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Rashid M, Rashid R, Gadewal N, Carethers JM, Koi M, Brim H, Ashktorab H. High-throughput sequencing and in-silico analysis confirm pathogenicity of novel MSH3 variants in African American colorectal cancer. Neoplasia 2024; 49:100970. [PMID: 38281411 PMCID: PMC10840101 DOI: 10.1016/j.neo.2024.100970] [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: 11/05/2023] [Revised: 12/19/2023] [Accepted: 01/08/2024] [Indexed: 01/30/2024]
Abstract
The maintenance of DNA sequence integrity is critical to avoid accumulation of cancer-causing mutations. Inactivation of DNA Mismatch Repair (MMR) genes (e.g., MLH1 and MSH2) is common among many cancers, including colorectal cancer (CRC) and is the driver of classic microsatellite instability (MSI) in tumors. Somatic MSH3 alterations have been linked to a specific form of MSI called elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) that is associated with patient poor prognosis and elevated among African American (AA) rectal cancer patients. Genetic variants of MSH3 and their pathogenicity vary among different populations, such as among AA, which are not well-represented in publicly available databases. Targeted exome sequencing of MSH3 among AA CRC samples followed by computational bioinformatic pipeline and molecular dynamic simulation analysis approach confirmed six identified MSH3 variants (c.G1237A, c.C2759T, c.G1397A, c.G2926A, c.C3028T, c.G3241A) that corresponded to MSH3 amino-acid changes (p.E413K; p.S466N; p.S920F; p.E976K; p.H1010Y; p.E1081K). All identified MSH3 variants were non-synonymous, novel, pathogenic, and show loss or gain of hydrogen bonding, ionic bonding, hydrophobic bonding, and disulfide bonding and have a deleterious effect on the structure of MSH3 protein. Some variants were located within the ATPase site of MSH3, affecting ATP hydrolysis that is critical for MSH3's function. Other variants were in the MSH3-MSH2 interacting domain, important for MSH3's binding to MSH2. Overall, our data suggest that these variants among AA CRC patients affect the function of MSH3 making them pathogenic and likely contributing to the development or advancement of CRC among AA. Further clarifying functional studies will be necessary to fully understand the impact of these variants on MSH3 function and CRC development in AA patients.
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Affiliation(s)
- Mudasir Rashid
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA
| | - Rumaisa Rashid
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA
| | - Nikhil Gadewal
- Bioinformatics and Computational Biology Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210, India
| | - John M Carethers
- Division of Gastroenterology and Hepatology, Department of Medicine, UC San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA; Moores Cancer Center, and Herbert Wertheim School of Public Health and Human Longevity Science, UC San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Minoru Koi
- Division of Gastroenterology and Hepatology, Department of Medicine, UC San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Hassan Brim
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA.
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Koi M, Leach BH, McGee S, Tseng-Rogenski SS, Burke CA, Carethers JM. Compound heterozygous MSH3 germline variants and associated tumor somatic DNA mismatch repair dysfunction. NPJ Precis Oncol 2024; 8:12. [PMID: 38243056 PMCID: PMC10798947 DOI: 10.1038/s41698-024-00511-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 12/08/2023] [Indexed: 01/21/2024] Open
Abstract
We describe here an individual from a fourth family with germline compound heterozygous MSH3 germline variants and its observed biological consequences. The patient was initially diagnosed with invasive moderately-differentiated adenocarcinoma of the colon at the age of 43. Germline multigene panel testing revealed a pathogenic variant MSH3 c.2436-1 G > A and a variant of (initial) uncertain significance MSH3 c.3265 A > T (p.Lys1089*). Germline genetic testing of family members confirm the variants are in trans with the c.2436-1 G > A variant of paternal and the c.3265 A > T variant of maternal origin. Tumor DNA exhibits low levels of microsatellite instability and elevated microsatellite alterations at selected tetranucleotide repeats (EMAST). Tissue immunohistochemical staining for MSH3 demonstrated variant MSH3 protein is present in the cytoplasm and cell membrane but not in the nucleus of normal and tumor epithelial cells. Furthermore, variant MSH3 is accompanied by loss of nuclear MSH6 and a reduced level of nuclear MSH2 in some tumor cells, suggesting that the variant MSH3 protein may inhibit binding of MSH6 to MSH2.
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Affiliation(s)
- Minoru Koi
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Division of Gastroenterology & Hepatology, Department of Medicine, and Moores Cancer Center, University of California at San Diego, San Diego, CA, USA
| | - Brandie H Leach
- Center for Personalized Genetic Healthcare, Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
- Sanford R. Weiss MD Center for Hereditary Colorectal Neoplasia, Cleveland Clinic, Cleveland, OH, USA
| | - Sarah McGee
- Center for Personalized Genetic Healthcare, Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
- Sanford R. Weiss MD Center for Hereditary Colorectal Neoplasia, Cleveland Clinic, Cleveland, OH, USA
| | - Stephanie S Tseng-Rogenski
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Carol A Burke
- Sanford R. Weiss MD Center for Hereditary Colorectal Neoplasia, Cleveland Clinic, Cleveland, OH, USA
- Department of Gastroenterology, Hepatology and Nutrition, Cleveland Clinic, Cleveland, OH, USA
| | - John M Carethers
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
- Division of Gastroenterology & Hepatology, Department of Medicine, and Moores Cancer Center, University of California at San Diego, San Diego, CA, USA.
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Tseng MC, Lee YH, Yen TB, Li SM. Genome-wide characterization of microsatellites in cobia Rachycentron canadum (Linnaeus, 1766): Survey and analysis of their abundance and diversity. JOURNAL OF FISH BIOLOGY 2024; 104:44-55. [PMID: 37658731 DOI: 10.1111/jfb.15552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/23/2023] [Accepted: 08/31/2023] [Indexed: 09/05/2023]
Abstract
The cobia Rachycentron canadum, mainly distributed in the warm waters of tropical and subtropical regions around the world, remains a fish of considerable economic importance. Detailed diversity and the number of microsatellite sequences in the cobia genome are still unintelligible. The primary aim of this work was to identify and quantify the miscellaneous SSR sequences in the cobia genome. More than 280,000 sequences were sequenced and screened using next-generation sequencing technology and microsatellite identification. Perfect mononucleotide repeats, dinucleotide microsatellites, and trinucleotide microsatellites contain (A)10 /(T)10 , (AC)6 /(TG)6 , and (AAT)5-32 as the largest number of motifs in each type of microsatellite, respectively. The tetranucleotide and pentanucleotide microsatellites (TTM and PTM) consist of the largest number of motifs of both (ATCT)5-32 and (TCAT)5-31 in TTMs, and (CTCTC)5-9 in PTMs, whereas the hexanucleotide microsatellites are rarely observed in the cobia genome. All c. 38000 sequences of composite microsatellites are extremely diverse, including compound (11.71%), interrupted compound (71.77%), complex (0.45%), and interrupted complex (16.07%). In this study, we developed a convenient and useful recording system for writing down and categorizing diverse composite microsatellite types. This system will provide great support for exploring repeat origins, evolutionary mechanisms, and the application of polymorphic microsatellites.
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Affiliation(s)
- Mei-Chen Tseng
- Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung 912, Taiwan, R.O.C
| | - Yen-Hung Lee
- Tungkang Aquaculture Research Center, Fisheries Research Institute, MOA, Pingtung 928, Taiwan, R.O.C
| | - Tsair-Bor Yen
- Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Pingtung 912, Taiwan, R.O.C
| | - Shu-Ming Li
- Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung 912, Taiwan, R.O.C
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Villy MC, Masliah-Planchon J, Schnitzler A, Delhomelle H, Buecher B, Filser M, Merchadou K, Golmard L, Melaabi S, Vacher S, Blanluet M, Suybeng V, Corsini C, Dhooge M, Hamzaoui N, Farelly S, Ait Omar A, Benamouzig R, Caumette V, Bahuau M, Cucherousset J, Allory Y, Stoppa-Lyonnet D, Bieche I, Colas C. MSH3: a confirmed predisposing gene for adenomatous polyposis. J Med Genet 2023; 60:1198-1205. [PMID: 37402566 DOI: 10.1136/jmg-2023-109341] [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: 04/25/2023] [Accepted: 06/18/2023] [Indexed: 07/06/2023]
Abstract
BACKGROUND The MSH3 gene is part of the DNA mismatch repair system, but has never been shown to be involved in Lynch syndrome. A first report of four patients from two families, bearing biallelic MSH3 germline variants, with a phenotype of attenuated colorectal adenomatous polyposis raised the question of its involvement in hereditary cancer predisposition. The patients' tumours exhibited elevated microsatellite alterations at selected tetranucleotide repeats (EMAST), a hallmark of MSH3 deficiency. METHODS We report five new unrelated patients with MSH3-associated polyposis. We describe their personal and familial history and study the EMAST phenotype in various normal and tumour samples, which are relevant findings based on the rarity of this polyposis subtype so far. RESULTS All patients had attenuated colorectal adenomatous polyposis, with duodenal polyposis in two cases. Both women had breast carcinomas. EMAST phenotype was present at various levels in different samples of the five patients, confirming the MSH3 deficiency, with a gradient of instability in polyps depending on their degree of dysplasia. The negative EMAST phenotype ruled out the diagnosis of germline MSH3 deficiency for two patients: one homozygous for a benign variant and one with a monoallelic large deletion. CONCLUSION This report lends further credence to biallelic MSH3 germline pathogenic variants being involved in colorectal and duodenal adenomatous polyposis. Large-scale studies may help clarify the tumour spectrum and associated risks. Ascertainment of EMAST may help with the interpretation of variants of unknown significance. We recommend adding MSH3 to dedicated diagnostic gene panels.
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Affiliation(s)
| | | | - Anne Schnitzler
- Department of Genetics, PSL University, Institut Curie, Paris, France
| | - Hélène Delhomelle
- Department of Genetics, PSL University, Institut Curie, Paris, France
| | - Bruno Buecher
- Department of Genetics, PSL University, Institut Curie, Paris, France
| | - Mathilde Filser
- Department of Genetics, PSL University, Institut Curie, Paris, France
| | | | - Lisa Golmard
- Department of Genetics, PSL University, Institut Curie, Paris, France
| | - Samia Melaabi
- Department of Genetics, PSL University, Institut Curie, Paris, France
| | - Sophie Vacher
- Department of Genetics, PSL University, Institut Curie, Paris, France
| | - Maud Blanluet
- Department of Genetics, PSL University, Institut Curie, Paris, France
| | - Voreak Suybeng
- Department of Genetics, PSL University, Institut Curie, Paris, France
| | - Carole Corsini
- Medical Genetics Department, Centre Hospitalier Regional Universitaire de Montpellier, Montpellier, France
| | - Marion Dhooge
- Oncogenetic Unit, Department of Gastroenterology, AP-HP Centre-Université de Paris, Hopital Cochin, Paris, France
| | - Nadim Hamzaoui
- Department of Genetics, AP-HP Centre-Université de Paris, Hospital Cochin, Paris, France
| | - Solenne Farelly
- Oncogenetic Unit, Department of Gastroenterology, AP-HP Centre-Université de Paris, Hopital Cochin, Paris, France
| | - Amal Ait Omar
- Department of Gastroenterology, Hôpital Avicenne, Bobigny, France
| | | | - Vincent Caumette
- Department of Genetics, Hôpitaux Universitaires Henri Mondor, Creteil, France
| | - Michel Bahuau
- Department of Genetics, Hôpitaux Universitaires Henri Mondor, Creteil, France
| | - Joël Cucherousset
- Department of Pathology, GHI Le Raincy-Montfermeil, Montfermeil, France
| | - Yves Allory
- Department of Pathology, Université Paris-Saclay, Institut Curie, Paris, France
| | | | - Ivan Bieche
- Department of Genetics, Université Paris Cité, Institut Curie, Paris, France
| | - Chrystelle Colas
- Department of Genetics, PSL University, Institut Curie, Paris, France
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Rock A, Uche A, Yoon J, Agulnik M, Chow W, Millis S. Bioinformatic Analysis of Recurrent Genomic Alterations and Corresponding Pathway Alterations in Ewing Sarcoma. J Pers Med 2023; 13:1499. [PMID: 37888109 PMCID: PMC10608227 DOI: 10.3390/jpm13101499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
Ewing Sarcoma (ES) is an aggressive, mesenchymal malignancy associated with a poor prognosis in the recurrent or metastatic setting with an estimated overall survival (OS) of <30% at 5 years. ES is characterized by a balanced, reciprocal chromosomal translocation involving the EWSR1 RNA-binding protein and ETS transcription factor gene (EWS-FLI being the most common). Interestingly, murine ES models have failed to produce tumors phenotypically representative of ES. Genomic alterations (GA) in ES are infrequent and may work synergistically with EWS-ETS translocations to promote oncogenesis. Aberrations in fibroblast growth factor receptor (FGFR4), a receptor tyrosine kinase (RTK) have been shown to contribute to carcinogenesis. Mouse embryonic fibroblasts (MEFs) derived from knock-in strain of homologous Fgfr4G385R mice display a transformed phenotype with enhanced TGF-induced mammary carcinogenesis. The association between the FGFRG388R SNV in high-grade soft tissue sarcomas has previously been demonstrated conferring a statistically significant association with poorer OS. How the FGFR4G388R SNV specifically relates to ES has not previously been delineated. To further define the genomic landscape and corresponding pathway alterations in ES, comprehensive genomic profiling (CGP) was performed on the tumors of 189 ES patients. The FGFR4G388R SNV was identified in a significant proportion of the evaluable cases (n = 97, 51%). In line with previous analyses, TP53 (n = 36, 19%), CDK2NA/B (n = 33, 17%), and STAG2 (n = 22, 11.6%) represented the most frequent alterations in our cohort. Co-occurrence of CDK2NA and STAG2 alterations was observed (n = 5, 3%). Notably, we identified a higher proportion of TP53 mutations than previously observed. The most frequent pathway alterations affected MAPK (n = 89, 24% of pathological samples), HRR (n = 75, 25%), Notch1 (n = 69, 23%), Histone/Chromatin remodeling (n = 57, 24%), and PI3K (n = 64, 20%). These findings help to further elucidate the genomic landscape of ES with a novel investigation of the FGFR4G388R SNV revealing frequent aberration.
