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Jiang C, Liu W, Jin Z, Lan L, Xu L, Du A, Peng S, Zeng Y, Wang H, Liao M, Zhou J. Construction and validation of "WCH-nomogram" for predicting the prognosis after resection of colorectal liver metastases. Cancer Med 2024; 13:e7222. [PMID: 38698687 PMCID: PMC11066479 DOI: 10.1002/cam4.7222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 03/18/2024] [Accepted: 04/14/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND The prognostic predictive tool for patients with colorectal liver metastasis (CRLM) is limited and the criteria for administering preoperative neoadjuvant chemotherapy in CRLM patients remain controversial. METHODS This study enrolled 532 CRLM patients at West China Hospital (WCH) from January 2009 to December 2019. Prognostic factors were identified from the training cohort to construct a WCH-nomogram and evaluating accuracy in the validation cohort. Receiver operating characteristic (ROC) curve analysis was used to compare the prediction accuracy with other existing prediction tools. RESULTS From the analysis of the training cohort, four independent prognostic risk factors, namely tumor marker score, KRAS mutation, primary lymph node metastasis, and tumor burden score were identified on which a WCH-nomogram was constructed. The C-index of the two cohorts were 0.674 (95% CI: 0.634-0.713) and 0.655 (95% CI: 0.586-0.723), respectively, which was better than the previously reported predication scores (CRS, m-CS and GAME score). ROC curves showed AUCs for predicting 1-, 3-, and 5-year overall survival (OS) of 0.758, 0.709, and 0.717 in the training cohort, and 0.860, 0.669, and 0.692 in the validation cohort, respectively. A cutoff value of 114.5 points was obtained for the WCH-nomogram total score based on the maximum Youden index of the ROC curve of 5-year OS. Risk stratification showed significantly better prognosis in the low-risk group, however, the high-risk group was more likely to benefit from neoadjuvant chemotherapy. CONCLUSIONS The WCH-nomogram demonstrates superior prognostic stratification compared to prior scoring systems, effectively identifying CRLM patients who may benefit the most from neoadjuvant chemotherapy.
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Affiliation(s)
- Chuang Jiang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Weixing Liu
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Zechuan Jin
- Department of Colorectal Cancer Center, West China HospitalSichuan UniversityChengduSichuanChina
| | - Ling Lan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Lin Xu
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Ao Du
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Song Peng
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Yong Zeng
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Haichuan Wang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Mingheng Liao
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
| | - Jin Zhou
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China HospitalSichuan UniversityChengduSichuanChina
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2
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Chan JM, Clendenning M, Joseland S, Georgeson P, Mahmood K, Joo JE, Walker R, Como J, Preston S, Chai SM, Chu YL, Meyers AL, Pope BJ, Duggan D, Fink JL, Macrae FA, Rosty C, Winship IM, Jenkins MA, Buchanan DD. Inherited BRCA1 and RNF43 pathogenic variants in a familial colorectal cancer type X family. Fam Cancer 2024; 23:9-21. [PMID: 38063999 PMCID: PMC10869370 DOI: 10.1007/s10689-023-00351-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/21/2023] [Indexed: 02/17/2024]
Abstract
Genetic susceptibility to familial colorectal cancer (CRC), including for individuals classified as Familial Colorectal Cancer Type X (FCCTX), remains poorly understood. We describe a multi-generation CRC-affected family segregating pathogenic variants in both BRCA1, a gene associated with breast and ovarian cancer and RNF43, a gene associated with Serrated Polyposis Syndrome (SPS). A single family out of 105 families meeting the criteria for FCCTX (Amsterdam I family history criteria with mismatch repair (MMR)-proficient CRCs) recruited to the Australasian Colorectal Cancer Family Registry (ACCFR; 1998-2008) that underwent whole exome sequencing (WES), was selected for further testing. CRC and polyp tissue from four carriers were molecularly characterized including a single CRC that underwent WES to determine tumor mutational signatures and loss of heterozygosity (LOH) events. Ten carriers of a germline pathogenic variant BRCA1:c.2681_2682delAA p.Lys894ThrfsTer8 and eight carriers of a germline pathogenic variant RNF43:c.988 C > T p.Arg330Ter were identified in this family. Seven members carried both variants, four of which developed CRC. A single carrier of the RNF43 variant met the 2019 World Health Organization (WHO2019) criteria for SPS, developing a BRAF p.V600 wildtype CRC. Loss of the wildtype allele for both BRCA1 and RNF43 variants was observed in three CRC tumors while a LOH event across chromosome 17q encompassing both genes was observed in a CRC. Tumor mutational signature analysis identified the homologous recombination deficiency (HRD)-associated COSMIC signatures SBS3 and ID6 in a CRC for a carrier of both variants. Our findings show digenic inheritance of pathogenic variants in BRCA1 and RNF43 segregating with CRC in a FCCTX family. LOH and evidence of BRCA1-associated HRD supports the importance of both these tumor suppressor genes in CRC tumorigenesis.
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Affiliation(s)
- James M Chan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | - Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Susan Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Shuyi Marci Chai
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Yen Lin Chu
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Aaron L Meyers
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
| | - Bernard J Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | - David Duggan
- Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - J Lynn Fink
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
- Australian Translational Genomics Centre, Queensland University of Technology, Brisbane, QLD, Australia
| | - Finlay A Macrae
- Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, VIC, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
- Envoi Pathology, Brisbane, QLD, Australia
- School of Medicine, University of Queensland, Herston, QLD, Australia
| | - Ingrid M Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, VIC, Australia
| | - Mark A Jenkins
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia.
- Centre for Cancer Research, University of Melbourne, The University of Melbourne, Parkville, VIC, Australia.
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia.
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3
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Joo JE, Chu YL, Georgeson P, Walker R, Mahmood K, Clendenning M, Meyers AL, Como J, Joseland S, Preston SG, Diepenhorst N, Toner J, Ingle DJ, Sherry NL, Metz A, Lynch BM, Milne RL, Southey MC, Hopper JL, Win AK, Macrae FA, Winship IM, Rosty C, Jenkins MA, Buchanan DD. Intratumoral presence of the genotoxic gut bacteria pks + E. coli, Enterotoxigenic Bacteroides fragilis, and Fusobacterium nucleatum and their association with clinicopathological and molecular features of colorectal cancer. Br J Cancer 2024; 130:728-740. [PMID: 38200234 PMCID: PMC10912205 DOI: 10.1038/s41416-023-02554-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND This study aimed to investigate clinicopathological and molecular tumour features associated with intratumoral pks+ Escherichia coli (pks+E.coli+), pks+E.coli- (non-E.coli bacteria harbouring the pks island), Enterotoxigenic Bacteroides fragilis (ETBF) and Fusobacterium nucleatum (F. nucleatum). METHODS We screened 1697 tumour-derived DNA samples from the Australasian Colorectal Cancer Family Registry, Melbourne Collaborative Cohort Study and the ANGELS study using targeted PCR. RESULTS Pks+E.coli+ was associated with male sex (P < 0.01) and APC:c.835-8 A > G somatic mutation (P = 0.03). The association between pks+E.coli+ and APC:c.835-8 A > G was specific to early-onset CRCs (diagnosed<45years, P = 0.02). The APC:c.835-A > G was not associated with pks+E.coli- (P = 0.36). F. nucleatum was associated with DNA mismatch repair deficiency (MMRd), BRAF:c.1799T>A p.V600E mutation, CpG island methylator phenotype, proximal tumour location, and high levels of tumour infiltrating lymphocytes (Ps < 0.01). In the stratified analysis by MMRd subgroups, F. nucleatum was associated with Lynch syndrome, MLH1 methylated and double MMR somatic mutated MMRd subgroups (Ps < 0.01). CONCLUSION Intratumoral pks+E.coli+ but not pks+E.coli- are associated with CRCs harbouring the APC:c.835-8 A > G somatic mutation, suggesting that this mutation is specifically related to DNA damage from colibactin-producing E.coli exposures. F. nucleatum was associated with both hereditary and sporadic MMRd subtypes, suggesting the MMRd tumour microenvironment is important for F. nucleatum colonisation irrespective of its cause.
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Affiliation(s)
- Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Yen Lin Chu
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Aaron L Meyers
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Susan G Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Natalie Diepenhorst
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Julie Toner
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Danielle J Ingle
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Norelle L Sherry
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia
| | - Andrew Metz
- Endoscopy Unit, Department of Gastroenterology and Hepatology, The Royal Melbourne Hospital, Parkville, VIC, Australia
- Melbourne Medical School, The University of Melbourne, Parkville, VIC, Australia
| | - Brigid M Lynch
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, VIC, Australia
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, VIC, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Finlay A Macrae
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, VIC, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, VIC, Australia
| | - Ingrid M Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, VIC, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
- Envoi Specialist Pathologists, Brisbane, QLD, Australia
- University of Queensland, Brisbane, QLD, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC, Australia.
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia.
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia.
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4
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Walker R, Mahmood K, Como J, Clendenning M, Joo JE, Georgeson P, Joseland S, Preston SG, Pope BJ, Chan JM, Austin R, Bojadzieva J, Campbell A, Edwards E, Gleeson M, Goodwin A, Harris MT, Ip E, Kirk J, Mansour J, Mar Fan H, Nichols C, Pachter N, Ragunathan A, Spigelman A, Susman R, Christie M, Jenkins MA, Pai RK, Rosty C, Macrae FA, Winship IM, Buchanan DD. DNA Mismatch Repair Gene Variant Classification: Evaluating the Utility of Somatic Mutations and Mismatch Repair Deficient Colonic Crypts and Endometrial Glands. Cancers (Basel) 2023; 15:4925. [PMID: 37894291 PMCID: PMC10605939 DOI: 10.3390/cancers15204925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Germline pathogenic variants in the DNA mismatch repair (MMR) genes (Lynch syndrome) predispose to colorectal (CRC) and endometrial (EC) cancer. Lynch syndrome specific tumor features were evaluated for their ability to support the ACMG/InSiGHT framework in classifying variants of uncertain clinical significance (VUS) in the MMR genes. Twenty-eight CRC or EC tumors from 25 VUS carriers (6xMLH1, 9xMSH2, 6xMSH6, 4xPMS2), underwent targeted tumor sequencing for the presence of microsatellite instability/MMR-deficiency (MSI-H/dMMR) status and identification of a somatic MMR mutation (second hit). Immunohistochemical testing for the presence of dMMR crypts/glands in normal tissue was also performed. The ACMG/InSiGHT framework reclassified 7/25 (28%) VUS to likely pathogenic (LP), three (12%) to benign/likely benign, and 15 (60%) VUS remained unchanged. For the seven re-classified LP variants comprising nine tumors, tumor sequencing confirmed MSI-H/dMMR (8/9, 88.9%) and a second hit (7/9, 77.8%). Of these LP reclassified variants where normal tissue was available, the presence of a dMMR crypt/gland was found in 2/4 (50%). Furthermore, a dMMR endometrial gland in a carrier of an MSH2 exon 1-6 duplication provides further support for an upgrade of this VUS to LP. Our study confirmed that identifying these Lynch syndrome features can improve MMR variant classification, enabling optimal clinical care.
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Affiliation(s)
- Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Melbourne Bioinformatics, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Jihoon E. Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Susan G. Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Bernard J. Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Melbourne Bioinformatics, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - James M. Chan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Rachel Austin
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4006, Australia; (R.A.); (H.M.F.)
| | - Jasmina Bojadzieva
- Clinical Genetics Unit, Austin Health, Melbourne, VIC 3084, Australia; (J.B.); (A.C.)
| | - Ainsley Campbell
- Clinical Genetics Unit, Austin Health, Melbourne, VIC 3084, Australia; (J.B.); (A.C.)
| | - Emma Edwards
- Familial Cancer Service, Westmead Hospital, Sydney, NSW 2145, Australia;
| | - Margaret Gleeson
- Hunter Family Cancer Service, Newcastle, NSW 2298, Australia; (M.G.); (J.K.); (A.R.)
| | - Annabel Goodwin
- Cancer Genetics Department, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (A.G.); (A.S.)
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2050, Australia
| | - Marion T. Harris
- Monash Health Familial Cancer Centre, Clayton, VIC 3168, Australia;
| | - Emilia Ip
- Cancer Genetics Service, Liverpool Hospital, Liverpool, NSW 2170, Australia;
| | - Judy Kirk
- Hunter Family Cancer Service, Newcastle, NSW 2298, Australia; (M.G.); (J.K.); (A.R.)
| | - Julia Mansour
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS 7000, Australia;
| | - Helen Mar Fan
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4006, Australia; (R.A.); (H.M.F.)
| | - Cassandra Nichols
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia; (C.N.); (N.P.)
| | - Nicholas Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia; (C.N.); (N.P.)
- Medical School, Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA 6009, Australia
- School of Medicine, Curtin University, Perth, WA 6102, Australia
| | - Abiramy Ragunathan
- Hunter Family Cancer Service, Newcastle, NSW 2298, Australia; (M.G.); (J.K.); (A.R.)
| | - Allan Spigelman
- Cancer Genetics Department, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (A.G.); (A.S.)
- St Vincent’s Cancer Genetics Unit, Sydney, NSW 2010, Australia
- Surgical Professorial Unit, UNSW Clinical School of Clinical Medicine, Sydney, NSW 2052, Australia
| | - Rachel Susman
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4006, Australia; (R.A.); (H.M.F.)
| | - Michael Christie
- Department of Medicine, Royal Melbourne Hospital, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia;
- Department of Pathology, The Royal Melbourne Hospital, Melbourne, VIC 3052, Australia
| | - Mark A. Jenkins
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Rish K. Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, AZ 85259, USA;
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Envoi Specialist Pathologists, Brisbane, QLD 4059, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD 4072, Australia
| | - Finlay A. Macrae
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Melbourne, VIC 3052, Australia; (F.A.M.); (I.M.W.)
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Melbourne, VIC 3052, Australia
- Department of Medicine, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Ingrid M. Winship
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Melbourne, VIC 3052, Australia; (F.A.M.); (I.M.W.)
- Department of Medicine, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia; (K.M.); (J.C.); (M.C.); (J.E.J.); (P.G.); (S.J.); (S.G.P.); (B.J.P.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Melbourne, VIC 3052, Australia; (F.A.M.); (I.M.W.)
