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Bratei AA, Stefan-van Staden RI. Pathological Features of Colorectal Adenocarcinoma Patients Related to MLH1. Cell Mol Bioeng 2024; 17:153-164. [PMID: 38737450 PMCID: PMC11082117 DOI: 10.1007/s12195-024-00797-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/30/2024] [Indexed: 05/14/2024] Open
Abstract
Background MLH1, one of the MMR proteins, is linked to DNA replication, its role being to repair the incorrect DNA sequences and to replace them with proper ones. The loss of the MLH1 gene expression is part of Lynch syndrome which can lead to a series of cancers like colorectal and endometrial ones. The aim of this paper is to correlate the levels of MLH1 in four different bio-logical fluids with clinicopathological features in colorectal cancer patients in order to predict them with high probability. Therefore, a mathematical model with given code in Matlab has been proposed to get the clinicopathological features with high probability by only introducing the values for MLH1 concentrations. All these data can be obtained in a very short time even before surgery which can be very helpful the surgeon and the oncologist. Methods Four types of samples (whole blood, saliva, urine and tissue) were analyzed using stochastic microsensors; concentrations of MLH1 were determined and compared with different macroscopic and micro-scopic pathological features to obtain mathematical models for early, non-invasive diagnostic of colorectal adenocarcinoma. Results There have been established criteria and mathematical models for tumor location, TNM grading system, depth of the tumor, lymphatic, vascular and perineural invasions and the presence of mucus in the tumoral mass. Conclusions By using whole blood, saliva and urine samples, the location can be approximated. The proposed mathematical models aimed to allow a minim/noninvasive characterization of the tumor and its location which can help the surgeon and the oncologist to choose faster the personalized treatment.
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Affiliation(s)
- Alexandru Adrian Bratei
- Faculty of Chemical Engineering and Biotechnologies, National University of Science and Technology POLITEHNICA Bucharest, Bucharest, Romania
- Laboratory of Electrochemistry and PATLAB, National Institute of Research for Electrochemistry and Condensed Matter, 060021 Bucharest-6, Romania
- Department of Pathology, Emergency University Hospital, Bucharest, Romania
- Department of Pathology, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu-Mures, 540139 Targu Mures, Romania
| | - Raluca-Ioana Stefan-van Staden
- Faculty of Chemical Engineering and Biotechnologies, National University of Science and Technology POLITEHNICA Bucharest, Bucharest, Romania
- Laboratory of Electrochemistry and PATLAB, National Institute of Research for Electrochemistry and Condensed Matter, 060021 Bucharest-6, Romania
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Mak S, Alexander JL, Clark SK, Hawkins M, Cuthill V, Latchford A, Monahan KJ. The Diagnostic Yield of Genetic Testing in Patients With Multiple Colorectal Adenomas: A Specialist Center Cohort Study. Clin Transl Gastroenterol 2024; 15:e00645. [PMID: 37856205 PMCID: PMC10810582 DOI: 10.14309/ctg.0000000000000645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/19/2023] [Indexed: 10/20/2023] Open
Abstract
INTRODUCTION Adenoma multiplicity is associated with increased colorectal cancer (CRC) risk. The utility of genetic testing in patients with multiple colorectal adenomas (MCRA) remains uncertain. We evaluated the diagnostic yield of mutations in polyposis- and CRC-associated genes in patients with MCRA. METHODS We performed a cross-sectional review of adult patients with 10-99 cumulative adenomas from the prospective database at the St Mark's Hospital Polyposis Registry and Family Cancer Clinic between 1999 and 2021. Genetic testing was performed for adenomatous polyposis-associated genes, hamartomatous polyposis-associated genes, and nonpolyposis colorectal cancer-associated genes. Clinicopathological outcomes were extracted for multiple logistic regression analysis. RESULTS Two hundred fifty-nine patients with MCRA (median age 61 [interquartile range 53-69] years) were identified. Sixty-six patients (25.5%) had a pathogenic variant or likely pathogenic variant, with APC and biallelic MUTYH mutations constituting the majority of identified pathogenic variant/likely pathogenic variants. Diagnostic yields were greater than 10% at any adenoma burden. In univariate analysis, higher adenoma burden and younger age were associated with higher yield (both P < 0.0001). In patients with MCRA with 10-19 adenomas without a relevant personal or family history of CRC, the diagnostic yield was nil. In multiple logistic regression analysis, higher adenoma burden, younger age, personal history of CRC, and first-degree familial history of CRC were associated with higher diagnostic yield. DISCUSSION Diagnostic yield of >10% at any adenoma burden supports current guidance for constitutional genetic testing in patients with MCRA, although the low yield in people older than 60 years with 10-19 adenomas suggests that a stratified approach might be appropriate.
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Affiliation(s)
- Sau Mak
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - James L. Alexander
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Susan K. Clark
- Family Cancer & Lynch Syndrome Clinic, St Mark's Centre for Familial Intestinal Cancer, St Mark's Hospital, London North West University Healthcare NHS Trust, London, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Menna Hawkins
- Family Cancer & Lynch Syndrome Clinic, St Mark's Centre for Familial Intestinal Cancer, St Mark's Hospital, London North West University Healthcare NHS Trust, London, UK
| | - Victoria Cuthill
- Family Cancer & Lynch Syndrome Clinic, St Mark's Centre for Familial Intestinal Cancer, St Mark's Hospital, London North West University Healthcare NHS Trust, London, UK
| | - Andrew Latchford
- Family Cancer & Lynch Syndrome Clinic, St Mark's Centre for Familial Intestinal Cancer, St Mark's Hospital, London North West University Healthcare NHS Trust, London, UK
| | - Kevin J. Monahan
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Family Cancer & Lynch Syndrome Clinic, St Mark's Centre for Familial Intestinal Cancer, St Mark's Hospital, London North West University Healthcare NHS Trust, London, UK
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Kim SR, Oldfield L, Tone A, Pollett A, Pedersen S, Wellum J, Cesari M, Lajkosz K, Pugh TJ, Ferguson SE. Comprehensive molecular assessment of mismatch repair deficiency in Lynch associated ovarian cancers using next generation sequencing panel. Int J Gynecol Cancer 2023:ijgc-2023-004815. [PMID: 37940339 DOI: 10.1136/ijgc-2023-004815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023] Open
Abstract
OBJECTIVES Abnormalities in mismatch repair have been described in ovarian cancer, but few studies have examined the causes of mismatch repair deficiency (MMRd). To address this, we completed targeted mutational and methylation sequencing on MMRd ovarian cancer cases. The objective of this study was to explore the molecular mechanism of MMRd using our targeted next generation sequencing panel. METHODS Newly diagnosed non-serous/mucinous ovarian cancers (n=215) were prospectively recruited from three cancer centers in Ontario, Canada, between 2015 and 2018. Tumors were reflexively assessed for mismatch repair protein by immunohistochemistry. Matched tumor-normal MMRd cases were analyzed on a custom next generation sequencing panel to identify germline and somatic mutations, copy number variants, rearrangements, and promoter methylation in mismatch repair and associated genes. RESULTS Of 215 cases, 28 (13%) were MMRd. The MMRd cohort had a median age of 52.3 years (range 33.6-62.2), with mostly stage I (50%) and grade 1 or 2 endometrioid histotype (57%). Of the 28 cases, 22 were available for molecular analysis, and Lynch syndrome was detected in 50% of MMRd cases (11/22; seven ovarian cancer and four synchronous ovarian and endometrial cancer: seven MSH6, two MLH1, one PMS2, and one MSH2). An explanation for the observed mismatch repair phenotype was available for 22/22 deficient cases, including 12 MLH1/PMS2 deficient (nine somatic methylation, one bi-allelic somatic deletion, and two pathogenic germline variant), one PMS2 deficient (one pathogenic germline variant), seven MSH6 deficient (seven pathogenic germline variant), and two MSH2/MSH6 deficient (one pathogenic germline variant and one bi-allelic somatic mutation). Concordance between clinical germline testing and panel sequencing results was 100%. CONCLUSIONS Use of our custom next generation sequencing panel allowed for the streamlined assessment of hereditary and somatic causes of MMRd in ovarian cancers.