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Affiliation(s)
- Adam Rock
- City of Hope Comprehensive Cancer Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA; (J.Y.); (M.A.)
| | - An Uche
- Alameda Health System, 1411 E. 31st St., Oakland, CA 94602, USA;
| | - Janet Yoon
- City of Hope Comprehensive Cancer Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA; (J.Y.); (M.A.)
| | - Mark Agulnik
- City of Hope Comprehensive Cancer Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA; (J.Y.); (M.A.)
| | - Warren Chow
- UCI Health, 101 The City Drive, South Orange, CA 92868, USA;
| | - Sherri Millis
- Foundation Medicine, Inc., 150 Second St., Cambridge, MA 02141, USA;
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Vuković Đerfi K, Salar A, Cacev T, Kapitanović S. EMAST Type of Microsatellite Instability-A Distinct Entity or Blurred Overlap between Stable and MSI Tumors. Genes (Basel) 2023; 14:1474. [PMID: 37510378 PMCID: PMC10380056 DOI: 10.3390/genes14071474] [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: 06/24/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Microsatellite instability (MSI) represents an accumulation of frameshifts in short tandem repeats, microsatellites, across the genome due to defective DNA mismatch repair (dMMR). MSI has been associated with distinct clinical, histological, and molecular features of tumors and has proven its prognostic and therapeutic value in different types of cancer. Recently, another type of microsatellite instability named elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) has been reported across many different tumors. EMAST tumors have been associated with chronic inflammation, higher tumor stage, and poor prognosis. Nevertheless, the clinical significance of EMAST and its relation to MSI remains unclear. It has been proposed that EMAST arises as a result of isolated MSH3 dysfunction or as a secondary event in MSI tumors. Even though previous studies have associated EMAST with MSI-low phenotype in tumors, recent studies show a certain degree of overlap between EMAST and MSI-high tumors. However, even in stable tumors, (MSS) frameshifts in microsatellites can be detected as a purely stochastic event, raising the question of whether EMAST truly represents a distinct type of microsatellite instability. Moreover, a significant fraction of patients with MSI tumors do not respond to immunotherapy and it can be speculated that in these tumors, EMAST might act as a modifying factor.
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Affiliation(s)
- Kristina Vuković Đerfi
- Laboratory for Personalized Medicine, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenicka cesta 54, 10000 Zagreb, Croatia
| | - Anamarija Salar
- Laboratory for Personalized Medicine, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenicka cesta 54, 10000 Zagreb, Croatia
| | - Tamara Cacev
- Laboratory for Personalized Medicine, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenicka cesta 54, 10000 Zagreb, Croatia
| | - Sanja Kapitanović
- Laboratory for Personalized Medicine, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenicka cesta 54, 10000 Zagreb, Croatia
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Maksimov MO, Wu C, Ashbrook DG, Villani F, Colonna V, Mousavi N, Ma N, Lu L, Pritchard JK, Goren A, Williams RW, Palmer AA, Gymrek M. A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice. Genome Res 2023; 33:689-702. [PMID: 37127331 PMCID: PMC10317118 DOI: 10.1101/gr.277576.122] [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: 12/08/2022] [Accepted: 04/26/2023] [Indexed: 05/03/2023]
Abstract
Short tandem repeats (STRs) are a class of rapidly mutating genetic elements typically characterized by repeated units of 1-6 bp. We leveraged whole-genome sequencing data for 152 recombinant inbred (RI) strains from the BXD family of mice to map loci that modulate genome-wide patterns of new mutations arising during parent-to-offspring transmission at STRs. We defined quantitative phenotypes describing the numbers and types of germline STR mutations in each strain and performed quantitative trait locus (QTL) analyses for each of these phenotypes. We identified a locus on Chromosome 13 at which strains inheriting the C57BL/6J (B) haplotype have a higher rate of STR expansions than those inheriting the DBA/2J (D) haplotype. The strongest candidate gene in this locus is Msh3, a known modifier of STR stability in cancer and at pathogenic repeat expansions in mice and humans, as well as a current drug target against Huntington's disease. The D haplotype at this locus harbors a cluster of variants near the 5' end of Msh3, including multiple missense variants near the DNA mismatch recognition domain. In contrast, the B haplotype contains a unique retrotransposon insertion. The rate of expansion covaries positively with Msh3 expression-with higher expression from the B haplotype. Finally, detailed analysis of mutation patterns showed that strains carrying the B allele have higher expansion rates, but slightly lower overall total mutation rates, compared with those with the D allele, particularly at tetranucleotide repeats. Our results suggest an important role for inherited variants in Msh3 in modulating genome-wide patterns of germline mutations at STRs.
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Affiliation(s)
- Mikhail O Maksimov
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Cynthia Wu
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California 92093, USA
| | - David G Ashbrook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Vincenza Colonna
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
- Institute of Genetics and Biophysics, National Research Council, Naples 80111, Italy
| | - Nima Mousavi
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Nichole Ma
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Alon Goren
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Abraham A Palmer
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92093, USA
- Department of Psychiatry, Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Melissa Gymrek
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA;
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92093, USA
- Department of Biomedical Informatics
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8
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Alfaro A, Zanabria D, Aguilar A, Jimenez-Solano SA, Zevallos A, Fajardo W. Gastric adenocarcinoma with high‑level microsatellite instability: A case report. Mol Clin Oncol 2023; 18:16. [PMID: 36798468 PMCID: PMC9926044 DOI: 10.3892/mco.2023.2612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 11/16/2022] [Indexed: 01/28/2023] Open
Abstract
Gastric cancer (GC) ranks fifth on the list of the most common malignancies worldwide. In Peru, gastric neoplasms are considered the second leading cause of mortality among males. Among the molecular subgroups of GC, microsatellite instability presents a favorable prognosis due to its hypermutated phenotype, which activates immunosurveillance. The present study describes the case of a 75-year-old patient, who was admitted in the hospital with a history of upper gastrointestinal bleeding and recurrent hospital admission, due to severe anemia. The patient presented with pale skin, normal vital functions, slight swelling of the lower extremities, and abdominal distention and bloating upon a physical examination. An endoscopic examination revealed an infiltrating circular ulcerated lesion. The histopathological analysis identified a moderately differentiated intestinal-type adenocarcinoma with pathological stage T3N0M0. Tumor genomic profiling demonstrated alterations in 15 different genes with a tumor mutational burden of 28 mutations/Mb. Finally, the patient underwent a partial gastrectomy without pre-operative chemotherapy. After 4 days, the patient presented with post-operative complications for which he was re-operated on. The patient did not survive. To the best of our knowledge, in the present case, pernicious anemia was an early sign of GC and a gastroscopy had to be performed. Furthermore, MutS homolog 3 alterations probably conditioned the presence of multiple frame-shift mutations.
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Affiliation(s)
- Alejandro Alfaro
- Department of Pathology, Hospital Nacional Dos de Mayo, Lima 15003, Peru
| | | | - Alfredo Aguilar
- Basic and Translational Research Unit, Oncosalud-AUNA, Lima 15036, Peru
| | - Sergio A. Jimenez-Solano
- Faculty of Natural Sciences and Mathematics, Universidad Nacional Federico Villarreal, Lima 15007, Peru
| | - Alejandra Zevallos
- School of Medicine, Universidad Privada San Juan Bautista, Lima 15067, Peru,Correspondence to: Professor Alejandra Zevallos, School of Medicine, Universidad Privada San Juan Bautista, Avenue José Antonio Lavalle N˚ 302-304 (Ex Hacienda Villa), Chorrillos, Lima 15067, Peru
| | - Williams Fajardo
- Department of Pathology, Hospital Nacional Dos de Mayo, Lima 15003, Peru,School of Medicine, Universidad Privada San Juan Bautista, Lima 15067, Peru
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Hao S, Tong J, Jha A, Risnik D, Lizardo D, Lu X, Goel A, Opresko PL, Yu J, Zhang L. Synthetical lethality of Werner helicase and mismatch repair deficiency is mediated by p53 and PUMA in colon cancer. Proc Natl Acad Sci U S A 2022; 119:e2211775119. [PMID: 36508676 PMCID: PMC9907101 DOI: 10.1073/pnas.2211775119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/01/2022] [Indexed: 12/15/2022] Open
Abstract
Synthetic lethality is a powerful approach for targeting oncogenic drivers in cancer. Recent studies revealed that cancer cells with microsatellite instability (MSI) require Werner (WRN) helicase for survival; however, the underlying mechanism remains unclear. In this study, we found that WRN depletion strongly induced p53 and its downstream apoptotic target PUMA in MSI colorectal cancer (CRC) cells. p53 or PUMA deletion abolished apoptosis induced by WRN depletion in MSI CRC cells. Importantly, correction of MSI abrogated the activation of p53/PUMA and cell killing, while induction of MSI led to sensitivity in isogenic CRC cells. Rare p53-mutant MSI CRC cells are resistant to WRN depletion due to lack of PUMA induction, which could be restored by wildtype (WT) p53 knock in or reconstitution. WRN depletion or treatment with the RecQ helicase inhibitor ML216 suppressed in vitro and in vivo growth of MSI CRCs in a p53/PUMA-dependent manner. ML216 treatment was efficacious in MSI CRC patient-derived xenografts. Interestingly, p53 gene remains WT in the majority of MSI CRCs. These results indicate a critical role of p53/PUMA-mediated apoptosis in the vulnerability of MSI CRCs to WRN loss, and support WRN as a promising therapeutic target in p53-WT MSI CRCs.
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Affiliation(s)
- Suisui Hao
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Jingshan Tong
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Anupma Jha
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
| | - Denise Risnik
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Darleny Lizardo
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Xinyan Lu
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA91010
| | - Patricia L. Opresko
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA15213
| | - Jian Yu
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Lin Zhang
- UPMC Hillman Cancer Center, Pittsburgh, PA15213
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
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10
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Inanaga S, Igase M, Sakai Y, Hagimori K, Sunahara H, Horikirizono H, Itamoto K, Baba K, Ohsato Y, Mizuno T. Relationship of microsatellite instability to mismatch repair deficiency in malignant tumors of dogs. J Vet Intern Med 2022; 36:1760-1769. [PMID: 35959511 PMCID: PMC9511092 DOI: 10.1111/jvim.16454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/10/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Microsatellite instability (MSI) is a type of genomic instability caused by mismatch repair deficiency (dMMR) in tumors. Studies on dMMR/MSI are limited, and the relationship between dMMR and MSI is unknown in tumors of dogs. OBJECTIVES We aimed to identify the frequency of dMMR/MSI by tumor type and evaluate the relationship between dMMR and MSI in tumors of dogs. ANIMALS In total, 101 dogs with 11 types of malignant tumors were included. METHODS We extracted DNA from fresh normal and tumor tissues. Twelve microsatellite loci from both normal and tumor DNA were amplified by PCR and detected by capillary electrophoresis. Each microsatellite (MS) was defined as MSI if a difference in product size between the tumor and normal DNA was detected. The dMMR was evaluated by immunohistochemistry with formalin-fixed paraffin-embedded tumor tissues. Next, we confirmed whether dMMR induces MSI by serial passaging of MMR gene knockout cell lines for 3 months. RESULTS Microsatellite instability was detected frequently in oral malignant melanoma. The number of MSI-positive markers was higher in cases with dMMR than in those with proficient MMR (P < .0001). Statistical analysis indicated that the occurrence of MSI in FH2305 might have relevance to dMMR. Furthermore, MSI occurred in dMMR cell lines 3 months after passaging. CONCLUSIONS AND CLINICAL IMPORTANCE Microsatellite instability and dMMR more frequently were found in oral malignant melanoma than in other tumors, and dMMR has relevance to MSI in both clinical cases and cell lines.
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Affiliation(s)
- Sakuya Inanaga
- Laboratory of Molecular Diagnostics and Therapeutics, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Masaya Igase
- Laboratory of Molecular Diagnostics and Therapeutics, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Yusuke Sakai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Hiroshi Sunahara
- Laboratory of Veterinary Surgery, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hiro Horikirizono
- Laboratory of Veterinary Radiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Kazuhito Itamoto
- Laboratory of Companion Animal Medicine, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Kenji Baba
- Laboratory of Veterinary Internal Medicine, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | | | - Takuya Mizuno
- Laboratory of Molecular Diagnostics and Therapeutics, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
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11
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Herz AL, Wisser S, Kohlruss M, Slotta-Huspenina J, Jesinghaus M, Grosser B, Steiger K, Novotny A, Hapfelmeier A, Schmidt T, Gaida MM, Weichert W, Keller G. Elevated microsatellite instability at selected tetranucleotide (EMAST) repeats in gastric cancer: a distinct microsatellite instability type with potential clinical impact? JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2022; 8:233-244. [PMID: 35099128 PMCID: PMC8977279 DOI: 10.1002/cjp2.257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/21/2022]
Abstract
We investigated the clinical impact of elevated microsatellite instability at selected tetranucleotide (EMAST) repeats in the context of neoadjuvant chemotherapy (CTx) in gastric/gastro‐oesophageal adenocarcinomas. We analysed 583 resected tumours (272 without and 311 after CTx) and 142 tumour biopsies before CTx. If at least two or three of the five tetranucleotide repeat markers tested showed instability, the tumours were defined as EMAST (2+) or EMAST (3+), respectively. Expression of mismatch repair proteins including MSH3 was analysed using immunohistochemistry. Microsatellite instability (MSI) and Epstein–Barr virus (EBV) positivity were determined using standard assays. EMAST (2+) and (3+) were detected in 17.8 and 11.5% of the tumours, respectively. The frequency of EMAST (2+) or (3+) in MSI‐high (MSI‐H) tumours was 96.2 or 92.5%, respectively, demonstrating a high overlap with this molecular subtype, and the association of EMAST and MSI status was significant (each overall p < 0.001). EMAST (2+ or 3+) alone in MSI‐H and EBV‐negative tumours demonstrated only a statistically significant association of EMAST (2+) positivity and negative lymph node status (42.3% in EMAST (2+) and 28.8% in EMAST negative, p = 0.045). EMAST alone by neither definition was significantly associated with overall survival (OS) of the patients. The median OS for EMAST (2+) patients was 40.0 months (95% confidence interval [CI] 16.4–63.6) compared with 38.7 months (95% CI 26.3–51.1) for the EMAST‐negative group (p = 0.880). The median OS for EMAST (3+) patients was 46.7 months (95% CI 18.2–75.2) and 38.7 months (95% CI 26.2–51.2) for the negative group (p = 0.879). No statistically significant association with response to neoadjuvant CTx was observed (p = 0.992 and p = 0.433 for EMAST (2+) and (3+), respectively). In conclusion, our results demonstrate a nearly complete intersection between MSI‐H and EMAST and they indicate that EMAST alone is not a distinct instability type associated with noticeable clinico‐pathological characteristics of gastric carcinoma patients.
