917 patients treated with non-ICI cancer-directed therapeutic approaches. We initially modelled the association of HLA amino-acid variation with overall survival in the MSK-IMPACT discovery cohort, followed by a detailed analysis of the association between HLA-A*03 and clinical outcomes in MSK-IMPACT, with replication in the additional cohorts (two further observational cohorts and five clinical trials). FINDINGS HLA-A*03 was associated in an additive manner with reduced overall survival after ICI treatment in the MSK-IMPACT cohort (HR 1·48 per HLA-A*03 allele [95% CI 1·20-1·82], p=0·00022), the validation DFCI Profile cohort (HR 1·22 per HLA-A*03 allele, 1·05-1·42; p=0·0097), and in the JAVELIN Solid Tumour clinical trial for bladder cancer (HR 1·36 per HLA-A*03 allele, 1·01-1·85; p=0·047). The HLA-A*03 effect was observed across ICI agents and tumour types, but not in patients treated with alternative therapies. Patients with HLA-A*03 had shorter progression-free survival in the pooled patient population from the three CheckMate clinical trials of nivolumab for renal cell carcinoma (HR 1·31, 1·01-1·71; p=0·044), but not in those receiving control (everolimus) therapies. Objective responses were observed in none of eight HLA-A*03 homozygotes in the ICI group (compared with 59 [26·6%] of 222 HLA-A*03 non-carriers and 13 (17·1%) of 76 HLA-A*03 heterozygotes). HLA-A*03 was associated with shorter progression-free survival in patients receiving ICI in the JAVELIN Renal 101 randomised clinical trial for renal cell carcinoma (avelumab plus axitinib; HR 1·59 per HLA-A*03 allele, 1·16-2·16; p=0·0036), but not in those receiving control (sunitinib) therapy. Objective responses were recorded in one (12·5%) of eight HLA-A*03 homozygotes in the ICI group (compared with 162 [63·8%] of 254 HLA-A*03 non-carriers and 40 [55·6%] of 72 HLA-A*03 heterozygotes). HLA-A*03 was associated with impaired outcome in meta-analysis of all 3335 patients treated with ICI at genome-wide significance (p=2·01 × 10-8) with no evidence of heterogeneity in effect (I2 0%, 95% CI 0-0·76) INTERPRETATION: HLA-A*03 is a predictive biomarker of poor response to ICI. Further evaluation of HLA-A*03 is warranted in randomised trials. HLA-A*03 carriage could be considered in decisions to initiate ICI in patients with cancer. FUNDING National Institutes of Health, Merck KGaA, and Pfizer.
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Affiliation(s)
- Vivek Naranbhai
- Massachusetts General Hospital, Boston, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Centre for the AIDS Programme of Research In South Africa, Durban, South Africa
| | - Mathias Viard
- Basic Science Programme, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | | | | | - Yuko Yuki
- Basic Science Programme, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Parantu Shah
- Bioinformatics, Department of Translational Medicine and Global Clinical Development, EMD Serono Research and Development Institute, Merck KGaA, Darmstadt, Germany
| | - Kevin Chin
- Immunooncology, EMD Serono Research and Development Institute, Merck KGaA, Darmstadt, Germany
| | | | | | | | | | | | - James L Gulley
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mary Carrington
- Basic Science Programme, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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24
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Polani S, Dean M, Lichter-Peled A, Hendrickson S, Tsang S, Fang X, Feng Y, Qiao W, Avni G, Kahila Bar-Gal G. Sequence Variant in the TRIM39-RPP21 Gene Readthrough is Shared Across a Cohort of Arabian Foals Diagnosed with Juvenile Idiopathic Epilepsy. J Genet Mutat Disord 2022; 1:103. [PMID: 35465405 PMCID: PMC9031527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Juvenile idiopathic epilepsy (JIE) is a self-limiting neurological disorder with a suspected genetic predisposition affecting young Arabian foals of the Egyptian lineage. The condition is characterized by tonic-clonic seizures with intermittent post-ictal blindness, in which most incidents are sporadic and unrecognized. This study aimed to identify genetic components shared across a local cohort of Arabian foals diagnosed with JIE via a combined whole genome and targeted resequencing approach: Initial whole genome comparisons between a small cohort of nine diagnosed foals (cases) and 27 controls from other horse breeds identified variants uniquely shared amongst the case cohort. Further validation via targeted resequencing of these variants, that pertain to non-intergenic regions, on additional eleven case individuals revealed a single 19bp deletion coupled with a triple-C insertion (Δ19InsCCC) within the TRIM39-RPP21 gene readthrough that was uniquely shared across all case individuals, and absent from three additional Arabian controls. Furthermore, we have confirmed recent findings refuting potential linkage between JIE and other inherited diseases in the Arabian lineage, and refuted the potential linkage between JIE and genes predisposing a similar disorder in human newborns. This is the first study to report a genetic variant to be shared in a sub-population cohort of Arabian foals diagnosed with JIE. Further evaluation of the sensitivity and specificity of the Δ19InsCCC allele within additional cohorts of the Arabian horse is warranted in order to validate its credibility as a marker for JIE, and to ascertain whether it has been introduced into other horse breeds by Arabian ancestry.
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Affiliation(s)
- S Polani
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - M Dean
- National Cancer Institute, Division of Cancer Epidemiology & Genetics, Laboratory of Translational Genomics, USA
| | - A Lichter-Peled
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - S Hendrickson
- Department of Biology, Shepherd University, Shepherdstown, USA
| | | | - X Fang
- BGI-Shenzhen, Shenzhen, China
| | - Y Feng
- BGI-Shenzhen, Shenzhen, China
| | - W Qiao
- BGI-Shenzhen, Shenzhen, China
| | - G Avni
- Medisoos Equine Clinic, Kibutz Magal, Israel
| | - G Kahila Bar-Gal
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
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25
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Abstract
Antimicrobial resistance (AMR) is a global health emergency affecting humans and animals, diminishing the effectiveness of medication used to treat illness. The agri-food sector has attracted increased attention for imprudent antimicrobial use (AMU) and its contribution to AMR. Thus, ascertaining farmers' and veterinarians' behaviours surrounding AMU is essential to address imprudent AMU and generate behaviour change within the agri-food sector. Therefore, the aim of this critical review is to investigate, assess and collate the current body of evidence to identify psychosocial factors including knowledge, understanding, perceptions, attitudes and behaviours surrounding AMU. Database searches were limited to articles utilizing qualitative and quantitative methodologies, available in English with no restriction on publication year. Of the 1156 articles identified, 103 were retained for this review. Findings on the psychosocial aspects were thematically analysed. Five key themes emerged from the data: (i) knowledge and awareness of antimicrobials; (ii) attitudes towards antimicrobials; (iii) influential relationships; (iv) resources; and (v) factors influencing AMU. Results indicated that to overcome barriers experienced by key stakeholders, a carefully considered, evidence-based approach, incorporating behaviour change theory, is required when designing intricate interventions/strategies, in order to elicit successful and sustained AMU behaviour change.
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Affiliation(s)
- C McKernan
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL,UK
| | - T Benson
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL,UK
| | - S Farrell
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL,UK
| | - M Dean
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL,UK
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26
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Jeffries A, Beck-Sagué CM, Marroquin-Garcia AB, Dean M, McCoy V, Cordova-Toma DA, Fenkl E, Madhivanan P. Cervical Visual Inspection with Acetic Acid (VIA) and Oncogenic Human Papillomavirus Screening in Rural Indigenous Guatemalan Women: Time to Rethink VIA. Int J Environ Res Public Health 2021; 18:ijerph182312406. [PMID: 34886133 PMCID: PMC8656883 DOI: 10.3390/ijerph182312406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/16/2021] [Accepted: 11/20/2021] [Indexed: 11/30/2022]
Abstract
Single-visit “screen-and-treat” strategies using visual inspection with acetic acid (VIA) and cryotherapy (liquid nitrous oxide ablation) in low-resource settings are commonly used to detect and treat precancerous lesions for cervical cancer prevention. This study compared VIA sensitivity and specificity in rural indigenous Guatemalan communities, to that of oncogenic human papillomavirus (HPV) testing for detection of precancerous changes, using cytology as the reference standard. Between 3–8 September 2017, trained nurses examined 222 women aged 23–58 years with VIA. Specimens for liquid-based cytology and HPV testing were obtained prior to VIA with a cytobrush and transported in PreservCyt to a US clinical laboratory. VIA and HPV test sensitivities were assessed as proportions of women with abnormal cytology that had abnormal VIA or HPV results, respectively, and specificities, as proportions with normal cytology with normal VIA or negative HPV tests. Of 222 women, 18 (8.1%) had abnormal cytology (1 carcinoma in a participant who received VIA-based cryotherapy in 2015, 4 high- and 5 low-grade squamous intraepithelial lesions, and 8 atypical squamous cells of undetermined significance (ASCUS)). Excluding ASCUS, sensitivities of VIA and HPV were 20.0% and 100%, respectively. VIA-based screening may not be acceptable for detecting precancerous lesions, and field cryotherapy for preventing malignancy. The World Health Organization recommended in 2021 “…using HPV DNA detection as the primary screening test rather than VIA or cytology”.