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5
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Joo JE, Mahmood K, Walker R, Georgeson P, Candiloro I, Clendenning M, Como J, Joseland S, Preston S, Graversen L, Wilding M, Field M, Lemon M, Wakeling J, Marfan H, Susman R, Isbister J, Edwards E, Bowman M, Kirk J, Ip E, McKay L, Antill Y, Hopper JL, Boussioutas A, Macrae FA, Dobrovic A, Jenkins MA, Rosty C, Winship IM, Buchanan DD. Identifying primary and secondary MLH1 epimutation carriers displaying low-level constitutional MLH1 methylation using droplet digital PCR and genome-wide DNA methylation profiling of colorectal cancers. Clin Epigenetics 2023; 15:95. [PMID: 37270516 PMCID: PMC10239107 DOI: 10.1186/s13148-023-01511-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/24/2023] [Indexed: 06/05/2023] Open
Abstract
BACKGROUND MLH1 epimutation is characterised by constitutional monoallelic MLH1 promoter hypermethylation, which can cause colorectal cancer (CRC). Tumour molecular profiles of MLH1 epimutation CRCs were used to classify germline MLH1 promoter variants of uncertain significance and MLH1 methylated early-onset CRCs (EOCRCs). Genome-wide DNA methylation and somatic mutational profiles of tumours from two germline MLH1: c.-11C > T and one MLH1: c.-[28A > G; 7C > T] carriers and three MLH1 methylated EOCRCs (< 45 years) were compared with 38 reference CRCs. Methylation-sensitive droplet digital PCR (ddPCR) was used to detect mosaic MLH1 methylation in blood, normal mucosa and buccal DNA. RESULTS Genome-wide methylation-based Consensus Clustering identified four clusters where the tumour methylation profiles of germline MLH1: c.-11C > T carriers and MLH1 methylated EOCRCs clustered with the constitutional MLH1 epimutation CRCs but not with the sporadic MLH1 methylated CRCs. Furthermore, monoallelic MLH1 methylation and APC promoter hypermethylation in tumour were observed in both MLH1 epimutation and germline MLH1: c.-11C > T carriers and MLH1 methylated EOCRCs. Mosaic constitutional MLH1 methylation in MLH1: c.-11C > T carriers and 1 of 3 MLH1 methylated EOCRCs was identified by methylation-sensitive ddPCR. CONCLUSIONS Mosaic MLH1 epimutation underlies the CRC aetiology in MLH1: c.-11C > T germline carriers and a subset of MLH1 methylated EOCRCs. Tumour profiling and ultra-sensitive ddPCR methylation testing can be used to identify mosaic MLH1 epimutation carriers.
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Affiliation(s)
- Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia.
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia.
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Ida Candiloro
- Beacon Biomarkers Lab, Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Susan Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Lise Graversen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Mathilda Wilding
- Department of Clinical Genetics, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Michael Field
- Department of Clinical Genetics, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Michelle Lemon
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Janette Wakeling
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- Tasman Health Care, Southport, QLD, Australia
| | - Helen Marfan
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Rachel Susman
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Joanne Isbister
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
| | - Emma Edwards
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Michelle Bowman
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Judy Kirk
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Emilia Ip
- Department of Cancer Genetics, Liverpool Hospital, Liverpool, NSW, Australia
| | - Lynne McKay
- The Cabrini Family Cancer Clinic, Cabrini Health, Malvern, VIC, Australia
| | - Yoland Antill
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
- The Cabrini Family Cancer Clinic, Cabrini Health, Malvern, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, VIC, Australia
| | - Alex Boussioutas
- Department of Gastroenterology, The Alfred Hospital, Melbourne, Parkville, VIC, 3010, Australia
- Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Finlay A Macrae
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, Australia
| | - Alexander Dobrovic
- Beacon Biomarkers Lab, Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, VIC, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
- Envoi Specialist Pathologists, Brisbane, Australia
- University of Queensland, Brisbane, Australia
| | - Ingrid M Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
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6
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Walker R, Mahmood K, Joo JE, Clendenning M, Georgeson P, Como J, Joseland S, Preston SG, Antill Y, Austin R, Boussioutas A, Bowman M, Burke J, Campbell A, Daneshvar S, Edwards E, Gleeson M, Goodwin A, Harris MT, Henderson A, Higgins M, Hopper JL, Hutchinson RA, Ip E, Isbister J, Kasem K, Marfan H, Milnes D, Ng A, Nichols C, O'Connell S, Pachter N, Pope BJ, Poplawski N, Ragunathan A, Smyth C, Spigelman A, Storey K, Susman R, Taylor JA, Warwick L, Wilding M, Williams R, Win AK, Walsh MD, Macrae FA, Jenkins MA, Rosty C, Winship IM, Buchanan DD. A tumor focused approach to resolving the etiology of DNA mismatch repair deficient tumors classified as suspected Lynch syndrome. J Transl Med 2023; 21:282. [PMID: 37101184 PMCID: PMC10134620 DOI: 10.1186/s12967-023-04143-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/19/2023] [Indexed: 04/28/2023] Open
Abstract
Routine screening of tumors for DNA mismatch repair (MMR) deficiency (dMMR) in colorectal (CRC), endometrial (EC) and sebaceous skin (SST) tumors leads to a significant proportion of unresolved cases classified as suspected Lynch syndrome (SLS). SLS cases (n = 135) were recruited from Family Cancer Clinics across Australia and New Zealand. Targeted panel sequencing was performed on tumor (n = 137; 80×CRCs, 33×ECs and 24xSSTs) and matched blood-derived DNA to assess for microsatellite instability status, tumor mutation burden, COSMIC tumor mutational signatures and to identify germline and somatic MMR gene variants. MMR immunohistochemistry (IHC) and MLH1 promoter methylation were repeated. In total, 86.9% of the 137 SLS tumors could be resolved into established subtypes. For 22.6% of these resolved SLS cases, primary MLH1 epimutations (2.2%) as well as previously undetected germline MMR pathogenic variants (1.5%), tumor MLH1 methylation (13.1%) or false positive dMMR IHC (5.8%) results were identified. Double somatic MMR gene mutations were the major cause of dMMR identified across each tumor type (73.9% of resolved cases, 64.2% overall, 70% of CRC, 45.5% of ECs and 70.8% of SSTs). The unresolved SLS tumors (13.1%) comprised tumors with only a single somatic (7.3%) or no somatic (5.8%) MMR gene mutations. A tumor-focused testing approach reclassified 86.9% of SLS into Lynch syndrome, sporadic dMMR or MMR-proficient cases. These findings support the incorporation of tumor sequencing and alternate MLH1 methylation assays into clinical diagnostics to reduce the number of SLS patients and provide more appropriate surveillance and screening recommendations.
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Affiliation(s)
- Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, 3051, Australia
| | - Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Susan G Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Yoland Antill
- Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, 3050, Australia
- Familial Cancer Centre, Cabrini Health, Malvern, VIC, 3144, Australia
- Familial Cancer Centre, Monash Health, Clayton, VIC, 3168, Australia
- Faculty of Medicine, Dentistry and Health Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Rachel Austin
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Alex Boussioutas
- Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Department of Gastroenterology, The Alfred Hospital, Melbourne, VIC, 3004, Australia
- Department of Medicine, The Royal Melbourne Hospital, Melbourne, VIC, 3010, Australia
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Parkville, VIC, 3000, Australia
| | - Michelle Bowman
- Familial Cancer Service, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Jo Burke
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, 7000, Australia
- School of Medicine, University of Tasmania, Sandy Bay, TAS, 7005, Australia
| | - Ainsley Campbell
- Clinical Genetics Unit, Austin Health, Melbourne, VIC, 3084, Australia
| | - Simin Daneshvar
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Emma Edwards
- Familial Cancer Service, Westmead Hospital, Sydney, NSW, 2145, Australia
| | | | - Annabel Goodwin
- Cancer Genetics Department, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia
- University of Sydney, Sydney, NSW, 2050, Australia
| | - Marion T Harris
- Monash Health Familial Cancer Centre, Clayton, VIC, 3168, Australia
| | - Alex Henderson
- Genetic Health Service, Wellington, Greater Wellington, 6242, New Zealand
- Wellington Hospital, Newtown, Greater Wellington, 6021, New Zealand
| | - Megan Higgins
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
- University of Queensland, St Lucia, QLD, 4067, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Ryan A Hutchinson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Emilia Ip
- Cancer Genetics Service, Liverpool Hospital, Liverpool, NSW, 2170, Australia
| | - Joanne Isbister
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, 3000, Australia
- Department of Medicine, The University of Melbourne, Melbourne, VIC, 3000, Australia
- Parkville Familial Cancer Centre, Peter McCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Kais Kasem
- Department of Clinical Pathology, Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Helen Marfan
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Di Milnes
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
- Royal Brisbane and Women's Hospital, Herston, QLD, 4029, Australia
| | - Annabelle Ng
- Cancer Genetics Department, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia
| | - Cassandra Nichols
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, 6008, Australia
| | - Shona O'Connell
- Monash Health Familial Cancer Centre, Clayton, VIC, 3168, Australia
| | - Nicholas Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, 6008, Australia
- Medical School, University of Western Australia, Perth, WA, 6009, Australia
- School of Medicine, Curtin University, Perth, WA, 6845, Australia
| | - Bernard J Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, 3051, Australia
| | - Nicola Poplawski
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Abiramy Ragunathan
- Familial Cancer Service, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Courtney Smyth
- Familial Cancer Centre, Monash Health, Clayton, VIC, 3168, Australia
| | - Allan Spigelman
- Hunter Family Cancer Service, Newcastle, NSW, 2298, Australia
- St Vincent's Cancer Genetics Unit, Sydney, NSW, 2290, Australia
- Surgical Professorial Unit, UNSW Clinical School of Clinical Medicine, Sydney, NSW, 2052, Australia
| | - Kirsty Storey
- Parkville Familial Cancer Centre, Peter McCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Rachel Susman
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Jessica A Taylor
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, 3000, Australia
| | - Linda Warwick
- ACT Genetic Service, The Canberra Hospital, Woden, ACT, 2606, Australia
| | - Mathilda Wilding
- Familial Cancer Service, Royal North Shore Hospital, St Leonards, NSW, 2065, Australia
| | - Rachel Williams
- Prince of Wales Clinical School, UNSW Medicine and Health, UNSW Sydney, Kensington, NSW, 2052, Australia
- Prince of Wales Hereditary Cancer Centre, Prince of Wales Hospital, Randwick, NSW, 2031, Australia
| | - Aung K Win
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, 3000, Australia
| | - Michael D Walsh
- Sullivan Nicolaides Pathology, Bowen Hills, QLD, 4006, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, 4072, Australia
| | - Finlay A Macrae
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, 3000, Australia
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Mark A Jenkins
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
- Envoi Specialist Pathologists, Brisbane, QLD, 4059, Australia
- University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ingrid M Winship
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, 3000, Australia
- Department of Medicine, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia.
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia.
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, 3000, Australia.
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7
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Walker R, Mahmood K, Joo JE, Clendenning M, Georgeson P, Como J, Joseland S, Preston SG, Antill Y, Austin R, Boussioutas A, Bowman M, Burke J, Campbell A, Daneshvar S, Edwards E, Gleeson M, Goodwin A, Harris MT, Henderson A, Higgins M, Hopper JL, Hutchinson RA, Ip E, Isbister J, Kasem K, Marfan H, Milnes D, Ng A, Nichols C, O’Connell S, Pachter N, Pope BJ, Poplawski N, Ragunathan A, Smyth C, Spigelman A, Storey K, Susman R, Taylor JA, Warwick L, Wilding M, Williams R, Win AK, Walsh MD, Macrae FA, Jenkins MA, Rosty C, Winship IM, Buchanan DD. A tumor focused approach to resolving the etiology of DNA mismatch repair deficient tumors classified as suspected Lynch syndrome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.27.23285541. [PMID: 36909643 PMCID: PMC10002795 DOI: 10.1101/2023.02.27.23285541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Routine screening of tumors for DNA mismatch repair (MMR) deficiency (dMMR) in colorectal (CRC), endometrial (EC) and sebaceous skin (SST) tumors leads to a significant proportion of unresolved cases classified as suspected Lynch syndrome (SLS). SLS cases (n=135) were recruited from Family Cancer Clinics across Australia and New Zealand. Targeted panel sequencing was performed on tumor (n=137; 80xCRCs, 33xECs and 24xSSTs) and matched blood-derived DNA to assess for microsatellite instability status, tumor mutation burden, COSMIC tumor mutational signatures and to identify germline and somatic MMR gene variants. MMR immunohistochemistry (IHC) and MLH1 promoter methylation were repeated. In total, 86.9% of the 137 SLS tumors could be resolved into established subtypes. For 22.6% of these resolved SLS cases, primary MLH1 epimutations (2.2%) as well as previously undetected germline MMR pathogenic variants (1.5%), tumor MLH1 methylation (13.1%) or false positive dMMR IHC (5.8%) results were identified. Double somatic MMR gene mutations were the major cause of dMMR identified across each tumor type (73.9% of resolved cases, 64.2% overall, 70% of CRC, 45.5% of ECs and 70.8% of SSTs). The unresolved SLS tumors (13.1%) comprised tumors with only a single somatic (7.3%) or no somatic (5.8%) MMR gene mutations. A tumor-focused testing approach reclassified 86.9% of SLS into Lynch syndrome, sporadic dMMR or MMR-proficient cases. These findings support the incorporation of tumor sequencing and alternate MLH1 methylation assays into clinical diagnostics to reduce the number of SLS patients and provide more appropriate surveillance and screening recommendations.