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Affiliation(s)
- Anna-Lina Herz
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Sarah Wisser
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Meike Kohlruss
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Julia Slotta-Huspenina
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Moritz Jesinghaus
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Pathology, University Hospital Marburg, Marburg, Germany
| | - Bianca Grosser
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Pathology and Molecular Diagnostics, University Hospital Augsburg, Augsburg, Germany
| | - Katja Steiger
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany.,German Cancer Consortium [DKTK], Partner Site Munich, Institute of Pathology, Munich, Germany
| | - Alexander Novotny
- Department of Surgery, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Alexander Hapfelmeier
- Institute for AI and Informatics in Medicine, Technical University of Munich, Munich, Germany.,Institute of General Practice and Health Services Research, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Thomas Schmidt
- Department of Surgery, University of Heidelberg, Heidelberg, Germany.,Department of Surgery, Universitätsklinikum Köln, Köln, Germany
| | - Matthias M Gaida
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Institute of Pathology, University Medical Center Mainz, Mainz, Germany
| | - Wilko Weichert
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany.,German Cancer Consortium [DKTK], Partner Site Munich, Institute of Pathology, Munich, Germany
| | - Gisela Keller
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany
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12
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Spectrum of DNA mismatch repair failures viewed through the lens of cancer genomics and implications for therapy. Clin Sci (Lond) 2022; 136:383-404. [PMID: 35274136 PMCID: PMC8919091 DOI: 10.1042/cs20210682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/02/2022] [Accepted: 02/28/2022] [Indexed: 12/15/2022]
Abstract
Genome sequencing can be used to detect DNA repair failures in tumors and learn about underlying mechanisms. Here, we synthesize findings from genomic studies that examined deficiencies of the DNA mismatch repair (MMR) pathway. The impairment of MMR results in genome-wide hypermutation and in the ‘microsatellite instability’ (MSI) phenotype—occurrence of indel mutations at short tandem repeat (microsatellite) loci. The MSI status of tumors was traditionally assessed by molecular testing of a selected set of MS loci or by measuring MMR protein expression levels. Today, genomic data can provide a more complete picture of the consequences on genomic instability. Multiple computational studies examined somatic mutation distributions that result from failed DNA repair pathways in tumors. These include analyzing the commonly studied trinucleotide mutational spectra of single-nucleotide variants (SNVs), as well as of other features such as indels, structural variants, mutation clusters and regional mutation rate redistribution. The identified mutation patterns can be used to rigorously measure prevalence of MMR failures across cancer types, and potentially to subcategorize the MMR deficiencies. Diverse data sources, genomic and pre-genomic, from human and from experimental models, suggest there are different ways in which MMR can fail, and/or that the cell-type or genetic background may result in different types of MMR mutational patterns. The spectrum of MMR failures may direct cancer evolution, generating particular sets of driver mutations. Moreover, MMR affects outcomes of therapy by DNA damaging drugs, antimetabolites, nonsense-mediated mRNA decay (NMD) inhibitors, and immunotherapy by promoting either resistance or sensitivity, depending on the type of therapy.
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13
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Prime editing efficiency and fidelity are enhanced in the absence of mismatch repair. Nat Commun 2022; 13:760. [PMID: 35140211 PMCID: PMC8828784 DOI: 10.1038/s41467-022-28442-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/26/2022] [Indexed: 02/07/2023] Open
Abstract
Prime editing (PE) is a powerful genome engineering approach that enables the introduction of base substitutions, insertions and deletions into any given genomic locus. However, the efficiency of PE varies widely and depends not only on the genomic region targeted, but also on the genetic background of the edited cell. Here, to determine which cellular factors affect PE efficiency, we carry out a focused genetic screen targeting 32 DNA repair factors, spanning all reported repair pathways. We show that, depending on cell line and type of edit, ablation of mismatch repair (MMR) affords a 2–17 fold increase in PE efficiency, across several human cell lines, types of edits and genomic loci. The accumulation of the key MMR factors MLH1 and MSH2 at PE sites argues for direct involvement of MMR in PE control. Our results shed new light on the mechanism of PE and suggest how its efficiency might be optimised. Prime Editing is a versatile genome engineering tool. Here, the authors identify the DNA repair pathway known as mismatch repair as inhibitory for Prime Editing, thus, loss of mismatch repair enhances the efficiency of Prime Editing.
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14
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Perne C, Peters S, Cartolano M, Horpaopan S, Grimm C, Altmüller J, Sommer AK, Hillmer AM, Thiele H, Odenthal M, Möslein G, Adam R, Sivalingam S, Kirfel J, Schweiger MR, Peifer M, Spier I, Aretz S. Variant profiling of colorectal adenomas from three patients of two families with MSH3-related adenomatous polyposis. PLoS One 2021; 16:e0259185. [PMID: 34843512 PMCID: PMC8629245 DOI: 10.1371/journal.pone.0259185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 10/14/2021] [Indexed: 12/12/2022] Open
Abstract
The spectrum of somatic genetic variation in colorectal adenomas caused by biallelic pathogenic germline variants in the MSH3 gene, was comprehensively analysed to characterise mutational signatures and identify potential driver genes and pathways of MSH3-related tumourigenesis. Three patients from two families with MSH3-associated polyposis were included. Whole exome sequencing of nine adenomas and matched normal tissue was performed. The amount of somatic variants in the MSH3-deficient adenomas and the pattern of single nucleotide variants (SNVs) was similar to sporadic adenomas, whereas the fraction of small insertions/deletions (indels) (21-42% of all small variants) was significantly higher. Interestingly, pathogenic somatic APC variants were found in all but one adenoma. The vast majority (12/13) of these were di-, tetra-, or penta-base pair (bp) deletions. The fraction of APC indels was significantly higher than that reported in patients with familial adenomatous polyposis (FAP) (p < 0.01) or in sporadic adenomas (p < 0.0001). In MSH3-deficient adenomas, the occurrence of APC indels in a repetitive sequence context was significantly higher than in FAP patients (p < 0.01). In addition, the MSH3-deficient adenomas harboured one to five (recurrent) somatic variants in 13 established or candidate driver genes for early colorectal carcinogenesis, including ACVR2A and ARID genes. Our data suggest that MSH3-related colorectal carcinogenesis seems to follow the classical APC-driven pathway. In line with the specific function of MSH3 in the mismatch repair (MMR) system, we identified a characteristic APC mutational pattern in MSH3-deficient adenomas, and confirmed further driver genes for colorectal tumourigenesis.
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Affiliation(s)
- Claudia Perne
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Maria Cartolano
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Sukanya Horpaopan
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Christina Grimm
- Institute for Translational Epigenetics, Medical Faculty and University Clinic Cologne, University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
- Berlin Institute of Health at Charité, Core Facility Genomics, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Anna K. Sommer
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Axel M. Hillmer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Margarete Odenthal
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Gabriela Möslein
- Zentrum für Hereditäre Tumore, BETHESDA Khs. Duisburg, Duisburg, Germany
| | - Ronja Adam
- Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Sugirthan Sivalingam
- Core Unit for Bioinformatics Data Analysis, Medical Faculty, University of Bonn, Bonn, Germany
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Jutta Kirfel
- Institute of Pathology, University of Lübeck, Lübeck, Germany
| | - Michal R. Schweiger
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute for Translational Epigenetics, Medical Faculty and University Clinic Cologne, University of Cologne, Cologne, Germany
| | - Martin Peifer
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
| | - Isabel Spier
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Stefan Aretz
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
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15
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Park Y, Jung JG, Yu ZC, Asaka R, Shen W, Wang Y, Jung WH, Tomaszewski A, Shimberg G, Chen Y, Parimi V, Gaillard S, Shih IM, Wang TL. A novel human endometrial epithelial cell line for modeling gynecological diseases and for drug screening. J Transl Med 2021; 101:1505-1512. [PMID: 34376780 PMCID: PMC8720294 DOI: 10.1038/s41374-021-00624-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/25/2021] [Indexed: 11/09/2022] Open
Abstract
Endometrium-related malignancies including uterine endometrioid carcinoma, ovarian clear cell carcinoma and ovarian endometrioid carcinoma are major types of gynecologic cancer, claiming more than 13,000 women's lives annually in the United States. In vitro cell models that recapitulate "normal" endometrial epithelial cells and their malignant counterparts are critically needed to facilitate the studies of pathogenesis in endometrium-related carcinomas. To achieve this objective, we have established a human endometrial epithelial cell line, hEM3, through immortalization and clonal selection from a primary human endometrium culture. hEM3 exhibits stable growth in vitro without senescence. hEM3 expresses protein markers characteristic of the endometrial epithelium, and they include PAX8, EpCAM, cytokeratin 7/8, and ER. hEM3 does not harbor pathogenic germline mutations in genes involving DNA mismatch repair (MMR) or homologous repair (HR) pathways. Despite its unlimited capacity of in vitro proliferation, hEM3 cells are not transformed, as they are not tumorigenic in immunocompromised mice. The cell line is amenable for gene editing, and we have established several gene-specific knockout clones targeting ARID1A, a tumor suppressor gene involved in the SWI/SNF chromatin remodeling. Drug screening demonstrates that both HDAC inhibitor and PARP inhibitor are effective in targeting cells with ARID1A deletion. Together, our data support the potential of hEM3 as a cell line model for studying the pathobiology of endometrium-related diseases and for developing effective precision therapies.
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Affiliation(s)
- Youngran Park
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jin-Gyoung Jung
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zheng-Cheng Yu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ryoichi Asaka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wenjing Shen
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yeh Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wei-Hung Jung
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Alicja Tomaszewski
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Geoff Shimberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yun Chen
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Vamsi Parimi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephanie Gaillard
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Tian-Li Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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16
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Laycock A, Kang A, Ang S, Texler M, Bentel J. Lack of correlation between MSH3 immunohistochemistry and microsatellite analysis for the detection of elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) in colorectal cancers. Hum Pathol 2021; 118:9-17. [PMID: 34537247 DOI: 10.1016/j.humpath.2021.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/02/2021] [Accepted: 09/10/2021] [Indexed: 12/24/2022]
Abstract
Immunohistochemical evaluation of mismatch repair protein (MMR) expression is an important screening tool in diagnostic pathology, where it is routinely used to identify subsets of colorectal cancers (CRCs) with either inherited or sporadic forms of microsatellite instability (MSI). MSH3 is not included in current MMR panels, although aberrant MSH3 expression is reported to occur in 40-60% of CRCs and is associated with elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) and a worse prognosis. In this study, we applied MSH3 immunohistochemistry and tetranucleotide MSI analysis to a cohort of 250 unselected CRCs to evaluate the potential use of the methods in routine practice. Partial, complete, and focal loss of nuclear MSH3 and its cytoplasmic mislocalization were evident in 67% of tumors, whereas MSI was evident in two to six of a panel of six tetranucleotide repeats in 46% of cases. However, concordance between MSH3 immunohistochemistry and tetranucleotide MSI results was only 61%, indicating the unsuitability of this combination of tests in routine pathology practice. MSH3 immunostaining was compromised in areas of tissue crush and autolysis, which are common in biopsy and surgical samples, potentially mitigating against its routine use. Although tetranucleotide MSI is clearly evident in a subset of CRCs, further development of validated sets of tetranucleotide repeats and either MSH3 or other immunohistochemical markers will be required to include EMAST testing in the routine evaluation of CRCs in clinical practice.
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Affiliation(s)
- Andrew Laycock
- PathWest Anatomical Pathology, Fiona Stanley Hospital, Perth, 6150 Western Australia, Australia; University of Notre Dame, Fremantle, 6160 Western Australia, Australia; Curtin University, Perth, 6102 Western Australia, Australia.
| | - Alexandra Kang
- PathWest Anatomical Pathology, Fiona Stanley Hospital, Perth, 6150 Western Australia, Australia
| | - Sophia Ang
- Clinical Services, Fiona Stanley Hospital, Perth, 6150 Western Australia, Australia
| | - Michael Texler
- PathWest Anatomical Pathology, Fiona Stanley Hospital, Perth, 6150 Western Australia, Australia
| | - Jacqueline Bentel
- PathWest Anatomical Pathology, Fiona Stanley Hospital, Perth, 6150 Western Australia, Australia
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17
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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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18
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Sychevskaya KA, Kravchenko SK, Risinskaya NV, Misyurina АЕ, Nikulina EE, Babaeva FE, Sudarikov AB. Microsatellite instability (MSI, EMAST) in the pathogenesis of follicular lymphoma. ONCOHEMATOLOGY 2021. [DOI: 10.17650/1818-8346-2021-16-2-56-69] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background. Genetic instability, an important phenomenon involved in oncogenic transformation and tumor progression, is associated with the insufficiency of the multicomponent DNA repair complex, in particular, the nucleotide mismatch repair (MMR) system. The MMR defect manifests itself as abnormalities in DNA microsatellite repeats, or microsatellite instability (MSI). In the studies of colorectal cancer, the role of MSI in prognostication of the disease, and defining the choice of specific therapy with immune checkpoint inhibitors has been proven.However, in lymphatic system tumors, the significance of this phenomenon is poorly understood. Determination of genetic instability in the onset of follicular lymphoma, a disease characterized by a heterogeneous course, may have prognostic value.Objective: to determine the genetic instability at the onset of follicular lymphoma.Materials and methods. Here we report an analysis of 24 microsatellite repeats and amelogenin loci in tumor cells of 46 follicular lymphoma patients.Results. In the studied cohort, lesions in microsatellite repeats were presented by MSI in 9 cases (19.6 %) and the loss of heterozygosity (LOH) in 19 cases (41.3 %). Most frequent lesions were found for the SE33 marker located at the q14 locus of chromosome 6. A significant association was shown between MSI and the double-hit follicular lymphoma group with rearrangements of the MYC and BCL2/BCL6 genes.Conclusion. Thus, our data indicate that the MSI phenomenon might be involved in the pathogenesis of the lymphatic tumors and particularly follicular lymphoma. However further studies on the expanded cohorts of patients are required to define the possible prognostic value of MSI in lymphatic tumors.