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Affiliation(s)
- Anne Jeffries
- Robert Stempel (RS) College of Public Health and Social Work, Florida International University (FIU), Miami, FL 33199, USA; (A.J.); (V.M.); (E.F.)
| | - Consuelo M. Beck-Sagué
- Robert Stempel (RS) College of Public Health and Social Work, Florida International University (FIU), Miami, FL 33199, USA; (A.J.); (V.M.); (E.F.)
- Correspondence: ; Tel.: +1-786-253-3928
| | | | - Michael Dean
- Laboratory of Translational Genomics, National Cancer Institute (NCI), National Institutes of Health, Rockville, MD 20850, USA;
| | - Virginia McCoy
- Robert Stempel (RS) College of Public Health and Social Work, Florida International University (FIU), Miami, FL 33199, USA; (A.J.); (V.M.); (E.F.)
| | | | - Eric Fenkl
- Robert Stempel (RS) College of Public Health and Social Work, Florida International University (FIU), Miami, FL 33199, USA; (A.J.); (V.M.); (E.F.)
| | - Purnima Madhivanan
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ 85724, USA;
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27
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Fu X, Lei H, Tao Y, Heselmeyer-Haddad K, Torres I, Dean M, Ried T, Schwartz R. Joint Clustering of Single-Cell Sequencing and Fluorescence In Situ Hybridization Data for Reconstructing Clonal Heterogeneity in Cancers. J Comput Biol 2021; 28:1035-1051. [PMID: 34612714 DOI: 10.1089/cmb.2021.0255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aneuploidy and whole genome duplication (WGD) events are common features of cancers associated with poor outcomes, but the ways they influence trajectories of clonal evolution are poorly understood. Phylogenetic methods for reconstructing clonal evolution from genomic data have proven a powerful tool for understanding how clonal evolution occurs in the process of cancer progression, but extant methods so far have limited the ability to resolve tumor evolution via ploidy changes. This limitation exists in part because single-cell DNA-sequencing (scSeq), which has been crucial to developing detailed profiles of clonal evolution, has difficulty in resolving ploidy changes and WGD. Multiplex interphase fluorescence in situ hybridization (miFISH) provides a more unambiguous signal of single-cell ploidy changes but it is limited to profiling small numbers of single markers. Here, we develop a joint clustering method to combine these two data sources with the goal of better resolving ploidy changes in tumor evolution. We develop a probabilistic framework to maximize the probability of latent variables given the pre-clustered datasets, which we optimize via Markov chain Monte Carlo sampling combined with linear regression. We validate the method by using simulated data derived from a glioblastoma (GBM) case profiled by both scSeq and miFISH. We further apply the method to two GBM cases with scSeq and miFISH data by reconstructing a phylogenetic tree from the joint clustering results, demonstrating their synergistic value in understanding how focal copy number changes and WGD events can collectively contribute to tumor progression.
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Affiliation(s)
- Xuecong Fu
- Department of Biological Sciences, and Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Haoyun Lei
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Yifeng Tao
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Irianna Torres
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Thomas Ried
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Russell Schwartz
- Department of Biological Sciences, and Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.,Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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Elegbede A, Gibson A, Pabani A, Dean M, Bebb G. P63.13 Long Term Survival Characteristics in SCLC Patients Receiving Atezolizumab and Chemotherapy. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Martos G, Bebb G, Pabani A, Gibson A, Dean M, Petersen L. P59.29 Frequency of PIK3CA Mutations and Therapeutic Outcomes in NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Elegbede A, Ezeife D, Gibson A, Dean M, Petersen L, Bebb G. P59.25 Prognostic and Treatment Characteristics of Metastatic KRAS G12C Mutant NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Gibson A, Dean M, Box A, Elegbede A, Bebb G. P59.06 Prognostic Nutritional Index in Real-World Patients Receiving Systemic Therapy for Driver Mutation-Positive Metastatic NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Guimarães Alves AC, Sukow NM, Adelman Cipolla G, Mendes M, Leal TP, Petzl-Erler ML, Lehtonen Rodrigues Souza R, Rainha de Souza I, Sanchez C, Santolalla M, Loesch D, Dean M, Machado M, Moon JY, Kaplan R, North KE, Weiss S, Barreto ML, Lima-Costa MF, Guio H, Cáceres O, Padilla C, Tarazona-Santos E, Mata IF, Dieguez E, Raggio V, Lescano A, Tumas V, Borges V, Ferraz HB, Rieder CR, Schumacher-Schuh A, Santos-Lobato BL, Chana-Cuevas P, Fernandez W, Arboleda G, Arboleda H, Arboleda-Bustos CE, O’Connor TD, Beltrame MH, Borda V. Tracing the Distribution of European Lactase Persistence Genotypes Along the Americas. Front Genet 2021; 12:671079. [PMID: 34630506 PMCID: PMC8493957 DOI: 10.3389/fgene.2021.671079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/23/2021] [Indexed: 01/26/2023] Open
Abstract
In adulthood, the ability to digest lactose, the main sugar present in milk of mammals, is a phenotype (lactase persistence) observed in historically herder populations, mainly Northern Europeans, Eastern Africans, and Middle Eastern nomads. As the -13910∗T allele in the MCM6 gene is the most well-characterized allele responsible for the lactase persistence phenotype, the -13910C > T (rs4988235) polymorphism is commonly evaluated in lactase persistence studies. Lactase non-persistent adults may develop symptoms of lactose intolerance when consuming dairy products. In the Americas, there is no evidence of the consumption of these products until the arrival of Europeans. However, several American countries' dietary guidelines recommend consuming dairy for adequate human nutrition and health promotion. Considering the extensive use of dairy and the complex ancestry of Pan-American admixed populations, we studied the distribution of -13910C > T lactase persistence genotypes and its flanking haplotypes of European origin in 7,428 individuals from several Pan-American admixed populations. We found that the -13910∗T allele frequency in Pan-American admixed populations is directly correlated with allele frequency of the European sources. Moreover, we did not observe any overrepresentation of European haplotypes in the -13910C > T flanking region, suggesting no selective pressure after admixture in the Americas. Finally, considering the dominant effect of the -13910∗T allele, our results indicate that Pan-American admixed populations are likely to have higher frequency of lactose intolerance, suggesting that general dietary guidelines deserve further evaluation across the continent.