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Affiliation(s)
- Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC 3051, Australia
| | - Jihoon E. Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Susan G. Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Yoland Antill
- Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC 3050, Australia
- Familial Cancer Centre, Cabrini Health, Malvern, VIC 3144, Australia
- Familial Cancer Centre, Monash Health, Clayton, VIC 3168, Australia
- Faculty of Medicine, Dentistry and Health Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Rachel Austin
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
| | - Alex Boussioutas
- Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
- Department of Gastroenterology, The Alfred Hospital, Melbourne, VIC 3004, Australia
- Department of Medicine, The Royal Melbourne Hospital, Melbourne, VIC 3010, Australia
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
| | - Michelle Bowman
- Familial Cancer Service, Westmead Hospital, Sydney, NSW 2145, Australia
| | - Jo Burke
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS 7000, Australia
- School of Medicine, University of Tasmania, Sandy Bay, TAS 7005 Australia
| | - Ainsley Campbell
- Clinical Genetics Unit, Austin Health, Melbourne, VIC 3084, Australia
| | - Simin Daneshvar
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Emma Edwards
- Familial Cancer Service, Westmead Hospital, Sydney, NSW 2145, Australia
| | | | - Annabel Goodwin
- Cancer Genetics Department, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- University of Sydney, Sydney, NSW 2050, Australia
| | - Marion T. Harris
- Monash Health Familial Cancer Centre, Clayton, VIC 3168, Australia
| | - Alex Henderson
- Genetic Health Service, Wellington, Greater Wellington, 6242, New Zealand
- Wellington Hospital, Newtown, Greater Wellington 6021, New Zealand
| | - Megan Higgins
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
- University of Queensland, St Lucia, QLD 4067, Australia
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, Melbourne, Victoria, 3010, Australia
| | - Ryan A. Hutchinson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Emilia Ip
- Cancer Genetics service, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Joanne Isbister
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC 3000, Australia
- Department of Medicine, The University of Melbourne, VIC 3000, Australia
- Parkville Familial Cancer Centre, Peter McCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Kais Kasem
- Department of Clinical Pathology, Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Helen Marfan
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
| | - Di Milnes
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
- Royal Brisbane and Women’s Hospital, Herston, QLD 4029, Australia
| | - Annabelle Ng
- Cancer Genetics Department, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Cassandra Nichols
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia
| | - Shona O’Connell
- Monash Health Familial Cancer Centre, Clayton, VIC 3168, Australia
| | - Nicholas Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia
- Medical School, University of Western Australia, Perth, WA 6009, Australia
- School of Medicine, Curtin University, Perth, WA 6845, Australia
| | - Bernard J. Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC 3051, Australia
| | - Nicola Poplawski
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | | | - Courtney Smyth
- Familial Cancer Centre, Monash Health, Clayton, VIC 3168, Australia
| | - Allan Spigelman
- Hunter Family Cancer Service, Newcastle, NSW 2298, Australia
- St Vincent’s Cancer Genetics Unit, Sydney, NSW 2290, Australia
- Surgical Professorial Unit, UNSW Clinical School of Clinical Medicine, Sydney, NSW 2052, Australia
| | - Kirsty Storey
- Parkville Familial Cancer Centre, Peter McCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Rachel Susman
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
| | - Jessica A. Taylor
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC 3000, Australia
| | - Linda Warwick
- ACT Genetic Service, The Canberra Hospital, Woden, ACT 2606, Australia
| | - Mathilda Wilding
- Familial Cancer Service, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Rachel Williams
- Prince of Wales Clinical School, UNSW Medicine and Health, UNSW Sydney, Kensington, NSW 2052, Australia
- Prince of Wales Hereditary Cancer Centre, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Aung K. Win
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, Melbourne, Victoria, 3010, Australia
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC 3000, Australia
| | - Michael D. Walsh
- Sullivan Nicolaides Pathology, Bowen Hills, QLD 4006, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4072, Australia
| | - Finlay A. Macrae
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC 3000, Australia
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Mark A. Jenkins
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, Melbourne, Victoria, 3010, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
- Envoi Specialist Pathologists, Brisbane, QLD 4059, Australia
- University of Queensland, Brisbane, QLD 4072, Australia
| | - Ingrid M. Winship
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC 3000, Australia
- Department of Medicine, The University of Melbourne, VIC 3000, Australia
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC 3000, Australia
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Chow RD, Michaels T, Bellone S, Hartwich TM, Bonazzoli E, Iwasaki A, Song E, Santin AD. Distinct Mechanisms of Mismatch-Repair Deficiency Delineate Two Modes of Response to Anti-PD-1 Immunotherapy in Endometrial Carcinoma. Cancer Discov 2023; 13:312-331. [PMID: 36301137 PMCID: PMC9905265 DOI: 10.1158/2159-8290.cd-22-0686] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/29/2022] [Accepted: 10/19/2022] [Indexed: 02/07/2023]
Abstract
Mismatch repair-deficient (MMRd) cancers have varied responses to immune-checkpoint blockade (ICB). We conducted a phase II clinical trial of the PD-1 inhibitor pembrolizumab in 24 patients with MMRd endometrial cancer (NCT02899793). Patients with mutational MMRd tumors (6 patients) had higher response rates and longer survival than those with epigenetic MMRd tumors (18 patients). Mutation burden was higher in tumors with mutational MMRd compared with epigenetic MMRd; however, within each category of MMRd, mutation burden was not correlated with ICB response. Pretreatment JAK1 mutations were not associated with primary resistance to pembrolizumab. Longitudinal single-cell RNA-seq of circulating immune cells revealed contrasting modes of antitumor immunity for mutational versus epigenetic MMRd cancers. Whereas effector CD8+ T cells correlated with regression of mutational MMRd tumors, activated CD16+ NK cells were associated with ICB-responsive epigenetic MMRd tumors. These data highlight the interplay between tumor-intrinsic and tumor-extrinsic factors that influence ICB response. SIGNIFICANCE The molecular mechanism of MMRd is associated with response to anti-PD-1 immunotherapy in endometrial carcinoma. Tumors with epigenetic MMRd or mutational MMRd are correlated with NK cell or CD8+ T cell-driven immunity, respectively. Classifying tumors by the mechanism of MMRd may inform clinical decision-making regarding cancer immunotherapy. This article is highlighted in the In This Issue feature, p. 247.
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Affiliation(s)
- Ryan D. Chow
- Department of Genetics, Yale University, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Corresponding authors: Correspondence to: Ryan D. Chow, Address: 850 West Campus Drive, ISTC 314, West Haven CT 06516, , Phone: 203-737-3825, Eric Song, Address: 300 Cedar Street, Suite S630, New Haven, CT 06519, , Phone: 203-785-2919, Alessandro D. Santin, Address: 333 Cedar Street, PO Box 208063, New Haven, CT 06511, , Phone: 203-737-2280
| | - Tai Michaels
- Department of Immunobiology, Yale University, New Haven, Connecticut, USA
| | - Stefania Bellone
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tobias M.P. Hartwich
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Elena Bonazzoli
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
| | - Eric Song
- Department of Immunobiology, Yale University, New Haven, Connecticut, USA
- Corresponding authors: Correspondence to: Ryan D. Chow, Address: 850 West Campus Drive, ISTC 314, West Haven CT 06516, , Phone: 203-737-3825, Eric Song, Address: 300 Cedar Street, Suite S630, New Haven, CT 06519, , Phone: 203-785-2919, Alessandro D. Santin, Address: 333 Cedar Street, PO Box 208063, New Haven, CT 06511, , Phone: 203-737-2280
| | - Alessandro D. Santin
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Corresponding authors: Correspondence to: Ryan D. Chow, Address: 850 West Campus Drive, ISTC 314, West Haven CT 06516, , Phone: 203-737-3825, Eric Song, Address: 300 Cedar Street, Suite S630, New Haven, CT 06519, , Phone: 203-785-2919, Alessandro D. Santin, Address: 333 Cedar Street, PO Box 208063, New Haven, CT 06511, , Phone: 203-737-2280
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9
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Walker R, Georgeson P, Mahmood K, Joo JE, Makalic E, Clendenning M, Como J, Preston S, Joseland S, Pope BJ, Hutchinson RA, Kasem K, Walsh MD, Macrae FA, Win AK, Hopper JL, Mouradov D, Gibbs P, Sieber OM, O'Sullivan DE, Brenner DR, Gallinger S, Jenkins MA, Rosty C, Winship IM, Buchanan DD. Evaluating Multiple Next-Generation Sequencing-Derived Tumor Features to Accurately Predict DNA Mismatch Repair Status. J Mol Diagn 2023; 25:94-109. [PMID: 36396080 PMCID: PMC10424255 DOI: 10.1016/j.jmoldx.2022.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/27/2022] [Accepted: 10/20/2022] [Indexed: 11/16/2022] Open
Abstract
Identifying tumor DNA mismatch repair deficiency (dMMR) is important for precision medicine. Tumor features, individually and in combination, derived from whole-exome sequenced (WES) colorectal cancers (CRCs) and panel-sequenced CRCs, endometrial cancers (ECs), and sebaceous skin tumors (SSTs) were assessed for their accuracy in detecting dMMR. CRCs (n = 300) with WES, where mismatch repair status was determined by immunohistochemistry, were assessed for microsatellite instability (MSMuTect, MANTIS, MSIseq, and MSISensor), Catalogue of Somatic Mutations in Cancer tumor mutational signatures, and somatic mutation counts. A 10-fold cross-validation approach (100 repeats) evaluated the dMMR prediction accuracy for i) individual features, ii) Lasso statistical model, and iii) an additive feature combination approach. Panel-sequenced tumors (29 CRCs, 22 ECs, and 20 SSTs) were assessed for the top performing dMMR predicting features/models using these three approaches. For WES CRCs, 10 features provided >80% dMMR prediction accuracy, with MSMuTect, MSIseq, and MANTIS achieving ≥99% accuracy. The Lasso model achieved 98.3% accuracy. The additive feature approach, with three or more of six of MSMuTect, MANTIS, MSIseq, MSISensor, insertion-deletion count, or tumor mutational signature small insertion/deletion 2 + small insertion/deletion 7 achieved 99.7% accuracy. For the panel-sequenced tumors, the additive feature combination approach of three or more of six achieved accuracies of 100%, 95.5%, and 100% for CRCs, ECs, and SSTs, respectively. The microsatellite instability calling tools performed well in WES CRCs; however, an approach combining tumor features may improve dMMR prediction in both WES and panel-sequenced data across tissue types.
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Affiliation(s)
- Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Susan Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Bernard J Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ryan A Hutchinson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Kais Kasem
- Department of Clinical Pathology, Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Michael D Walsh
- Sullivan Nicolaides Pathology, Bowen Hills, Queensland, Australia
| | - Finlay A Macrae
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, Victoria, Australia; Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Aung K Win
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Dmitri Mouradov
- Personalized Oncology Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Peter Gibbs
- Personalized Oncology Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia; Department of Medical Oncology, Western Health, Melbourne, Victoria, Australia
| | - Oliver M Sieber
- Personalized Oncology Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia; Department of Surgery, The University of Melbourne, Parkville, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Dylan E O'Sullivan
- Department of Oncology, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Darren R Brenner
- Department of Oncology, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada; Department of Cancer Epidemiology and Prevention Research, Alberta Health Services, Calgary, Alberta, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Mark A Jenkins
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Envoi Specialist Pathologists, Brisbane, Queensland, Australia; University of Queensland, Brisbane, Queensland, Australia
| | - Ingrid M Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, Victoria, Australia.
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10
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Pan S, Cox H, Willmott J, Mundt E, Gorringe H, Landon M, Bowles KR, Coffee B, Roa BB, Mancini-DiNardo D. Discordance between germline genetic findings and abnormal tumor immunohistochemistry staining of mismatch repair proteins in individuals with suspected Lynch syndrome. Front Oncol 2023; 13:1069467. [PMID: 36793599 PMCID: PMC9923021 DOI: 10.3389/fonc.2023.1069467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
Background and Aims Tumor immunohistochemical staining (IHC) of DNA mismatch repair (MMR) proteins is often used to guide germline genetic testing and variant classification for patients with suspected Lynch syndrome. This analysis examined the spectrum of germline findings in a cohort of individuals showing abnormal tumor IHC. Methods We assessed individuals with reported abnormal IHC findings and referred for testing with a six-gene syndrome-specific panel (n=703). Pathogenic variants (PVs) and variants of uncertain significance (VUS) in MMR genes were designated expected/unexpected relative to IHC results. Results The PV positive rate was 23.2% (163/703; 95% confidence interval [CI], 20.1%-26.5%); 8.0% (13/163; 95% CI, 4.3%-13.3%) of PV carriers had a PV in an unexpected MMR gene. Overall, 121 individuals carried VUS in MMR genes expected to be mutated based on IHC results. Based on independent evidence, in 47.1% (57/121; 95% CI, 38.0%-56.4%) of these individuals the VUSs were later reclassified as benign and in 14.0% (17/121; 95% CI, 8.4%-21.5%) of these individuals the VUSs were reclassified as pathogenic. Conclusions Among patients with abnormal IHC findings, IHC-guided single-gene genetic testing may miss 8% of individuals with Lynch syndrome. In addition, in patients with VUS identified in MMR genes predicted to be mutated by IHC, extreme caution must be taken when the IHC results are considered in variant classification.
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Affiliation(s)
- Shujuan Pan
- Myriad Genetic Laboratories, Inc., Salt Lake City, UT, United States
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11
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Bartley AN, Mills AM, Konnick E, Overman M, Ventura CB, Souter L, Colasacco C, Stadler ZK, Kerr S, Howitt BE, Hampel H, Adams SF, Johnson W, Magi-Galluzzi C, Sepulveda AR, Broaddus RR. Mismatch Repair and Microsatellite Instability Testing for Immune Checkpoint Inhibitor Therapy: Guideline From the College of American Pathologists in Collaboration With the Association for Molecular Pathology and Fight Colorectal Cancer. Arch Pathol Lab Med 2022; 146:1194-1210. [PMID: 35920830 DOI: 10.5858/arpa.2021-0632-cp] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2022] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The US Food and Drug Administration (FDA) approved immune checkpoint inhibitor therapy for patients with advanced solid tumors that have DNA mismatch repair defects or high levels of microsatellite instability; however, the FDA provided no guidance on which specific clinical assays should be used to determine mismatch repair status. OBJECTIVE.— To develop an evidence-based guideline to identify the optimal clinical laboratory test to identify defects in DNA mismatch repair in patients with solid tumor malignancies who are being considered for immune checkpoint inhibitor therapy. DESIGN.— The College of American Pathologists convened an expert panel to perform a systematic review of the literature and develop recommendations. Using the National Academy of Medicine-endorsed Grading of Recommendations Assessment, Development and Evaluation approach, the recommendations were derived from available evidence, strength of that evidence, open comment feedback, and expert panel consensus. Mismatch repair immunohistochemistry, microsatellite instability derived from both polymerase chain reaction and next-generation sequencing, and tumor mutation burden derived from large panel next-generation sequencing were within scope. RESULTS.— Six recommendations and 3 good practice statements were developed. More evidence and evidence of higher quality were identified for colorectal cancer and other cancers of the gastrointestinal (GI) tract than for cancers arising outside the GI tract. CONCLUSIONS.— An optimal assay depends on cancer type. For most cancer types outside of the GI tract and the endometrium, there was insufficient published evidence to recommend a specific clinical assay. Absent published evidence, immunohistochemistry is an acceptable approach readily available in most clinical laboratories.