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Affiliation(s)
- K. A. Sychevskaya
- National Medical Research Center for Hematology, Ministry of Health of Russia
| | - S. K. Kravchenko
- National Medical Research Center for Hematology, Ministry of Health of Russia
| | - N. V. Risinskaya
- National Medical Research Center for Hematology, Ministry of Health of Russia
| | - А. Е. Misyurina
- National Medical Research Center for Hematology, Ministry of Health of Russia
| | - E. E. Nikulina
- National Medical Research Center for Hematology, Ministry of Health of Russia
| | - F. E. Babaeva
- National Medical Research Center for Hematology, Ministry of Health of Russia
| | - A. B. Sudarikov
- National Medical Research Center for Hematology, Ministry of Health of Russia
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de Castro E Gloria H, Jesuíno Nogueira L, Bencke Grudzinski P, da Costa Ghignatti PV, Guecheva TN, Motta Leguisamo N, Saffi J. Olaparib-mediated enhancement of 5-fluorouracil cytotoxicity in mismatch repair deficient colorectal cancer cells. BMC Cancer 2021; 21:448. [PMID: 33888065 PMCID: PMC8063290 DOI: 10.1186/s12885-021-08188-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/12/2021] [Indexed: 02/07/2023] Open
Abstract
Background The advances in colorectal cancer (CRC) treatment include the identification of deficiencies in Mismatch Repair (MMR) pathway to predict the benefit of adjuvant 5-fluorouracil (5-FU) and oxaliplatin for stage II CRC and immunotherapy. Defective MMR contributes to chemoresistance in CRC. A growing body of evidence supports the role of Poly-(ADP-ribose) polymerase (PARP) inhibitors, such as Olaparib, in the treatment of different subsets of cancer beyond the tumors with homologous recombination deficiencies. In this work we evaluated the effect of Olaparib on 5-FU cytotoxicity in MMR-deficient and proficient CRC cells and the mechanisms involved. Methods Human colon cancer cell lines, proficient (HT29) and deficient (HCT116) in MMR, were treated with 5-FU and Olaparib. Cytotoxicity was assessed by MTT and clonogenic assays, apoptosis induction and cell cycle progression by flow cytometry, DNA damage by comet assay. Adhesion and transwell migration assays were also performed. Results Our results showed enhancement of the 5-FU citotoxicity by Olaparib in MMR-deficient HCT116 colon cancer cells. Moreover, the combined treatment with Olaparib and 5-FU induced G2/M arrest, apoptosis and polyploidy in these cells. In MMR proficient HT29 cells, the Olaparib alone reduced clonogenic survival, induced DNA damage accumulation and decreased the adhesion and migration capacities. Conclusion Our results suggest benefits of Olaparib inclusion in CRC treatment, as combination with 5-FU for MMR deficient CRC and as monotherapy for MMR proficient CRC. Thus, combined therapy with Olaparib could be a strategy to overcome 5-FU chemotherapeutic resistance in MMR-deficient CRC.
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Affiliation(s)
- Helena de Castro E Gloria
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Sarmento Leite st 245, Porto Alegre, RS, Brazil
| | - Laura Jesuíno Nogueira
- Cardiology Institute of Rio Grande do Sul/ University Foundation of Cardiology (ICFUC), Porto Alegre, RS, Brazil
| | - Patrícia Bencke Grudzinski
- Cardiology Institute of Rio Grande do Sul/ University Foundation of Cardiology (ICFUC), Porto Alegre, RS, Brazil
| | | | - Temenouga Nikolova Guecheva
- Cardiology Institute of Rio Grande do Sul/ University Foundation of Cardiology (ICFUC), Porto Alegre, RS, Brazil
| | - Natalia Motta Leguisamo
- Cardiology Institute of Rio Grande do Sul/ University Foundation of Cardiology (ICFUC), Porto Alegre, RS, Brazil
| | - Jenifer Saffi
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Sarmento Leite st 245, Porto Alegre, RS, Brazil.
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20
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Comprehensive Genomic Characterization of Fifteen Early-Onset Lynch-Like Syndrome Colorectal Cancers. Cancers (Basel) 2021; 13:cancers13061259. [PMID: 33809179 PMCID: PMC7999079 DOI: 10.3390/cancers13061259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary The most prevalent type of hereditary colorectal cancer is called Lynch syndrome and it is characterized by a tumor phenotype called microsatellite instability (MSI). This disease is a consequence of germline (inheritable) variants in any of the four mismatch repair (MMR) DNA genes, being their identification essential to ensure their appropriate diagnosis and implementation of preventive measurements. Nevertheless, only 50% of patients with MSI and suspected Lynch syndrome actually carry a germline pathogenic variant in an MMR gene that explains the clinical entity. The remaining 50% are termed Lynch-like syndrome, and their causes remain unknown. In this work, we tried to elucidate the molecular mechanisms that underlie this rare entity in a group of early-onset Lynch-like syndrome colorectal cancer, through whole-exome sequencing of germline and tumor samples. We observed that one-third of these patients have somatic alterations in genes associated with the MMR system and that these could be the mechanism causing their unexplained MSI. Furthermore, we found that patients who showed biallelic somatic alterations also carried germline variants in new candidate genes associated with DNA repair functions and that this could be, partly, the cause of the early onset in this cohort. Abstract Lynch-like syndrome (LLS) is an increasingly common clinical challenge with an underlying molecular basis mostly unknown. To shed light onto it, we focused on a very young LLS early-onset colorectal cancer (CRC) cohort (diagnosis ≤ 40 y.o.), performing germline and tumor whole-exome sequencing (WES) of 15 patients, and additionally analyzing their corresponding tumor mutational burden (TMB) and mutational signatures. We identified four cases (27%) with double somatic putative variants in mismatch repair (MMR) core genes, as well as three additional cases (20%) with double MSH3 somatic alterations in tumors with unexplained MSH2/MSH6 loss of expression, and two cases (13%) with POLD1 potential biallelic alterations. Average TMB was significantly higher for LLS cases with double somatic alterations. Lastly, nine predicted deleterious variants in genes involved in the DNA repair functions and/or previously associated with CRC were found in nine probands, four of which also showed MMR biallelic somatic inactivation. In conclusion, we contribute new insights into LLS CRC, postulating MSH3 and POLD1 double somatic alterations as an underlying cause of a microsatellite instability (MSI) phenotype, proposing intrinsic biological differences between LLS with and without somatic alterations, and suggesting new predisposing candidate genes in this scenario.
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21
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Kondelin J, Martin S, Katainen R, Renkonen-Sinisalo L, Lepistö A, Koskensalo S, Böhm J, Mecklin JP, Cajuso T, Hänninen UA, Välimäki N, Ravantti J, Rajamäki K, Palin K, Aaltonen LA. No evidence of EMAST in whole genome sequencing data from 248 colorectal cancers. Genes Chromosomes Cancer 2021; 60:463-473. [PMID: 33527622 DOI: 10.1002/gcc.22941] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/20/2022] Open
Abstract
Microsatellite instability (MSI) is caused by defective DNA mismatch repair (MMR), and manifests as accumulation of small insertions and deletions (indels) in short tandem repeats of the genome. Another form of repeat instability, elevated microsatellite alterations at selected tetranucleotide repeats (EMAST), has been suggested to occur in 50% to 60% of colorectal cancer (CRC), of which approximately one quarter are accounted for by MSI. Unlike for MSI, the criteria for defining EMAST is not consensual. EMAST CRCs have been suggested to form a distinct subset of CRCs that has been linked to a higher tumor stage, chronic inflammation, and poor prognosis. EMAST CRCs not exhibiting MSI have been proposed to show instability of di- and trinucleotide repeats in addition to tetranucleotide repeats, but lack instability of mononucleotide repeats. However, previous studies on EMAST have been based on targeted analysis of small sets of marker repeats, often in relatively few samples. To gain insight into tetranucleotide instability on a genome-wide level, we utilized whole genome sequencing data from 227 microsatellite stable (MSS) CRCs, 18 MSI CRCs, 3 POLE-mutated CRCs, and their corresponding normal samples. As expected, we observed tetranucleotide instability in all MSI CRCs, accompanied by instability of mono-, di-, and trinucleotide repeats. Among MSS CRCs, some tumors displayed more microsatellite mutations than others as a continuum, and no distinct subset of tumors with the previously proposed molecular characters of EMAST could be observed. Our results suggest that tetranucleotide repeat mutations in non-MSI CRCs represent stochastic mutation events rather than define a distinct CRC subclass.
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Affiliation(s)
- Johanna Kondelin
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Samantha Martin
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Riku Katainen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Laura Renkonen-Sinisalo
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Anna Lepistö
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Selja Koskensalo
- The HUCH Gastrointestinal Clinic, Helsinki University Central Hospital, Helsinki, Finland
| | - Jan Böhm
- Department of Pathology, Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Jukka-Pekka Mecklin
- Department of Education and Research, Jyväskylä Central Hospital, Jyväskylä, Finland.,Department Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Tatiana Cajuso
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Ulrika A Hänninen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Niko Välimäki
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Janne Ravantti
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Kristiina Rajamäki
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lauri A Aaltonen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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22
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Raeker MO, Carethers JM. Immunological Features with DNA Microsatellite Alterations in Patients with Colorectal Cancer. JOURNAL OF CANCER IMMUNOLOGY 2020; 2:116-127. [PMID: 33000102 DOI: 10.33696/cancerimmunol.2.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Competent human DNA mismatch repair (MMR) corrects DNA polymerase mistakes made during cell replication to maintain complete DNA fidelity in daughter cells; faulty DNA MMR occurs in the setting of inflammation and neoplasia, creating base substitutions (e.g. point mutations) and frameshift mutations at DNA microsatellite sequences in progeny cells. Frameshift mutations at DNA microsatellite sequences are a detected biomarker termed microsatellite instability (MSI) for human disease, as this marker can prognosticate and determine therapeutic approaches for patients with cancer. There are two types of MSI: MSI-High (MSI-H), defined by frameshifts at mono- and di-nucleotide microsatellite sequences, and elevated microsatellite alterations at selected tetranucleotide repeats or EMAST, defined by frameshifts in di- and tetranucleotide microsatellite sequences but not mononucleotide sequences. Patients with colorectal cancers (CRCs) manifesting MSI-H demonstrate improved survival over patients without an MSI-H tumor, driven by the generation of immunogenic neoantigens caused by novel truncated proteins from genes whose sequences contain coding microsatellites; these patients' tumors contain hundreds of somatic mutations, and show responsiveness to treatment with immune checkpoint inhibitors. Patients with CRCs manifesting EMAST demonstrate poor survival over patients without an EMAST tumor, and may be driven by a more dominant defect in double strand break repair attributed to the MMR protein MSH3 over its frameshift correcting function; these patients' tumors often have a component of inflammation (and are also termed inflammation-associated microsatellite alterations) and show less somatic mutations and lack coding mononucleotide frameshift mutations that seem to generate the neoantigens seen in the majority of MSI-H tumors. Overall, both types of MSI are biomarkers that can prognosticate patients with CRC, can be tested for simultaneously in marker panels, and informs the approach to specific therapy including immunotherapy for their cancers.
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Affiliation(s)
- Maide O Raeker
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - John M Carethers
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.,Department of Human Genetics and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
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23
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Inflammation-Associated Microsatellite Alterations Caused by MSH3 Dysfunction Are Prevalent in Ulcerative Colitis and Increase With Neoplastic Advancement. Clin Transl Gastroenterol 2020; 10:e00105. [PMID: 31789935 PMCID: PMC6970556 DOI: 10.14309/ctg.0000000000000105] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES: Inflammation-associated microsatellite alterations (also known as elevated microsatellite alterations at selected tetranucleotide repeats [EMAST]) result from IL-6–induced nuclear-to-cytosolic displacement of the DNA mismatch repair (MMR) protein MSH3, allowing frameshifts of dinucleotide or longer microsatellites within DNA. MSH3 also engages homologous recombination to repair double-strand breaks (DSBs), making MSH3 deficiency contributory to both EMAST and DSBs. EMAST is observed in cancers, but given its genesis by cytokines, it may be present in non-neoplastic inflammatory conditions. We examined ulcerative colitis (UC), a preneoplastic condition from prolonged inflammatory duration. METHODS: We assessed 70 UC colons without neoplasia, 5 UC specimens with dysplasia, 14 UC-derived colorectal cancers (CRCs), and 19 early-stage sporadic CRCs for microsatellite instability (MSI) via multiplexed polymerase chain reaction capable of simultaneous detection of MSI-H, MSI-L, and EMAST. We evaluated UC specimens for MSH3 expression via immunohistochemistry. RESULTS: UC, UC with dysplasia, and UC-derived CRCs demonstrated dinucleotide or longer microsatellite frameshifts, with UC showing coincident reduction of nuclear MSH3 expression. No UC specimen, with or without neoplasia, demonstrated mononucleotide frameshifts. EMAST frequency was higher in UC-derived CRCs than UC (71.4% vs 31.4%, P = 0.0045) and higher than early-stage sporadic CRCs (66.7% vs 26.3%, P = 0.0426). EMAST frequency was higher with UC duration >8 years compared with ≤8 years (40% vs 16%, P = 0.0459). DISCUSSION: Inflammation-associated microsatellite alterations/EMAST are prevalent in UC and signify genomic mutations in the absence of neoplasia. Duration of disease and advancement to neoplasia increases frequency of EMAST. MSH3 dysfunction is a potential contributory pathway toward neoplasia in UC that could be targeted by therapeutic intervention.
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Park Y, Kim DW, Hong YJ, Park KU, Nam SK, Na HY, Lee HS, Kim MH, Oh HK, Kang SB. Is elevated microsatellite alterations at selected tetranucleotide repeats (EMAST)-negative/MSI-high colorectal cancer a distinct subtype of the disease? J Surg Oncol 2020; 122:1462-1469. [PMID: 32779222 DOI: 10.1002/jso.26157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/26/2020] [Indexed: 11/11/2022]
Abstract
BACKGROUND AND OBJECTIVES Microsatellite instability (MSI) plays a prognostic and predictive role in colorectal cancer (CRC). Elevated microsatellite alterations at selected tetranucleotide repeats (EMAST), a novel type of MSI, was recently identified. METHODS A retrospective analysis of a prospective cohort database was performed. Patients who attempted curative surgery for MSI-high (MSI-H) CRC and had available testing results of EMAST were included for analysis. The difference in clinical characteristics, immunohistochemistry profile, and 3-year recurrence-free and overall survival between EMAST-negative and EMAST-positive tumors was measured. RESULTS EMAST status was successfully evaluated in 86 cases among patients who received EMAST testing, and only 16.3% (14/86) of these patients were EMAST-negative/MSI-H. Patients with EMAST-negative tumors were younger; their tumors exhibited well differentiation, less venous invasion, and greater mutS homolog 3 expression. There was no distant metastasis or cancer-specific death among EMAST-negative patients. Yet no statistically significant difference was found between the two groups in 3-year overall or recurrence-free survival. CONCLUSIONS Patients with EMAST-negative/MSI-H CRC seem to have different clinicopathological characteristics. Future large-scale studies could clarify the role of EMAST genotype as a sub-classifier of MSI-H CRC.