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Affiliation(s)
- Ana Cecília Guimarães Alves
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Programa de Pós-Graduação em Genética, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Natalie Mary Sukow
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Gabriel Adelman Cipolla
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Marla Mendes
- Laboratório de Diversidade Genética Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thiago P. Leal
- Laboratório de Diversidade Genética Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Programa de Pós-Graduação em Genética, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Ricardo Lehtonen Rodrigues Souza
- Programa de Pós-Graduação em Genética, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Laboratório de Polimorfismos e Ligação, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Ilíada Rainha de Souza
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Laboratório de Polimorfismos Genéticos, Departamento de Biologia Celular, Embriologia e Genética, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Cesar Sanchez
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
| | - Meddly Santolalla
- Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Douglas Loesch
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Moara Machado
- Laboratório de Diversidade Genética Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Scott Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Mauricio L. Barreto
- Universidade Federal da Bahia, Instituto de Saúde Coletiva, Salvador, Brazil
- Fundação Oswaldo Cruz, Centro de Integração de Dados e Conhecimentos para Saúde (Cidacs), Salvador, Brazil
| | - M. Fernanda Lima-Costa
- Fundação Oswaldo Cruz, Instituto René Rachou, Belo Horizonte, Brazil
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Saúde Pública, Belo Horizonte, Brazil
| | - Heinner Guio
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
- Facultad de Ciencias de la Salud, Universidad de Huánuco, Huánuco, Peru
| | - Omar Cáceres
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
- Carrera de Medicina Humana, Facultad de Ciencias de la Salud, Universidad Científica del Sur, Lima, Peru
| | - Carlos Padilla
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
| | - Eduardo Tarazona-Santos
- Laboratório de Diversidade Genética Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ignacio F. Mata
- Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
- Department of Neurology, University of Washington, Seattle, WA, United States
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, OH, United States
| | - Elena Dieguez
- Neurology Institute, Universidad de la República, Montevideo, Uruguay
| | - Víctor Raggio
- Department of Genetics, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Andres Lescano
- Neurology Institute, Universidad de la República, Montevideo, Uruguay
| | - Vitor Tumas
- Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vanderci Borges
- Movement Disorders Unit, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Henrique B. Ferraz
- Movement Disorders Unit, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Carlos R. Rieder
- Departamento de Neurologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Artur Schumacher-Schuh
- Serviço de Neurologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Departamento de Farmacologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Pedro Chana-Cuevas
- CETRAM, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Santiago, Chile
| | - William Fernandez
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Gonzalo Arboleda
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Humberto Arboleda
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Carlos E. Arboleda-Bustos
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
- Program for Personalized and Genomic Medicine, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
- Department of Medicine, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Marcia Holsbach Beltrame
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Programa de Pós-Graduação em Genética, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Victor Borda
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
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Higgin R, Dean M, Qureshi A, Hancock N. Outcomes following the delayed management of open tibial fractures. Injury 2021; 52:2434-2438. [PMID: 34158158 DOI: 10.1016/j.injury.2021.05.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/10/2021] [Accepted: 05/26/2021] [Indexed: 02/02/2023]
Abstract
AIMS National guidelines set standards for the definitive management of open fractures within 72 h. This study aims to investigate our outcomes where this timeline was unachievable for most cases due to a split-site orthoplastic service. PATIENTS & METHODS 116 consecutive Gustilo-Anderson grade IIIB & IIIC open tibial fractures presenting to our major trauma centre (MTC) between September 2012 and April 2018 were reviewed. The mean follow up was 46 months (17 to 88). 110 (95%) were grade IIIB and 6 (5%) grade IIIC. The most common injury mechanism included road traffic accidents (59%) and falls (28%). Primary outcomes were recorded according to; timing of initial debridement and definitive cover, rates of superficial and deep infection, non-union and amputation. Subgroups were statistically analysed according to time to initial debridement, definitive soft-tissue cover and injury severity score (ISS). RESULTS The mean time to initial debridement was 11.3 h (2.9 to 38.9) and definitive soft-tissue cover 9.9 days (0 to 37). We recorded rates of: superficial infection; 42 cases (36%), deep infection; 14 cases (12%) and non-union requiring revision; 19 cases (16%). There were 20 amputations (17%) with 9 (8.6%) performed early and 11 (9.5%) delayed. Subgroup analysis showed higher rates of superficial infection (50%, p = 0.002) and amputation (26.6%, p = 0.01) for those debrided <12 h. A greater presenting ISS related to a delay to definitive cover >7 days (p = 0.05). Primary outcomes trended worse for those covered >7 days but did not reach significance. CONCLUSION Major trauma patients are particularly vulnerable to poor outcomes resulting from the delay in definitive management of open fractures. MTC's need resources and a co-located orthoplastic service to achieve national standards and better outcomes. Current guidelines do not advise for the management of patients where a delay in definitive surgery is anticipated.
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Affiliation(s)
- Ryan Higgin
- Trauma & Orthopaedic Department, University Hospital Southampton, Tremona Road, Southampton SO16 6YD United Kingdom.
| | - Michael Dean
- Trauma & Orthopaedic Department, University Hospital Southampton, Tremona Road, Southampton SO16 6YD United Kingdom
| | - Amir Qureshi
- Trauma & Orthopaedic Department, University Hospital Southampton, Tremona Road, Southampton SO16 6YD United Kingdom.
| | - Nicholas Hancock
- Trauma & Orthopaedic Department, University Hospital Southampton, Tremona Road, Southampton SO16 6YD United Kingdom.
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Lei H, Gertz EM, Schäffer AA, Fu X, Tao Y, Heselmeyer-Haddad K, Torres I, Li G, Xu L, Hou Y, Wu K, Shi X, Dean M, Ried T, Schwartz R. Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data. Bioinformatics 2021; 37:4704-4711. [PMID: 34289030 PMCID: PMC8665747 DOI: 10.1093/bioinformatics/btab504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 05/19/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Computational reconstruction of clonal evolution in cancers has become a crucial tool for understanding how tumors initiate and progress and how this process varies across patients. The field still struggles, however, with special challenges of applying phylogenetic methods to cancers, such as the prevalence and importance of copy number alteration (CNA) and structural variation (SV) events in tumor evolution, which are difficult to profile accurately by prevailing sequencing methods in such a way that subsequent reconstruction by phylogenetic inference algorithms is accurate. RESULTS In the present work, we develop computational methods to combine sequencing with multiplex interphase fluorescence in situ hybridization (miFISH) to exploit the complementary advantages of each technology in inferring accurate models of clonal CNA evolution accounting for both focal changes and aneuploidy at whole-genome scales. By integrating such information in an integer linear programming (ILP) framework, we demonstrate on simulated data that incorporation of FISH data substantially improves accurate inference of focal CNA and ploidy changes in clonal evolution from deconvolving bulk sequence data. Analysis of real glioblastoma data for which FISH, bulk sequence, and single cell sequence are all available confirms the power of FISH to enhance accurate reconstruction of clonal copy number evolution in conjunction with bulk and optionally single-cell sequence data. AVAILABILITY Source code is available on Github at https://github.com/CMUSchwartzLab/FISH_deconvolution.
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Affiliation(s)
- Haoyun Lei
- Computational Biology Dept, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - E Michael Gertz
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xuecong Fu
- Shenzhen Luohu People's Hospital, Shenzhen, 518000, China
| | - Yifeng Tao
- Computational Biology Dept, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Irianna Torres
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Guibo Li
- Department of Biology, University of Copenhagen, Copenhagen, 1599, Denmark
| | - Liqin Xu
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Soltofts Plads, 2800 Kongens Lyngby, Denmark
| | - Yong Hou
- Department of Biology, University of Copenhagen, Copenhagen, 1599, Denmark
| | - Kui Wu
- Department of Biology, University of Copenhagen, Copenhagen, 1599, Denmark
| | - Xulian Shi
- Shenzhen Luohu People's Hospital, Shenzhen, 518000, China
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, U.S. National Institutes of Health, Gaithersburg, MD, 20814, USA
| | - Thomas Ried
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Russell Schwartz
- Computational Biology Dept, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Dept. of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
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Rossi N, Dean M. Abstract 48: Characterization of Human Papillomavirus (HPV) Sequence and Integration and Analysis of Immune Response Genes for Application in Guatemalan Cervical Cancer. Cancer Epidemiol Biomarkers Prev 2021. [DOI: 10.1158/1538-7755.asgcr21-48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Purpose: Cervical cancer is a significant cause of mortality in Guatemala due to inefficient screening and late diagnosis. We are developing new technologies to improve the analysis of HPV-positive cervical tumors in Guatemala. The goal is to enhance understanding of HPV infection, tumor progression, and therapeutics development.
Methods: We established a cohort of 700 Guatemalan cervical cancer patients with blood, fresh-frozen tumors, and clinical data. To optimize techniques, we extracted DNA and RNA from 20 cervical cancer cell lines. Long-read whole genome and transcriptome sequencing, and long-range PCR, were performed on cervical cancer DNA. HPV and HLA gene sequences were aligned to reference genomes.
Results: Complete HPV sequences were compiled, HPV subtypes determined, and integration sites identified in cell lines with single and multiple integration events. HLA types of the class I genes were determined from the complete gene sequence, mutations detected, and HLA homozygosity. RNA was used for long-read whole transcriptome analysis of HPV and cellular genes. These results establish the use of long-read sequencing technology to characterize both HLA and host genomes. Paired Guatemalan tumor and blood DNA was successfully used for full HLA gene sequencing and mutation analysis. In addition, the complete HPV genome sequence was resolved. Binding of HPV peptides was predicted using the HPV and HLA sequences. These peptides identify the specific HPV epitopes potentially presented on the cell surface.