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Affiliation(s)
- Soyoun Rachel Kim
- Princess Margaret Cancer Center/University Health Network/Sinai Health Systems, Toronto, Ontario, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, Canada
- Gynecologic Oncology, Princess Margaret Hospital Cancer Center, Toronto, Ontario, Canada
| | - Leslie Oldfield
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alicia Tone
- Gynecologic Oncology, Princess Margaret Hospital Cancer Center, Toronto, Ontario, Canada
| | - Aaron Pollett
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Stephanie Pedersen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Johanna Wellum
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Matthew Cesari
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Katherine Lajkosz
- Department of Biostatistics, University of Toronto, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, University Health Network, Toronto, Ontario, Canada
| | - Sarah Elizabeth Ferguson
- Princess Margaret Cancer Center/University Health Network/Sinai Health Systems, Toronto, Ontario, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, Canada
- Gynecologic Oncology, Princess Margaret Hospital Cancer Center, Toronto, Ontario, Canada
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Trujillo-Rojas MA, Ayala-Madrigal MDLL, Gutiérrez-Angulo M, González-Mercado A, Moreno-Ortiz JM. Diagnosis of patients with Lynch syndrome lacking the Amsterdam II or Bethesda criteria. Hered Cancer Clin Pract 2023; 21:21. [PMID: 37864171 PMCID: PMC10589993 DOI: 10.1186/s13053-023-00266-0] [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: 06/02/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Lynch Syndrome (LS) is an autosomal dominant inheritance disorder characterized by genetic predisposition to develop cancer, caused by pathogenic variants in the genes of the mismatch repair system. Cases are detected by implementing the Amsterdam II and the revised Bethesda criteria, which are based on family history. MAIN BODY Patients who meet the criteria undergo posterior tests, such as germline DNA sequencing, to confirm the diagnosis. However, these criteria have poor sensitivity, as more than one-quarter of patients with LS do not meet the criteria. It is very likely that the lack of sensitivity of the criteria is due to the incomplete penetrance of this syndrome. The penetrance and risk of developing a particular type of cancer are highly dependent on the affected gene and probably of the variant. Patients with variants in low-penetrance genes have a lower risk of developing a cancer associated with LS, leading to families with unaffected generations and showing fewer clear patterns. This study focuses on describing genetic aspects of LS cases that underlie the lack of sensitivity of the clinical criteria used for its diagnosis. CONCLUSION Universal screening could be an option to address the problem of underdiagnosis.
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Affiliation(s)
- Miguel Angel Trujillo-Rojas
- Doctorado en Genética Humana e Instituto de Genética Humana "Dr. Enrique Corona Rivera", Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada #950, Col. Independencia, Guadalajara, C.P. 44340, Jalisco, México
| | - María de la Luz Ayala-Madrigal
- Instituto de Genética Humana "Dr. Enrique Corona Rivera", Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Sierra Mojada #950, Col. Independencia, Guadalajara, C.P. 44340, Jalisco, México
| | - Melva Gutiérrez-Angulo
- Departamento de Ciencias de la Salud, Centro Universitario de los Altos, Universidad de Guadalajara, Av. Rafael Casillas Aceves #1200. Tepatitlán de Morelos, C.P. 47620, Jalisco, México
| | - Anahí González-Mercado
- Instituto de Genética Humana "Dr. Enrique Corona Rivera", Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Sierra Mojada #950, Col. Independencia, Guadalajara, C.P. 44340, Jalisco, México
| | - José Miguel Moreno-Ortiz
- Instituto de Genética Humana "Dr. Enrique Corona Rivera", Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Sierra Mojada #950, Col. Independencia, Guadalajara, C.P. 44340, Jalisco, México.
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Luo Q, Zhou P, Chang S, Huang Z, Zeng X. Construction and validation of a prognostic model for colon adenocarcinoma based on bile acid metabolism-related genes. Sci Rep 2023; 13:12728. [PMID: 37543674 PMCID: PMC10404223 DOI: 10.1038/s41598-023-40020-z] [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: 05/20/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023] Open
Abstract
Colon adenocarcinoma (COAD), one of the common clinical cancers, exhibits high morbidity and mortality, and its pathogenesis and treatment are still underdeveloped. Numerous studies have demonstrated the involvement of bile acids in tumour development, while the potential role of their metabolism in the tumor microenvironment (TME) has not been explored. A collection of 481 genes related to bile acid metabolism were obtained, and The Cancer Genome Atlas-based COAD risk model was developed using the least absolute shrinkage selection operator (LASSO) regression analysis. The Gene Expression Omnibus dataset was used to validate the results. The predictive performance of the model was verified using column line plots, principal component analysis and receiver operating characteristic curves. Then, we analysed the differences between the high- and low-risk groups from training set based on clinical characteristics, immune cell infiltration, immune-related functions, chemotherapeutic drug sensitivity and immunotherapy efficacy. Additionally, we constructed a protein-protein interaction network to screen for target genes, which were further investigated in terms of differential immune cell distribution. A total of 234 bile acids-related differentially expressed genes were obtained between normal and tumour colon tissues. Among them, 111 genes were upregulated and 123 genes were down-regulated in the tumour samples. Relying on the LASSO logistic regression algorithm, we constructed a model of bile acid risk score, comprising 12 genes: CPT2, SLCO1A2, CD36, ACOX1, CDKN2A, HADH, GABRD, LEP, TIMP1, MAT1A, SLC6A15 and PPARGC1A. This model was validated in the GEO-COAD set. Age and risk score were observed to be independent prognostic factors in patients with COAD. Genes related to bile acid metabolism in COAD were closely related to bile secretion, intestinal transport, steroid and fatty acid metabolism. Furthermore, the high-risk group was more sensitive to Oxaliplatin than the low-risk group. Finally, the three target genes screened were closely associated with immune cells. We identified a set of 12 genes (CPT2, SLCO1A2, CD36, ACOX1, CDKN2A, HADH, GABRD, LEP, TIMP1, MAT1A, SLC6A15, and PPARGC1A) associated with bile acid metabolism and developed a bile acid risk score model using LASSO regression analysis. The model demonstrated good predictive performance and was validated using an independent dataset. Our findings revealed that the bile acid risk score were independent prognostic factors in COAD patients.
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Affiliation(s)
- Qinghua Luo
- Department of Anorectal Surgery, Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, China.
| | - Ping Zhou
- Department of Anorectal Surgery, Jiangxi Hospital of Integrated Traditional Chinese and Western Medicine, Nanchang, China
| | - Shuangqing Chang
- Department of Anorectal Surgery, Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, China
| | - Zhifang Huang
- Department of Anorectal Surgery, Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, China
| | - Xuebo Zeng
- Department of Brain Diseases, Shenzhen Pingle Orthopaedic Hospital, Shenzhen, China
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O'Brien TD, Potter AB, Driscoll CC, Goh G, Letaw JH, McCabe S, Thanner J, Kulkarni A, Wong R, Medica S, Week T, Buitrago J, Larson A, Camacho KJ, Brown K, Crist R, Conrad C, Evans-Dutson S, Lutz R, Mitchell A, Anur P, Serrato V, Shafer A, Marriott LK, Hamman KJ, Mulford A, Wiszniewski W, Sampson JE, Adey A, O'Roak BJ, Harrington CA, Shannon J, Spellman PT, Richards CS. Population screening shows risk of inherited cancer and familial hypercholesterolemia in Oregon. Am J Hum Genet 2023; 110:1249-1265. [PMID: 37506692 PMCID: PMC10432140 DOI: 10.1016/j.ajhg.2023.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
The Healthy Oregon Project (HOP) is a statewide effort that aims to build a large research repository and influence the health of Oregonians through providing no-cost genetic screening to participants for a next-generation sequencing 32-gene panel comprising genes related to inherited cancers and familial hypercholesterolemia. This type of unbiased population screening can detect at-risk individuals who may otherwise be missed by conventional medical approaches. However, challenges exist for this type of high-throughput testing in an academic setting, including developing a low-cost high-efficiency test and scaling up the clinical laboratory for processing large numbers of samples. Modifications to our academic clinical laboratory including efficient test design, robotics, and a streamlined analysis approach increased our ability to test more than 1,000 samples per month for HOP using only one dedicated HOP laboratory technologist. Additionally, enrollment using a HIPAA-compliant smartphone app and sample collection using mouthwash increased efficiency and reduced cost. Here, we present our experience three years into HOP and discuss the lessons learned, including our successes, challenges, opportunities, and future directions, as well as the genetic screening results for the first 13,670 participants tested. Overall, we have identified 730 pathogenic/likely pathogenic variants in 710 participants in 24 of the 32 genes on the panel. The carrier rate for pathogenic/likely pathogenic variants in the inherited cancer genes on the panel for an unselected population was 5.0% and for familial hypercholesterolemia was 0.3%. Our laboratory experience described here may provide a useful model for population screening projects in other states.