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Affiliation(s)
- Yeshong Park
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Duck-Woo Kim
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Yun Ji Hong
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Soo Kyung Nam
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Hee Young Na
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Min Hyun Kim
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Heung-Kwon Oh
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Sung-Bum Kang
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
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The Human DNA Mismatch Repair Protein MSH3 Contains Nuclear Localization and Export Signals That Enable Nuclear-Cytosolic Shuttling in Response to Inflammation. Mol Cell Biol 2020; 40:MCB.00029-20. [PMID: 32284349 DOI: 10.1128/mcb.00029-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/07/2020] [Indexed: 12/16/2022] Open
Abstract
Inactivation of DNA mismatch repair propels colorectal cancer (CRC) tumorigenesis. CRCs exhibiting elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) show reduced nuclear MutS homolog 3 (MSH3) expression with surrounding inflammation and portend poor patient outcomes. MSH3 reversibly exits from the nucleus to the cytosol in response to the proinflammatory cytokine interleukin-6 (IL-6), suggesting that MSH3 may be a shuttling protein. In this study, we manipulated three putative nuclear localization (NLS1 to -3) and two potential nuclear export signals (NES1 and -2) within MSH3. We found that both NLS1 and NLS2 possess nuclear import function, with NLS1 responsible for nuclear localization within full-length MSH3. We also found that NES1 and NES2 work synergistically to maximize nuclear export, with both being required for IL-6-induced MSH3 export. We examined a 27-bp deletion (Δ27bp) within the polymorphic exon 1 that occurs frequently in human CRC cells and neighbors NLS1. With oxidative stress, MSH3 with this deletion (Δ27bp MSH3) localizes to the cytoplasm, suggesting that NLS1 function in Δ27bp MSH3 is compromised. Overall, MSH3's shuttling in response to inflammation enables accumulation in the cytoplasm; reduced nuclear MSH3 increases EMAST and DNA damage. We suggest that polymorphic sequences adjacent to NLS1 may enhance cytosolic retention, which has clinical implications for inflammation-associated neoplastic processes.
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26
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Zhang Z, Duan FX, Gu GL, Yu PF. Mutation analysis of related genes in hamartoma polyp tissue of Peutz-Jeghers syndrome. World J Gastroenterol 2020; 26:1926-1937. [PMID: 32390703 PMCID: PMC7201153 DOI: 10.3748/wjg.v26.i16.1926] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/29/2020] [Accepted: 04/04/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Peutz-Jeghers syndrome (PJS) is a rare disease with clinical manifestations of pigmented spots on the lips, mucous membranes and extremities, scattered gastrointestinal polyps, and susceptibility to tumors. The clinical heterogeneity of PJS is obvious, and the relationship between clinical phenotype and genotype is still unclear.
AIM To investigate the mutation status of hereditary colorectal tumor-associated genes in hamartoma polyp tissue of PJS patients and discuss its relationship with the clinicopathological data of PJS.
METHODS Twenty patients with PJS were randomly selected for this study and were treated in the Air Force Medical Center (former Air Force General Hospital) PLA between 2008 and 2017. Their hamartoma polyp tissues were used for APC, AXIN2, BMPR1A, EPCAM, MLH1, MLH3, MSH2, MSH6, MUTYH, PMS1, PMS2, PTEN, SMAD4, and LKB1/STK11 gene sequencing using next-generation sequencing technology. The correlations between the sequencing results and clinical pathological data of PJS were analyzed.
RESULTS Fourteen types of LKB1/STK11 mutations were detected in 16 cases (80.0%), of which 8 new mutations were found (3 types of frameshift deletion mutations: c.243delG, c.363_364delGA, and c.722delC; 2 types of frameshift insertions: c. 144_145insGCAAG, and c.454_455insC; 3 types of splice site mutations: c.464+1G>T, c.464+1G>A, and c.598-1G>A); 9 cases (45.0%) were found to have 18 types of heterozygous mutations in the remaining 13 genes except LKB1/STK11. Of these, MSH2: c.792+1G>A, MSH6: c.3689C>G, c.4001+13C>CTTAC, PMS1: c.46C>t, and c.922G>A were new mutations.
CONCLUSION The genetic mutations in hamartoma polyp tissue of PJS are complex and diverse. Moreover, other gene mutations in PJS hamartoma polyp tissue were observed, with the exception of LKB1/STK11 gene, especially the DNA mismatch repair gene (MMR). Colorectal hamartoma polyps with LKB1/STK11 mutations were larger in diameter than those with other gene mutations.
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Affiliation(s)
- Zhi Zhang
- Air Force Clinical College (Air Force Medical Center) of Anhui Medical University, Beijing 100142, China
| | - Fu-Xiao Duan
- Department of General Surgery, the General Hospital of Northern Theater Command PLA, Shenyang 110016, Liaoning Province, China
| | - Guo-Li Gu
- Department of General Surgery, Air Force Medical Center, PLA, Beijing 100142, China
| | - Peng-Fei Yu
- Department of General Surgery, Air Force Medical Center, PLA, Beijing 100142, China
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The Clinicopathological Features and Genetic Mutations in Gastric Cancer Patients According to EMAST and MSI Status. Cancers (Basel) 2020; 12:cancers12030551. [PMID: 32120855 PMCID: PMC7139949 DOI: 10.3390/cancers12030551] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 01/22/2023] Open
Abstract
Background: There has been no report regarding the clinicopathological features and genetic mutations regarding elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) in gastric cancer (GC). Methods: The correlation among EMAST status, microsatellite instability (MSI) status, mutations of common GC-related genes and 16 DNA repair-associated genes, and the clinicopathological features were analyzed. Results: Among the 360 GC patients enrolled, there were 76 (21.1%) with EMAST+ tumors and 284 with EMAST− tumors, and 59 (16.4%) were MSI-high (MSI-H) tumors, and 301 were microsatellite stable (MSS) tumors. Patients with EMAST+ tumors exhibited an earlier pathological T category and had more genetic mutations in the PI3K/AKT pathway, ARID1A and DNA repair-associated genes than those with EMAST− tumors. Patients with MSI-H tumors have more genetic mutations in the PI3K/AKT pathway and DNA repair-associated genes than those with MSS tumors. In the subgroup analysis for MSI-H GC, EMAST+ tumors were associated with earlier pathological T and N categories, earlier TNM stages, higher frequency of DNA-repair-associated genetic mutations, and a better survival rate than EMAST− tumors. Conclusions:PI3K/AKT pathway mutations may play an important role in EMAST+ and/or MSI-H GC. EMAST+/MSI-H tumors seem to represent a different subtype of gastric cancer from EMAST−/MSI-H tumors.
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28
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Raeker MÖ, Pierre-Charles J, Carethers JM. Tetranucleotide Microsatellite Mutational Behavior Assessed in Real Time: Implications for Future Microsatellite Panels. Cell Mol Gastroenterol Hepatol 2020; 9:689-704. [PMID: 31982570 PMCID: PMC7163322 DOI: 10.1016/j.jcmgh.2020.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND & AIMS Fifty percent of colorectal cancers show elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) and are associated with inflammation, metastasis, and poor patient outcome. EMAST results from interleukin 6-induced nuclear-to-cytosolic displacement of the DNA mismatch repair protein Mutated S Homolog 3, allowing frameshifts of dinucleotide and tetranucleotide but not mononucleotide microsatellites. Unlike mononucleotide frameshifts that universally shorten in length, we previously observed expansion and contraction frameshifts at tetranucleotide sequences. Here, we developed cell models to assess tetranucleotide frameshifts in real time. METHODS We constructed plasmids containing native (AAAG)18 and altered-length ([AAAG]15 and [AAAG]12) human D9S242 locus that placed enhanced green fluorescent protein +1 bp/-1 bp out-of-frame for protein translation and stably transfected into DNA mismatch repair-deficient cells for clonal selection. We used flow cytometry to detect enhanced green fluorescent protein-positive cells to measure mutational behavior. RESULTS Frameshift mutation rates were 31.6 to 71.1 × 10-4 mutations/cell/generation and correlated with microsatellite length (r2 = 0.986, P = .0375). Longer repeats showed modestly higher deletion over insertion rates, with both equivalent for shorter repeats. Accumulation of more deletion frameshifts contributed to a distinct mutational bias for each length (overall: 77.8% deletions vs 22.2% insertions), likely owing to continual deletional mutation of insertions. Approximately 78.9% of observed frameshifts were 1 AAAG repeat, 16.1% were 2 repeats, and 5.1% were 3 or more repeats, consistent with a slipped strand mispairing mutation model. CONCLUSIONS Tetranucleotide frameshifts show a deletion bias and undergo more than 1 deletion event via intermediates, with insertions converted into deletions. Tetranucleotide markers added to traditional microsatellite instability panels will be able to determine both EMAST and classic microsatellite instability, but needs to be assessed by multiple markers to account for mutational behavior and intermediates.
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Affiliation(s)
- Maide Ö Raeker
- Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jovan Pierre-Charles
- Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - John M Carethers
- Department of Human Genetics and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.
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Lorca V, Garre P. Current status of the genetic susceptibility in attenuated adenomatous polyposis. World J Gastrointest Oncol 2019; 11:1101-1114. [PMID: 31908716 PMCID: PMC6937445 DOI: 10.4251/wjgo.v11.i12.1101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/18/2019] [Accepted: 10/14/2019] [Indexed: 02/05/2023] Open
Abstract
Adenomatous polyposis (AP) is classified according to cumulative adenoma number in classical AP (CAP) and attenuated AP (AAP). Genetic susceptibility is the major risk factor in CAP due to mutations in the known high predisposition genes APC and MUTYH. However, the contribution of genetic susceptibility to AAP is lower and less understood. New predisposition genes have been recently proposed, and some of them have been validated, but their scarcity hinders accurate risk estimations and prevalence calculations. AAP is a heterogeneous condition in terms of severity, clinical features and heritability. Therefore, clinicians do not have strong discriminating criteria for the recommendation of the genetic study of known predisposition genes, and the detection rate is low. Elucidation and knowledge of new AAP high predisposition genes are of great importance to offer accurate genetic counseling to the patient and family members. This review aims to update the genetic knowledge of AAP, and to expound the difficulties involved in the genetic analysis of a highly heterogeneous condition such as AAP.
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Affiliation(s)
- Víctor Lorca
- Laboratorio de Oncología Molecular, Grupo de Investigación Clínica y Traslacional en Oncología, Hospital Clínico San Carlos, Madrid 28040, Spain
| | - Pilar Garre
- Laboratorio de Oncología Molecular, Servicio de Oncología, Hospital Clínico San Carlos, Madrid 28040, Spain
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Watson MM, Lea D, Hagland HR, Søreide K. Elevated Microsatellite Alterations at Selected Tetranucleotides (EMAST) Is Not Attributed to MSH3 Loss in Stage I-III Colon cancer: An Automated, Digitalized Assessment by Immunohistochemistry of Whole Slides and Hot Spots. Transl Oncol 2019; 12:1583-1588. [PMID: 31677491 PMCID: PMC6930943 DOI: 10.1016/j.tranon.2019.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/08/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION EMAST is a poorly understood form of microsatellite instability (MSI) in colorectal cancer (CRC) for which loss of MSH3 has been proposed as the underlying mechanism, based on experimental studies. We aimed to evaluate whether MSH3 loss is associated with EMAST in CRC. METHODS A consecutive cohort of patients with stage I-III CRC. Digital image analysis using heatmap-derived hot spots investigated MSH3 expression by immunohistochemistry. Fragment analysis of multiplex PCR was used to assess MSI and EMAST, and results cross-examined with MSH3 protein expression. RESULTS Of 152 patients, EMAST was found in 50 (33%) and exclusively in the colon. Most EMAST-positive cancers had instability at all 5 markers, and EMAST overlapped with MSI-H in 42/50 cases (84%). The most frequently altered tetranucleotide markers were D8S321 (38.2% of tumors) and D20S82 (34.4%). Subjective evaluation of MSH3 expression by IHC in tumor found ≤10% negative tumor cells in all samples, most being ≤5% negative. Digital analysis improved the detection but showed a similar spread of MSH3 loss (range 0.1-15.7%, mean 2.2%). Hotspot MSH3 negativity ranged between 0.1 to 95.0%, (mean 8.6%) with significant correlation with the whole slide analysis (Spearman's rho=0.677 P<.001). Loss of MSH3 expression did not correlate with EMAST. CONCLUSIONS In a well-defined cohort of patients with CRC, loss of MSH3 was not associated with EMAST. Further investigation into the mechanisms leading to EMAST in CRC is needed.