Conclusion: Long-read RNA and DNA sequencing technology allow the determination of the complete HPV sequence, integration, and HLA class I typing and mutation analysis. HLA typing provides essential information on an individual's immune response. These techniques and analyses are being applied to tumor samples from women in Guatemala to aid in the development of targeted treatments. These methods are portable and could be employed in low- and middle-income countries.
Citation Format: Nicole Rossi, Michael Dean. Characterization of Human Papillomavirus (HPV) Sequence and Integration and Analysis of Immune Response Genes for Application in Guatemalan Cervical Cancer [abstract]. In: Proceedings of the 9th Annual Symposium on Global Cancer Research; Global Cancer Research and Control: Looking Back and Charting a Path Forward; 2021 Mar 10-11. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2021;30(7 Suppl):Abstract nr 48.
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Gonzalez N, Rao N, Dean M, Prokunina-Olsson L, Baris D, Schwenn M, Johnson A, Rothman N, Silverman D, Koutros S. Abstract 861: Diesel engine exhaust is associated with TP53 mutations and high-risk non-muscle invasive bladder cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Second to cigarette smoking, occupational exposures are a leading risk factor for the development of bladder cancer. Occupational exposure to diesel exhaust in particular has been linked to increased bladder cancer risk in several epidemiologic studies. To provide insight into possible mechanisms that influence this association, we examined the relationship between diesel exhaust and somatic mutations in bladder tumors.
Methods: Targeted sequencing of frequently mutated genes in bladder cancer was conducted in formalin-fixed paraffin-embedded bladder tumors from a population-based case-control study in New England. Lifetime occupational histories combined with exposure-oriented questions were used to estimate cumulative exposure to respirable elemental carbon (REC), a primary index for diesel exhaust. REC exposure was modeled both continuously (per 100 μg/m3-yrs) and categorically (by tertiles). Two-stage polytomous logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) to evaluate etiologic heterogeneity by tumor subtypes using data on 797 cases and 1,418 controls.
Results: We observed significant heterogeneity in the relationship between diesel exhaust and risk of bladder cancer by TP53 mutation status (p-heterogeneity=0.013). When comparing patients with TP53+ tumors to controls, there was a strong association with increasing cumulative REC exposure (ORTertile 1 vs. Unexposed=1.4, 95% CI=0.7, 2.8; ORTertile 2 vs. Unexposed=1.3, 95% CI=0.6, 2.7; ORTertile 3 vs. Unexposed=2.8, 95% CI=1.4, 5.7; p-trend=0.003), while there was no apparent association between cumulative REC exposure and bladder cancer among patients with wild-type TP53 tumors (p-trend=0.603). Subtype analyses that incorporate clinical features (stage: non-muscle invasive/muscle-invasive and grade: low-grade/high-grade) with TP53 mutation, also indicate etiologic heterogeneity in the relationship between diesel exhaust and bladder cancer (p-het=0.002), with the strongest association observed between increasing cumulative REC and risk of bladder cancer among cases with non-muscle invasive, high-grade tumors (including carcinoma in situ) with TP53 mutations (OR per 100 μg/m3-yrs =1.14, 95% CI=1.00, 1.29).
Conclusions: Our results suggest that diesel engine exhaust may influence bladder cancer risk by impacting the cell cycle, especially among patients with high-risk non-muscle invasive tumors that are more likely to progress to invasive disease. More work will be needed to understand the impact of diesel-generated oxidative stress on tumor suppressor genes like TP53 and cell cycle regulation in the development of bladder cancer.
Citation Format: Nicole Gonzalez, Nina Rao, Michael Dean, Ludmila Prokunina-Olsson, Dalsu Baris, Molly Schwenn, Alison Johnson, Nathaniel Rothman, Debra Silverman, Stella Koutros. Diesel engine exhaust is associated with TP53 mutations and high-risk non-muscle invasive bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 861.
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Affiliation(s)
| | - Nina Rao
- 1National Cancer Institute, Bethesda, MD
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Ren M, Orozco A, Shao K, Albanez A, Ortiz J, Cao B, Wang L, Barreda L, Alvarez CS, Garland L, Wu D, Chung CC, Wang J, Frone M, Ralon S, Argueta V, Orozco R, Gharzouzi E, Dean M. Germline variants in hereditary breast cancer genes are associated with early age at diagnosis and family history in Guatemalan breast cancer. Breast Cancer Res Treat 2021; 189:533-539. [PMID: 34196900 PMCID: PMC8357728 DOI: 10.1007/s10549-021-06305-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022]
Abstract
Purpose Mutations in hereditary breast cancer genes play an important role in the risk for cancer. Methods Cancer susceptibility genes were sequenced in 664 unselected breast cancer cases from Guatemala. Variants were annotated with ClinVar and VarSome. Results A total of 73 out of 664 subjects (11%) had a pathogenic variant in a high or moderate penetrance gene. The most frequently mutated genes were BRCA1 (37/664, 5.6%) followed by BRCA2 (15/664, 2.3%), PALB2 (5/664, 0.8%), and TP53 (5/664, 0.8%). Pathogenic variants were also detected in the moderate penetrance genes ATM, BARD1, CHEK2, and MSH6. The high ratio of BRCA1/BRCA2 mutations is due to two potential founder mutations: BRCA1 c.212 + 1G > A splice mutation (15 cases) and BRCA1 c.799delT (9 cases). Cases with pathogenic mutations had a significantly earlier age at diagnosis (45 vs 51 years, P < 0.001), are more likely to have had diagnosis before menopause, and a higher percentage had a relative with any cancer (51% vs 37%, P = 0.038) or breast cancer (33% vs 15%, P < 0.001). Conclusions Hereditary breast cancer mutations were observed among Guatemalan women, and these women are more likely to have early age at diagnosis and family history of cancer. These data suggest the use of genetic testing in breast cancer patients and those at high risk as part of a strategy to reduce breast cancer mortality in Guatemala. Supplementary Information The online version contains supplementary material available at 10.1007/s10549-021-06305-5.
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Affiliation(s)
- Megan Ren
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, USA
| | - Anali Orozco
- Instituto Cancerologia, Guatemala City, Guatemala
| | - Kang Shao
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, People's Republic of China
| | | | - Jeremy Ortiz
- Instituto Cancerologia, Guatemala City, Guatemala
| | - Boyang Cao
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, People's Republic of China
| | - Lusheng Wang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, People's Republic of China.,Department of Computer Science, City University of Hong Kong, Kowloon, SAR, Hong Kong, People's Republic of China
| | - Lilian Barreda
- Hospital General San Juan de Dios, Guatemala City, Guatemala
| | - Christian S Alvarez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, USA
| | - Lisa Garland
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Gaithersburg, MD, USA
| | - Dongjing Wu
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Gaithersburg, MD, USA
| | - Charles C Chung
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Gaithersburg, MD, USA.,Office of Biostatistics and Epidemiology (OBE), Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Silver Spring, MD , 20993-0002, USA
| | - Jiahui Wang
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Gaithersburg, MD, USA
| | - Megan Frone
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, USA
| | - Sergio Ralon
- Hospital General San Juan de Dios, Guatemala City, Guatemala
| | - Victor Argueta
- Hospital General San Juan de Dios, Guatemala City, Guatemala
| | - Roberto Orozco
- Hospital General San Juan de Dios, Guatemala City, Guatemala.
| | | | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, USA.