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Affiliation(s)
- Timothy D O'Brien
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Amiee B Potter
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Catherine C Driscoll
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA; Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Gregory Goh
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA; Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - John H Letaw
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Sarah McCabe
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jane Thanner
- Information Technology Group, Oregon Health & Science University, Portland, OR 97201, USA
| | - Arpita Kulkarni
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rossana Wong
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Samuel Medica
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA
| | - Tiana Week
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jacob Buitrago
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA
| | - Aaron Larson
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA
| | - Katie Johnson Camacho
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Kim Brown
- Knight Cancer Institute, Community Outreach and Engagement, Oregon Health & Science University, Portland, OR 97201, USA
| | - Rachel Crist
- Knight Cancer Institute, Community Outreach and Engagement, Oregon Health & Science University, Portland, OR 97201, USA
| | - Casey Conrad
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Sara Evans-Dutson
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Ryan Lutz
- Knight Cancer Institute, Community Outreach and Engagement, Oregon Health & Science University, Portland, OR 97201, USA
| | - Asia Mitchell
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Pavana Anur
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Vanessa Serrato
- Knight Cancer Institute, Community Outreach and Engagement, Oregon Health & Science University, Portland, OR 97201, USA
| | - Autumn Shafer
- University of Oregon, School of Journalism and Communication, Portland, OR 97209, USA
| | | | - K J Hamman
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Amelia Mulford
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Wojciech Wiszniewski
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jone E Sampson
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Andrew Adey
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA; Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Brian J O'Roak
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christina A Harrington
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA; Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jackilen Shannon
- Knight Cancer Institute, Community Outreach and Engagement, Oregon Health & Science University, Portland, OR 97201, USA; Division of Oncological Sciences, Oregon Health & Science University, Portland, OR 97239, USA
| | - Paul T Spellman
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA; Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - C Sue Richards
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA; Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA.
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Wu M, Hao S, Wang X, Su S, Du S, Zhou S, Yang R, Du H. A pyroptosis-related gene signature that predicts immune infiltration and prognosis in colon cancer. Front Oncol 2023; 13:1173181. [PMID: 37503314 PMCID: PMC10369052 DOI: 10.3389/fonc.2023.1173181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023] Open
Abstract
Background Colon cancer (CC) is a highly heterogeneous malignancy associated with high morbidity and mortality. Pyroptosis is a type of programmed cell death characterized by an inflammatory response that can affect the tumor immune microenvironment and has potential prognostic and therapeutic value. The aim of this study was to evaluate the association between pyroptosis-related gene (PRG) expression and CC. Methods Based on the expression profiles of PRGs, we classified CC samples from The Cancer Gene Atlas and Gene Expression Omnibus databases into different clusters by unsupervised clustering analysis. The best prognostic signature was screened and established using least absolute shrinkage and selection operator (LASSO) and multivariate COX regression analyses. Subsequently, a nomogram was established based on multivariate COX regression analysis. Next, gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were performed to explore the potential molecular mechanisms between the high- and low-risk groups and to explore the differences in clinicopathological characteristics, gene mutation characteristics, abundance of infiltrating immune cells, and immune microenvironment between the two groups. We also evaluated the association between common immune checkpoints and drug sensitivity using risk scores. The immunohistochemistry staining was utilized to confirm the expression of the selected genes in the prognostic model in CC. Results The 1163 CC samples were divided into two clusters (clusters A and B) based on the expression profiles of the 33 PRGs. Genes with prognostic value were screened from the DEGs between the two clusters, and an eight PRGs prognostic model was constructed. GSEA and GSVA of the high- and low-risk groups revealed that they were mainly enriched in inflammatory response-related pathways. Compared to those in the low-risk group, patients in the high-risk group had worse overall survival, an immunosuppressive microenvironment, and worse sensitivity to immunotherapy and drug treatment. Conclusion Our findings provide a foundation for future research targeting pyroptosis and new insights into prognosis and immunotherapy from the perspective of pyroptosis in CC.
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Affiliation(s)
- Mingjian Wu
- Department of Gastrointestinal Surgery, Panyu Maternal and Child Care Service Centre of Guangzhou (He Xian Memorial Affiliated Hospital of Southern Medical University), Guangzhou, China
| | - Shuai Hao
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xiaoxiang Wang
- The First Clinical Medical College, Guangdong Medical University, Zhanjiang, Zhanjiang, Guangdong, China
| | - Shuguang Su
- Department of Pathology, Panyu Maternal and Child Care Service Centre of Guangzhou (He Xian Memorial Affiliated Hospital of Southern Medical University), Guangzhou, China
| | - Siyuan Du
- Department of Pathology, Panyu Maternal and Child Care Service Centre of Guangzhou (He Xian Memorial Affiliated Hospital of Southern Medical University), Guangzhou, China
| | - Sitong Zhou
- Department of Dermatology, The First People’s Hospital of Foshan, Foshan, Guangdong, China
| | - Ronghua Yang
- Department of Burn and Plastic Surgery, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, Guangdong, China
| | - Hanpeng Du
- Department of Gastrointestinal Surgery, Panyu Maternal and Child Care Service Centre of Guangzhou (He Xian Memorial Affiliated Hospital of Southern Medical University), Guangzhou, China
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Xu X, Liang JH, Xu QC, Yin XY. Development and Verification of a novel cuproptosis- and immune-associated based prognostic genetic signature for pancreatic ductal adenocarcinoma. Clin Res Hepatol Gastroenterol 2023; 47:102089. [PMID: 36707046 DOI: 10.1016/j.clinre.2023.102089] [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: 07/22/2022] [Revised: 12/21/2022] [Accepted: 01/23/2023] [Indexed: 01/26/2023]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDAC) is a malignancy with a dismal prognosis. Cuproptosis, a novel mechanism mediated by protein lipoylation, results in acute proteotoxic stress and ultimately cell death. However, the clinical impacts of cuproptosis-associated genes and their relationship with immune status in PDAC have not been documented. In this study, we aimed at constructing a cuproptosis- and immune-associated prognostic signature to stratify and predict the prognosis for PDAC patients. METHODS The gene expression profiles of 176 PDAC patients from The Cancer Genome Atlas and 167 normal pancreas tissues from the Genotype-Tissue Expression Project were analyzed for differentially expressed genes (DEGs) between PDAC and normal tissues. Pearson correlation analyses were performed to screen out cuproptosis- and immune-associated DEGs. The risk signature of DEGs was constructed using the least absolute shrinkage and selection operator (LASSO) Cox regression analysis, which was validated in the Gene Expression Omnibus (GEO) cohort (n = 114). The immune characteristics in the two risk groups were evaluated using single-sample gene set enrichment analysis and ESTIMATE algorithms. RESULTS A total of 91 cuproptosis- and immune-associated DEGs were screened out, and eight prognostic-related genes were identified using LASSO Cox regression. The prognostic-related genes were then used to construct a risk scoring model, which stratified patients into low- and high-risk groups and were further verified in the external GEO database. The patients in the high-risk group had significantly shorter overall survival than those in the low-risk group. A nomogram based on the risk signature was then constructed. Immune infiltration evaluation suggested that immune status was more activated in the low-risk group. The mutation spectrum also differed between high- and low-risk groups. CONCLUSIONS Our cuproptosis- and immune-associated genetic risk signature could be a prognostic biomarker for PDAC. Cuproptosis might be a promising therapeutic target for PDAC.
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Affiliation(s)
- Xiang Xu
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Jia-Hua Liang
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Qiong-Cong Xu
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Xiao-Yu Yin
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China.