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Affiliation(s)
- Angela N Bartley
- From the Department of Pathology, St. Joseph Mercy Hospital, Ann Arbor, Michigan (Bartley)
| | - Anne M Mills
- From the Department of Pathology, University of Virginia, Charlottesville (Mills)
| | - Eric Konnick
- From the Department of Laboratory Medicine and Pathology, University of Washington, Seattle (Konnick)
| | - Michael Overman
- From the Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston (Overman)
| | - Christina B Ventura
- From Surveys, College of American Pathologists, Northfield, Illinois (Ventura, Colasacco)
| | - Lesley Souter
- From Methodology Consultant, Smithville, Ontario, Canada (Souter)
| | - Carol Colasacco
- From Surveys, College of American Pathologists, Northfield, Illinois (Ventura, Colasacco)
| | - Zsofia K Stadler
- From the Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York (Stadler)
| | - Sarah Kerr
- From Hospital Pathology Associates, PA, Minneapolis, Minnesota (Kerr)
| | - Brooke E Howitt
- From the Department of Pathology, Stanford University, Stanford, California (Howitt)
| | - Heather Hampel
- From the Department of Internal Medicine, The Ohio State University, Columbus (Hampel)
| | - Sarah F Adams
- From the Department of Obstetrics & Gynecology, University of New Mexico, Albuquerque (Adams)
| | - Wenora Johnson
- From Fight Colorectal Cancer, Springfield, Missouri (Johnson)
| | - Cristina Magi-Galluzzi
- From the Department of Pathology, University of Alabama at Birmingham, Birmingham (Magi-Galluzzi)
| | - Antonia R Sepulveda
- From the Department of Pathology, George Washington University, Washington, District of Columbia (Sepulveda)
| | - Russell R Broaddus
- From the Department of Pathology & Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill (Broaddus)
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12
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Abu-Ghazaleh N, Kaushik V, Gorelik A, Jenkins M, Macrae F. Worldwide prevalence of Lynch syndrome in patients with colorectal cancer: Systematic review and meta-analysis. Genet Med 2022; 24:971-985. [PMID: 35177335 DOI: 10.1016/j.gim.2022.01.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 10/19/2022] Open
Abstract
PURPOSE Lynch syndrome (LS) is the most common hereditary colorectal cancer (CRC) syndrome, with an estimated prevalence of 2% to 3% of CRC. A prevalence study is needed to provide accurate estimates of the true prevalence of LS. METHODS MEDLINE (Ovid), Embase, and Web of Science were searched. Prevalence was calculated by random effects meta-analysis models. I2 score was used to assess heterogeneity across studies. Meta-regression was performed for between-study variance. RESULTS A total of 51 studies were included in this review. The overall pooled yield of LS screening was 2.2% based on all methods of detection. Studies performing germline tests on all participants with CRC reported higher prevalence (5.1%) as opposed to studies only performing germline tests on participants with tumors with mismatch repair deficiency (1.6%) or microsatellite instability (1.1%). Selected cohorts of CRC had a higher prevalence of germline LS diagnoses. CONCLUSION LS prevalence across multiple ethnic, geographic, and clinical populations is remarkably similar. Universal germline testing of patients presenting with cancer identifies that most CRCs are attributed to LS. Young patients presenting with CRC and those who fulfill criteria for a familial risk provide the highest returns for LS identification. Our study supports the universal germline CRC screening for LS.
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Affiliation(s)
- Nadine Abu-Ghazaleh
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Colorectal Cancer and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia.
| | - Varun Kaushik
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Colorectal Cancer and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Alexandra Gorelik
- Department of Colorectal Cancer and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia; Monash Department of Clinical Epidemiology, Cabrini Institute, Malvern, Victoria, Australia
| | - Mark Jenkins
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Finlay Macrae
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Colorectal Cancer and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia
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13
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Antill Y, Buchanan DD, Scott CL. Mismatch repair and clinical response to immune checkpoint inhibitors in endometrial cancer. Cancer 2021; 128:1157-1161. [PMID: 34875102 PMCID: PMC9300166 DOI: 10.1002/cncr.34024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/09/2021] [Accepted: 10/14/2021] [Indexed: 12/19/2022]
Abstract
Endometrial cancer is common, and a subset recurs and requires additional treatment. Some of these are recognized as being susceptible to immune therapies and are said to have mismatch repair deficiency (dMMR). However, this clinical trial highlights which cases are more likely to respond well: those containing mutations in genes known as Lynch genes and also some with mutations in POLE/POLD1 (“ultra‐hypermutation” genes). In contrast, the majority of dMMR endometrial cancers have silencing or DNA methylation of one of these genes, MLH1, and do not seem to be as responsive to single‐agent immune therapy. The availability of combination therapies may be important to consider for these women.
This hypothesis‐driving study highlights the need for further evaluation of the interaction between immune checkpoint inhibitor therapy responses and the mechanism of DNA mismatch repair (MMR) deficiency. Although MMR gene germline pathogenic variant carriers and Lynch‐like tumors with double somatic MMR gene mutations are highly likely to respond to a single‐agent immune checkpoint inhibitor (ICI), those with MLH1 hypermethylation may benefit from additional agents to induce an ICI response.
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Affiliation(s)
- Yoland Antill
- Department of Medical Oncology, Cabrini Health, Malvern, Victoria, Australia.,Faculty of Medicine, Dentistry, and Health Sciences, Monash University, Melbourne, Victoria, Australia.,Familial Cancer Centre, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Familial Cancer Centre, Royal Melbourne Hospital, Parkville, Victoria, Australia.,Colorectal Oncogenomics Group, Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia.,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia.,Genomic Medicine, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Clare L Scott
- Familial Cancer Centre, Royal Melbourne Hospital, Parkville, Victoria, Australia.,Cancer Biology and Stem Cells Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.,Royal Women's Hospital, Parkville, Victoria, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia.,Sir Peter MacCallum Cancer Centre, Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
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14
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Georgeson P, Pope BJ, Rosty C, Clendenning M, Mahmood K, Joo JE, Walker R, Hutchinson R, Preston S, Como J, Joseland S, Win AK, Macrae FA, Hopper JL, Mouradov D, Gibbs P, Sieber OM, O’Sullivan DE, Brenner DR, Gallinger S, Jenkins MA, Winship IM, Buchanan DD. Evaluating the utility of tumour mutational signatures for identifying hereditary colorectal cancer and polyposis syndrome carriers. Gut 2021; 70:2138-2149. [PMID: 33414168 PMCID: PMC8260632 DOI: 10.1136/gutjnl-2019-320462] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/08/2020] [Accepted: 12/12/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Germline pathogenic variants (PVs) in the DNA mismatch repair (MMR) genes and in the base excision repair gene MUTYH underlie hereditary colorectal cancer (CRC) and polyposis syndromes. We evaluated the robustness and discriminatory potential of tumour mutational signatures in CRCs for identifying germline PV carriers. DESIGN Whole-exome sequencing of formalin-fixed paraffin-embedded (FFPE) CRC tissue was performed on 33 MMR germline PV carriers, 12 biallelic MUTYH germline PV carriers, 25 sporadic MLH1 methylated MMR-deficient CRCs (MMRd controls) and 160 sporadic MMR-proficient CRCs (MMRp controls) and included 498 TCGA CRC tumours. COSMIC V3 single base substitution (SBS) and indel (ID) mutational signatures were assessed for their ability to differentiate CRCs that developed in carriers from non-carriers. RESULTS The combination of mutational signatures SBS18 and SBS36 contributing >30% of a CRC's signature profile was able to discriminate biallelic MUTYH carriers from all other non-carrier control CRCs with 100% accuracy (area under the curve (AUC) 1.0). SBS18 and SBS36 were associated with specific MUTYH variants p.Gly396Asp (p=0.025) and p.Tyr179Cys (p=5×10-5), respectively. The combination of ID2 and ID7 could discriminate the 33 MMR PV carrier CRCs from the MMRp control CRCs (AUC 0.99); however, SBS and ID signatures, alone or in combination, could not provide complete discrimination (AUC 0.79) between CRCs from MMR PV carriers and sporadic MMRd controls. CONCLUSION Assessment of SBS and ID signatures can discriminate CRCs from biallelic MUTYH carriers and MMR PV carriers from non-carriers with high accuracy, demonstrating utility as a potential diagnostic and variant classification tool.
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Affiliation(s)
- Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Bernard J. Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia,Melbourne Bioinformatics, The University of Melbourne, Carlton, Victoria, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia,Envoi Pathology, Brisbane, Queensland, Australia,University of Queensland, School of Medicine, Herston, Queensland, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia,Melbourne Bioinformatics, The University of Melbourne, Carlton, Victoria, Australia
| | - Jihoon E. Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Ryan Hutchinson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Susan Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Aung K. Win
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia,Centre for Epidemiology and Biostatistics, The University of Melbourne, Carlton, Victoria, Australia
| | - Finlay A. Macrae
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia,Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Carlton, Victoria, Australia
| | - Dmitry Mouradov
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, Victoria, Australia,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Peter Gibbs
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, Victoria, Australia,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia,Department of Medical Oncology, Western Health, Victoria, Australia
| | - Oliver M. Sieber
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, Victoria, Australia,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia,Department of Surgery, The University of Melbourne, Parkville, Victoria, Australia,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Dylan E. O’Sullivan
- Department of Oncology, University of Calgary, Calgary, Canada,Department of Community Health Sciences, University of Calgary, Calgary, Canada
| | - Darren R. Brenner
- Department of Oncology, University of Calgary, Calgary, Canada,Department of Community Health Sciences, University of Calgary, Calgary, Canada,Department of Cancer Epidemiology and Prevention Research, Alberta Health Services, Calgary, Canada
| | - Steve Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada,Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Mark A. Jenkins
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia,Centre for Epidemiology and Biostatistics, The University of Melbourne, Carlton, Victoria, Australia
| | - Ingrid M. Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia,Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia,Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
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15
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den Elzen N, Joseland SL, Saya S, Jonnagadla S, Isbister J, Winship I, Buchanan DD. "Left in limbo": Exploring how patients with colorectal cancer interpret and respond to a suspected Lynch syndrome diagnosis. Hered Cancer Clin Pract 2021; 19:43. [PMID: 34656160 PMCID: PMC8520179 DOI: 10.1186/s13053-021-00201-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/01/2021] [Indexed: 12/30/2022] Open
Abstract
Background A diagnosis of suspected Lynch syndrome (SLS) is given when a tumour displays characteristics consistent with Lynch syndrome (LS), but no germline pathogenic variant is identified. This inconclusive diagnosis results in uncertainty around appropriate cancer risk management. This qualitative study explored how patients with CRC interpret and respond to an SLS diagnosis. Methods Semi-structured telephone interviews were conducted with 15 patients with CRC who received an SLS diagnosis, recruited from cancer genetics services across Australia. Interviews were transcribed verbatim and analysed using thematic analysis. Participant responses were compared with appointment summary letters from cancer genetics services. Results Participants’ interpretations of genetic test results were found to vary widely. While this variation often aligned with variation in interpretations by cancer genetics services, participants also had difficulties with the complexity and recall of genetic test results. Participants had a range of psychological responses to the uncertainty that their results presented, from relief to disappointment and doubt. Cancer risk perceptions also varied widely, with participants’ interpretations of their genetic test results just one of several influencing factors. Despite this variability, almost all participants adhered to cancer risk management advice, although different participants received different advice. All participants also communicated any cancer risk management advice to first-degree relatives, motivated by protecting them, but information communicated was not always consistent with advice received. Conclusions Our study findings highlight the variability in patients’ interpretations of their diagnosis, cancer risk management and family communication when a diagnosis of SLS is received, and provide novel insights into how healthcare professionals can better support patients with SLS.
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Affiliation(s)
- Nicole den Elzen
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, 305 Grattan Street, Parkville, Victoria, 3010, Australia.,The University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Sharelle L Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, 305 Grattan Street, Parkville, Victoria, 3010, Australia.,The University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Sibel Saya
- The University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia.,Department of General Practice, The University of Melbourne, Parkville, Victoria, Australia
| | - Sowmya Jonnagadla
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, 305 Grattan Street, Parkville, Victoria, 3010, Australia.,The University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Joanne Isbister
- Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ingrid Winship
- Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia.,Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, 305 Grattan Street, Parkville, Victoria, 3010, Australia. .,The University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia. .,Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia.
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16
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Meessen S, Currey N, Jahan Z, Parker HW, Jenkins MA, Buchanan DD, Hopper JL, Segelov E, Dahlstrom JE, Kohonen-Corish MRJ. Tetranucleotide and Low Microsatellite Instability Are Inversely Associated with the CpG Island Methylator Phenotype in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13143529. [PMID: 34298744 PMCID: PMC8308094 DOI: 10.3390/cancers13143529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 01/19/2023] Open
Abstract
Simple Summary A type of DNA mismatch repair defect known as “elevated microsatellite alterations at selected tetranucleotide repeats” (EMAST) is found across many different cancers. Tetranucleotide microsatellite instability, which is caused by MSH3 mismatch repair gene/protein loss-of-function, shares a molecular basis with “low microsatellite instability” (MSI-L) in colorectal cancer. Tetranucleotide microsatellite instability is also a byproduct of “high microsatellite instability” (MSI-H) that arises from deficiency of mismatch repair due to MSH2, MSH6, MLH1 or PMS2 gene alterations. MSH3-related EMAST is emerging as a biomarker of poor prognosis in colorectal cancer and needs to be clearly differentiated from MSI-H. Here, we show that tumours with non-MSI-H-related EMAST or MSI-L rarely show concordant promoter methylation of multiple marker genes. Colorectal tumours that are positive for a single (1/5) tetranucleotide repeat marker are an important subset of the EMAST spectrum. Abstract MSH3 gene or protein deficiency or loss-of-function in colorectal cancer can cause a DNA mismatch repair defect known as “elevated microsatellite alterations at selected tetranucleotide repeats” (EMAST). A high percentage of MSI-H tumors exhibit EMAST, while MSI-L is also linked with EMAST. However, the distribution of CpG island methylator phenotype (CIMP) within the EMAST spectrum is not known. Five tetranucleotide repeat and five MSI markers were used to classify 100 sporadic colorectal tumours for EMAST, MSI-H and MSI-L according to the number of unstable markers detected. Promoter methylation was determined using methylation-specific PCR for MSH3, MCC, CDKN2A (p16) and five CIMP marker genes. EMAST was found in 55% of sporadic colorectal carcinomas. Carcinomas with only one positive marker (EMAST-1/5, 26%) were associated with advanced tumour stage, increased lymph node metastasis, MSI-L and lack of CIMP-H. EMAST-2/5 (16%) carcinomas displayed some methylation but MSI was rare. Carcinomas with ≥3 positive EMAST markers (13%) were more likely to have a proximal colon location and be MSI-H and CIMP-H. Our study suggests that EMAST/MSI-L is a valuable prognostic and predictive marker for colorectal carcinomas that do not display the high methylation phenotype CIMP-H.
