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Song Y, Loomans-Kropp H, Baugher RN, Somerville B, Baxter SS, Kerr TD, Plona TM, Mellott SD, Young TB, Lawhorn HE, Wei L, Hu Q, Liu S, Hutson A, Pinto L, Potter JD, Sei S, Gelincik O, Lipkin SM, Gebert J, Kloor M, Shoemaker RH. Frameshift mutations in peripheral blood as a biomarker for surveillance of lynch syndrome. J Natl Cancer Inst 2024:djae060. [PMID: 38466935 DOI: 10.1093/jnci/djae060] [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] [Received: 12/04/2023] [Revised: 02/06/2024] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Lynch syndrome (LS) is a hereditary cancer predisposition syndrome caused by germline mutations in DNA mismatch repair (MMR) genes, which lead to high microsatellite instability (MSI-H) and frameshift mutations (FSMs) at coding mononucleotide repeats (cMNRs) in the genome. Recurrent FSMs in these regions are thought to play a central role in the increased risk of various cancers. However, there are no biomarkers currently available for the surveillance of MSI-H-associated cancers. METHODS An FSM-based biomarker panel was developed and validated by targeted next generation sequencing of supernatant DNA from cultured MSI-H colorectal cancer cells. This supported selection of 122-FSM targets as potential biomarkers. This biomarker panel was then tested using matched tumor, adjacent normal tissue, and buffy coat (53 samples), and blood-derived cell-free DNA (cfDNA; 38 samples) obtained from 45 cases of MSI-H/MMR deficient (MMRd) patients/carriers. cfDNA from 84 healthy individuals was also sequenced to assess background noise. RESULTS Recurrent FSMs at cMNRs were detectable not only in tumors, but also in cfDNA from MSI-H/MMRd cases including a LS carrier with a varying range of target detection (up to 85.2%), whereas they were virtually undetectable in healthy individuals. ROC analysis showed high sensitivity and specificity (AUC = 0.94) of the investigated panel. CONCLUSIONS We demonstrated that FSMs can be detected in cfDNA from MSI-H/MMRd cases and asymptomatic carriers. The 122-target FSM panel described here has promise as a tool for improved surveillance of MSI-H/MMRd carriers with the potential to reduce the frequency of invasive screening methods for this high-cancer-risk cohort.
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Affiliation(s)
- Yurong Song
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Ryan N Baugher
- CLIA Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brandon Somerville
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shaneen S Baxter
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Travis D Kerr
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Teri M Plona
- CLIA Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephanie D Mellott
- CLIA Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Todd B Young
- CLIA Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Heidi E Lawhorn
- CLIA Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lei Wei
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Alan Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Ligia Pinto
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
- School of Public Health, University of Washington, Seattle, WA, USA
| | - Shizuko Sei
- Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | - Ozkan Gelincik
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Steven M Lipkin
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Robert H Shoemaker
- Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
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Song Y, Baxter S, Dai L, Sanders C, Loomans-Kropp H, Somerville B, Baugher RN, Mellott SD, Young TB, Lawhorn HE, Plona TM, Xu B, Wei L, Hu Q, Liu S, Hutson A, Karim B, Difilippantonio S, Pinto L, Kloor M, Lipkin SM, Sei S, Shoemaker RH. Abstract 6518: Time course genomic characterization reveals progressive accumulation of mutations during tumor development in a Lynch syndrome mouse model. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6518] [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
DNA mismatch repair (MMR) genes (e.g., MLH1, MSH2, MSH6, PMS2, and EPCAM) play an important role in maintaining genomic stability during DNA replication and recombination. Deficiency in MMR resulting from mutations in these genes leads to mutations in microsatellite regions throughout the genome (microsatellite instability; MSI) and in cancer driver oncogenes or tumor suppressor genes, which accumulate over time and eventually lead to cancer formation. Monoallelic germline mutation in MMR genes causes Lynch syndrome (LS). Among LS-related cancer types, the lifetime risk for colorectal cancer (CRC) is the highest (~80%). Frameshift mutations (FSMs) in coding microsatellites produce neoantigens, which have been shown to elicit immune responses. It was thus postulated that they can serve as vaccine targets. To develop a prophylactic vaccine and prevention strategy for this high-risk population, we characterized a LS mouse model (Msh2LoxP/LoxP;Villin-Cre) to determine whether these mice recapitulate the human LS oncogenic process. We found that tumor development was already notable at 7-8 months of age and median survival was 11.5 months. Histopathological analysis showed that tumors were adenoma or adenocarcinoma mixed with mucinous features. Using a targeted sequencing approach, a panel of FSMs in mononucleotide regions were identified in both tumors and histologically normal mucosa, suggesting that Msh2 deletion and FSMs were not sufficient for tumor development. In addition, Apc, Ctnnb, and Trp53 mutations were also observed with low frequency in organoids derived from these tumors, indicating that other driver mutations may be required for tumor initiation and progression, and most FSMs detected in tumors and mucosa were probably passenger mutations. To determine if fecal samples can be used to monitor the FSM load, fecal DNA from different time points was sequenced. We found that FSMs can be detected at 1month of age although the number of FSMs was relatively low compared to that from older mice, indicating that FSMs accumulate over time. MSI detection via fragment analysis confirmed that these tumors were MSI-H. Interestingly, mucosa and fecal samples from a time course study showed progressive increase in microsatellite instability, suggesting the possibility of using MSI score for disease monitoring. Our preliminary data indicates that combined fecal FSM status and MSI score can be potentially used as a biomarker to monitor the tumor development and disease progression for LS colorectal cancer.