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Johnson Y, Goldberg P, Moodley J, Algar U, Thomson S, Sinanovic E, Ramesar R. A comparative cost analysis of two screening strategies for colorectal cancer in Lynch Syndrome in a South African tertiary hospital. Cancer Causes Control 2023; 34:161-169. [PMID: 36355273 DOI: 10.1007/s10552-022-01645-z] [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: 12/22/2021] [Accepted: 10/11/2022] [Indexed: 11/11/2022]
Abstract
AIM Lynch Syndrome (LS) individuals have a 25-75% lifetime risk of developing colorectal cancer. Colonoscopy screening decreases this risk. This study compared the cost of Strategy 1: screening colonoscopy for 1st degree relatives of patients that met the Revised Bethesda Criteria (i.e., probands) to Strategy 2: screening colonoscopy for 1st degree relatives of probands with genetic mutations for Lynch Syndrome based in a resource-constrained health care system. METHOD A comparative, health care provider perspective, cost analysis was conducted at a tertiary hospital, using a micro-costing, ingredient approach. Forty probands that underwent genetic testing between November 01, 2014 and October 30, 2015 and their first-degree relatives were costed according to Strategy 1 and Strategy 2. Unit costs of colonoscopy and genetic testing were estimated and used to calculate and compare the total costs per strategy in South African rand (R) converted to UK pounds (£). Sensitivity analyses were performed on colonoscopy adherence, relatives' positivity, and variable discount rates. RESULTS The cost for Strategy 1 amounted to £653 344/R6 161 035 compared to £49 327/R 465 155 for Strategy 2 (Discount rate 3%; Adherence 75%; and Positivity rate of relatives 45%). Base case analysis indicated a difference of 92% less in the total cost for Strategy 2 compared to Strategy 1. Sensitivity analyses showed that the difference in cost between the two strategies was not sensitive to variations in adherence, positivity or discount rates. CONCLUSION Colonoscopy screening for LS and at-risk family members was tenfold less costly when combined with genetic analysis. The logistics of rolling out this strategy nationally should be investigated.
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Affiliation(s)
- Yasmina Johnson
- Pharmacy Services, Department of Health, Western Cape, Dorp Street, Cape Town, South Africa
| | - Paul Goldberg
- Colorectal Unit, Groote Schuur Hospital, Health Sciences Faculty, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa
| | - Jennifer Moodley
- Cancer Research Initiative and School of Public Health and Family Medicine, Health Sciences Faculty, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa
| | - Ursula Algar
- Colorectal Unit, Groote Schuur Hospital, Health Sciences Faculty, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa
| | - Sandie Thomson
- Division of Medical Gastroenterology, Health Sciences Faculty, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa
| | - Edina Sinanovic
- Health Economics Unit, Health Economics Division, School of Public Health and Family Medicine, Health Sciences Faculty, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa
| | - Raj Ramesar
- MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Institute for Infectious Diseases and Molecular Medicine, Department of Pathology, Health Sciences Faculty, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa.
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Williams MH, Hadjinicolaou AV, Norton B, Kader R, Lovat LB. Lynch syndrome: from detection to treatment. Front Oncol 2023; 13:1166238. [PMID: 37197422 PMCID: PMC10183578 DOI: 10.3389/fonc.2023.1166238] [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: 02/15/2023] [Accepted: 04/11/2023] [Indexed: 05/19/2023] Open
Abstract
Lynch syndrome (LS) is an inherited cancer predisposition syndrome associated with high lifetime risk of developing tumours, most notably colorectal and endometrial. It arises in the context of pathogenic germline variants in one of the mismatch repair genes, that are necessary to maintain genomic stability. LS remains underdiagnosed in the population despite national recommendations for empirical testing in all new colorectal and endometrial cancer cases. There are now well-established colorectal cancer surveillance programmes, but the high rate of interval cancers identified, coupled with a paucity of high-quality evidence for extra-colonic cancer surveillance, means there is still much that can be achieved in diagnosis, risk-stratification and management. The widespread adoption of preventative pharmacological measures is on the horizon and there are exciting advances in the role of immunotherapy and anti-cancer vaccines for treatment of these highly immunogenic LS-associated tumours. In this review, we explore the current landscape and future perspectives for the identification, risk stratification and optimised management of LS with a focus on the gastrointestinal system. We highlight the current guidelines on diagnosis, surveillance, prevention and treatment and link molecular disease mechanisms to clinical practice recommendations.
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Affiliation(s)
- Madeleine H. Williams
- Department of Gastroenterology, Guy’s and St. Thomas NHS Foundation Trust, London, United Kingdom
| | - Andreas V. Hadjinicolaou
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Andreas V. Hadjinicolaou,
| | - Benjamin C. Norton
- Department of Gastroenterology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Rawen Kader
- Wellcome-EPSRC Centre for Interventional and Surgical Sciences, University College London, London, United Kingdom
| | - Laurence B. Lovat
- Wellcome-EPSRC Centre for Interventional and Surgical Sciences, University College London, London, United Kingdom
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11
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Identification and validation of a pyroptosis-related prognostic model for colorectal cancer. Funct Integr Genomics 2022; 23:21. [PMID: 36564624 DOI: 10.1007/s10142-022-00935-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/14/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
In this study, we explored the pyroptosis-related biomarkers and signatures of colorectal cancer (CRC). Gene expression profiles were downloaded from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA)-COADREAD and were analyzed for differentially expressed genes (DEGs). DEGs in CRC‒pyroptosis-related genes (CRC‒PRGs) were obtained by intersecting DEGs associated with CRC and PRGs. The CRC‒PRGs were verified; functional enrichment analysis was performed with Gene Ontology (GO) followed by cluster analysis. Cox analyses and LASSO regression were used in TCGA dataset to construct a prognostic model for patients with CRC. A prognostic risk assessment model was constructed and efficacy was evaluated. Decision curve analysis was utilized to assess the role of the Lasso-Cox regression prognostic model for clinical utility at 1, 3, and 5 years. Twelve CRC‒PRGs were identified as prognostic pyroptosis-related DEGs. CXCL8, IL13RA2, MELK, and POP1 were selected as prognostic genes to construct features with a good prognostic performance in GEO and TCGA. Functional enrichment indicated that the 4-gene signature might be involved in CRC tumorigenesis and development through various pathways by playing a prognostic role in CRC. Furthermore, the results of the immune landscape analysis showed that the expression of CXCL8 and IL13RA2 in TCGA-COADREAD dataset was positively correlated with significant differential enrichment of most immune cells. A novel prognostic model consisting of four key genes, CXCL8, IL13RA2, MELK, and POP1, can accurately predict the survival of patients with CRC. This finding may provide a new perspective for the treatment of pyroptosis-related CRC.
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12
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Guan Y, Pathak S, Ballard D, Veluswamy JK, McCullough LE, McBride CM, Gornick MC. Testing a deliberative democracy method with citizens of African ancestry to weigh pros and cons of targeted screening for hereditary breast and ovarian cancer risk. Front Public Health 2022; 10:984926. [PMID: 36424974 PMCID: PMC9679525 DOI: 10.3389/fpubh.2022.984926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
Abstract
Background Democratic deliberation (DD), a strategy to foster co-learning among researchers and communities, could be applied to gain informed public input on health policies relating to genomic translation. Purpose We evaluated the quality of DD for gaining informed community perspectives regarding targeting communities of African Ancestry (AAn) for Hereditary Breast and Ovarian Cancer (HBOC) screening in Georgia. Methods We audiotaped a 2.5 day conference conducted via zoom in March 2021 to examine indicators of deliberation quality based on three principles: (1) inclusivity (diverse viewpoints based on participants' demographics, cancer history, and civic engagement), (2) consideration of factual information (balanced and unbiased expert testimonies, participant perceived helpfulness), and (3) deliberation (speaking opportunities, adoption of a societal perspective on the issue, reasoned justification of ideas, and participant satisfaction). Results We recruited 24 participants who reflected the diversity of views and life experiences of citizens of AAn living in Georgia. The expert testimony development process we undertook for creating balanced factual information was endorsed by experts' feedback. Deliberation process evaluation showed that while participation varied (average number of statements = 24, range: 3-62), all participants contributed. Participants were able to apply expert information and take a societal perspective to deliberate on the pros and cons of targeting individuals of AAn for HBOC screening in Georgia. Conclusions The rigorous process of public engagement using deliberative democracy approach can successfully engage a citizenry with diverse and well-informed views, do so in a relatively short time frame and yield perspectives based on high quality discussion.