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Alvarez CS, Hernández E, Escobar K, Villagrán CI, Kroker-Lobos MF, Rivera-Andrade A, Smith JW, Egner PA, Lazo M, Freedman ND, Guallar E, Dean M, Graubard BI, Groopman JD, Ramírez-Zea M, McGlynn KA. Aflatoxin B 1 exposure and liver cirrhosis in Guatemala: a case-control study. BMJ Open Gastroenterol 2021; 7:bmjgast-2020-000380. [PMID: 32641287 PMCID: PMC7342465 DOI: 10.1136/bmjgast-2020-000380] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023] Open
Abstract
Objective In Guatemala, cirrhosis is among the 10 leading causes of death, and mortality rates have increased lately. The reasons for this heavy burden of disease are not clear as the prevalence of prominent risk factors, such as hepatitis B virus, hepatitis C virus and heavy alcohol consumption, appears to be low. Aflatoxin B1 (AFB1) exposure, however, appears to be high, and thus could be associated with the high burden of cirrhosis. Whether AFB1 increases the risk of cirrhosis in the absence of viral infection, however, is not clear. Design Cirrhosis cases (n=100) from two major referral hospitals in Guatemala City were compared with controls (n=200) from a cross-sectional study. Logistic regression was used to estimate the ORs and 95% CIs of cirrhosis and quintiles of AFB1 in crude and adjusted models. A sex-stratified analysis was also conducted. Results The median AFB1 level was significantly higher among the cases (11.4 pg/mg) than controls (5.11 pg/mg). In logistic regression analyses, higher levels of AFB1 was associated with cirrhosis (quintile 5 vs quintile 1, OR: 11.55; 95% CI 4.05 to 32.89). No attenuation was observed with adjustment by sex, ethnicity, hepatitis B virus status, and heavy alcohol consumption. A significantly increasing trend in association was observed in both models (p trend <0.01). Additionally, the cirrhosis–AFB1 association was more prominent among men. Conclusions The current study found a significant positive association between AFB1 exposure and cirrhosis. Mitigation of AFB1 exposure and a better understanding of additional risk factors may be important to reduce the burden of cirrhosis in Guatemala.
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Affiliation(s)
- Christian S Alvarez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Elisa Hernández
- Centro de Investigaciones Biomédicas, Facultad de Ciencias Médicas, Universidad de San Carlos de Guatemala, Guatemala, Guatemala
| | - Kira Escobar
- Centro de Investigaciones Biomédicas, Facultad de Ciencias Médicas, Universidad de San Carlos de Guatemala, Guatemala, Guatemala
| | - Carmen I Villagrán
- Centro de Investigaciones Biomédicas, Facultad de Ciencias Médicas, Universidad de San Carlos de Guatemala, Guatemala, Guatemala
| | - María F Kroker-Lobos
- INCAP Research Center for the Prevention of Chronic Diseases, Institute of Nutrition of Central America and Panama, Guatemala, Guatemala
| | - Alvaro Rivera-Andrade
- INCAP Research Center for the Prevention of Chronic Diseases, Institute of Nutrition of Central America and Panama, Guatemala, Guatemala
| | - Joshua W Smith
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Patricia A Egner
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Mariana Lazo
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Eliseo Guallar
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Barry I Graubard
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - John D Groopman
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Manuel Ramírez-Zea
- INCAP Research Center for the Prevention of Chronic Diseases, Institute of Nutrition of Central America and Panama, Guatemala, Guatemala
| | - Katherine A McGlynn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
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39
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Moore A, Machiela MJ, Machado M, Wang SS, Kane E, Slager SL, Zhou W, Carrington M, Lan Q, Milne RL, Birmann BM, Adami HO, Albanes D, Arslan AA, Becker N, Benavente Y, Bisanzi S, Boffetta P, Bracci PM, Brennan P, Brooks-Wilson AR, Canzian F, Caporaso N, Clavel J, Cocco P, Conde L, Cox DG, Cozen W, Curtin K, De Vivo I, de Sanjose S, Foretova L, Gapstur SM, Ghesquières H, Giles GG, Glenn M, Glimelius B, Gao C, Habermann TM, Hjalgrim H, Jackson RD, Liebow M, Link BK, Maynadie M, McKay J, Melbye M, Miligi L, Molina TJ, Monnereau A, Nieters A, North KE, Offit K, Patel AV, Piro S, Ravichandran V, Riboli E, Salles G, Severson RK, Skibola CF, Smedby KE, Southey MC, Spinelli JJ, Staines A, Stewart C, Teras LR, Tinker LF, Travis RC, Vajdic CM, Vermeulen RCH, Vijai J, Weiderpass E, Weinstein S, Doo NW, Zhang Y, Zheng T, Chanock SJ, Rothman N, Cerhan JR, Dean M, Camp NJ, Yeager M, Berndt SI. Genome-wide homozygosity and risk of four non-Hodgkin lymphoma subtypes. J Transl Genet Genom 2021; 5:200-217. [PMID: 34622145 PMCID: PMC8494431 DOI: 10.20517/jtgg.2021.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
AIM Recessive genetic variation is thought to play a role in non-Hodgkin lymphoma (NHL) etiology. Runs of homozygosity (ROH), defined based on long, continuous segments of homozygous SNPs, can be used to estimate both measured and unmeasured recessive genetic variation. We sought to examine genome-wide homozygosity and NHL risk. METHODS We used data from eight genome-wide association studies of four common NHL subtypes: 3061 chronic lymphocytic leukemia (CLL), 3814 diffuse large B-cell lymphoma (DLBCL), 2784 follicular lymphoma (FL), and 808 marginal zone lymphoma (MZL) cases, as well as 9374 controls. We examined the effect of homozygous variation on risk by: (1) estimating the fraction of the autosome containing runs of homozygosity (FROH); (2) calculating an inbreeding coefficient derived from the correlation among uniting gametes (F3); and (3) examining specific autosomal regions containing ROH. For each, we calculated beta coefficients and standard errors using logistic regression and combined estimates across studies using random-effects meta-analysis. RESULTS We discovered positive associations between FROH and CLL (β = 21.1, SE = 4.41, P = 1.6 × 10-6) and FL (β = 11.4, SE = 5.82, P = 0.02) but not DLBCL (P = 1.0) or MZL (P = 0.91). For F3, we observed an association with CLL (β = 27.5, SE = 6.51, P = 2.4 × 10-5). We did not find evidence of associations with specific ROH, suggesting that the associations observed with FROH and F3 for CLL and FL risk were not driven by a single region of homozygosity. CONCLUSION Our findings support the role of recessive genetic variation in the etiology of CLL and FL; additional research is needed to identify the specific loci associated with NHL risk.
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Affiliation(s)
- Amy Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Moara Machado
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Sophia S Wang
- Division of Health Analytics, City of Hope Beckman Research Institute, Duarte, CA 91010, USA
| | - Eleanor Kane
- Department of Health Sciences, University of York, York YO10 5DD, UK
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD 20877, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD 20892, USA
- Ragon Institute of MGH, Cambridge, MA 02139, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria 3800, Australia
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17176, Sweden
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Institute of Health and Society, Clinical Effectiveness Research Group, University of Oslo, Oslo 0315, Norway
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alan A Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, NY 10016, USA
- Department of Population Health, New York University School of Medicine, New York, NY 10016, USA
- Perlmutter Comprehensive Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Nikolaus Becker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg 69120, Germany
| | - Yolanda Benavente
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona 08036, Spain
| | - Simonetta Bisanzi
- Regional Cancer Prevention Laboratory, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence 50139, Italy
| | - Paolo Boffetta
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Medical and Surgical Sciences, University of Bologna, Bologna 41026, Italy
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94118, USA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon 69372, France
| | - Angela R Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z1L3, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jacqueline Clavel
- Center of Research in Epidemiology and Statistics Sorbonne Paris Cité (CRESS), UMR1153, INSERM, Villejuif 75004, France
| | - Pierluigi Cocco
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - David G Cox
- INSERM U1052, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon 69008, France
| | - Wendy Cozen
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Karen Curtin
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Immaculata De Vivo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Silvia de Sanjose
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona 08036, Spain
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno 656 53, Czech Republic
| | - Susan M Gapstur
- Department of Population Science, American Cancer Society, Atlanta, GA 30303, USA
| | - Hervè Ghesquières
- Department of Hematology, Centre Léon Bérard, Lyon 69008, France
- INSERM U1052, Cancer Research Center of Lyon, Lyon-1 University, Pierre-Bénite Cedex 69008, France
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria 3800, Australia
| | - Martha Glenn
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75105, Sweden
| | - Chi Gao
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Henrik Hjalgrim