Funded by the National Cancer Institute, National Institutes of Health, under Contract No. HHSN261201500003I
Citation Format: Yurong Song, Shaneen Baxter, Lisheng Dai, Chelsea Sanders, Holli Loomans-Kropp, Brandon Somerville, Ryan N. Baugher, Stephanie D. Mellott, Todd B. Young, Heidi E. Lawhorn, Teri M. Plona, Bingfang Xu, Lei Wei, Qiang Hu, Song Liu, Alan Hutson, Baktiar Karim, Simone Difilippantonio, Ligia Pinto, Matthias Kloor, Steven M. Lipkin, Shizuko Sei, Robert H. Shoemaker. Time course genomic characterization reveals progressive accumulation of mutations during tumor development in a Lynch syndrome mouse model. [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 6518.
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Affiliation(s)
- Yurong Song
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Shaneen Baxter
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Lisheng Dai
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Chelsea Sanders
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | | | - Ryan N. Baugher
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | - Todd B. Young
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Heidi E. Lawhorn
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Teri M. Plona
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Bingfang Xu
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Lei Wei
- 3Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Qiang Hu
- 3Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Song Liu
- 3Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Alan Hutson
- 3Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Baktiar Karim
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | - Ligia Pinto
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | | | - Shizuko Sei
- 6Division of Cancer Prevention, Bethesda, MD
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Dwyer AJ, Murphy CC, Boland CR, Garcia R, Hampel H, Limburg P, Lowery J, Zauber AG, Waring S, Worrall S, Perea J, Siegel R, Lee J, Molmenti C, Sears CL, Buckhaults P, Hayes R, Hussan H, de Miranda N, Palles C, Diaz L, Song M, Cercek A, Lieu CH, Patel SG, Karlitz JJ, Cao Y, Demb J, Blatchford P, Risendal B, Staples ES, Wali A, Daschner P, Loomans-Kropp H, Flores R, Levell CL, Wehling K, Martin J, Pesmen C, Kuchar V, Soisson R, Davis A, Ahnen D. A Summary of the Fight Colorectal Cancer Working Meeting: Exploring Risk Factors and Etiology of Sporadic Early-Age Onset Colorectal Cancer. Gastroenterology 2019; 157:280-288. [PMID: 31095950 PMCID: PMC10601967 DOI: 10.1053/j.gastro.2019.04.049] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Andrea J Dwyer
- University of Colorado Denver-Anschutz Medical Campus, Denver, Colorado.
| | | | | | | | - Heather Hampel
- The Ohio State University Medical Center. Columbus, Ohio
| | | | - Jan Lowery
- University of Colorado, Denver, Colorado
| | - Ann G Zauber
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | - Jose Perea
- Surgery Department, Fundación Jiménez Díaz University Hospital, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | | | | | - Christine Molmenti
- Feinstein Institute for Medical Research, Northwell Health, Manhattan, New York
| | - Cynthia L Sears
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | - Hisham Hussan
- Ohio State University Wexner Medical Center, Columbus, Ohio
| | | | - Claire Palles
- University of Birmingham, Birmingham, United Kingdom
| | - Luis Diaz
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Andrea Cercek
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Swati G Patel
- University of Colorado Anschutz Medical Center, Aurora, Colorado; Rocky Mountain Regional Veterans Affairs Hospital, Denver, Colorado
| | | | - Yin Cao
- Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Josh Demb
- University of California San Diego, San Diego, California
| | | | | | | | - Anil Wali
- National Cancer Institute, Bethesda, Maryland
| | | | | | - R Flores
- National Institutes of Health, Bethesda, Maryland
| | | | - Karen Wehling
- Research Advocate, Fight Colorectal Cancer, Austin, Texas
| | - Jessica Martin
- Research Advocate, Fight Colorectal Cancer, Austin, Texas
| | - Curt Pesmen
- Research Advocate, Fight Colorectal Cancer, Austin, Texas
| | - Violet Kuchar
- Patient Advocate, Fight Colorectal Cancer, Austin, Texas
| | | | - Anjee Davis
- Fight Colorectal Cancer, Springfield, Missouri
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