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Affiliation(s)
- Yue Guan
- Department of Behavioral, Social, and Health Education Sciences, Rollins School of Public Health, Emory University, Atlanta, GA, United States,*Correspondence: Yue Guan
| | - Sarita Pathak
- Department of Behavioral, Social, and Health Education Sciences, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Denise Ballard
- Department of Behavioral, Social, and Health Education Sciences, Rollins School of Public Health, Emory University, Atlanta, GA, United States,Winship Cancer Institute of Emory University, Atlanta, GA, United States
| | | | - Lauren E. McCullough
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Colleen M. McBride
- Department of Behavioral, Social, and Health Education Sciences, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Michele C. Gornick
- Department of Behavioral, Social, and Health Education Sciences, Rollins School of Public Health, Emory University, Atlanta, GA, United States
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Mighton C, Shickh S, Aguda V, Krishnapillai S, Adi-Wauran E, Bombard Y. From the patient to the population: Use of genomics for population screening. Front Genet 2022; 13:893832. [PMID: 36353115 PMCID: PMC9637971 DOI: 10.3389/fgene.2022.893832] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/26/2022] [Indexed: 10/22/2023] Open
Abstract
Genomic medicine is expanding from a focus on diagnosis at the patient level to prevention at the population level given the ongoing under-ascertainment of high-risk and actionable genetic conditions using current strategies, particularly hereditary breast and ovarian cancer (HBOC), Lynch Syndrome (LS) and familial hypercholesterolemia (FH). The availability of large-scale next-generation sequencing strategies and preventive options for these conditions makes it increasingly feasible to screen pre-symptomatic individuals through public health-based approaches, rather than restricting testing to high-risk groups. This raises anew, and with urgency, questions about the limits of screening as well as the moral authority and capacity to screen for genetic conditions at a population level. We aimed to answer some of these critical questions by using the WHO Wilson and Jungner criteria to guide a synthesis of current evidence on population genomic screening for HBOC, LS, and FH.
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Affiliation(s)
- Chloe Mighton
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Salma Shickh
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Vernie Aguda
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Centre for Medical Education, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Suvetha Krishnapillai
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Ella Adi-Wauran
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Yvonne Bombard
- Genomics Health Services Research Program, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
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14
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Ma Y, Lin C, Liu S, Wei Y, Ji C, Shi F, Lin F, Zhou Z. Radiomics features based on internal and marginal areas of the tumor for the preoperative prediction of microsatellite instability status in colorectal cancer. Front Oncol 2022; 12:1020349. [PMID: 36276101 PMCID: PMC9583004 DOI: 10.3389/fonc.2022.1020349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
Objectives To explore whether the preoperative CT radiomics can predict the status of microsatellite instability (MSI) in colorectal cancer (CRC) patients and identify the region with the most stable and high-efficiency radiomics features. Methods This retrospective study involved 230 CRC patients with preoperative computed tomography scans and available MSI status between December 2019 and October 2021. Image segmentation and radiomic feature extraction were performed as follows. First, slices with the maximum tumor area (region of interest, ROI) were manually contoured. Subsequently, each ROI was shrunk inward by 1, 2, and 3 mm, respectively, where the remaining ROIs were considered as the internal region of the tumor (named as IROI1, IROI2, and IROI3), and the shrunk regions were considered as marginal regions of the tumor (named as MROI1, MROI2, and MROI3). Finally, radiomics features were extracted from each of the ROI. The intraclass correlation coefficient and least absolute shrinkage and selection operator method were used to choose the most reliable and relevant features of MSI status. Clinical, radiomics, and combined clinical radiomics models have been established. Calibration curve and decision curve analyses (DCA) were generated to explore the correction effect and assess the clinical applicability of the above models, respectively. Results In the testing cohort, the radiomics model based on IROI3 yielded the highest average area under the curve (AUC) value of 0.908, compared with the remaining radiomics models. Additionally, hypertension and N stage were considered as clinically independent factors of MSI status. The combined clinical radiomics model achieved excellent diagnostic efficacy (AUC: 0.928; sensitivity: 0.840; specificity: 0.867) in the testing cohort, as well as favorable calibration and clinical utility by calibration curve and DCA analyses. Conclusions The IROI3 model, which is based on a 3-mm shrink in the largest areas of the tumor, could noninvasively reflect the heterogeneity and genetic instability within the tumor. This suggests that it is an important biomarker for the preoperative prediction of MSI status. The model can extract more robust and effective radiomics features, which lays a foundation for the radiomics study of hollow organs, such as in CRC.
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Affiliation(s)
- Yi Ma
- Department of Radiology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Changsong Lin
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Song Liu
- Department of Radiology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Ying Wei
- Department of Research and Development, Shanghai United Imaging Intelligence Co., Ltd., Shanghai, China
| | - Changfeng Ji
- Department of Radiology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Feng Shi
- Department of Research and Development, Shanghai United Imaging Intelligence Co., Ltd., Shanghai, China
| | - Fan Lin
- Department of Cell Biology, Nanjing Medical University, Nanjing, China
- *Correspondence: Fan Lin, ; Zhengyang Zhou,
| | - Zhengyang Zhou
- Department of Radiology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
- *Correspondence: Fan Lin, ; Zhengyang Zhou,
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15
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Ritterhouse LL, Gogakos T. Molecular Biomarkers of Response to Cancer Immunotherapy. Clin Lab Med 2022; 42:469-484. [DOI: 10.1016/j.cll.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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New Genetic Technologies in Diagnosis and Treatment of Cancer of Unknown Primary. Cancers (Basel) 2022; 14:cancers14143429. [PMID: 35884492 PMCID: PMC9318615 DOI: 10.3390/cancers14143429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 11/25/2022] Open
Abstract
Simple Summary The NGS and other molecular techniques creates huge hopes for effective CUP patients treatment and to select them for molecularly targeted therapies (agnostic therapies) and immunotherapy. Development of diagnostic technologies and biologically targeted therapies could make CUP’ patients access to modern therapies and change their outcome. Abstract Cancer of unknown primary (CUP) represents a rare oncological and heterogeneous disease in which one or more metastases are present, but the location of the primary site is unknown. Pathological diagnosis, using immunohistochemistry, of such metastatic materials is challenging and frequently does not allow for determining the tissue of origin (ToO). The selection of systemic therapy in patients with CUP is usually based on empiric grounds, and the prognosis is generally unfavourable. New molecular techniques could identify the tissue of origin and be used to select systemic agnostic therapies in various malignancies with specific molecular abnormalities. Targetable driver mutations or gene rearrangements in cancer cells may be identified using various molecular assays, of which particularly valuable are next-generation sequencing techniques. These assays may identify tumour sources and allow personalized treatments. However, current guidelines for CUP management do not recommend routine testing of gene expression and epigenetic factors. This is mainly due to the insufficient evidence supporting the improvement of CUP’s prognosis by virtue of this approach. This review summarizes the advantages and disadvantages of new genetic techniques in CUP diagnostics and proposes updating the recommendations for CUP management.