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Affiliation(s)
- Martin M Watson
- Gastrointestinal Translational Research Unit, Laboratory for Molecular Medicine, Stavanger University Hospital, Gerd Ragna Bloch Thorsens Gate 8, 4011, Stavanger, Norway; Department of Gastrointestinal Surgery, Stavanger University Hospital, Gerd Ragna Bloch Thorsens Gate 8, 4011, Stavanger, Norway; Department of Clinical Medicine, University of Bergen, Bergen, Norway.
| | - Dordi Lea
- Gastrointestinal Translational Research Unit, Laboratory for Molecular Medicine, Stavanger University Hospital, Gerd Ragna Bloch Thorsens Gate 8, 4011, Stavanger, Norway; Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Pathology, Stavanger University Hospital, Gerd Ragna Bloch Thorsens Gate 8, 4011, Stavanger, Norway
| | - Hanne R Hagland
- Gastrointestinal Translational Research Unit, Laboratory for Molecular Medicine, Stavanger University Hospital, Gerd Ragna Bloch Thorsens Gate 8, 4011, Stavanger, Norway; Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Norway
| | - Kjetil Søreide
- Gastrointestinal Translational Research Unit, Laboratory for Molecular Medicine, Stavanger University Hospital, Gerd Ragna Bloch Thorsens Gate 8, 4011, Stavanger, Norway; Department of Gastrointestinal Surgery, Stavanger University Hospital, Gerd Ragna Bloch Thorsens Gate 8, 4011, Stavanger, Norway; Department of Clinical Medicine, University of Bergen, Bergen, Norway
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Chang SC, Lan YT, Lin PC, Yang SH, Lin CH, Liang WY, Chen WS, Jiang JK, Lin JK. Patterns of germline and somatic mutations in 16 genes associated with mismatch repair function or containing tandem repeat sequences. Cancer Med 2019; 9:476-486. [PMID: 31769227 PMCID: PMC6970039 DOI: 10.1002/cam4.2702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/19/2019] [Accepted: 10/28/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND We assumed that targeted next-generation sequencing (NGS) of mismatch repair-associated genes could improve the detection of driving mutations in colorectal cancers (CRC) with microsatellite instability (MSI) and microsatellite alterations at selected tetranucleotide repeats (EMAST) and clarify the somatic mutation patterns of CRC subtypes. MATERIAL AND METHODS DNAs from tumors and white blood cells were obtained from 81 patients with EMAST(+)/MSI-high (MSI-H), 78 patients with EMAST(+)/microsatellite stable (MSS), and 72 patients with EMAST(-)/MSI-H. The germline and somatic mutations were analyzed with a 16-genes NGS panel. RESULTS In total, 284 germline mutations were identified in 161 patients. The most common mutations were in EPCAM (24.8%), MSH6 (24.2%), MLH1 (21.7%), and AXIN2 (21.7%). Germline mutations of AXIN2, POLE, POLD1, and TGFBR2 also resulted in EMAST and MSI. EMAST(+)/MSI-H tumors had a significant higher mutation number (205.9 ± 95.2 mut/MB) than tumors that were only EMAST(+) or MSI-H (118.6 ± 64.2 and 106.2 ± 54.5 mut/MB, respectively; both P < .001). In patients with AXIN2 germline mutations, the number of pathological somatic mutations in the tumors was significantly higher than those without AXIN2 germline mutations (176.7 ± 94.2 mut/MB vs 139.6 ± 85.0 mut/MB, P = .002). CONCLUSION Next-generation sequencing could enhance the detection of familial CRC. The somatic mutation burden might result from not only the affected genes in germline mutations but also through the dysfunction of downstream effectors. The AXIN2 gene might associate with hypermutation in tumors. Further in vitro experiments to confirm the causal relationship is deserved.
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Affiliation(s)
- Shih-Ching Chang
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yuan-Tzu Lan
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Pei-Ching Lin
- Department of Clinical Pathology, Yang-Ming Branch, Taipei City Hospital, Taipei, Taiwan.,Department of Health and Welfare, University of Taipei, Taipei, Taiwan
| | - Shung-Haur Yang
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,National Yang-Ming University Hospital, Yilan, Taiwan
| | - Chien-Hsing Lin
- Division of Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan
| | - Wen-Yi Liang
- Department of Pathology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Wei-Shone Chen
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jeng-Kai Jiang
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jen-Kou Lin
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
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Watson MM, Kanani A, Lea D, Khajavi RB, Søreide JA, Kørner H, Hagland HR, Søreide K. Elevated Microsatellite Alterations at Selected Tetranucleotides (EMAST) in Colorectal Cancer is Associated with an Elderly, Frail Phenotype and Improved Recurrence-Free Survival. Ann Surg Oncol 2019; 27:1058-1067. [PMID: 31686344 DOI: 10.1245/s10434-019-08048-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Elevated microsatellite alterations at selected tetranucleotides (EMAST) is a poorly investigated form of microsatellite instability (MSI) in colorectal cancer (CRC). OBJECTIVE The aim of this study was to investigate the clinicopathological features of EMAST in CRC and its relation to outcome. METHODS A population-based, consecutive cohort of surgically treated stage I-III CRC patients investigated for high-frequency MSI (MSI-H) and EMAST. Clinicopathological differences were reported as odds ratios (OR) and survival was presented as hazard ratios (HR) with 95% confidence intervals (CIs). RESULTS Of 161 patients included, 25% were aged > 79 years. There was a large overlap in the prevalence of EMAST (31.7%) and MSI-H (27.3%) [82.4% of EMAST were also MSI-H]. EMAST had the highest prevalence in the proximal colon (OR 15.9, 95% CI 5.6-45.1; p < 0.001) and in women (OR 4.1, 95% CI 1.9-8.6; p < 0.001), and were poorly differentiated (OR 5.0, 95% CI 2.3-10.7; p < 0.001). Compared with EMAST-negative patients, EMAST-positive patients were older (median age 77 vs. 69 years; p < 0.001), leaner (median weight 67.5 vs. 77 kg; p = 0.001), had significantly higher rates of hypoalbuminemia (24% vs. 6%; OR 2.3, 95% CI 1.5-3.6; p = 0.002) and anemia (45% vs. 20%; OR 3.3, 95% CI 1.6-6.8; p = 0.001), and had elevated preoperative C-reactive protein (CRP) levels (51% vs. 34%; OR 1.9, 95% CI 1.0-3.9; p = 0.046). Improved recurrence-free survival was found in both MSI-H and EMAST subtypes. In multivariable analysis, node status (pN +), together with elevated CRP and MSI-positive, were the strongest prognostic factors for recurrence-free survival. CONCLUSIONS EMAST in CRC is associated with an older, leaner, and frailer phenotype with a lower risk of recurrence. The relevance of, and putative mechanisms to, EMAST warrants further investigation.
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Affiliation(s)
- Martin M Watson
- Gastrointestinal Translational Research Unit, Laboratory for Molecular Biology, Stavanger University Hospital, Stavanger, Norway.,Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Arezo Kanani
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
| | - Dordi Lea
- Gastrointestinal Translational Research Unit, Laboratory for Molecular Biology, Stavanger University Hospital, Stavanger, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway.,Department of Pathology, Stavanger University Hospital, Stavanger, Norway
| | - Ramesh B Khajavi
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
| | - Jon Arne Søreide
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hartwig Kørner
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hanne R Hagland
- Gastrointestinal Translational Research Unit, Laboratory for Molecular Biology, Stavanger University Hospital, Stavanger, Norway.,Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
| | - Kjetil Søreide
- Gastrointestinal Translational Research Unit, Laboratory for Molecular Biology, Stavanger University Hospital, Stavanger, Norway. .,Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway. .,Department of Clinical Medicine, University of Bergen, Bergen, Norway.
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Mohammadpour S, Goodarzi HR, Jafarinia M, Porhoseingholi MA, Nazemalhosseini‐Mojarad E. EMAST status as a beneficial predictor of fluorouracil‐based adjuvant chemotherapy for Stage II/III colorectal cancer. J Cell Physiol 2019; 235:3604-3611. [DOI: 10.1002/jcp.29249] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 08/23/2019] [Indexed: 01/19/2023]
Affiliation(s)
- Somayeh Mohammadpour
- Department of Biology, Fars Science and Research Branch Islamic Azad University Marvdasht Iran
- Department of Biology, Marvdasht Branch Islamic Azad University Marvdasht Iran
| | - Hamed R. Goodarzi
- Department of Biology, Marvdasht Branch Islamic Azad University Marvdasht Iran
| | - Mojtaba Jafarinia
- Department of Biology, Marvdasht Branch Islamic Azad University Marvdasht Iran
| | - Mohammad A. Porhoseingholi
- Department of Bio‐Statistics, Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases Shahid Beheshti University of Medical Sciences Tehran Iran
| | - Ehsan Nazemalhosseini‐Mojarad
- Department of Gastrointestinal (GI) Cancer, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases Shahid Beheshti University of Medical Sciences Tehran Iran
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Chen MH, Chang SC, Lin PC, Yang SH, Lin CC, Lan YT, Lin HH, Lin CH, Lai JI, Liang WY, Lu ML, Yang MH, Chao Y. Combined Microsatellite Instability and Elevated Microsatellite Alterations at Selected Tetranucleotide Repeats (EMAST) Might Be a More Promising Immune Biomarker in Colorectal Cancer. Oncologist 2019; 24:1534-1542. [PMID: 31292272 DOI: 10.1634/theoncologist.2019-0171] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/06/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The form of microsatellite instability (MSI) affecting tetranucleotide repeats known as elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) has emerged as a new potential biomarker in multiple cancers. In colorectal cancer (CRC), the correlation between EMAST and MSI mutations remain inconclusive. MATERIALS AND METHODS We evaluated 1,505 patients with CRC using five EMAST markers (D20S82, D20S85, D8S321, D9S242, and MYCL1) and the Bethesda panel of MSI markers. Most commonly, mutations involved in CRCs were identified by MassArray Assay, and DNA repair genes were analyzed by next-generation sequencing. Clinical characteristics and prognostic relevance were correlated with EMAST and MSI. RESULTS Tumors that were EMAST positive and MSI high (MSI-H) were detected in 159 (10.6%) and 154 (10.2%) of 1,505 patients with CRC. Patients were divided into four groups according to EMAST and MSI status (EMAST-positive and MSI-H, EMAST-positive and microsatellite-stable [MSS], EMAST-negative and MSI-H, and EMAST-negative and MSS). The EMAST-positive and MSI-H group was associated with female predominance, higher prevalence of proximal colon tumors, early stage tumors, poorly differentiated tumors, mucinous histology, and higher incidence of mutations in PI3KCA, BRAF, TGFBR, PTEN, and AKT1 compared with other groups. Furthermore, compared with only EMAST-positive tumors or only MSI-H tumors, tumors that were both EMAST-positive and MSI-H had a higher frequency of MLH1, MSH3, MSH6, PMS2, and EXO1 gene mutations. Finally, the presence of EMAST-positive and MSI-H tumors was a good prognostic indicator in CRC. CONCLUSION High mutations in several DNA repair genes in EMAST-positive and MSI-H tumors suggest that this subtype of CRC might be more suitable for treatment with immune therapy. IMPLICATIONS FOR PRACTICE Elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) is a unique molecular subtype of colorectal cancer (CRC). The current study demonstrated that the EMAST-positive and MSI-high (MSI-H) group was associated with female predominance, higher prevalence of proximal colon tumors, early stage tumors, poorly differentiated tumors, mucinous histology, and higher incidence of mutations in PI3KCA, BRAF, TGFBR, PTEN, and AKT1 compared with other groups. Most importantly, high mutations in DNA repair genes and MSI-related genes in EMAST-positive and MSI-H tumors suggest that this subtype of CRC might be more suitable for treatment with immune therapy compared with MSI-H tumors alone.
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Affiliation(s)
- Ming-Huang Chen
- Division of Medical Oncology, Center for Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Shih-Ching Chang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Pei-Ching Lin
- Department of Clinical Pathology, Yang-Ming Branch, Taipei City Hospital, Taipei, Taiwan
- Department of Health and Welfare, University of Taipei, Taipei, Taiwan
| | - Shung-Haur Yang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chun-Chi Lin
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yuan-Tzu Lan
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Hung-Hsin Lin
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chien-Hsing Lin
- Division of Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan
| | - Jiun-I Lai
- Division of Medical Oncology, Center for Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Wen-Yi Liang
- Department of Pathology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Meng-Lun Lu
- Division of Medical Oncology, Center for Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Muh-Hwa Yang
- Division of Medical Oncology, Center for Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yee Chao
- Division of Medical Oncology, Center for Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
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Determination of Mismatch Repair Status in Human Cancer and Its Clinical Significance: Does One Size Fit All? Adv Anat Pathol 2019; 26:270-279. [PMID: 30932972 DOI: 10.1097/pap.0000000000000234] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The clinical management of cancers has progressed rapidly into the immunopathology era, with the unprecedented histology-agnostic approval of pembrolizumab in mismatch repair (MMR) deficient tumors. Despite the significant recent achievements in the treatment of these patients, however, the identification of clinically relevant subclasses of cancers based on the MMR status remains a major challenge. Many investigations have assessed the role of different diagnostic tools, including immunohistochemistry, microsatellite instability, and tumor mutational burden in both prognostic and therapeutic settings, with heterogenous results. To date, there are no tumor-specific guidelines or companion diagnostic tests for MMR assessment, and this analysis is often performed with locally developed methods. In this review, we provide a comprehensive overview of the current state-of-knowledge of MMR alterations in syndromic and sporadic tumors and discuss the available armamentarium for MMR pathologic characterization, from morphology to high-throughput molecular tools.
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Flower M, Lomeikaite V, Ciosi M, Cumming S, Morales F, Lo K, Hensman Moss D, Jones L, Holmans P, Monckton DG, Tabrizi SJ. MSH3 modifies somatic instability and disease severity in Huntington's and myotonic dystrophy type 1. Brain 2019; 142:awz115. [PMID: 31216018 PMCID: PMC6598626 DOI: 10.1093/brain/awz115] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/31/2019] [Accepted: 02/27/2019] [Indexed: 12/22/2022] Open
Abstract
The mismatch repair gene MSH3 has been implicated as a genetic modifier of the CAG·CTG repeat expansion disorders Huntington's disease and myotonic dystrophy type 1. A recent Huntington's disease genome-wide association study found rs557874766, an imputed single nucleotide polymorphism located within a polymorphic 9 bp tandem repeat in MSH3/DHFR, as the variant most significantly associated with progression in Huntington's disease. Using Illumina sequencing in Huntington's disease and myotonic dystrophy type 1 subjects, we show that rs557874766 is an alignment artefact, the minor allele for which corresponds to a three-repeat allele in MSH3 exon 1 that is associated with a reduced rate of somatic CAG·CTG expansion (P = 0.004) and delayed disease onset (P = 0.003) in both Huntington's disease and myotonic dystrophy type 1, and slower progression (P = 3.86 × 10-7) in Huntington's disease. RNA-Seq of whole blood in the Huntington's disease subjects found that repeat variants are associated with MSH3 and DHFR expression. A transcriptome-wide association study in the Huntington's disease cohort found increased MSH3 and DHFR expression are associated with disease progression. These results suggest that variation in the MSH3 exon 1 repeat region influences somatic expansion and disease phenotype in Huntington's disease and myotonic dystrophy type 1, and suggests a common DNA repair mechanism operates in both repeat expansion diseases.