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen 2300, Denmark
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH 43210, USA
| | - Mark Liebow
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Brian K Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Marc Maynadie
- U1231, Registre des Hémopathies Malignes de Côte d'Or, University of Burgundy and Dijon University Hospital, Dijon 21070, France
| | - James McKay
- International Agency for Research on Cancer (IARC), Lyon 69372, France
| | - Mads Melbye
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen 2300, Denmark
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lucia Miligi
- Environmental and Occupational Epidemiology Branch-Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence 50139, Italy
| | - Thierry J Molina
- Department of Pathology, AP-HP, Necker Enfants Malades, Université Paris Descartes, EA 7324, Sorbonne Paris Cité 75015, France
| | - Alain Monnereau
- Center of Research in Epidemiology and Statistics Sorbonne Paris Cité (CRESS), UMR1153, INSERM, Villejuif 75004, France
- Registre des Hémopathies Malignes de la Gironde, Institut Bergonié, Bordeaux Cedex 33076, France
| | - Alexandra Nieters
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Baden-Württemberg 79108, Germany
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alpa V Patel
- Department of Population Science, American Cancer Society, Atlanta, GA 30303, USA
| | - Sara Piro
- Environmental and Occupational Epidemiology Branch-Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence 50139, Italy
| | - Vignesh Ravichandran
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London W2 1PG, UK
| | - Gilles Salles
- INSERM U1052, Cancer Research Center of Lyon, Lyon-1 University, Pierre-Bénite Cedex 69008, France
- Department of Hematology, Hospices Civils de Lyon, Pierre Benite Cedex 69495, France
- Department of Hematology, Université Lyon-1, Pierre Benite Cedex 69495, France
| | - Richard K Severson
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Christine F Skibola
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Karin E Smedby
- Department of Medicine, Solna, Karolinska Institutet, Stockholm 17176, Sweden
- Hematology Center, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - John J Spinelli
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia V5Z1L3, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada
| | - Anthony Staines
- School of Nursing, Psychotherapy and Community Health, Dublin City University, Dublin 9, Ireland
| | - Carolyn Stewart
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA 30303, USA
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98117, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Claire M Vajdic
- Centre for Big Data Research in Health, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Roel C H Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CG, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nicole Wong Doo
- Concord Clinical School, University of Sydney, Concord, New South Wales 2139, Australia
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06520, USA
| | - Tongzhang Zheng
- Department of Epidemiology, Brown University, Providence, RI 02903, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD 20877, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
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40
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Nepal C, Zhu B, O’Rourke CJ, Bhatt DK, Lee D, Song L, Wang D, Van Dyke A, Choo-Wosoba H, Liu Z, Hildesheim A, Goldstein AM, Dean M, LaFuente-Barquero J, Lawrence S, Mutreja K, Olanich ME, Bermejo JL, Ferreccio C, Roa JC, Rashid A, Hsing AW, Gao YT, Chanock SJ, Araya JC, Andersen JB, Koshiol J. Integrative molecular characterisation of gallbladder cancer reveals micro-environment-associated subtypes. J Hepatol 2021; 74:1132-1144. [PMID: 33276026 PMCID: PMC8058239 DOI: 10.1016/j.jhep.2020.11.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/21/2020] [Accepted: 11/16/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Gallbladder cancer (GBC) is the most common type of biliary tract cancer, but the molecular mechanisms involved in gallbladder carcinogenesis remain poorly understood. In this study, we applied integrative genomics approaches to characterise GBC and explore molecular subtypes associated with patient survival. METHODS We profiled the mutational landscape of GBC tumours (whole-exome sequencing on 92, targeted sequencing on 98, in total 190 patients). In a subset (n = 45), we interrogated the matched transcriptomes, DNA methylomes, and somatic copy number alterations. We explored molecular subtypes identified through clustering tumours by genes whose expression was associated with survival in 47 tumours and validated subtypes on 34 publicly available GBC cases. RESULTS Exome analysis revealed TP53 was the most mutated gene. The overall mutation rate was low (median 0.82 Mut/Mb). APOBEC-mediated mutational signatures were more common in tumours with higher mutational burden. Aflatoxin-related signatures tended to be highly clonal (present in ≥50% of cancer cells). Transcriptome-wide survival association analysis revealed a 95-gene signature that stratified all GBC patients into 3 subtypes that suggested an association with overall survival post-resection. The 2 poor-survival subtypes were associated with adverse clinicopathologic features (advanced stage, pN1, pM1), immunosuppressive micro-environments (myeloid-derived suppressor cell accumulation, extensive desmoplasia, hypoxia) and T cell dysfunction, whereas the good-survival subtype showed the opposite features. CONCLUSION These data suggest that the tumour micro-environment and immune profiles could play an important role in gallbladder carcinogenesis and should be evaluated in future clinical studies, along with mutational profiles. LAY SUMMARY Gallbladder cancer is highly fatal, and its causes are poorly understood. We evaluated gallbladder tumours to see if there were differences between tumours in genetic information such as DNA and RNA. We found evidence of aflatoxin exposure in these tumours, and immune cells surrounding the tumours were associated with survival.
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Affiliation(s)
- Chirag Nepal
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, NIH, USA
| | - Colm J O’Rourke
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Deepak Kumar Bhatt
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Donghyuk Lee
- Division of Cancer Epidemiology and Genetics, NIH, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, NIH, USA
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, NIH, USA
| | | | | | - Zhiwei Liu
- Division of Cancer Epidemiology and Genetics, NIH, USA
| | | | | | - Michael Dean
- Division of Cancer Epidemiology and Genetics, NIH, USA
| | - Juan LaFuente-Barquero
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Scott Lawrence
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Karun Mutreja
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mary E Olanich
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | - Catterina Ferreccio
- Department of Public Health, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, 8330077 Chile and Advanced Center for Chronic Diseases (ACCDiS), FONDAP, Santiago, 8380492 Chile
| | - Juan Carlos Roa
- Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, 8330024 Chile
| | - Asif Rashid
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ann W Hsing
- Stanford Cancer Institute and Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford, California, USA
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | | | - Juan Carlos Araya
- Hospital Dr. Hernán Henríquez Aravena, Temuco, 4780000 Chile,Department of Pathology, Faculty of Medicine, Universidad de La Frontera, Temuco, 4780000 Chile,Advanced Center for Chronic Diseases (ACCDiS), FONDAP, Santiago, 8380492 Chile
| | - Jesper B Andersen
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Denmark.
| | - Jill Koshiol
- Division of Cancer Epidemiology and Genetics, NIH, Rockville, MD, USA.
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41
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Yeager M, Machiela MJ, Kothiyal P, Dean M, Bodelon C, Suman S, Wang M, Mirabello L, Nelson CW, Zhou W, Palmer C, Ballew B, Colli LM, Freedman ND, Dagnall C, Hutchinson A, Vij V, Maruvka Y, Hatch M, Illienko I, Belayev Y, Nakamura N, Chumak V, Bakhanova E, Belyi D, Kryuchkov V, Golovanov I, Gudzenko N, Cahoon EK, Albert P, Drozdovitch V, Little MP, Mabuchi K, Stewart C, Getz G, Bazyka D, Berrington de Gonzalez A, Chanock SJ. Lack of transgenerational effects of ionizing radiation exposure from the Chernobyl accident. Science 2021; 372:725-729. [PMID: 33888597 DOI: 10.1126/science.abg2365] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/12/2021] [Indexed: 12/15/2022]
Abstract
Effects of radiation exposure from the Chernobyl nuclear accident remain a topic of interest. We investigated germline de novo mutations (DNMs) in children born to parents employed as cleanup workers or exposed to occupational and environmental ionizing radiation after the accident. Whole-genome sequencing of 130 children (born 1987-2002) and their parents did not reveal an increase in the rates, distributions, or types of DNMs relative to the results of previous studies. We find no elevation in total DNMs, regardless of cumulative preconception gonadal paternal [mean = 365 milligrays (mGy), range = 0 to 4080 mGy] or maternal (mean = 19 mGy, range = 0 to 550 mGy) exposure to ionizing radiation. Thus, we conclude that, over this exposure range, evidence is lacking for a substantial effect on germline DNMs in humans, suggesting minimal impact from transgenerational genetic effects.