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Park JS, Park JW, Shin S, Lee ST, Shin SJ, Min BS, Park SJ, Park JJ, Cheon JH, Kim WH, Kim TI. Application of Multigene Panel Testing in Patients With High Risk for Hereditary Colorectal Cancer: A Descriptive Report Focused on Genotype-Phenotype Correlation. Dis Colon Rectum 2022; 65:793-803. [PMID: 34897210 DOI: 10.1097/dcr.0000000000002039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND The genetic test solely based on the clinical features of hereditary colorectal cancer has limitations in clinical practice. OBJECTIVE This study aimed to analyze the results of comprehensive multigene panel tests based on clinical findings. DESIGN This was a cross-sectional study based on a prospectively compiled database. SETTING The study was conducted at a tertiary hospital. PATIENTS A total of 381 patients with high risk for hereditary colorectal cancer syndromes were enrolled between March 2014 and December 2019. MAIN OUTCOME MEASURES The primary outcome was to describe the mutational spectrum based on genotype-phenotype concordance and discordance. RESULTS Germline mutations were identified in 89 patients for polyposis hereditary colorectal cancer genes (76 in APC; 4 in PTEN; 4 in STK11; 3 in BMPR1A; 1 in POLE; 1 in POLD1), 89 patients for nonpolyposis hereditary colorectal cancer genes (41 in MLH1; 40 in MSH2; 6 in MSH6; and 2 in PMS2), and 12 patients for other cancer predisposition genes (1 in ATM; 2 in BRCA1; 1 in BRCA2; 1 in BRIP1; 1 in MLH3; 1 in NBN; 1 in PMS1; 1 in PTCH1; 1 in TP53; and 2 in monoallelic MUTYH). If we had used direct sequencing tests of 1 or 2 major genes based on phenotype, 48 (25.3%) of 190 mutations would not have been detected due to technical differences (12.1%), less frequent genotype (4.2%), unclear phenotype (3.7%), and genotype-phenotype discordance (4.7%). The genotype-phenotype discordance is probably linked to compound heterozygote, less distinctive phenotype, and insufficient information for colorectal cancer risk. LIMITATIONS This study included a small number of patients with insufficient follow-up duration. CONCLUSIONS A comprehensive multigene panel is expected to identify more genetic mutations than phenotype-based direct sequencing, with special utility for unclear phenotype or genotype-phenotype discordance. See Video Abstract at http://links.lww.com/DCR/B844. APLICACIN DE PRUEBAS DE PANEL MULTIGNICO EN PACIENTES CON ALTO RIESGO DE CNCER COLORRECTAL HEREDITARIO INFORME DESCRIPTIVO ENFOCADO EN LA CORRELACIN GENOTIPOFENOTIPO ANTECEDENTES:La prueba genética basada únicamente en la característica clínica del cáncer colorrectal hereditario tiene limitaciones en la práctica clínica.OBJETIVO:Este estudio tuvo como objetivo analizar el resultado de pruebas integrales de panel multigénico basadas en hallazgos clínicos.DISEÑO:Este fue un estudio transversal basado en una base de datos recopilada prospectivamente.AJUSTE:El estudio se realizó en un hospital terciario.PACIENTES:Se inscribió un total de 381 pacientes con alto riesgo de síndromes de cáncer colorrectal hereditario entre marzo del 2014 y diciembre del 2019.PRINCIPALES MEDIDAS DE RESULTADO:El resultado principal fue describir el espectro mutacional basado en la concordancia y discordancia genotipo-fenotipo.RESULTADOS:Se identificaron mutaciones de la línea germinal en 89 pacientes para genes de cáncer colorrectal hereditario con poliposis (76 en APC; 4 en PTEN; 4 en STK11; 3 en BMPR1A; 1 en POLE; 1 en POLD1), 89 pacientes para genes de CCR hereditario sin poliposis (41 en MLH1; 40 en MSH2; 6 en MSH6; y 2 en PMS2) y 12 pacientes por otro gen de predisposición al cáncer (1 en ATM; 2 en BRCA1; 1 en BRCA2; 1 en BRIP1; 1 en MLH3; 1 en NBN; 1 en PMS1; 1 en PTCH1; 1 en TP53; y 2 en MUTYH monoalélico). Si hubiéramos utilizado pruebas de secuenciación directa de uno o dos genes principales basados en el fenotipo, 48 (25,3%) de 190 mutaciones no se habrían detectado debido a diferencias técnicas (12,1%), genotipo menos frecuente (4,2%), fenotipo poco claro (3,7%) y discordancia genotipo-fenotipo (4,7%). La discordancia genotipo-fenotipo probablemente esté relacionada con el heterocigoto compuesto, el fenotipo menos distintivo y la información insuficiente para el riesgo de cáncer colorrectal.LIMITACIONES:Este estudio incluyó una pequeña cantidad de pacientes con una duración de seguimiento insuficiente.CONCLUSIONES:Se espera que un panel multigénico completo identifique más mutaciones genéticas que la secuenciación directa basada en el fenotipo, con especial utilidad para la discordancia de fenotipo o genotipo-fenotipo poco clara. Consulte Video Resumen en http://links.lww.com/DCR/B844. Traducción- Dr. Francisco M. Abarca-Rendon).
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Affiliation(s)
- Ji Soo Park
- Hereditary Cancer Clinic, Cancer Prevention Center, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Won Park
- Division of Gastroenterology, Department of Internal Medicine, and Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Saeam Shin
- Hereditary Cancer Clinic, Cancer Prevention Center, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung-Tae Lee
- Hereditary Cancer Clinic, Cancer Prevention Center, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sang Joon Shin
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Byung Soh Min
- Department of Surgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Soo Jung Park
- Division of Gastroenterology, Department of Internal Medicine, and Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae Jun Park
- Hereditary Cancer Clinic, Cancer Prevention Center, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
- Division of Gastroenterology, Department of Internal Medicine, and Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae Hee Cheon
- Division of Gastroenterology, Department of Internal Medicine, and Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Won Ho Kim
- Division of Gastroenterology, Department of Internal Medicine, and Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Tae Il Kim
- Hereditary Cancer Clinic, Cancer Prevention Center, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
- Division of Gastroenterology, Department of Internal Medicine, and Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
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Mighton C, Lerner‐Ellis J. Principles of molecular testing for hereditary cancer. Genes Chromosomes Cancer 2022; 61:356-381. [DOI: 10.1002/gcc.23048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Chloe Mighton
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Genomics Health Services Research Program Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto Toronto ON Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health University of Toronto Toronto ON Canada
| | - Jordan Lerner‐Ellis
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada
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Serrated Colorectal Lesions: An Up-to-Date Review from Histological Pattern to Molecular Pathogenesis. Int J Mol Sci 2022; 23:ijms23084461. [PMID: 35457279 PMCID: PMC9032676 DOI: 10.3390/ijms23084461] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/16/2022] [Accepted: 04/17/2022] [Indexed: 12/10/2022] Open
Abstract
Until 2010, colorectal serrated lesions were generally considered as harmless lesions and reported as hyperplastic polyps (HPs) by pathologists and gastroenterologists. However, recent evidence showed that they may bear the potential to develop into colorectal carcinoma (CRC). Therefore, the World Health Organization (WHO) classification has identified four categories of serrated lesions: hyperplastic polyps (HPs), sessile serrated lesions (SSLs), traditional serrated adenoma (TSAs) and unclassified serrated adenomas. SSLs with dysplasia and TSAs are the most common precursors of CRC. CRCs arising from serrated lesions originate via two different molecular pathways, namely sporadic microsatellite instability (MSI) and the CpG island methylator phenotype (CIMP), the latter being considered as the major mechanism that drives the serrated pathway towards CRC. Unlike CRCs arising through the adenoma-carcinoma pathway, APC-inactivating mutations are rarely shown in the serrated neoplasia pathway.
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Lee JK, Kwon WK, Hong SN, Chang DK, Kim HC, Jang JH, Kim JW. Necessity of Multiplex Ligation Probe Amplification in Genetic Tests: Germline variant analysis of the APC gene in familial adenomatous polyposis patients. Cancer Genet 2022; 262-263:95-101. [DOI: 10.1016/j.cancergen.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/10/2022] [Accepted: 02/09/2022] [Indexed: 11/02/2022]
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21
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Xu X, Liang JH, Li JH, Xu QC, Yin XY. Values of a novel pyroptosis-related genetic signature in predicting outcome and immune status of pancreatic ductal adenocarcinoma. Gastroenterol Rep (Oxf) 2022; 10:goac051. [PMID: 36196256 PMCID: PMC9522386 DOI: 10.1093/gastro/goac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/18/2022] [Accepted: 08/14/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Pyroptosis is an emerging form of programmed cell death associated with progression in malignancies. Yet, there are few studies reporting on the association between pancreatic ductal adenocarcinoma (PDAC) and pyroptosis. Therefore, we aimed to construct a pyroptosis-related genetic signature to predict the clinical outcome and immune status in PDAC patients.
Methods
RNA-seq data of 176 PDAC patients from The Cancer Genome Atlas (TCGA) and 167 PDAC patients from the Genotype-Tissue Expression Project were analysed for pyroptosis-related differentially expressed genes (DEGs) between PDAC and normal pancreas. The risk signature of DEGs was analysed using the least absolute shrinkage and selection operator (LASSO) Cox regression analysis and its accuracy was validated in the Gene Expression Omnibus (GEO) cohort (n = 190). Functional enrichment analyses were performed to explore the mechanisms of the DEGs. The immune characteristics were evaluated using single-sample gene set enrichment analysis and ESTIMATE algorithms for each group.
Results
A nine-gene risk signature was generated from LASSO Cox regression analysis and classified PDAC patients into either a high- or low-risk group according to the median risk score. The high-risk group had significantly shorter overall survival than the low-risk group and it was verified in the external GEO database. A nomogram based on the risk signature was constructed and showed an ideal prediction performance. Functional enrichment analyses revealed that pyroptosis might regulate the tumor immune microenvironment in PDAC. Immune infiltration evaluation suggested that immune status was more activated in the low-risk group than in the high-risk group.
Conclusion
The risk signature encompassing nine pyroptosis-related genes may be a prognostic marker for PDAC. Pyroptosis might affect the prognosis of PDAC patients via regulating the tumor immune microenvironment.