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Affiliation(s)
- Michael Flower
- Department of Neurodegenerative Disease and Dementia Research Institute, UCL, UK
| | - Vilija Lomeikaite
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, UK
| | - Marc Ciosi
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, UK
| | - Sarah Cumming
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, UK
| | - Fernando Morales
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, UK
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, Costa Rica
| | - Kitty Lo
- School of Mathematics and Statistics, University of Sydney, Australia
| | - Davina Hensman Moss
- Department of Neurodegenerative Disease and Dementia Research Institute, UCL, UK
| | - Lesley Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, UK
| | - Darren G Monckton
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, UK
| | - Sarah J Tabrizi
- Department of Neurodegenerative Disease and Dementia Research Institute, UCL, UK
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Abstract
Functional genomics approaches can overcome limitations-such as the lack of identification of robust targets and poor clinical efficacy-that hamper cancer drug development. Here we performed genome-scale CRISPR-Cas9 screens in 324 human cancer cell lines from 30 cancer types and developed a data-driven framework to prioritize candidates for cancer therapeutics. We integrated cell fitness effects with genomic biomarkers and target tractability for drug development to systematically prioritize new targets in defined tissues and genotypes. We verified one of our most promising dependencies, the Werner syndrome ATP-dependent helicase, as a synthetic lethal target in tumours from multiple cancer types with microsatellite instability. Our analysis provides a resource of cancer dependencies, generates a framework to prioritize cancer drug targets and suggests specific new targets. The principles described in this study can inform the initial stages of drug development by contributing to a new, diverse and more effective portfolio of cancer drug targets.
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Behan FM, Iorio F, Picco G, Gonçalves E, Beaver CM, Migliardi G, Santos R, Rao Y, Sassi F, Pinnelli M, Ansari R, Harper S, Jackson DA, McRae R, Pooley R, Wilkinson P, van der Meer D, Dow D, Buser-Doepner C, Bertotti A, Trusolino L, Stronach EA, Saez-Rodriguez J, Yusa K, Garnett MJ. Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens. Nature 2019; 568:511-516. [PMID: 30971826 DOI: 10.1038/s41586-019-1103-9] [Citation(s) in RCA: 685] [Impact Index Per Article: 137.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 03/08/2019] [Indexed: 12/15/2022]
Abstract
Functional genomics approaches can overcome limitations-such as the lack of identification of robust targets and poor clinical efficacy-that hamper cancer drug development. Here we performed genome-scale CRISPR-Cas9 screens in 324 human cancer cell lines from 30 cancer types and developed a data-driven framework to prioritize candidates for cancer therapeutics. We integrated cell fitness effects with genomic biomarkers and target tractability for drug development to systematically prioritize new targets in defined tissues and genotypes. We verified one of our most promising dependencies, the Werner syndrome ATP-dependent helicase, as a synthetic lethal target in tumours from multiple cancer types with microsatellite instability. Our analysis provides a resource of cancer dependencies, generates a framework to prioritize cancer drug targets and suggests specific new targets. The principles described in this study can inform the initial stages of drug development by contributing to a new, diverse and more effective portfolio of cancer drug targets.
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Affiliation(s)
- Fiona M Behan
- Wellcome Sanger Institute, Cambridge, UK.,Open Targets, Cambridge, UK
| | - Francesco Iorio
- Wellcome Sanger Institute, Cambridge, UK.,Open Targets, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | | | | | - Giorgia Migliardi
- Candiolo Cancer Institute-FPO, IRCCS, Turin, Italy.,Department of Oncology, University of Torino, Turin, Italy
| | - Rita Santos
- GlaxoSmithKline Research and Development, Stevenage, UK
| | - Yanhua Rao
- GlaxoSmithKline Research and Development, Collegeville, PA, USA
| | | | - Marika Pinnelli
- Candiolo Cancer Institute-FPO, IRCCS, Turin, Italy.,Department of Oncology, University of Torino, Turin, Italy
| | | | | | | | | | | | | | | | - David Dow
- Open Targets, Cambridge, UK.,GlaxoSmithKline Research and Development, Stevenage, UK
| | - Carolyn Buser-Doepner
- Open Targets, Cambridge, UK.,GlaxoSmithKline Research and Development, Collegeville, PA, USA
| | - Andrea Bertotti
- Candiolo Cancer Institute-FPO, IRCCS, Turin, Italy.,Department of Oncology, University of Torino, Turin, Italy
| | - Livio Trusolino
- Candiolo Cancer Institute-FPO, IRCCS, Turin, Italy.,Department of Oncology, University of Torino, Turin, Italy
| | - Euan A Stronach
- Open Targets, Cambridge, UK.,GlaxoSmithKline Research and Development, Stevenage, UK
| | - Julio Saez-Rodriguez
- Open Targets, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.,Faculty of Medicine, Joint Research Centre for Computational Biomedicine, RWTH Aachen University, Aachen, Germany.,Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Bioquant, Heidelberg, Germany.,Heidelberg University Hospital, Heidelberg, Germany
| | - Kosuke Yusa
- Wellcome Sanger Institute, Cambridge, UK. .,Open Targets, Cambridge, UK. .,Stem Cell Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
| | - Mathew J Garnett
- Wellcome Sanger Institute, Cambridge, UK. .,Open Targets, Cambridge, UK.
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Ashktorab H, Azimi H, Varma S, Lee EL, Laiyemo AO, Nickerson ML, Brim H. Driver genes exome sequencing reveals distinct variants in African Americans with colorectal neoplasia. Oncotarget 2019; 10:2607-2624. [PMID: 31080553 PMCID: PMC6498998 DOI: 10.18632/oncotarget.26721] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/31/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in the United States. African Americans are disproportionately affected by CRC. Our hypothesis is that driver genes with known and novel mutations have an impact on CRC outcome in this population. Therefore, we investigated the variants' profiles in a panel of 15 CRC genes. PATIENTS & METHODS Colorectal specimens (n=140) were analyzed by targeted exome sequencing using an Ion Torrent platform. Detected variants were validated in 36 samples by Illumina sequencing. The novel status of the validated variants was determined by comparison to publicly available databases. Annotated using ANNOVAR and in-silico functional analysis of these variants were performed to determine likely pathogenic variants. RESULTS Overall, 121 known and novel variants were validated: APC (27%), AMER1 (3%), ARID1 (7%), MSH3 (12%), MSH6 (10%), BRAF (4%), KRAS (6%), FBXW7 (4%), PIK3CA (6%), SMAD4 (5%), SOX9 (2%), TCF7L2 (2%), TGFBR2 (5%), TP53 (7%). From these validated variants, 12% were novel in 8 genes (AMER1, APC, ARID1A, BRAF, MSH6, PIK3CA, SMAD4, and TCF7L2). Of the validated variants, 23% were non-synonymous, 14% were stopgains, 24% were synonymous and 39% were intronic variants. CONCLUSION We here report the specifics of variants' profiles of African Americans with colorectal lesions. Validated variants showed that Tumor Suppressor Genes (TSGs) APC and ARID1 and DNA Mismatch repair (MMR) genes MSH3 and MSH6 are the genes with the highest numbers of validated variants. Oncogenes KRAS and PIK3CA are also altered and likely participate in the increased proliferative potential of the mutated colonic epithelial cells in this population.
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Affiliation(s)
- Hassan Ashktorab
- Department of Medicine, Cancer Center, Howard University, Washington, DC, USA
| | - Hamed Azimi
- Department of Medicine, Cancer Center, Howard University, Washington, DC, USA
| | | | - Edward L. Lee
- Department of Pathology, Howard University College of Medicine, Washington, DC, USA
| | - Adeyinka O. Laiyemo
- Department of Medicine, Cancer Center, Howard University, Washington, DC, USA
| | - Michael L. Nickerson
- Laboratory of Translational Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Hassan Brim
- Department of Pathology, Howard University College of Medicine, Washington, DC, USA
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40
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Chan EM, Shibue T, McFarland JM, Gaeta B, Ghandi M, Dumont N, Gonzalez A, McPartlan JS, Li T, Zhang Y, Bin Liu J, Lazaro JB, Gu P, Piett CG, Apffel A, Ali SO, Deasy R, Keskula P, Ng RWS, Roberts EA, Reznichenko E, Leung L, Alimova M, Schenone M, Islam M, Maruvka YE, Liu Y, Roper J, Raghavan S, Giannakis M, Tseng YY, Nagel ZD, D'Andrea A, Root DE, Boehm JS, Getz G, Chang S, Golub TR, Tsherniak A, Vazquez F, Bass AJ. WRN helicase is a synthetic lethal target in microsatellite unstable cancers. Nature 2019; 568:551-556. [PMID: 30971823 PMCID: PMC6580861 DOI: 10.1038/s41586-019-1102-x] [Citation(s) in RCA: 232] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 02/27/2019] [Indexed: 01/08/2023]
Abstract
Synthetic lethality-an interaction between two genetic events through which the co-occurrence of these two genetic events leads to cell death, but each event alone does not-can be exploited for cancer therapeutics1. DNA repair processes represent attractive synthetic lethal targets, because many cancers exhibit an impairment of a DNA repair pathway, which can lead to dependence on specific repair proteins2. The success of poly(ADP-ribose) polymerase 1 (PARP-1) inhibitors in cancers with deficiencies in homologous recombination highlights the potential of this approach3. Hypothesizing that other DNA repair defects would give rise to synthetic lethal relationships, we queried dependencies in cancers with microsatellite instability (MSI), which results from deficient DNA mismatch repair. Here we analysed data from large-scale silencing screens using CRISPR-Cas9-mediated knockout and RNA interference, and found that the RecQ DNA helicase WRN was selectively essential in MSI models in vitro and in vivo, yet dispensable in models of cancers that are microsatellite stable. Depletion of WRN induced double-stranded DNA breaks and promoted apoptosis and cell cycle arrest selectively in MSI models. MSI cancer models required the helicase activity of WRN, but not its exonuclease activity. These findings show that WRN is a synthetic lethal vulnerability and promising drug target for MSI cancers.
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Affiliation(s)
- Edmond M Chan
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Nancy Dumont
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | - Tianxia Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yanxi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jie Bin Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jean-Bernard Lazaro
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Peili Gu
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Cortt G Piett
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Annie Apffel
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Syed O Ali
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Rebecca Deasy
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Paula Keskula
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Raymond W S Ng
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Emma A Roberts
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Elizaveta Reznichenko
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Lisa Leung
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Maria Alimova
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Mirazul Islam
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yosef E Maruvka
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Yang Liu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jatin Roper
- Department of Medicine, Division of Gastroenterology, Duke University, Durham, NC, USA
| | - Srivatsan Raghavan
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Marios Giannakis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yuen-Yi Tseng
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Zachary D Nagel
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Alan D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jesse S Boehm
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gad Getz
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Todd R Golub
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Francisca Vazquez
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Adam J Bass
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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41
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Lieb S, Blaha-Ostermann S, Kamper E, Rippka J, Schwarz C, Ehrenhöfer-Wölfer K, Schlattl A, Wernitznig A, Lipp JJ, Nagasaka K, van der Lelij P, Bader G, Koi M, Goel A, Neumüller RA, Peters JM, Kraut N, Pearson MA, Petronczki M, Wöhrle S. Werner syndrome helicase is a selective vulnerability of microsatellite instability-high tumor cells. eLife 2019; 8:43333. [PMID: 30910006 PMCID: PMC6435321 DOI: 10.7554/elife.43333] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/14/2019] [Indexed: 12/31/2022] Open
Abstract
Targeted cancer therapy is based on exploiting selective dependencies of tumor cells. By leveraging recent functional screening data of cancer cell lines we identify Werner syndrome helicase (WRN) as a novel specific vulnerability of microsatellite instability-high (MSI-H) cancer cells. MSI, caused by defective mismatch repair (MMR), occurs frequently in colorectal, endometrial and gastric cancers. We demonstrate that WRN inactivation selectively impairs the viability of MSI-H but not microsatellite stable (MSS) colorectal and endometrial cancer cell lines. In MSI-H cells, WRN loss results in severe genome integrity defects. ATP-binding deficient variants of WRN fail to rescue the viability phenotype of WRN-depleted MSI-H cancer cells. Reconstitution and depletion studies indicate that WRN dependence is not attributable to acute loss of MMR gene function but might arise during sustained MMR-deficiency. Our study suggests that pharmacological inhibition of WRN helicase function represents an opportunity to develop a novel targeted therapy for MSI-H cancers.
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Affiliation(s)
- Simone Lieb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | - Janine Rippka
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | | | - Jesse J Lipp
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Kota Nagasaka
- Research Institute of Molecular Pathology, Vienna, Austria
| | | | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Minoru Koi
- Division of Gastroenterology, Department of Internal Medicine, Comprehensive Cancer Center, University of Michigan, Ann Arbor, United States
| | - Ajay Goel
- Center for Gastrointestinal Research, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, United States
| | | | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
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42
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Kategaya L, Perumal SK, Hager JH, Belmont LD. Werner Syndrome Helicase Is Required for the Survival of Cancer Cells with Microsatellite Instability. iScience 2019; 13:488-497. [PMID: 30898619 PMCID: PMC6441948 DOI: 10.1016/j.isci.2019.02.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/28/2018] [Accepted: 02/06/2019] [Indexed: 02/08/2023] Open
Abstract
Werner syndrome protein (WRN) is a RecQ enzyme involved in the maintenance of genome integrity. Germline loss-of-function mutations in WRN led to premature aging and predisposition to cancer. We evaluated synthetic lethal (SL) interactions between WRN and another human RecQ helicase, BLM, with DNA damage response genes in cancer cell lines. We found that WRN was SL with a DNA mismatch repair protein MutL homolog 1, loss of which is associated with high microsatellite instability (MSI-H). MSI-H cells exhibited increased double-stranded DNA breaks, altered cell cycles, and decreased viability in response to WRN knockdown, in contrast to microsatellite stable (MSS) lines, which tolerated depletion of WRN. Although WRN is the only human RecQ enzyme with a distinct exonuclease domain, only loss of helicase activity drives the MSI SL interaction. This SL interaction in MSI cancer cells positions WRN as a relevant therapeutic target in patients with MSI-H tumors.
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Affiliation(s)
- Lorn Kategaya
- Biology Department, IDEAYA Biosciences, 7000 Sierra Point Boulevard, South San Francisco, CA 94080, USA.
| | - Senthil K Perumal
- Biology Department, IDEAYA Biosciences, 7000 Sierra Point Boulevard, South San Francisco, CA 94080, USA
| | - Jeffrey H Hager
- Biology Department, IDEAYA Biosciences, 3033 Science Park Road, Suite 250, San Diego, CA 92121, USA
| | - Lisa D Belmont
- Biology Department, IDEAYA Biosciences, 7000 Sierra Point Boulevard, South San Francisco, CA 94080, USA.