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Affiliation(s)
- Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA. .,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Prachi Kothiyal
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA.,SymbioSeq LLC, Arlington, VA 20148, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Clara Bodelon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Shalabh Suman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Mingyi Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Chase W Nelson
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.,Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Cameron Palmer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Bari Ballew
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Leandro M Colli
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA.,Department of Medical Imaging, Hematology, and Oncology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, 14049-900, Brazil
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Casey Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Vibha Vij
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Yosi Maruvka
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Maureen Hatch
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Iryna Illienko
- National Research Centre for Radiation Medicine, 53 Yu. Illienka Street, Kyiv, 04050, Ukraine
| | - Yuri Belayev
- National Research Centre for Radiation Medicine, 53 Yu. Illienka Street, Kyiv, 04050, Ukraine
| | - Nori Nakamura
- Department of Molecular Biosciences, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima, 732-0815, Japan
| | - Vadim Chumak
- National Research Centre for Radiation Medicine, 53 Yu. Illienka Street, Kyiv, 04050, Ukraine
| | - Elena Bakhanova
- National Research Centre for Radiation Medicine, 53 Yu. Illienka Street, Kyiv, 04050, Ukraine
| | - David Belyi
- National Research Centre for Radiation Medicine, 53 Yu. Illienka Street, Kyiv, 04050, Ukraine
| | - Victor Kryuchkov
- Burnasyan Federal Medical and Biophysical Centre, 46 Zhivopisnaya Street, Moscow, 123182, Russia
| | - Ivan Golovanov
- Burnasyan Federal Medical and Biophysical Centre, 46 Zhivopisnaya Street, Moscow, 123182, Russia
| | - Natalia Gudzenko
- National Research Centre for Radiation Medicine, 53 Yu. Illienka Street, Kyiv, 04050, Ukraine
| | - Elizabeth K Cahoon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Paul Albert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Vladimir Drozdovitch
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Mark P Little
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Kiyohiko Mabuchi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Chip Stewart
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Gad Getz
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Dimitry Bazyka
- National Research Centre for Radiation Medicine, 53 Yu. Illienka Street, Kyiv, 04050, Ukraine
| | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA.
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42
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Koutros S, Rao N, Moore LE, Nickerson ML, Lee D, Zhu B, Pardo LA, Baris D, Schwenn M, Johnson A, Jones K, Garcia-Closas M, Prokunina-Olsson L, Silverman DT, Rothman N, Dean M. Targeted Deep Sequencing of Bladder Tumors Reveals Novel Associations between Cancer Gene Mutations and Mutational Signatures with Major Risk Factors. Clin Cancer Res 2021; 27:3725-3733. [PMID: 33849962 DOI: 10.1158/1078-0432.ccr-20-4419] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/26/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Exome- and whole-genome sequencing of muscle-invasive bladder cancer has revealed important insights into the molecular landscape; however, there are few studies of non-muscle-invasive bladder cancer with detailed risk factor information. EXPERIMENTAL DESIGN We examined the relationship between smoking and other bladder cancer risk factors and somatic mutations and mutational signatures in bladder tumors. Targeted sequencing of frequently mutated genes in bladder cancer was conducted in 322 formalin-fixed paraffin-embedded bladder tumors from a population-based case-control study. Logistic regression was used to calculate odds ratios (OR) and 95% confidence intervals (CI), evaluating mutations and risk factors. We used SignatureEstimation to extract four known single base substitution mutational signatures and Poisson regression to calculate risk ratios (RR) and 95% CIs, evaluating signatures and risk factors. RESULTS Non-silent KDM6A mutations were more common in females than males (OR = 1.83; 95% CI, 1.05-3.19). There was striking heterogeneity in the relationship between smoking status and established single base substitution signatures: current smoking status was associated with greater ERCC2-Signature mutations compared with former (P = 0.024) and never smoking (RR = 1.40; 95% CI, 1.09-1.80; P = 0.008), former smoking was associated with greater APOBEC-Signature13 mutations (P = 0.05), and never smoking was associated with greater APOBEC-Signature2 mutations (RR = 1.54; 95% CI, 1.17-2.01; P = 0.002). There was evidence that smoking duration (the component most strongly associated with bladder cancer risk) was associated with ERCC2-Signature mutations and APOBEC-Signature13 mutations among current (P trend = 0.005) and former smokers (P = 0.0004), respectively. CONCLUSIONS These data quantify the contribution of bladder cancer risk factors to mutational burden and suggest different signature enrichments among never, former, and current smokers.
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Affiliation(s)
- Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland.
| | - Nina Rao
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Lee E Moore
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Michael L Nickerson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Donghyuk Lee
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Bin Zhu
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Larissa A Pardo
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Dalsu Baris
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | | | | | - Kristine Jones
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland
| | - Montserrat Garcia-Closas
- Office of the Director, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Debra T Silverman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland.,Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Bethesda, Maryland
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43
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Groopman JD, Smith JW, Rivera-Andrade A, Alvarez CS, Kroker-Lobos MF, Egner PA, Gharzouzi E, Dean M, McGlynn KA, Ramírez-Zea M. Aflatoxin and the Etiology of Liver Cancer and Its Implications for Guatemala. WORLD MYCOTOXIN J 2021; 14:305-317. [PMID: 35096197 PMCID: PMC8797158 DOI: 10.3920/wmj2020.2641] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
During the 60 years since the first scientific reports about a relation between aflatoxin exposure and adverse health consequences, both in animals and humans, there has been a remarkable number of basic, clinical and population science studies characterizing the impact of this mycotoxin on diseases such as liver cancer. Many of these human investigations to date have focused on populations residing in Asia and Africa due to the high incidence of liver cancer and high exposures to aflatoxin. These studies formed the basis for the International Agency for Research on Cancer to classify the aflatoxins as Group 1 known human carcinogens. In addition, aflatoxin contamination levels have been used in international commodity trade to set the price of various staples such as maize and groundnuts. While there have been many case-control and prospective cohort studies of liver cancer risk over the years there have been remarkably few investigations focused on liver cancer in Latin America. Our interdisciplinary and multiple institutional collaborative has been developing a long-term strategy to characterize the role of aflatoxin and other mycotoxins as health risk factors in Guatemala and neighboring countries. This paper summarizes a number of the investigations to date and provides a roadmap of our strategies for the near term to discern the emergent etiology of liver cancer in this region. With these data in hand public health-based prevention strategies could be strategically implemented and conducted to lower the impact of these mycotoxins on human health.
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Affiliation(s)
- John D. Groopman
- Departments of Environmental Health and Engineering and Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, U.S.A
| | - Joshua W. Smith
- Departments of Environmental Health and Engineering and Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, U.S.A
| | - Alvaro Rivera-Andrade
- INCAP Research Center for the Prevention of Chronic Diseases, Institute of Nutrition of Central America and Panama, Guatemala City, Guatemala
| | - Christian S. Alvarez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, U.S.A
| | - María F. Kroker-Lobos
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, U.S.A
| | - Patricia A. Egner
- Departments of Environmental Health and Engineering and Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, U.S.A
| | | | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, U.S.A
| | - Katherine A. McGlynn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, U.S.A
| | - Manuel Ramírez-Zea
- INCAP Research Center for the Prevention of Chronic Diseases, Institute of Nutrition of Central America and Panama, Guatemala City, Guatemala
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44
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Kim J, Gianferante M, Karyadi DM, Hartley SW, Frone MN, Luo W, Robison LL, Armstrong GT, Bhatia S, Dean M, Yeager M, Zhu B, Song L, Sampson JN, Yasui Y, Leisenring WM, Brodie SA, de Andrade KC, Fortes FP, Goldstein AM, Khincha PP, Machiela MJ, McMaster ML, Nickerson ML, Oba L, Pemov A, Pinheiro M, Rotunno M, Santiago K, Wegman-Ostrosky T, Diver WR, Teras L, Freedman ND, Hicks BD, Zhu B, Wang M, Jones K, Hutchinson AA, Dagnall C, Savage SA, Tucker MA, Chanock SJ, Morton LM, Stewart DR, Mirabello L. Frequency of Pathogenic Germline Variants in Cancer-Susceptibility Genes in the Childhood Cancer Survivor Study. JNCI Cancer Spectr 2021; 5:pkab007. [PMID: 34308104 PMCID: PMC8023430 DOI: 10.1093/jncics/pkab007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/01/2020] [Accepted: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Background Pediatric cancers are the leading cause of death by disease in children despite improved survival rates overall. The contribution of germline genetic susceptibility to pediatric cancer survivors has not been extensively characterized. We assessed the frequency of pathogenic or likely pathogenic (P/LP) variants in 5451 long-term pediatric cancer survivors from the Childhood Cancer Survivor Study. Methods Exome sequencing was conducted on germline DNA from 5451 pediatric cancer survivors (cases who survived ≥5 years from diagnosis; n = 5105 European) and 597 European cancer-free adults (controls). Analyses focused on comparing the frequency of rare P/LP variants in 237 cancer-susceptibility genes and a subset of 60 autosomal dominant high-to-moderate penetrance genes, for both case-case and case-control comparisons. Results Of European cases, 4.1% harbored a P/LP variant in high-to-moderate penetrance autosomal dominant genes compared with 1.3% in controls (2-sided P = 3 × 10-4). The highest frequency of P/LP variants was in genes typically associated with adult onset rather than pediatric cancers, including BRCA1/2, FH, PALB2, PMS2, and CDKN2A. A statistically significant excess of P/LP variants, after correction for multiple tests, was detected in patients with central nervous system cancers (NF1, SUFU, TSC1, PTCH2), Wilms tumor (WT1, REST), non-Hodgkin lymphoma (PMS2), and soft tissue sarcomas (SDHB, DICER1, TP53, ERCC4, FGFR3) compared with other pediatric cancers. Conclusion In long-term pediatric cancer survivors, we identified P/LP variants in cancer-susceptibility genes not previously associated with pediatric cancer as well as confirmed known associations. Further characterization of variants in these genes in pediatric cancer will be important to provide optimal genetic counseling for patients and their families.