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Affiliation(s)
- Xiang Xu
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, P. R. China
| | - Jia-Hua Liang
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, P. R. China
| | - Jian-Hui Li
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, P. R. China
| | - Qiong-Cong Xu
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, P. R. China
| | - Xiao-Yu Yin
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, P. R. China
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22
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Tran VT, Nguyen ST, Pham XD, Phan TH, Nguyen VC, Nguyen HT, Nguyen HP, Doan PTT, Le TA, Nguyen BT, Jasmine TX, Nguyen DS, Nguyen HDL, Nguyen NM, Do DX, Tran VU, Nguyen HHT, Le MP, Nguyen YN, Do TTT, Truong DK, Tang HS, Phan MD, Nguyen HN, Giang H, Tu LN. Pathogenic Variant Profile of Hereditary Cancer Syndromes in a Vietnamese Cohort. Front Oncol 2022; 11:789659. [PMID: 35070997 PMCID: PMC8767154 DOI: 10.3389/fonc.2021.789659] [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: 10/05/2021] [Accepted: 12/09/2021] [Indexed: 12/30/2022] Open
Abstract
Background Hereditary cancer syndromes (HCS) are responsible for 5-10% of cancer cases. Genetic testing to identify pathogenic variants associated with cancer predisposition has not been routinely available in Vietnam. Consequently, the prevalence and genetic landscape of HCS remain unknown. Methods 1165 Vietnamese individuals enrolled in genetic testing at our laboratory in 2020. We performed analysis of germline mutations in 17 high- and moderate- penetrance genes associated with HCS by next generation sequencing. Results A total of 41 pathogenic variants in 11 genes were detected in 3.2% individuals. The carrier frequency was 4.2% in people with family or personal history of cancer and 2.6% in those without history. The percentage of mutation carriers for hereditary colorectal cancer syndromes was 1.3% and for hereditary breast and ovarian cancer syndrome was 1.6%. BRCA1 and BRCA2 mutations were the most prevalent with the positive rate of 1.3% in the general cohort and 5.1% in breast or ovarian cancer patients. Most of BRCA1 mutations located at the BRCA C-terminus domains and the top recurrent mutation was NM_007294.3:c.5251C>T (p.Arg1751Ter). One novel variant NM_000038.6(APC):c.6665C>A (p.Pro2222His) was found in a breast cancer patient with a strong family history of cancer. A case study of hereditary cancer syndrome was illustrated to highlight the importance of genetic testing. Conclusion This is the first largest analysis of carrier frequency and mutation spectrum of HCS in Vietnam. The findings demonstrate the clinical significance of multigene panel testing to identify carriers and their at-risk relatives for better cancer surveillance and management strategies.
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Affiliation(s)
| | - Sao Trung Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | - Huu Thinh Nguyen
- University Medical Center Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Huu Phuc Nguyen
- University Medical Center Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Phuong Thao Thi Doan
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | - Duy Sinh Nguyen
- Department of Oncology, Faculty of Medicine, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hong-Dang Luu Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Ngoc Mai Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Duy Xuan Do
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Vu Uyen Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hue Hanh Thi Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Minh Phong Le
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Yen Nhi Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | | | | | - Hung Sang Tang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Minh-Duy Phan
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hoai-Nghia Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Lan N Tu
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
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23
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Zeinalian M, Miar P, Tabatabaiefar M, Abdollahi Z, Noruzi M, Kazemi M, Naimi A, Emami M, Izadi S. BAT25, ACVR2, and TGFBR2 mononucleotide STR markers: A triplex panel for microsatellite instability testing in colorectal tumors. Adv Biomed Res 2022; 11:79. [DOI: 10.4103/abr.abr_205_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 12/11/2021] [Accepted: 03/12/2022] [Indexed: 11/04/2022] Open
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24
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Garcia-Pelaez J, Barbosa-Matos R, São José C, Sousa S, Gullo I, Hoogerbrugge N, Carneiro F, Oliveira C. Gastric cancer genetic predisposition and clinical presentations: Established heritable causes and potential candidate genes. Eur J Med Genet 2021; 65:104401. [PMID: 34871783 DOI: 10.1016/j.ejmg.2021.104401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 11/10/2021] [Accepted: 11/28/2021] [Indexed: 12/12/2022]
Abstract
Tumour risk syndromes (TRS) are characterized by an increased risk of early-onset cancers in a familial context. High cancer risk is mostly driven by loss-of-function variants in a single cancer-associated gene. Presently, predisposition to diffuse gastric cancer (DGC) is explained by CDH1 and CTNNA1 pathogenic and likely pathogenic variants (P/LP), causing Hereditary Diffuse Gastric Cancer (HDGC); while APC promoter 1B single nucleotide variants predispose to Gastric Adenocarcinoma and Proximal Polyposis of the Stomach (GAPPS). Familial Intestinal Gastric Cancer (FIGC), recognized as a GC-predisposing disease, remains understudied and genetically unsolved. GC can also occur in the spectrum of other TRS. Identification of heritable causes allows defining diagnostic testing criteria, helps to clinically classify GC families into the appropriate TRS, and allows performing pre-symptomatic testing identifying at-risk individuals for downstream surveillance, risk reduction and/or treatment. However, most of HDGC, some GAPPS, and most FIGC patients/families remain unsolved, expecting a heritable factor to be discovered. The missing heritability in GC-associated tumour risk syndromes (GC-TRS) is likely explained not by a single major gene, but by a diversity of genes, some, predisposing to other TRS. This would gain support if GC-enriched small families or apparently isolated early-onset GC cases were hiding a family history compatible with another TRS. Herein, we revisited current knowledge on GC-TRS, and searched in the literature for individuals/families bearing P/LP variants predisposing for other TRS, but whose probands display a clinical presentation and/or family history also fitting GC-TRS criteria. We found 27 families with family history compatible with HDGC or FIGC, harbouring 28 P/LP variants in 16 TRS-associated genes, mainly associated with DNA repair. PALB2 or BRCA2 were the most frequently mutated candidate genes in individuals with family history compatible with HDGC and FIGC, respectively. Consolidation of PALB2 and BRCA2 as HDGC- or FIGC-associated genes, respectively, holds promise and worth additional research. This analysis further highlighted the influence, that proband's choice and small or unreported family history have, for a correct TRS diagnosis, genetic screening, and disease management. In this review, we provide a rational for identification of particularly relevant candidate genes in GC-TRS.
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Affiliation(s)
- José Garcia-Pelaez
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Doctoral Programme in Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Rita Barbosa-Matos
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; International Doctoral Programme in Molecular and Cellular Biotechnology Applied to Health Sciences from Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Celina São José
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Doctoral Programme in Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Sónia Sousa
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Irene Gullo
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; FMUP - Faculty of Medicine of the University of Porto, Porto, Portugal; Centro Hospitalar e Universitário S. João, Porto, Portugal
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Fátima Carneiro
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; FMUP - Faculty of Medicine of the University of Porto, Porto, Portugal; Centro Hospitalar e Universitário S. João, Porto, Portugal
| | - Carla Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; FMUP - Faculty of Medicine of the University of Porto, Porto, Portugal.
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25
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Zhuang Z, Cai H, Lin H, Guan B, Wu Y, Zhang Y, Liu X, Zhuang J, Guan G. Development and Validation of a Robust Pyroptosis-Related Signature for Predicting Prognosis and Immune Status in Patients with Colon Cancer. JOURNAL OF ONCOLOGY 2021; 2021:5818512. [PMID: 34840571 PMCID: PMC8616665 DOI: 10.1155/2021/5818512] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/24/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Pyroptosis has been confirmed as a type of inflammatory programmed cell death in recent years. However, the prognostic role of pyroptosis in colon cancer (CC) remains unclear. METHODS Dataset TCGA-COAD which came from the TCGA portal was taken as the training cohort. GSE17538 from the GEO database was treated as validation cohorts. Differential expression genes (DEGs) between normal and tumor tissues were confirmed. Patients were classified into two subgroups according to the expression characteristics of pyroptosis-related DEGs. The LASSO regression analysis was used to build the best prognostic signature, and its reliability was validated using Kaplan-Meier, ROC, PCA, and t-SNE analyses. And a nomogram based on the multivariate Cox analysis was developed. The enrichment analysis was performed in the GO and KEGG to investigate the potential mechanism. In addition, we explored the difference in the abundance of infiltrating immune cells and immune microenvironment between high- and low-risk groups. And we also predicted the association of common immune checkpoints with risk scores. Finally, we verified the expression of the pyroptosis-related hub gene at the protein level by immunohistochemistry. RESULTS A total of 23 pyroptosis-related DEGs were identified in the TCGA cohort. Patients were classified into two molecular clusters (MC) based on DEGs. Kaplan-Meier survival analysis indicated that patients with MC1 represented significantly poorer OS than patients with MC2. 13 overall survival- (OS-) related DEGs in MCs were used to construct the prognostic signature. Patients in the high-risk group exhibited poorer OS compared to those in the low-risk group. Combined with the clinical features, the risk score was found to be an independent prognostic factor of CC patients. The above results are verified in the external dataset GSE17538. A nomogram was established and showed excellent performance. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that the varied prognostic performance between high- and low-risk groups may be related to the immune response mediated by local inflammation. Further analysis showed that the high-risk group has stronger immune cell infiltration and lower tumor purity than the low-risk group. Through the correlation between risk score and immune checkpoint expression, T-cell immunoglobulin and mucin domain-containing protein 3 (TIM-3) was predicted as a potential therapeutic target for the high-risk group. CONCLUSION The 13-gene signature was associated with OS, immune cells, tumor purity, and immune checkpoints in CC patients, and it could provide the basis for immunotherapy and predicting prognosis and help clinicians make decisions for individualized treatment.