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Affiliation(s)
- Sabine Meessen
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (S.M.); (N.C.)
| | - Nicola Currey
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (S.M.); (N.C.)
| | - Zeenat Jahan
- The Woolcock Institute of Medical Research, The University of Sydney, Sydney, NSW 2037, Australia; (Z.J.); (H.W.P.)
| | - Hannah W. Parker
- The Woolcock Institute of Medical Research, The University of Sydney, Sydney, NSW 2037, Australia; (Z.J.); (H.W.P.)
- Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Mark A. Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC 3000, Australia; (M.A.J.); (J.L.H.)
| | - Daniel D. Buchanan
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3010, Australia;
- University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, VIC 3010, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Melbourne, VIC 3010, Australia
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC 3000, Australia; (M.A.J.); (J.L.H.)
| | - Eva Segelov
- Department of Oncology, Monash University and Monash Health, Melbourne, VIC 3168, Australia;
| | - Jane E. Dahlstrom
- ACT Pathology, The Canberra Hospital and Australian National University Medical School, Canberra, ACT 2605, Australia;
| | - Maija R. J. Kohonen-Corish
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (S.M.); (N.C.)
- The Woolcock Institute of Medical Research, The University of Sydney, Sydney, NSW 2037, Australia; (Z.J.); (H.W.P.)
- Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
- Microbiome Research Centre, St George & Sutherland Clinical School, UNSW Sydney, Sydney, NSW 2217, Australia
- School of Medicine, Western Sydney University, Sydney, NSW 2751, Australia
- Correspondence:
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17
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Aswath K, Welch J, Gubbi S, Veeraraghavan P, Avadhanula S, Gara SK, Dikoglu E, Merino M, Raffeld M, Xi L, Kebebew E, Klubo-Gwiezdzinska J. Co-Occurrence of Familial Non-Medullary Thyroid Cancer (FNMTC) and Hereditary Non-Polyposis Colorectal Cancer (HNPCC) Associated Tumors-A Cohort Study. Front Endocrinol (Lausanne) 2021; 12:653401. [PMID: 34326811 PMCID: PMC8315151 DOI: 10.3389/fendo.2021.653401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/11/2021] [Indexed: 12/11/2022] Open
Abstract
Familial non-medullary thyroid cancer (FNMTC) is a form of endocrine malignancy exhibiting an autosomal dominant mode of inheritance with largely unknown germline molecular mechanism. Hereditary nonpolyposis colorectal cancer syndrome (HNPCC) is another hereditary autosomal dominant cancer syndrome which, if proven to be caused by germline mutations in mismatch repair genes (MMR)-MLHL, MSH2, MSH6, PMS2, and EPCAM-is called Lynch syndrome (LS). LS results in hereditary predisposition to a number of cancers, especially colorectal and endometrial cancers. Tumors in LS are characterized by microsatellite instability (MSI) and/or loss of MMR protein expression in immunohistochemistry (IHC). MSI is a rare event in thyroid cancer (TC), although it is known to occur in up to 2.5% of sporadic follicular TC cases. There are limited data on the role of germline MMR variants FNMTC. The goal of this study was to analyze the potential clinical and molecular association between HNPCC and FNMTC. We performed a cohort study analyzing the demographic, clinical, and pathologic data of 43 kindreds encompassing 383 participants (104 affected, 279 unaffected), aged 43.5 [7-99] years with FNMTC, and performed high-throughput whole-exome sequencing (WES) of peripheral blood DNA samples of selected 168 participants (54 affected by FNMTC and 114 unaffected). Total affected by thyroid cancer members per family ranged between 2 and 9 patients. FNMTC was more prevalent in women (68.3%) and characterized by a median tumor size of 1.0 [0.2-5.0] cm, multifocal growth in 44%, and gross extrathyroidal extension in 11.3%. Central neck lymph node metastases were found in 40.3% of patients at presentation, 12.9% presented with lateral neck lymph node metastases, and none had distant metastases. Family history screening revealed one Caucasian family meeting the clinical criteria for FNMTC and HNPCC, with five members affected by FNMTC and at least eight individuals reportedly unaffected by HNPCC-associated tumors. In addition, two family members were affected by melanoma. Genome Analysis Tool Kit (GATK) pipeline was used in variant analysis. Among 168 sequenced participants, a heterozygous missense variant in the MSH2 gene (rs373226409; c.2120G>A; p.Cys707Tyr) was detected exclusively in FNMTC- HNPCC- kindred. In this family, the sequencing was performed in one member affected by FNMTC, HPNCC-associated tumors and melanoma, one member affected solely by HNPCC-associated tumor, and one member with FNMTC only, as well as seven unaffected family members. The variant was present in all three affected adults, and in two unaffected children of the affected member, under the age of 18 years, and was absent in non-affected adults. This variant is predicted to be damaging/pathogenic in 17/20 in-silico models. However, immunostaining performed on the thyroid tumor tissue of two affected by FNMTC family members revealed intact nuclear expression of MSH2, and microsatellite stable status in both tumors that were tested. Although the MSH2 p.Cys707Tyr variant is rare with a minor allele frequency (MAF) of 0.00006 in Caucasians; it is more common in the South Asian population at 0.003 MAF. Therefore, the MSH2 variant observed in this family is unlikely to be an etiologic factor of thyroid cancer and a common genetic association between FNMTC and HNPCC has not yet been identified. This is the first report known to us on the co-occurrence of FNMTC and HNPCC. The co-occurrence of FNMTC and HNPCC-associated tumors is a rare event and although presented in a single family in our large FNMTC cohort, a common genetic background between the two comorbidities could not be established.
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Affiliation(s)
- Kshama Aswath
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - James Welch
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sriram Gubbi
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Padmasree Veeraraghavan
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Shirisha Avadhanula
- Department of Endocrinology, Diabetes and Metabolism, Cleveland Clinic, Cleveland, OH, United States
| | - Sudheer Kumar Gara
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Esra Dikoglu
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Maria Merino
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Mark Raffeld
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Liqiang Xi
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Electron Kebebew
- Department of Surgery, Stanford University, Stanford, CA, United States
| | - Joanna Klubo-Gwiezdzinska
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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Joo JE, Clendenning M, Wong EM, Rosty C, Mahmood K, Georgeson P, Winship IM, Preston SG, Win AK, Dugué PA, Jayasekara H, English D, Macrae FA, Hopper JL, Jenkins MA, Milne RL, Giles GG, Southey MC, Buchanan DD. DNA Methylation Signatures and the Contribution of Age-Associated Methylomic Drift to Carcinogenesis in Early-Onset Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13112589. [PMID: 34070516 PMCID: PMC8199056 DOI: 10.3390/cancers13112589] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The role of DNA methylation in the carcinogenesis of colorectal cancer (CRC) diagnosed <50 years of age (early-onset CRC or EOCRC) is currently unknown. In this study, we investigated the genome-wide DNA methylation of 97 tumour and 54 normal colonic mucosa samples from people with EOCRC with the aim of identifying unique DNA methylation signatures and determining the role of ageing-related DNA methylation drift and age-acceleration in EOCRC aetiology. We found extensive DNA methylation alterations associated with EOCRC carcinogenesis, including a unique signature comprising 234 loci compared with CRCs from people >50 years of age. CpGs that undergo ageing-related methylation drift were significantly altered in EOCRC, and accelerated ageing was also evident in normal mucosa from people with EOCRC. Our study is the first study to identify unique DNA methylation changes in EOCRC, contributing novel information that may aid future efforts towards EOCRC prevention. Abstract We investigated aberrant DNA methylation (DNAm) changes and the contribution of ageing-associated methylomic drift and age acceleration to early-onset colorectal cancer (EOCRC) carcinogenesis. Genome-wide DNAm profiling using the Infinium HM450K on 97 EOCRC tumour and 54 normal colonic mucosa samples was compared with: (1) intermediate-onset CRC (IOCRC; diagnosed between 50–70 years; 343 tumour and 35 normal); and (2) late-onset CRC (LOCRC; >70 years; 318 tumour and 40 normal). CpGs associated with age-related methylation drift were identified using a public dataset of 231 normal mucosa samples from people without CRC. DNAm-age was estimated using epiTOC2. Common to all three age-of-onset groups, 88,385 (20% of all CpGs) CpGs were differentially methylated between tumour and normal mucosa. We identified 234 differentially methylated genes that were unique to the EOCRC group; 13 of these DMRs/genes were replicated in EOCRC compared with LOCRCs from TCGA. In normal mucosa from people without CRC, we identified 28,154 CpGs that undergo ageing-related DNAm drift, and of those, 65% were aberrantly methylated in EOCRC tumours. Based on the mitotic-based DNAm clock epiTOC2, we identified age acceleration in normal mucosa of people with EOCRC compared with normal mucosa from the IOCRC, LOCRC groups (p = 3.7 × 10−16) and young people without CRC (p = 5.8 × 10−6). EOCRC acquires unique DNAm alterations at 234 loci. CpGs associated with ageing-associated drift were widely affected in EOCRC without needing the decades-long accrual of DNAm drift as commonly seen in intermediate- and late-onset CRCs. Accelerated ageing in normal mucosa from people with EOCRC potentially underlies the earlier age of diagnosis in CRC carcinogenesis.
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Affiliation(s)
- Jihoon E. Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Melbourne 3010, Australia; (J.E.J.); (M.C.); (C.R.); (K.M.); (P.G.); (S.G.P.); (H.J.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Melbourne 3000, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Melbourne 3010, Australia; (J.E.J.); (M.C.); (C.R.); (K.M.); (P.G.); (S.G.P.); (H.J.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Melbourne 3000, Australia
| | - Ee Ming Wong
- Precision Medicine, Monash Health, Monash University, Clayton, Melbourne 3800, Australia; (E.M.W.); (P.-A.D.); (R.L.M.); (G.G.G.); (M.C.S.)
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Melbourne 3010, Australia; (J.E.J.); (M.C.); (C.R.); (K.M.); (P.G.); (S.G.P.); (H.J.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Melbourne 3000, Australia
- School of Medicine, University of Queensland, Herston, Brisbane 4006, Australia
- Envoi Pathology, Brisbane 4059, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Melbourne 3010, Australia; (J.E.J.); (M.C.); (C.R.); (K.M.); (P.G.); (S.G.P.); (H.J.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Melbourne 3000, Australia
- Melbourne Bioinformatics, The University of Melbourne, Parkville, Melbourne 3010, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Melbourne 3010, Australia; (J.E.J.); (M.C.); (C.R.); (K.M.); (P.G.); (S.G.P.); (H.J.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Melbourne 3000, Australia
| | - Ingrid M. Winship
- Department of Medicine, The Royal Melbourne Hospital, University of Melbourne, Parkville, Melbourne 3050, Australia; (I.M.W.); (F.A.M.)
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne 3050, Australia
| | - Susan G. Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Melbourne 3010, Australia; (J.E.J.); (M.C.); (C.R.); (K.M.); (P.G.); (S.G.P.); (H.J.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Melbourne 3000, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne 3010, Australia; (A.K.W.); (D.E.); (J.L.H.); (M.A.J.)
| | - Pierre-Antoine Dugué
- Precision Medicine, Monash Health, Monash University, Clayton, Melbourne 3800, Australia; (E.M.W.); (P.-A.D.); (R.L.M.); (G.G.G.); (M.C.S.)
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne 3010, Australia; (A.K.W.); (D.E.); (J.L.H.); (M.A.J.)
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne 3004, Australia
| | - Harindra Jayasekara
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Melbourne 3010, Australia; (J.E.J.); (M.C.); (C.R.); (K.M.); (P.G.); (S.G.P.); (H.J.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Melbourne 3000, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne 3004, Australia
| | - Dallas English
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne 3010, Australia; (A.K.W.); (D.E.); (J.L.H.); (M.A.J.)
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne 3004, Australia
| | - Finlay A. Macrae
- Department of Medicine, The Royal Melbourne Hospital, University of Melbourne, Parkville, Melbourne 3050, Australia; (I.M.W.); (F.A.M.)
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne 3050, Australia
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, Melbourne 3050, Australia
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne 3010, Australia; (A.K.W.); (D.E.); (J.L.H.); (M.A.J.)
| | - Mark A. Jenkins
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne 3010, Australia; (A.K.W.); (D.E.); (J.L.H.); (M.A.J.)
| | - Roger L. Milne
- Precision Medicine, Monash Health, Monash University, Clayton, Melbourne 3800, Australia; (E.M.W.); (P.-A.D.); (R.L.M.); (G.G.G.); (M.C.S.)
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne 3010, Australia; (A.K.W.); (D.E.); (J.L.H.); (M.A.J.)
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne 3004, Australia
| | - Graham G. Giles
- Precision Medicine, Monash Health, Monash University, Clayton, Melbourne 3800, Australia; (E.M.W.); (P.-A.D.); (R.L.M.); (G.G.G.); (M.C.S.)
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne 3010, Australia; (A.K.W.); (D.E.); (J.L.H.); (M.A.J.)
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne 3004, Australia
| | - Melissa C. Southey
- Precision Medicine, Monash Health, Monash University, Clayton, Melbourne 3800, Australia; (E.M.W.); (P.-A.D.); (R.L.M.); (G.G.G.); (M.C.S.)