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Affiliation(s)
- Jung Kim
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Matthew Gianferante
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Danielle M Karyadi
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Stephen W Hartley
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Megan N Frone
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Wen Luo
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St.
Jude Children’s Research Hospital, Memphis, TN, USA
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St.
Jude Children’s Research Hospital, Memphis, TN, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship,
University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St.
Jude Children’s Research Hospital, Memphis, TN, USA
| | - Wendy M Leisenring
- Cancer Prevention and Clinical Statistics Programs,
Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Seth A Brodie
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kelvin C de Andrade
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Fernanda P Fortes
- International Research Center, A.C. Camargo Cancer
Center, São Paulo, Brazil
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Payal P Khincha
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Mary L McMaster
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Michael L Nickerson
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Leatrisse Oba
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Alexander Pemov
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Melissa Rotunno
- Division of Cancer Control and Population Sciences,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Karina Santiago
- International Research Center, A.C. Camargo Cancer
Center, São Paulo, Brazil
| | - Talia Wegman-Ostrosky
- Basic Research Subdirection, Instituto Nacional de
Cancerología (INCan), Mexico City, Mexico
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer
Society, Atlanta, GA, USA
| | - Lauren Teras
- Epidemiology Research Program, American Cancer
Society, Atlanta, GA, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy A Hutchinson
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Casey Dagnall
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
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45
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Gouveia MH, Borda V, Leal TP, Moreira RG, Bergen AW, Kehdy FSG, Alvim I, Aquino MM, Araujo GS, Araujo NM, Furlan V, Liboredo R, Machado M, Magalhaes WCS, Michelin LA, Rodrigues MR, Rodrigues-Soares F, Sant Anna HP, Santolalla ML, Scliar MO, Soares-Souza G, Zamudio R, Zolini C, Bortolini MC, Dean M, Gilman RH, Guio H, Rocha J, Pereira AC, Barreto ML, Horta BL, Lima-Costa MF, Mbulaiteye SM, Chanock SJ, Tishkoff SA, Yeager M, Tarazona-Santos E. Origins, Admixture Dynamics, and Homogenization of the African Gene Pool in the Americas. Mol Biol Evol 2021; 37:1647-1656. [PMID: 32128591 DOI: 10.1093/molbev/msaa033] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The Transatlantic Slave Trade transported more than 9 million Africans to the Americas between the early 16th and the mid-19th centuries. We performed a genome-wide analysis using 6,267 individuals from 25 populations to infer how different African groups contributed to North-, South-American, and Caribbean populations, in the context of geographic and geopolitical factors, and compared genetic data with demographic history records of the Transatlantic Slave Trade. We observed that West-Central Africa and Western Africa-associated ancestry clusters are more prevalent in northern latitudes of the Americas, whereas the South/East Africa-associated ancestry cluster is more prevalent in southern latitudes of the Americas. This pattern results from geographic and geopolitical factors leading to population differentiation. However, there is a substantial decrease in the between-population differentiation of the African gene pool within the Americas, when compared with the regions of origin from Africa, underscoring the importance of historical factors favoring admixture between individuals with different African origins in the New World. This between-population homogenization in the Americas is consistent with the excess of West-Central Africa ancestry (the most prevalent in the Americas) in the United States and Southeast-Brazil, with respect to historical-demography expectations. We also inferred that in most of the Americas, intercontinental admixture intensification occurred between 1750 and 1850, which correlates strongly with the peak of arrivals from Africa. This study contributes with a population genetics perspective to the ongoing social, cultural, and political debate regarding ancestry, admixture, and the mestizaje process in the Americas.
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Affiliation(s)
- Mateus H Gouveia
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Instituto de Pesquisa Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, MG, Brazil.,Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD
| | - Victor Borda
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Thiago P Leal
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Departamento de Estatística, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rennan G Moreira
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Laboratório de Genômica, Centro de Laboratórios Multiusuário (CELAM), ICB, UFMG, Belo Horizonte, MG, Brazil
| | - Andrew W Bergen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD
| | - Fernanda S G Kehdy
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Laboratório de Hanseníase, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Isabela Alvim
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marla M Aquino
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gilderlanio S Araujo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará - Campus Guamá, Belém, PA, Brazil
| | - Nathalia M Araujo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Vinicius Furlan
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Instituto de Ciências Exatas e Tecnológicas, Universidade Federal de Viçosa, Campus UFV-Florestal, Florestal, MG, Brazil
| | - Raquel Liboredo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Moara Machado
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Wagner C S Magalhaes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Núcleo de Ensino e Pesquisas do Instituto Mário Penna - NEP-IMP, Bairro Luxemburgo, Belo Horizonte, MG, Brazil
| | - Lucas A Michelin
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maíra R Rodrigues
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Fernanda Rodrigues-Soares
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Hanaisa P Sant Anna
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Melbourne Integrative Genomics, The University of Melbourne, Melbourne, VIC, Australia
| | - Meddly L Santolalla
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marília O Scliar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Giordano Soares-Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Roxana Zamudio
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Camila Zolini
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Beagle, Belo Horizonte, MG, Brazil.,Mosaico Translational Genomics Initiative, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maria Catira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Michael Dean
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Robert H Gilman
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD.,Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Jorge Rocha
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,CIBIO/InBIO: Research Center in Biodiversity and Genetic Resources, Vairão, Portugal
| | | | - Mauricio L Barreto
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, BA, Brazil.,Center of Data and Knowledge Integration for Health (CIDACS), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil
| | - Bernardo L Horta
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Maria F Lima-Costa
- Instituto de Pesquisa Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, MG, Brazil
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD
| | - Sarah A Tishkoff
- Department of Genetics and Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Mosaico Translational Genomics Initiative, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Universidad Peruana Cayetano Heredia, Lima, Peru.,Instituto de Estudos Avançados Transdisciplinares, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Mejia A, Arias Perez W, Zambrano Y, Gómez Pulgarín S, Tejada Moreno J, Gónzales L, Jaramillo R, Rodas Y, Navarro E, Ossa A, Borrero M, Angel G, Cock-Rada A, Rinaldi S, Romieu I, Dean M, Sanchez G. Frequency and spectrum of mutations in the BRCA1, BRCA2, PALB2, P53, PTEN, CHEK2, CDH1 genes in women from 3 cities of Colombia. Breast 2021. [DOI: 10.1016/s0960-9776(21)00259-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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47
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Gibson A, Tudor R, Dean M, Elegbede A, D'Silva A, Hao D, Bebb D. P89.12 Real World Outcomes in EGFR-Mutant Relapsed and De Novo Stage IV Non-Small Cell Lung Cancer (NSCLC). J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.1278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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48
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Anaka M, Gibson A, Dean M, Elegbede A, Petersen L, Tudor R, Sangha R, Bebb D. FP02.03 Changing Survival and Treatment Patterns in Patients Aged 80 or Older with Stage IV Non-Small Cell Lung Cancer (NSCLC). J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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49
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Elegbede A, Gibson A, Dean M, Box A, Bebb D. P36.05 Metastatic NSCLC Outcomes With Guideline-Recommended Treatment By KRAS Subtype. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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50
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Elegbede A, Gibson A, Dean M, Bebb D. P50.01 A Year Experience With Atezolizumab Plus Chemotherapy For Small Cell Lung Cancer In Alberta, Canada. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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