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Torshizi Esfahani A, Seyedna SY, Nazemalhosseini Mojarad E, Majd A, Asadzadeh Aghdaei H. MSI-L/EMAST is a predictive biomarker for metastasis in colorectal cancer patients. J Cell Physiol 2018; 234:13128-13136. [PMID: 30549036 DOI: 10.1002/jcp.27983] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 11/21/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Microsatellite instability (MSI) is a prognostic marker in colorectal cancer (CRC). The biological significance of MSI-low (MSI-L) phenotype and its differences with microsatellite stable (MSS) phenotype remains unclear. The aim of this study is indicating the role of mononucleotide repeat in identifying MSI-L and revealing the association of MSI-L with elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) and oncologic outcome in CRC patients. METHODS MSI and EMAST status were analyzed using three quasimonomorphic panel (BAT-25, BAT-26, and NR-27) and five tetranucleotide repeats (D20S82, D20S85, D9S242, D8S321, and MYCL1), respectively, by capillary electrophoresis method without the need to fluorescent primers. The associations of MSI status with clinicopathological features, EMAST status, metastasis, and overall survival (OS) were investigated. RESULTS Among 159 CRC patient 22.0% were MSI-H, 40.3% were MSS, 37.7% were MSI-L, and 41.5% showed EMAST + phenotype. MSI-L were associated with advanced stages, EMAST+ tumors and worse OS ( p ≤ 0.001). Metastasis was relatively common in MSI-L/EMAST + CRCs and BAT-25 were the most unstable marker in these tumors. CONCLUSIONS MSI-L tumors have different clinicopathological features from MSS and MSI-H tumors. The MSI-L phenotype is a worse prognostic biomarker in CRC and when accompanied by EMAST could be a predictor for metastasis.
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Affiliation(s)
- Amir Torshizi Esfahani
- Department of Biology, Faculty of Biological Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Seyed Yoosef Seyedna
- Department of Biology, Faculty of Biological Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Department of Cancer, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ahmad Majd
- Department of Molecular Medicine, Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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44
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Mori T, Hamaya Y, Uotani T, Yamade M, Iwaizumi M, Furuta T, Miyajima H, Osawa S, Sugimoto K. Prevalence of elevated microsatellite alterations at selected tetranucleotide repeats in pancreatic ductal adenocarcinoma. PLoS One 2018; 13:e0208557. [PMID: 30532127 PMCID: PMC6285458 DOI: 10.1371/journal.pone.0208557] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/19/2018] [Indexed: 01/29/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) prognosis remains poor even after complete resection owing to no valuable biomarkers for recurrence and chemosensitivity. Tumors not expressing MSH3 show elevated microsatellite alterations at selected tetranucleotide repeats (EMAST). EMAST reportedly occurs in several tumors. In colorectal cancer (CRC), EMAST was reportedly correlated with 5-fluorouracil (5-FU) sensitivity. However, EMAST prevalence in PDAC and its significance as a prognostic biomarker are unknown. This study aimed to investigate EMAST prevalence in PDAC and the associations between EMAST and pathological factors, EMAST and prognosis, and EMAST and MSH3 expression via immunohistochemistry (IHC). We assessed 40 PDAC patients undergoing surgery. Genomic DNA was extracted from tumors and normal tissues. EMAST and microsatellite instability-high (MSI-H) were analyzed using five polymorphic tetranucleotide markers and five mononucleotide markers, respectively. Tumor sections were stained for MSH3, and staining intensity was evaluated via the Histoscore (H-score). Eighteen of 40 (45%) PDAC patients were EMAST-positive; however, none were MSI-H-positive. Clinicopathological characteristics including overall survival (OS) and recurrence-free survival (RFS) were not significantly different between EMAST-positive and EMAST-negative patients (P = 0.45, 0.98 respectively). IHC was performed to evaluate MSH3 protein expression levels for the PDAC tissue specimens. H-scores of EMAST-positive patients ranged from 0 to 300 (median, 40) and those of EMAST-negative patients ranged from 0 to 300 (median, 170). MSH3 protein was not significantly downregulated in EMAST-positive patients (P = 0.07). This study is a preliminary study and the number of cases investigated was small, and thus, study of a larger cohort will reveal the clinical implication of EMAST.
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Affiliation(s)
- Taiki Mori
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yasushi Hamaya
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
- * E-mail:
| | - Takahiro Uotani
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mihoko Yamade
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Moriya Iwaizumi
- Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takahisa Furuta
- Center for Clinical Research, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hiroaki Miyajima
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Satoshi Osawa
- Department of Endoscopic and Photodynamic Medicine, Hamamatsu, Japan
| | - Ken Sugimoto
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
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45
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A new method for discovering EMAST sequences in animal models of cancer. Sci Rep 2018; 8:13764. [PMID: 30214002 PMCID: PMC6137214 DOI: 10.1038/s41598-018-32057-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/31/2018] [Indexed: 01/28/2023] Open
Abstract
Elevated Microsatellite Alterations at Selected Tetranucleotide repeats (EMAST) occur in up to 60% of colorectal cancers and may associate with aggressive and advanced disease in patients. Although EMAST occurs in many cancer types, current understanding is limited due to the lack of an animal model. Reported here is the design and implementation of an algorithm for detecting EMAST repeats in mice. This algorithm incorporates properties of known human EMAST sequences to identify repeat sequences in animal genomes and was able to identify EMAST-like sequences in the mouse. Seven of the identified repeats were analyzed further in a colon cancer mouse model and six of the seven displayed EMAST instability characteristic of that seen in human colorectal cancers. In conclusion, the algorithm developed successfully identified EMAST repeats in an animal genome and, for the first time, EMAST has been shown to occur in a mouse model of colon cancer.
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46
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Expression of NOX Family Genes and Their Clinical Significance in Colorectal Cancer. Dig Dis Sci 2018; 63:2332-2340. [PMID: 29781053 DOI: 10.1007/s10620-018-5121-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/10/2018] [Indexed: 12/09/2022]
Abstract
BACKGROUND The NADPH oxidase (NOX) family is overexpressed in many cancers and is associated with cancer cell proliferation and metastasis; however, little is known about the role of the NOX family in colorectal cancer (CRC). AIMS To identify the expression of the NOX family in CRC and to investigate the relationship between the expression of NOXs with the prognosis of the patients. METHODS In the TCGA data portal, mRNA expression data were obtained from 41 normal samples and 458 CRC samples to analyze mRNA expression and gene alteration. We compared the survival differences according to the degree of expression of NOX family in CRC patients and performed Gene Set Enrichment Analysis (GSEA). RESULTS The mRNA expression of NOX1, 3, 4, and DUOX1, 2 was significantly increased in the colorectal adenocarcinoma. Especially, the higher T and N stage, the more NOX4 expression was significantly increased. Survival analyses showed that NOX4 and NOX5 were associated with poor prognosis; however, NOX1 and DUOX2 were significantly associated with better prognosis. In the results of GSEA of CRC patients, the NOX4 gene was significantly associated with Angiogenesis, EMT and notch signaling. CONCLUSIONS The NOX family is overexpressed in CRC and is associated with the prognosis of the patient. Therefore, NOX family can predict CRC patient survival and the role of the NOX family as a molecular target in the treatment of CRC.
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47
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Duan FX, Gu GL, Yang HR, Yu PF, Zhang Z. Must Peutz-Jeghers syndrome patients have the LKB1/STK11 gene mutation? A case report and review of the literature. World J Clin Cases 2018; 6:224-232. [PMID: 30148152 PMCID: PMC6107527 DOI: 10.12998/wjcc.v6.i8.224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/23/2018] [Accepted: 05/13/2018] [Indexed: 02/05/2023] Open
Abstract
Peutz-Jeghers syndrome (PJS) is an autosomal dominant inherited disease, which is characterized by mucocutaneous pigmentation and multiple gastrointestinal hamartoma polyps. The germline mutation of LKB1/STK11 gene on chromosome 19p13.3 is considered to be the hereditary cause of PJS. However, must a patient with PJS have the LKB1/STK11 gene mutation? We here report a case of a male patient who had typical manifestations of PJS and a definite family history, but did not have LKB1/STK11 gene mutation. By means of high-throughput sequencing technology, only mutations in APC gene (c.6662T > C: p.Met2221Thr) and MSH6 gene (c.3488A > T: p.Glu1163Val) were detected. The missense mutations in APC and MSH6 gene may lead to abnormalities in structure and function of their expression products, and may result in the occurrence of PJS. This study suggests that some other genetic disorders may cause PJS besides LKB1/STK11 gene mutation.
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Affiliation(s)
- Fu-Xiao Duan
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
| | - Guo-Li Gu
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
| | - Hai-Rui Yang
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
| | - Peng-Fei Yu
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
| | - Zhi Zhang
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
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48
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Abstract
Lynch Syndrome (LS) is the most common dominantly inherited colorectal cancer (CRC) predisposition and is caused by a heterozygous germline defect in one of the DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6, or PMS2. High microsatellite instability (MSI-H) and loss of MMR protein expression in tumours reflecting a defective MMR are indicators for LS, as well as a positive family history of early onset CRC. MSH2 and MSH6 form a major functional heterodimer, and MSH3 is an alternative binding partner for MSH2. So far, the role of germline MSH3 variants remains unclear, as to our knowledge heterozygous truncating variants are not regarded causative for LS, but were detected in patients with CRC, and recently biallelic MSH3 defects have been identified in two patients with adenomatous polyposis. By gene screening we investigated the role of MSH3 in 11 LS patients with truncating MSH6 germline variants and an unexplained MSH2 protein loss in their corresponding MSI-H tumours. We report the first two LS patients harbouring heterozygous germline variants c.1035del and c.2732T>G in MSH3 coincidentally with truncating variants in MSH6. In the patient with truncating germline variants in MSH3 and MSH6, two additional somatic second hits in both genes abrogate all binding partners for the MSH2 protein which might subsequently be degraded. The clinical relevance of MSH3 germline variants is currently under re-evaluation, and heterozygous MSH3 defects alone do not seem to induce a LS phenotype, but might aggravate the MSH6 phenotype in affected family members.
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49
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Wodarz D, Goel A, Boland CR, Komarova NL. Effect of aspirin on tumour cell colony formation and evolution. J R Soc Interface 2018; 14:rsif.2017.0374. [PMID: 28878032 DOI: 10.1098/rsif.2017.0374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 08/14/2017] [Indexed: 12/21/2022] Open
Abstract
Aspirin is known to reduce the risk of colorectal cancer (CRC) incidence, but the underlying mechanisms are not fully understood. In a previous study, we quantified the in vitro growth kinetics of different CRC tumour cell lines treated with varying doses of aspirin, measuring the rate of cell division and cell death. Here, we use these measured parameters to calculate the chances of successful clonal expansion and to determine the evolutionary potential of the tumour cell lines in the presence and absence of aspirin. The calculations indicate that aspirin increases the probability that a single tumour cell fails to clonally expand. Further, calculations suggest that aspirin increases the evolutionary potential of an expanding tumour cell colony. An aspirin-treated tumour cell population is predicted to result in the accumulation of more mutations (and is thus more virulent and more difficult to treat) than a cell population of the same size that grew without aspirin. This indicates a potential trade-off between delaying the onset of cancer and increasing its evolutionary potential through chemoprevention. Further work needs to investigate to what extent these findings apply to in vivo settings, and to what degree they contribute to the epidemiologically documented aspirin-mediated protection.
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Affiliation(s)
- Dominik Wodarz
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92617, USA .,Department of Mathematics, University of California, Rowland Hall, Irvine, CA 92617, USA
| | - Ajay Goel
- Center for Gastroenterological Research, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas TX, USA
| | - C Richard Boland
- University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Natalia L Komarova
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92617, USA.,Department of Mathematics, University of California, Rowland Hall, Irvine, CA 92617, USA
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50
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Koi M, Okita Y, Carethers JM. Fusobacterium nucleatum Infection in Colorectal Cancer: Linking Inflammation, DNA Mismatch Repair and Genetic and Epigenetic Alterations. J Anus Rectum Colon 2018; 2:37-46. [PMID: 30116794 PMCID: PMC6090547 DOI: 10.23922/jarc.2017-055] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 01/30/2018] [Indexed: 12/13/2022] Open
Abstract
It has been recently reported that the population of Fusobacterium, particularly Fusobacterium nucleatum (Fn), is overrepresented in colorectal cancers and adenomas. The promoting effects of Fn infection on adenoma and/or carcinoma formation have been shown in ApcMin/+mice. Characteristics of Fn-associated CRC were identified through studies using human CRC cohorts, and include right-sided colon location, CpG island methylation phenotype-high (CIMP-H), high level of microsatellite instability (MSI-H), and poor patient prognosis. A subset of Fn-associated CRC exhibits a low level of microsatellite instability (MSI-L) and elevated microsatellite alterations in selected tetra-nucleotide repeats (EMAST) induced by translocation of MSH3 from the nucleus to the cytoplasm in response to oxidative DNA damage or inflammatory signals. The association between CIMP/MSI-H and Fn-infection can be explained by the role of the mismatch repair (MMR) protein complex formed between MSH2 and MSH6 (MutSα) to repair aberrant bases generated by ROS to form 7,8-dihydro-8-oxo-guanine (8-oxoG). Clustered 8-oxoGs formed at CpG-rich regions including promoters by ROS is refractory to base excision repair (BER). Under these conditions, MutSα initiates repair in cooperation with DNA methyltransferases (DNMTs) and the polycomb repressive complex 4 (PRC4). DNMTs at damaged sites methylate CpG islands to repress transcription of target genes and promote repair reactions. Thus, continuous generation of ROS through chronic Fn infection may initiate 1) CIMP-positive adenoma and carcinoma in an MSH2/MSH6-dependent manner, and/or 2) MSI-L/EMAST CRC in an MSH3-dependent manner. The poor prognosis of Fn-associated CRC can be explained by Fn-induced immune-evasion and/or chemo-resistance.
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Affiliation(s)
- Minoru Koi
- Division of Gastroenterology, Department of Internal Medicine, and Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yoshiki Okita
- Division of Gastroenterology, Department of Internal Medicine, and Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - John M Carethers
- Division of Gastroenterology, Department of Internal Medicine, and Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
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