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne 3004, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, Melbourne 3010, Australia
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Melbourne 3010, Australia; (J.E.J.); (M.C.); (C.R.); (K.M.); (P.G.); (S.G.P.); (H.J.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Melbourne 3000, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne 3050, Australia
- Correspondence: ; Tel.: +61-3-8559-7004
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19
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Pope BJ, Clendenning M, Rosty C, Mahmood K, Georgeson P, Joo JE, Walker R, Hutchinson RA, Jayasekara H, Joseland S, Como J, Preston S, Spurdle AB, Macrae FA, Win AK, Hopper JL, Jenkins MA, Winship IM, Buchanan DD. Germline and Tumor Sequencing as a Diagnostic Tool To Resolve Suspected Lynch Syndrome. J Mol Diagn 2021; 23:358-371. [PMID: 33383211 PMCID: PMC7927277 DOI: 10.1016/j.jmoldx.2020.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 11/13/2020] [Accepted: 12/15/2020] [Indexed: 12/22/2022] Open
Abstract
Patients in whom mismatch repair (MMR)-deficient cancer develops in the absence of pathogenic variants of germline MMR genes or somatic hypermethylation of the MLH1 gene promoter are classified as having suspected Lynch syndrome (SLS). Germline whole-genome sequencing (WGS) and targeted and genome-wide tumor sequencing were applied to identify the underlying cause of tumor MMR deficiency in SLS. Germline WGS was performed on samples from 14 cancer-affected patients with SLS, including two sets of first-degree relatives. MMR genes were assessed for germline pathogenic variants, including complex structural rearrangements and noncoding variants. Tumor tissue was assessed for somatic MMR gene mutations using targeted, whole-exome sequencing or WGS. Germline WGS identified pathogenic MMR variants in 3 of the 14 cases (21.4%), including a 9.5-megabase inversion disrupting MSH2 in a mother and daughter. Excluding these 3 MMR carriers, tumor sequencing identified at least two somatic MMR gene mutations in 8 of 11 tumors tested (72.7%). In a second mother-daughter pair, a somatic cause of tumor MMR deficiency was supported by the presence of double somatic MSH2 mutations in their respective tumors. More than 70% of SLS cases had double somatic MMR mutations in the absence of germline pathogenic variants in the MMR or other DNA repair-related genes on WGS, and, therefore, were confidently assigned a noninherited cause of tumor MMR deficiency.
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Affiliation(s)
- Bernard J Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Melbourne Bioinformatics, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Envoi Specialist Pathologists, Brisbane, Queensland, Australia; School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Melbourne Bioinformatics, The University of Melbourne, Parkville, Victoria, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Ryan A Hutchinson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Harindra Jayasekara
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Division of Cancer Epidemiology, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Susan Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Amanda B Spurdle
- Molecular Cancer Epidemiology Laboratory, Berghofer Medical Research Institute, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Finlay A Macrae
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Parkville, Victoria, Australia; Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Aung K Win
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, Victoria, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Parkville, Victoria, Australia; Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia.
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20
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Diagnosis of Lynch Syndrome and Strategies to Distinguish Lynch-Related Tumors from Sporadic MSI/dMMR Tumors. Cancers (Basel) 2021; 13:cancers13030467. [PMID: 33530449 PMCID: PMC7865821 DOI: 10.3390/cancers13030467] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Microsatellite instability (MSI) is a hallmark of Lynch syndrome (LS)-related tumors but is not specific, as most of MSI/mismatch repair-deficient (dMMR) tumors are sporadic. Therefore, the identification of MSI/dMMR requires additional diagnostic tools to identify LS. In this review, we address the hallmarks of LS and present recent advances in diagnostic and screening strategies to identify LS patients. We also discuss the pitfalls associated with current strategies, which should be taken into account in order to improve the diagnosis of LS. Abstract Microsatellite instability (MSI) is a hallmark of Lynch syndrome (LS)-related tumors but is not specific to it, as approximately 80% of MSI/mismatch repair-deficient (dMMR) tumors are sporadic. Methods leading to the diagnosis of LS have considerably evolved in recent years and so have tumoral tests for LS screening and for the discrimination of LS-related to MSI-sporadic tumors. In this review, we address the hallmarks of LS, including the clinical, histopathological, and molecular features. We present recent advances in diagnostic and screening strategies to identify LS patients. We also discuss the pitfalls associated with the current strategies, which should be taken into account to improve the diagnosis of LS and avoid inappropriate clinical management.
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21
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Neumeyer S, Hua X, Seibold P, Jansen L, Benner A, Burwinkel B, Halama N, Berndt SI, Phipps AI, Sakoda LC, Schoen RE, Slattery ML, Chan AT, Gala M, Joshi AD, Ogino S, Song M, Herpel E, Bläker H, Kloor M, Scherer D, Ulrich A, Ulrich CM, Win AK, Figueiredo JC, Hopper JL, Macrae F, Milne RL, Giles GG, Buchanan DD, Peters U, Hoffmeister M, Brenner H, Newcomb PA, Chang-Claude J. Genetic Variants in the Regulatory T cell-Related Pathway and Colorectal Cancer Prognosis. Cancer Epidemiol Biomarkers Prev 2020; 29:2719-2728. [PMID: 33008876 PMCID: PMC7976673 DOI: 10.1158/1055-9965.epi-20-0714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/29/2020] [Accepted: 09/28/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND High numbers of lymphocytes in tumor tissue, including T regulatory cells (Treg), have been associated with better colorectal cancer survival. Tregs, a subset of CD4+ T lymphocytes, are mediators of immunosuppression in cancer, and therefore variants in genes related to Treg differentiation and function could be associated with colorectal cancer prognosis. METHODS In a prospective German cohort of 3,593 colorectal cancer patients, we assessed the association of 771 single-nucleotide polymorphisms (SNP) in 58 Treg-related genes with overall and colorectal cancer-specific survival using Cox regression models. Effect modification by microsatellite instability (MSI) status was also investigated because tumors with MSI show greater lymphocytic infiltration and have been associated with better prognosis. Replication of significant results was attempted in 2,047 colorectal cancer patients of the International Survival Analysis in Colorectal Cancer Consortium (ISACC). RESULTS A significant association of the TGFBR3 SNP rs7524066 with more favorable colorectal cancer-specific survival [hazard ratio (HR) per minor allele: 0.83; 95% confidence interval (CI), 0.74-0.94; P value: 0.0033] was replicated in ISACC (HR: 0.82; 95% CI, 0.68-0.98; P value: 0.03). Suggestive evidence for association was found with two IL7 SNPs, rs16906568 and rs7845577. Thirteen SNPs with differential associations with overall survival according to MSI in the discovery analysis were not confirmed. CONCLUSIONS Common genetic variation in the Treg pathway implicating genes such as TGFBR3 and IL7 was shown to be associated with prognosis of colorectal cancer patients. IMPACT The implicated genes warrant further investigation.
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Affiliation(s)
- Sonja Neumeyer
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Xinwei Hua
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- School of Public Health, University of Washington, Seattle, Washington
| | - Petra Seibold
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lina Jansen
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Burwinkel
- Division of Molecular Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Gynecology and Obstetrics, Molecular Biology of Breast Cancer, University of Heidelberg, Heidelberg, Germany
| | - Niels Halama
- Department of Medical Oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Tissue Imaging and Analysis Center, National Center for Tumor Diseases, BIOQUANT, University of Heidelberg, Heidelberg, Germany
- Institute for Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Epidemiology Department, University of Washington, Seattle, Washington
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Mingyang Song
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Esther Herpel
- NCT Tissue Bank, National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hendrik Bläker
- Institute of Pathology, Charité University Medicine, Berlin, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Dominique Scherer
- Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Heidelberg, Germany
| | - Alexis Ulrich
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, University of Heidelberg, Germany
| | - Cornelia M Ulrich
- Huntsman Cancer Institute, Population Sciences, Salt Lake City, Utah
- Department of Population Health Sciences, University of Utah, Salt Lake City, Utah
| | - Aung K Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Melbourne, Australia
| | - Jane C Figueiredo
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles California
| | - John L Hopper
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Victoria, Australia
| | - Finlay Macrae
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Victoria, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Melbourne, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Melbourne, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Polly A Newcomb
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Cancer Epidemiology Group, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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22
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Worldwide variation in lynch syndrome screening: case for universal screening in low colorectal cancer prevalence areas. Fam Cancer 2020; 20:145-156. [PMID: 32914371 DOI: 10.1007/s10689-020-00206-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023]
Abstract
To perform a systematic assessment of universal Lynch syndrome (LS) screening yield in colorectal cancer (CRC) patients around the world. Universal screening for LS is recommended in all CRC patients. However, the variation in yield of LS screening in the setting of significant global variation in CRC prevalence is unknown. A systematic review of articles in the MEDLINE database was performed to identify studies performing universal screening for LS. All cases with microsatellite instability (MSI-H) or missing one or more proteins on immunohistochemistry (IHC) were considered screening positive. The overall pooled yield of universal LS screening in 97 study arms from 89 identified studies was 11.9% (5649/47545) and the overall pooled percentage of confirmed LS patients was 1.8% (682/37220). LS screening positivity varied significantly based on geographic region (Kruskal Wallis test, p < 0.001) and reported 5-year CRC prevalence in the country (Fisher's exact, p < 0.001). Significant inverse correlation was found between LS screening positivity and 5-year CRC prevalence (Pearson correlation, r = - 0.56, p < 0.001). The overall yield of LS screening was 15.00% (382/2553) and rate of confirmed LS was 7.7% (113/1475) in LS screening done in patients ≤ 50 years (16 studies). There is significant geographic variation in LS screening positivity with higher yield in countries with lower prevalence of CRC. Our results highlight the importance of universal LS screening in younger patients and low CRC prevalence countries.
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Ikenoue T, Arai M, Ishioka C, Iwama T, Kaneko S, Matsubara N, Moriya Y, Nomizu T, Sugano K, Tamura K, Tomita N, Yoshida T, Sugihara K, Naruse H, Yamaguchi K, Nojima M, Nakamura Y, Furukawa Y. Importance of gastric cancer for the diagnosis and surveillance of Japanese Lynch syndrome patients. J Hum Genet 2019; 64:1187-1194. [DOI: 10.1038/s10038-019-0674-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/11/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
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Li D, Hoodfar E, Jiang SF, Udaltsova N, Pham NP, Jodesty Y, Armstrong MA, Hung YY, Baker RJ, Postlethwaite D, Ladabaum U, Levin TR, Corley DA, Bergoffen J. Comparison of Universal Versus Age-Restricted Screening of Colorectal Tumors for Lynch Syndrome Using Mismatch Repair Immunohistochemistry: A Cohort Study. Ann Intern Med 2019; 171:19-26. [PMID: 31181578 DOI: 10.7326/m18-3316] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Guidelines recommend screening all patients with newly diagnosed colorectal cancer (CRC) for Lynch syndrome (LS). However, the efficiency of universal LS screening in elderly populations has not been well studied. OBJECTIVE To compare the performance of age-restricted and universal LS screening using reflex mismatch repair (MMR) immunohistochemistry (IHC) of CRC tumors. DESIGN Retrospective cohort study. SETTING A large, diverse, community-based health care system. PARTICIPANTS 3891 persons with newly diagnosed CRC who had LS screening between 2011 and 2016. MEASUREMENTS Diagnostic yield of different LS screening strategies. RESULTS Sixty-three LS cases (diagnostic yield, 1.62%) were identified by universal screening, with only 5 (7.9%) detected after age 70 years and 1 (1.6%) detected after age 80 years. When all patients with CRC who had universal screening were used as the denominator, 58 LS cases (diagnostic yield, 1.49% [95% CI, 1.13% to 1.92%]) were identified in patients with CRC diagnosed at or before age 70 years, 60 LS cases (diagnostic yield, 1.54% [CI, 1.18% to 1.98%]) were identified in those with CRC diagnosed at or before age 75 years, and 62 LS cases (diagnostic yield, 1.59% [CI, 1.22% to 2.04%]) were identified in those with CRC diagnosed at or before age 80 years. Using 75 years as the upper age limit for screening missed 3 of 63 (4.8%) LS cases but resulted in 1053 (27.1%) fewer cases requiring tumor MMR IHC. Using 80 years as the upper age limit missed 1 of 63 (1.6%) LS cases and resulted in 668 (17.2%) fewer cases requiring tumor MMR IHC. LIMITATION Persons who were eligible for but did not complete germline analysis were excluded from calculations of performance characteristics. CONCLUSION The incremental diagnostic yield decreased substantially after age 70 to 75 years. Stopping reflex CRC screening for LS after age 80 years may be reasonable because of very low efficiency, particularly in resource-limited settings, but this merits further investigation. Studies evaluating the effect of diagnosing LS in elderly persons on their family members are needed. PRIMARY FUNDING SOURCE Kaiser Permanente Northern California Division of Research.
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Affiliation(s)
- Dan Li
- Kaiser Permanente Northern California, Santa Clara, California, and Kaiser Permanente Northern California, Oakland, California (D.L.)
| | | | - Sheng-Fang Jiang
- Kaiser Permanente Northern California, Oakland, California (S.J., N.U., M.A.A., Y.H., D.P., D.A.C.)
| | - Natalia Udaltsova
- Kaiser Permanente Northern California, Oakland, California (S.J., N.U., M.A.A., Y.H., D.P., D.A.C.)
| | - Nhung P Pham
- Kaiser Permanente Northern California, Santa Clara, California (N.P.P., Y.J.)
| | - Yves Jodesty
- Kaiser Permanente Northern California, Santa Clara, California (N.P.P., Y.J.)
| | - Mary Anne Armstrong
- Kaiser Permanente Northern California, Oakland, California (S.J., N.U., M.A.A., Y.H., D.P., D.A.C.)
| | - Yun-Yi Hung
- Kaiser Permanente Northern California, Oakland, California (S.J., N.U., M.A.A., Y.H., D.P., D.A.C.)
| | - Robin J Baker
- Kaiser Permanente Northern California, San Francisco, California (R.J.B.)
| | - Debbie Postlethwaite
- Kaiser Permanente Northern California, Oakland, California (S.J., N.U., M.A.A., Y.H., D.P., D.A.C.)
| | - Uri Ladabaum
- Stanford University School of Medicine, Stanford, California (U.L.)
| | - Theodore R Levin
- Kaiser Permanente Northern California, Walnut Creek, California (T.R.L.)
| | - Douglas A Corley
- Kaiser Permanente Northern California, Oakland, California (S.J., N.U., M.A.A., Y.H., D.P., D.A.C.)
| | - JoAnn Bergoffen
- Kaiser Permanente Northern California, San Jose, California (J.B.)
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25
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Georgeson P, Walsh MD, Clendenning M, Daneshvar S, Pope BJ, Mahmood K, Joo JE, Jayasekara H, Jenkins MA, Winship IM, Buchanan DD. Tumor mutational signatures in sebaceous skin lesions from individuals with Lynch syndrome. Mol Genet Genomic Med 2019; 7:e00781. [PMID: 31162827 PMCID: PMC6625139 DOI: 10.1002/mgg3.781] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/16/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Muir-Torre syndrome is defined by the development of sebaceous skin lesions in individuals who carry a germline mismatch repair (MMR) gene mutation. Loss of expression of MMR proteins is frequently observed in sebaceous skin lesions, but MMR-deficiency alone is not diagnostic for carrying a germline MMR gene mutation. METHODS Whole exome sequencing was performed on three MMR-deficient sebaceous lesions from individuals with MSH2 gene mutations (Lynch syndrome) and three MMR-proficient sebaceous lesions from individuals without Lynch syndrome with the aim of characterizing the tumor mutational signatures, somatic mutation burden, and microsatellite instability status. Thirty predefined somatic mutational signatures were calculated for each lesion. RESULTS Signature 1 was ubiquitous across the six lesions tested. Signatures 6 and 15, associated with defective DNA MMR, were significantly more prevalent in the MMR-deficient lesions from the MSH2 carriers compared with the MMR-proficient non-Lynch sebaceous lesions (mean ± SD=41.0 ± 8.2% vs. 2.3 ± 4.0%, p = 0.0018). Tumor mutation burden was, on average, significantly higher in the MMR-deficient lesions compared with the MMR-proficient lesions (23.3 ± 11.4 vs. 1.8 ± 0.8 mutations/Mb, p = 0.03). All four sebaceous lesions observed in sun exposed areas of the body demonstrated signature 7 related to ultraviolet light exposure. CONCLUSION Tumor mutational signatures 6 and 15 and somatic mutation burden were effective in differentiating Lynch-related from non-Lynch sebaceous lesions.
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Affiliation(s)
- Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Vic., Australia.,Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, Vic., Australia
| | | | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Vic., Australia.,Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, Vic., Australia
| | - Simin Daneshvar
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Vic., Australia.,Dorevitch Pathology, Frankston Hospital, Frankston, Vic., Australia
| | - Bernard J Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Vic., Australia.,Melbourne Bioinformatics, The University of Melbourne, Carlton, Vic., Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Vic., Australia.,Melbourne Bioinformatics, The University of Melbourne, Carlton, Vic., Australia
| | - Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Vic., Australia.,Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, Vic., Australia
| | - Harindra Jayasekara
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Vic., Australia.,Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, Vic., Australia.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Vic., Australia.,Centre for Alcohol Policy Research, La Trobe University, Melbourne, Vic., Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Vic., Australia
| | - Ingrid M Winship
- Department of Medicine, The University of Melbourne, Parkville, Vic., Australia.,Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Vic., Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Vic., Australia.,Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, Vic., Australia.,Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Vic., Australia
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26
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Joo JE, Jayasekara H, Wong EM, Clendenning M, Rosty C, Winship IM, Jenkins MA, Hopper JL, English DR, Milne RL, Giles GG, Southey MC, Buchanan DD. Assessing the ProMCol classifier as a prognostic marker for non-metastatic colorectal cancer within the Melbourne Collaborative Cohort Study. Gut 2019; 68:761-762. [PMID: 29574407 DOI: 10.1136/gutjnl-2018-316122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 03/06/2018] [Accepted: 03/14/2018] [Indexed: 12/08/2022]
Affiliation(s)
- Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia.,Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Melbourne, Victoria, Australia
| | - Harindra Jayasekara
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia.,Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Melbourne, Victoria, Australia.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Alcohol Policy Research, La Trobe University, Melbourne, Victoria, Australia
| | - Ee Ming Wong
- Precision Medicine, Monash University, Clayton, Victoria, Australia.,Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia.,Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Melbourne, Victoria, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia.,Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Melbourne, Victoria, Australia.,Envoi Pathology, Brisbane, Queensland, Australia.,School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Ingrid M Winship
- Department of Medicine, The University of Melbourne, Melbourne, Victoria, Australia.,Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Carlton, Victoria, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Carlton, Victoria, Australia
| | - Dallas R English
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, The University of Melbourne, Carlton, Victoria, Australia
| | - Roger L Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, The University of Melbourne, Carlton, Victoria, Australia
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, The University of Melbourne, Carlton, Victoria, Australia
| | - Melissa C Southey
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Melbourne, Victoria, Australia.,Precision Medicine, Monash University, Clayton, Victoria, Australia.,Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia.,Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Melbourne, Victoria, Australia.,Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, The University of Melbourne, Carlton, Victoria, Australia
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27
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Yozu M, Kumarasinghe MP, Brown IS, Gill AJ, Rosty C. Australasian Gastrointestinal Pathology Society (AGPS) consensus guidelines for universal defective mismatch repair testing in colorectal carcinoma. Pathology 2019; 51:233-239. [DOI: 10.1016/j.pathol.2018.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 11/18/2018] [Accepted: 11/25/2018] [Indexed: 01/28/2023]
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28
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Kašubová I, Kalman M, Jašek K, Burjanivová T, Malicherová B, Vaňochová A, Meršaková S, Lasabová Z, Plank L. Stratification of patients with colorectal cancer without the recorded family history. Oncol Lett 2019; 17:3649-3656. [PMID: 30881489 PMCID: PMC6403522 DOI: 10.3892/ol.2019.10018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 12/20/2018] [Indexed: 12/28/2022] Open
Abstract
Colorectal cancer (CRC) is a multifactorial disease and one of the most malignant tumours. In addition to the sporadic form, familial occurrences, particularly hereditary non-polyposis CRC-Lynch syndrome (LS)-are often observed. LS is caused by a germline mutation in mismatch repair (MMR) genes, whose task it is to correct errors in the DNA structure that result from its replication. The aim of the present study was to stratify CRC patients using molecular diagnostics and next generation sequencing, according to the chosen criteria [positive for microsatellite instability (MSI) and negative for a BRAF mutation and MutL homolog 1 (MLH1) methylation], and subsequently to detect pathological germline mutations in MMR genes in Slovak patients. To exclude patients with MSI from further testing, the present study detected the BRAF V600E mutation and examined MLH1 methylation status. From the 300 CRC patients, 37 cases with MSI were identified. In the MSI-positive samples, 13 cases of BRAF V600E mutation were recorded. In 24 BRAF-negative patients, 11 cases of epigenetic methylation of MLH1 and 12 cases without MLH1 methylation suspected for LS were detected, and it was not possible to analyse the methylation phenotype of 1 sample. Thus, the present study reports the novel deletion of four nucleotides, 1627_1630del AAAG (Glu544Lysfs*26) in MSH6, probably associated with LS. A second case with a nonsense mutation in MSH was also detected, namely MMR_c.1030C>T (p.Q344X).
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Affiliation(s)
- Ivana Kašubová
- Division of Oncology, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin, Biomedical Center Martin, SK-03601 Martin, Slovakia
| | - Michal Kalman
- Department of Pathological Anatomy, Jessenius Faculty of Medicine in Martin and University Hospital in Martin, SK-03659 Martin, Slovakia
| | - Karin Jašek
- Division of Oncology, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin, Biomedical Center Martin, SK-03601 Martin, Slovakia
| | - Tatiana Burjanivová
- Division of Oncology, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin, Biomedical Center Martin, SK-03601 Martin, Slovakia
| | - Bibiana Malicherová
- Division of Oncology, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin, Biomedical Center Martin, SK-03601 Martin, Slovakia
| | - Andrea Vaňochová
- Department of Molecular Biology, Jessenius Faculty of Medicine in Martin, SK-03601 Martin, Slovakia
| | - Sandra Meršaková
- Division of Oncology, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin, Biomedical Center Martin, SK-03601 Martin, Slovakia
| | - Zora Lasabová
- Division of Oncology, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin, Biomedical Center Martin, SK-03601 Martin, Slovakia.,Department of Molecular Biology, Jessenius Faculty of Medicine in Martin, SK-03601 Martin, Slovakia
| | - Lukáš Plank
- Department of Pathological Anatomy, Jessenius Faculty of Medicine in Martin and University Hospital in Martin, SK-03659 Martin, Slovakia
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29
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Mascarenhas L, Shanley S, Mitchell G, Spurdle AB, Macrae F, Pachter N, Buchanan DD, Ward RL, Fox S, Duxbury E, Driessen R, Boussioutas A. Current mismatch repair deficiency tumor testing practices and capabilities: A survey of Australian pathology providers. Asia Pac J Clin Oncol 2018; 14:417-425. [PMID: 30294856 DOI: 10.1111/ajco.13076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 06/17/2018] [Indexed: 12/13/2022]
Abstract
AIM & METHODS An electronic survey of the Royal College of Pathologists of Australasia accredited pathology services was conducted to assess Lynch syndrome tumor screening practices and to identify barriers and capabilities to screen newly diagnosed colorectal and endometrial tumors in Australia. RESULTS Australia lacks a national policy for universal mismatch repair-deficient (dMMR) testing of incident colorectal and endometrial tumors cases. Routine Lynch syndrome tumor screening program for colorectal and/or endometrial tumors was applied by 95% (37/39) of laboratories. Tumor dMMR screening methods varied; MMR protein immunohistochemistry (IHC) alone was undertaken by 77% of 39 laboratories, 18% performed both IHC and microsatellite instability testing, 5% did not have the capacity to perform in-house testing. For colorectal tumors, 47% (17/36) reported following a universal approach without age limit, 30% (11/36) tested only "red flag" cases; 6% (3/36) on clinician request only. For endometrial tumors, 37% (12/33) reported clinician request generated testing, 27% (9/33) were screening only "red flag" cases, and 12% (4/33) carried out universal screening without an age criteria. BRAF V600E mutation testing of colorectal tumors demonstrating aberrant MLH1 protein expression by IHC was the most common secondary tumor test, with 53% of laboratories performing the test; 15% of laboratories also applied the BRAF V600E test to endometrial tumors with aberrant MLH1 expression despite no evidence for its utility. Tumor testing for MLH1 promoter methylation was performed by less than 15% laboratories. CONCLUSION Although use of tumor screening for evidence of dMMR is widely available, protocols for its use in Australia vary widely. This national survey provides a snapshot of the current availability and practice of tumor dMMR screening and identifies the need for a uniform national testing policy.
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Affiliation(s)
- Lyon Mascarenhas
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Susan Shanley
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Gillian Mitchell
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Finlay Macrae
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Nicholas Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia, Australia
- School of Medicine & Pharmacology, University of Western Australia, WA, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Robyn L Ward
- Office of Deputy Vice Chancellor (Research), University of Queensland, Brisbane, Queensland, Australia
| | - Stephen Fox
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | | | - Rebecca Driessen
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Alex Boussioutas
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia
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30
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Cenin DR, Naber SK, Lansdorp‐Vogelaar I, Jenkins MA, Buchanan DD, Preen DB, Ee HC, O'Leary P. Costs and outcomes of Lynch syndrome screening in the Australian colorectal cancer population. J Gastroenterol Hepatol 2018; 33:1737-1744. [PMID: 29645364 PMCID: PMC6403824 DOI: 10.1111/jgh.14154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 03/22/2018] [Accepted: 03/24/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND AND AIM Individuals with Lynch syndrome (LS) are at increased risk of LS-related cancers including colorectal cancer (CRC). CRC tumor screening for mismatch repair (MMR) deficiency is recommended in Australia to identify LS, although its cost-effectiveness has not been assessed. We aim to determine the cost-effectiveness of screening individuals with CRC for LS at different age-at-diagnosis thresholds. METHODS We developed a decision analysis model to estimate yield and costs of LS screening. Age-specific probabilities of LS diagnosis were based on Australian data. Two CRC tumor screening pathways were assessed (MMR immunohistochemistry followed by MLH1 methylation (MLH1-Pathway) or BRAF V600E testing (BRAF-Pathway) if MLH1 expression was lost) for four age-at-diagnosis thresholds-screening < 50, screening < 60, screening < 70, and universal screening. RESULTS Per 1000 CRC cases, screening < 50 identified 5.2 LS cases and cost $A7041 per case detected in the MLH1-Pathway. Screening < 60 increased detection by 1.5 cases for an incremental cost of $A25 177 per additional case detected. Screening < 70 detected 1.6 additional cases at an incremental cost of $A40 278 per additional case detected. Compared with screening < 70, universal screening detected no additional LS cases but cost $A158 724 extra. The BRAF-Pathway identified the same number of LS cases for higher costs. CONCLUSIONS The MLH1-Pathway is more cost-effective than BRAF-Pathway for all age-at-diagnosis thresholds. MMR immunohistochemistry tumor screening in individuals diagnosed with CRC aged < 70 years resulted in higher LS case detection at a reasonable cost. Further research into the yield of LS screening in CRC patients ≥ 70 years is needed to determine if universal screening is justified.
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Affiliation(s)
- Dayna R Cenin
- Department of Public HealthErasmus Medical CenterRotterdamThe Netherlands,Faculty of Health SciencesCurtin UniversityPerthWestern AustraliaAustralia,Centre for Health Services Research, School of Population and Global HealthThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Steffie K Naber
- Department of Public HealthErasmus Medical CenterRotterdamThe Netherlands
| | | | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global HealthUniversity of MelbourneMelbourneVictoriaAustralia
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global HealthUniversity of MelbourneMelbourneVictoriaAustralia,Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of PathologyUniversity of MelbourneParkvilleVictoriaAustralia,Genetic Medicine and Familial Cancer CentreThe Royal Melbourne HospitalParkvilleVictoriaAustralia,Victorian Comprehensive Cancer CentreUniversity of Melbourne Centre for Cancer ResearchParkvilleVictoriaAustralia
| | - David B Preen
- Centre for Health Services Research, School of Population and Global HealthThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Hooi C Ee
- Department of GastroenterologySir Charles Gairdner HospitalPerthWestern AustraliaAustralia
| | - Peter O'Leary
- Faculty of Health SciencesCurtin UniversityPerthWestern AustraliaAustralia,School of Women's and Infants' HealthThe University of Western AustraliaPerthWestern AustraliaAustralia,PathWest Laboratory MedicineQE2 Medical CentreNedlandsWestern AustraliaAustralia
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31
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Pai RK, Dudley B, Karloski E, Brand RE, O’Callaghan N, Rosty C, Buchanan DD, Jenkins MA, Thibodeau SN, French AJ, Lindor NM, Pai RK. DNA mismatch repair protein deficient non-neoplastic colonic crypts: a novel indicator of Lynch syndrome. Mod Pathol 2018; 31:1608-1618. [PMID: 29884888 PMCID: PMC6396289 DOI: 10.1038/s41379-018-0079-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/20/2018] [Accepted: 04/22/2018] [Indexed: 02/06/2023]
Abstract
Lynch syndrome is the most common form of hereditary colorectal carcinoma. However, establishing the diagnosis of Lynch syndrome is challenging, and ancillary studies that distinguish between sporadic DNA mismatch repair (MMR) protein deficiency and Lynch syndrome are needed, particularly when germline mutation studies are inconclusive. The aim of this study was to determine if MMR protein-deficient non-neoplastic intestinal crypts can help distinguish between patients with and without Lynch syndrome. We evaluated the expression of MMR proteins in non-neoplastic intestinal mucosa obtained from colorectal surgical resection specimens from patients with Lynch syndrome-associated colorectal carcinoma (n = 52) and patients with colorectal carcinoma without evidence of Lynch syndrome (n = 70), including sporadic MMR protein-deficient colorectal carcinoma (n = 30), MMR protein proficient colorectal carcinoma (n = 30), and "Lynch-like" syndrome (n = 10). MMR protein-deficient non-neoplastic colonic crypts were identified in 19 of 122 (16%) patients. MMR protein-deficient colonic crypts were identified in 18 of 52 (35%) patients with Lynch syndrome compared to only 1 of 70 (1%) patients without Lynch syndrome (p < 0.001). This one patient had "Lynch-like" syndrome and harbored two MSH2-deficient non-neoplastic colonic crypts. MMR protein-deficient non-neoplastic colonic crypts were not identified in patients with sporadic MMR protein-deficient or MMR protein proficient colorectal carcinoma. Our findings suggest that MMR protein-deficient colonic crypts are a novel indicator of Lynch syndrome, and evaluation for MMR protein-deficient crypts may be a helpful addition to Lynch syndrome diagnostics.
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Affiliation(s)
- Rish K. Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, Arizona
| | - Beth Dudley
- Department of Internal Medicine, Division of Gastroenterology, Hereditary Tumor Program, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Eve Karloski
- Department of Internal Medicine, Division of Gastroenterology, Hereditary Tumor Program, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Randall E. Brand
- Department of Internal Medicine, Division of Gastroenterology, Hereditary Tumor Program, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Neil O’Callaghan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia.,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia.,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia,Envoi Specialist Pathologists, Herston, QLD, Australia.,University of Queensland, School of Medicine, Herston, QLD, Australia
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia.,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia,Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Mark A. Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria 3010 Australia
| | | | - Amy J. French
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN
| | - Noralane M. Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, USA
| | - Reetesh K. Pai
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA
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32
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Wang A, McCracken J, Li Y, Xu L. The practice of universal screening for Lynch syndrome in newly diagnosed endometrial carcinoma. Health Sci Rep 2018; 1:e43. [PMID: 30623082 PMCID: PMC6266449 DOI: 10.1002/hsr2.43] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/14/2018] [Accepted: 03/28/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Lynch syndrome (LS) accounts for 5% of all endometrial cancer (EC) cases and 4% of all lifetime risk of developing colorectal cancer. While current guidelines recommend LS screening for all patients with newly diagnosed colorectal cancer, there is no such guideline for screening patients with EC. DISCUSSION This review addresses LS screening and discusses algorithms for testing patients in the setting of newly diagnosed EC. CONCLUSION The successful diagnosis of LS has important implications, including prevention of LS-associated cancers among relatives and immunotherapy recommendations for patients with advanced EC and loss of expression of mismatch repair immunohistochemistry and microsatellite instability positive following failure of traditional treatment.
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Affiliation(s)
- Aifen Wang
- Department of Obstetrics and Gynecology, Zhangjiagang HospitalNanjing University of Chinese MedicineJiangsuChina215600
| | - Jenna McCracken
- Department of PathologyDuke University School of MedicineDurhamNCUSA
| | - Yanjing Li
- Department of PathologyDuke University School of MedicineDurhamNCUSA
| | - Lingfan Xu
- Department of PathologyDuke University School of MedicineDurhamNCUSA
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Jenkins MA, Win AK, Templeton AS, Angelakos MS, Buchanan DD, Cotterchio M, Figueiredo JC, Thibodeau SN, Baron JA, Potter JD, Hopper JL, Casey G, Gallinger S, Le Marchand L, Lindor NM, Newcomb PA, Haile RW. Cohort Profile: The Colon Cancer Family Registry Cohort (CCFRC). Int J Epidemiol 2018; 47:387-388i. [PMID: 29490034 PMCID: PMC5913593 DOI: 10.1093/ije/dyy006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/19/2017] [Accepted: 01/15/2018] [Indexed: 01/02/2023] Open
Affiliation(s)
- Mark A Jenkins
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
- Genetic Medicine, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Allyson S Templeton
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Maggie S Angelakos
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
- Genetic Medicine, Royal Melbourne Hospital, Parkville, VIC, Australia
- Colorectal Oncogenomics Group, University of Melbourne, Parkville, VIC, Australia
| | | | - Jane C Figueiredo
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - John A Baron
- Department of Medicine, University of North Carolina School of Medicine, and Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- School of Public Health, University of Washington, Seattle, WA, USA
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | | | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- School of Public Health, University of Washington, Seattle, WA, USA
| | - Robert W Haile
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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34
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Lorans M, Dow E, Macrae FA, Winship IM, Buchanan DD. Update on Hereditary Colorectal Cancer: Improving the Clinical Utility of Multigene Panel Testing. Clin Colorectal Cancer 2018; 17:e293-e305. [PMID: 29454559 DOI: 10.1016/j.clcc.2018.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/17/2017] [Accepted: 01/09/2018] [Indexed: 12/30/2022]
Abstract
Colorectal cancer (CRC), one of the most common cancers, is a major public health issue globally, especially in Westernized countries. Up to 35% of CRCs are thought to be due to heritable factors, but currently only 5% to 10% of CRCs are attributable to high-risk mutations in known CRC susceptibility genes, predominantly the mismatch repair genes (Lynch syndrome) and adenomatous polyposis coli gene (APC; familial adenomatous polyposis). In this era of precision medicine, high-risk mutation carriers, when identified, can be offered various risk management options that prevent cancers and improve survival, including risk-reducing medication, screening for early detection, and surgery. The practice of clinical genetics is currently transitioning from phenotype-directed single gene testing to multigene panels, now offered by numerous providers. For CRC, the genes included across these panels vary, ranging from well established, clinically actionable susceptibility genes with quantified magnitude of risk, to genes that lack extensive validation or have less evidence of association with CRC and, therefore, have minimal clinical utility. The current lack of consensus regarding inclusion of genes in CRC panels presents challenges in patient counseling and management, particularly when a variant in a less validated gene is identified. Furthermore, there remain considerable challenges regarding variant interpretation even for the well established CRC susceptibility genes. Ironically though, only through more widespread testing and the accumulation of large international data sets will sufficient information be generated to (i) enable well powered studies to determine if a gene is associated with CRC susceptibility, (ii) to develop better models for variant interpretation and (iii) to facilitate clinical translation.
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Affiliation(s)
- Marie Lorans
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Eryn Dow
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Finlay A Macrae
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia; Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia.
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35
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Clendenning M, Huang A, Jayasekara H, Lorans M, Preston S, O'Callaghan N, Pope BJ, Macrae FA, Winship IM, Milne RL, Giles GG, English DR, Hopper JL, Win AK, Jenkins MA, Southey MC, Rosty C, Buchanan DD. Somatic mutations of the coding microsatellites within the beta-2-microglobulin gene in mismatch repair-deficient colorectal cancers and adenomas. Fam Cancer 2018; 17:91-100. [PMID: 28616688 PMCID: PMC6129400 DOI: 10.1007/s10689-017-0013-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In colorectal cancers (CRCs) with tumour mismatch repair (MMR) deficiency, genes involved in the host immune response that contain microsatellites in their coding regions, including beta-2-microglobulin (B2M), can acquire mutations that may alter the immune response, tumour progression and prognosis. We screened the coding microsatellites within B2M for somatic mutations in MMR-deficient CRCs and adenomas to determine associations with tumour subtypes, clinicopathological features and survival. Incident MMR-deficient CRCs from Australasian Colorectal Cancer Family Registry (ACCFR) and the Melbourne Collaborative Cohort Study participants (n = 144) and 63 adenomas from 41 MMR gene mutation carriers from the ACCFR were screened for somatic mutations within five coding microsatellites of B2M. Hazard ratios (HR) and 95% confidence intervals (CI) for overall survival by B2M mutation status were estimated using Cox regression, adjusting for age at CRC diagnosis, sex, AJCC stage and grade. B2M mutations occurred in 30 (20.8%) of the 144 MMR-deficient CRCs (29% of the MLH1-methylated, 17% of the Lynch syndrome and 9% of the suspected Lynch CRCs). No B2M mutations were identified in the 63 adenomas tested. B2M mutations differed by site, stage, grade and lymphocytic infiltration although none reached statistical significance (p > 0.05). The HR for overall survival for B2M mutated CRC was 0.65 (95% CI 0.29-1.48) compared with B2M wild-type. We observed differences in B2M mutation status in MMR-deficient CRC by tumour subtypes, site, stage, grade, immune infiltrate and for overall survival that warrant further investigation in larger studies before B2M mutation status can be considered to have clinical utility.
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Affiliation(s)
- Mark Clendenning
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Alvin Huang
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Harindra Jayasekara
- Cancer Epidemiology Centre, Cancer Council Victoria, St Kilda, VIC, 3182, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Alcohol Policy Research, La Trobe University, Melbourne, VIC, 3000, Australia
| | - Marie Lorans
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Susan Preston
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Neil O'Callaghan
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Bernard J Pope
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Finlay A Macrae
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, VIC, 3010, Australia
- Department of Medicine, The University of Melbourne, Parkville, VIC, 3010, Australia
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, 3010, Australia
| | - Ingrid M Winship
- Department of Medicine, The University of Melbourne, Parkville, VIC, 3010, Australia
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, 3010, Australia
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, St Kilda, VIC, 3182, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, St Kilda, VIC, 3182, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Dallas R English
- Cancer Epidemiology Centre, Cancer Council Victoria, St Kilda, VIC, 3182, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Epidemiology and Institute of Health and Environment, School of Public Health, Seoul National University, Seoul, South Korea
| | - Aung K Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, 3010, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Envoi Specialist Pathologists, Herston, QLD, 4006, Australia
- School of Medicine, University of Queensland, Herston, QLD, 4006, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, 3010, Australia.
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36
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Risk of colorectal cancer for carriers of a germ-line mutation in POLE or POLD1. Genet Med 2017; 20:890-895. [PMID: 29120461 PMCID: PMC5943186 DOI: 10.1038/gim.2017.185] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 08/17/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Germ-line mutations in the exonuclease domains of the POLE and POLD1 genes are associated with an increased, but yet unquantified, risk of colorectal cancer (CRC). METHODS We identified families with POLE or POLD1 variants by searching PubMed for relevant studies prior to October 2016 and by genotyping 669 population-based CRC cases diagnosed in patients under 60 years of age, from the Australasian Colorectal Cancer Family Registry. We estimated the age-specific cumulative risks (penetrance) using a modified segregation analysis. RESULTS We observed 67 CRCs (mean age at diagnosis = 50.2 (SD = 13.8) years) among 364 first- and second-degree relatives from 41 POLE families, and 6 CRCs (mean age at diagnosis = 39.7 (SD = 6.83) years) among 69 relatives from 9 POLD1 families. We estimated risks of CRC up to the age of 70 years (95% confidence interval) for males and females, respectively, to be 28% (95% CI, 10–42%) and 21% (95% CI, 7–33%) for POLE mutation carriers and 90% (95% CI, 33–99%) and 82% (95% CI, 26–99%) for POLD1 mutation carriers. CONCLUSION CRC risks for POLE mutation carriers are sufficiently high to warrant consideration of colonoscopy screening and implementation of management guidelines recommended for MSH6 mutation carriers in cases of Lynch syndrome. Refinement of estimates of CRC risk for POLD1 carriers is needed; however, clinical management recommendations could follow those made for POLE carriers.
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Pokharel HP, Hacker NF, Andrews L. Hereditary gynaecologic cancers in Nepal: a proposed model of care to serve high risk populations in developing countries. Hered Cancer Clin Pract 2017; 15:12. [PMID: 28936272 PMCID: PMC5604345 DOI: 10.1186/s13053-017-0072-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 09/05/2017] [Indexed: 12/15/2022] Open
Abstract
Background Endometrial, ovarian and breast cancers are paradigms for global health disparity. Women living in the developing world continue to present in later stages of disease and have fewer options for treatment than those in developed countries. Risk reducing surgery is of proven benefit for women at high risk of gynaecological cancer. There is no specific model for identification and management of such women in the developing world. Methods We have integrated data from our published audit of a major gynaecological oncology centre at Royal Hospital for Women in Australia, with data from our survey and a focus group discussion of Nepalese gynaecological health care professionals regarding genetic testing, and findings from the literature. These data have been used to identify current barriers to multidisciplinary gynaecological oncology care in developing nations, and to develop a model to integrate hereditary cancer services into cancer care in Nepal, as a paradigm for other developing nations. Results The ability to identify women with hereditary gynaecological cancer in developing nations is influenced by their late presentation (if active management is declined or not appropriate), limited access to specialised services and cultural and financial barriers. In order to include genetic assessment in multidisciplinary gynaecological cancer care, education needs to be provided to all levels of health care providers to enable reporting of family history, and appropriate ordering of investigations. Training of genetic counsellors is needed to assist in the interpretation of results and extending care to unaffected at-risk relatives. Novel approaches will be required to overcome geographic and financial barriers, including mainstreaming of genetic testing, telephone counselling, use of mouth swabs and utilisation of international laboratories. Conclusion Women in Nepal have yet to receive benefits from the advances in early cancer diagnosis and management. There is a potential of extending the benefits of hereditary cancer diagnosis in Nepal due to the rapid fall in the cost of genetic testing and the ability to collect DNA from a buccal swab through appropriate training of the gynaecological carers.
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Affiliation(s)
- Hanoon P Pokharel
- Gynaecologic Cancer Centre, Royal Hospital for Women, Sydney, Australia.,School of Women's and Children's Health, UNSW, Sydney, Australia.,Department of Obstetrics and Gynaecology, B.P Koirala Institute of Health Sciences, Dharan, Nepal
| | - Neville F Hacker
- Gynaecologic Cancer Centre, Royal Hospital for Women, Sydney, Australia.,School of Women's and Children's Health, UNSW, Sydney, Australia
| | - Lesley Andrews
- Hereditary Cancer Clinic, Prince of Wales Hospital, Sydney, Australia.,School of Medicine, UNSW, Sydney, Australia
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