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Affiliation(s)
- Zhicheng Zhuang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Huajun Cai
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Hexin Lin
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Bingjie Guan
- Department of Radiation Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Yong Wu
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Yiyi Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Xing Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Jinfu Zhuang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Guoxian Guan
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
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26
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O'Shea R, Rankin NM, Kentwell M, Gleeson M, Tucker KM, Hampel H, Taylor N, Lewis S. Stakeholders' views of integrating universal tumour screening and genetic testing for colorectal and endometrial cancer into routine oncology. Eur J Hum Genet 2021; 29:1634-1644. [PMID: 33811254 PMCID: PMC8560784 DOI: 10.1038/s41431-021-00871-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/07/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022] Open
Abstract
Mainstream genetic testing in routine oncology care requires implementation research to inform intervention design. In Australia, funding is available for oncology health professionals (OHP) to organise genetic testing (GT) for eligible colorectal and endometrial cancer patients as part of their routine care. To assess the health system ability to incorporate this practice change, we conducted an implementation survey using the Consolidated Framework for Implementation Research (CFIR). The online survey was available from April to September 2020 to OHP and genetic health professional (GHP). In total, 198 respondents attempted the survey, with 158 completed and 27 partial responses: 26% were GHP, 66% OHP and 8% pathologists. Of all responders, 50% were female, mainly practicing in public hospital settings (57%) in an urban location (80%) and with an 18-60 years plus age range. The majority of respondents saw the relative advantage of aligning GT to abnormal universal tumour screening (UTS) results, with 77% of GHP and 78% of OHP agreeing it would streamline care for patients. There was disagreement across healthcare professional groups about knowledge and self-efficacy, with 45% of GHP not viewing oncologists as 'feeling confident' to use genetic test results for treatment management decisions, while 62% of OHP felt confident in their ability. Both OHP and GHP's indicated embedding a genetic counsellor in oncology or having a genetics point of contact to support integrating of GT through UTS as favourable interventions. Implementation research findings allow for the design of targeted interventions and a model for GT integration into oncology.
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Affiliation(s)
- Rosie O'Shea
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.
- Discipline of Genetic Counselling, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia.
| | - Nicole M Rankin
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Maira Kentwell
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Oncology, Royal Women's Hospital Parkville, Melbourne, VIC, Australia
| | | | - Katherine M Tucker
- Hereditary Cancer Clinic, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Natalie Taylor
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Cancer Research Division, Cancer Council, Sydney, NSW, Australia
| | - Sarah Lewis
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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27
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Georgeson P, Pope BJ, Rosty C, Clendenning M, Mahmood K, Joo JE, Walker R, Hutchinson R, Preston S, Como J, Joseland S, Win AK, Macrae FA, Hopper JL, Mouradov D, Gibbs P, Sieber OM, O’Sullivan DE, Brenner DR, Gallinger S, Jenkins MA, Winship IM, Buchanan DD. Evaluating the utility of tumour mutational signatures for identifying hereditary colorectal cancer and polyposis syndrome carriers. Gut 2021; 70:2138-2149. [PMID: 33414168 PMCID: PMC8260632 DOI: 10.1136/gutjnl-2019-320462] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/08/2020] [Accepted: 12/12/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Germline pathogenic variants (PVs) in the DNA mismatch repair (MMR) genes and in the base excision repair gene MUTYH underlie hereditary colorectal cancer (CRC) and polyposis syndromes. We evaluated the robustness and discriminatory potential of tumour mutational signatures in CRCs for identifying germline PV carriers. DESIGN Whole-exome sequencing of formalin-fixed paraffin-embedded (FFPE) CRC tissue was performed on 33 MMR germline PV carriers, 12 biallelic MUTYH germline PV carriers, 25 sporadic MLH1 methylated MMR-deficient CRCs (MMRd controls) and 160 sporadic MMR-proficient CRCs (MMRp controls) and included 498 TCGA CRC tumours. COSMIC V3 single base substitution (SBS) and indel (ID) mutational signatures were assessed for their ability to differentiate CRCs that developed in carriers from non-carriers. RESULTS The combination of mutational signatures SBS18 and SBS36 contributing >30% of a CRC's signature profile was able to discriminate biallelic MUTYH carriers from all other non-carrier control CRCs with 100% accuracy (area under the curve (AUC) 1.0). SBS18 and SBS36 were associated with specific MUTYH variants p.Gly396Asp (p=0.025) and p.Tyr179Cys (p=5×10-5), respectively. The combination of ID2 and ID7 could discriminate the 33 MMR PV carrier CRCs from the MMRp control CRCs (AUC 0.99); however, SBS and ID signatures, alone or in combination, could not provide complete discrimination (AUC 0.79) between CRCs from MMR PV carriers and sporadic MMRd controls. CONCLUSION Assessment of SBS and ID signatures can discriminate CRCs from biallelic MUTYH carriers and MMR PV carriers from non-carriers with high accuracy, demonstrating utility as a potential diagnostic and variant classification tool.
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Affiliation(s)
- Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Bernard J. Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia,Melbourne Bioinformatics, The University of Melbourne, Carlton, Victoria, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia,Envoi Pathology, Brisbane, Queensland, Australia,University of Queensland, School of Medicine, Herston, Queensland, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia,Melbourne Bioinformatics, The University of Melbourne, Carlton, Victoria, Australia
| | - Jihoon E. Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Ryan Hutchinson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Susan Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Aung K. Win
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia,Centre for Epidemiology and Biostatistics, The University of Melbourne, Carlton, Victoria, Australia
| | - Finlay A. Macrae
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia,Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Carlton, Victoria, Australia
| | - Dmitry Mouradov
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, Victoria, Australia,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Peter Gibbs
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, Victoria, Australia,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia,Department of Medical Oncology, Western Health, Victoria, Australia
| | - Oliver M. Sieber
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, Victoria, Australia,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia,Department of Surgery, The University of Melbourne, Parkville, Victoria, Australia,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Dylan E. O’Sullivan
- Department of Oncology, University of Calgary, Calgary, Canada,Department of Community Health Sciences, University of Calgary, Calgary, Canada
| | - Darren R. Brenner
- Department of Oncology, University of Calgary, Calgary, Canada,Department of Community Health Sciences, University of Calgary, Calgary, Canada,Department of Cancer Epidemiology and Prevention Research, Alberta Health Services, Calgary, Canada
| | - Steve Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada,Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Mark A. Jenkins
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia,Centre for Epidemiology and Biostatistics, The University of Melbourne, Carlton, Victoria, Australia
| | - Ingrid M. Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia,Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia,University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia,Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
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28
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POLE, POLD1, and NTHL1: the last but not the least hereditary cancer-predisposing genes. Oncogene 2021; 40:5893-5901. [PMID: 34363023 DOI: 10.1038/s41388-021-01984-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023]
Abstract
POLE, POLD1, and NTHL1 are involved in DNA replication and have recently been recognized as hereditary cancer-predisposing genes, because their alterations are associated with colorectal cancer and other tumors. POLE/POLD1-associated syndrome shows an autosomal dominant inheritance, whereas NTHL1-associated syndrome follows an autosomal recessive pattern. Although the prevalence of germline monoallelic POLE/POLD1 and biallelic NTHL1 pathogenic variants is low, they determine different phenotypes with a broad tumor spectrum overlapping that of other hereditary conditions like Lynch Syndrome or Familial Adenomatous Polyposis. Endometrial and breast cancers, and probably ovarian and brain tumors are also associated with POLE/POLD1 alterations, while breast cancer and other unusual tumors are correlated with NTHL1 pathogenic variants. POLE-mutated colorectal and endometrial cancers are associated with better prognosis and may show favorable responses to immunotherapy. Since POLE/POLD1-mutated tumors show a high tumor mutational burden producing an increase in neoantigens, the identification of POLE/POLD1 alterations could help select patients suitable for immunotherapy treatment. In this review, we will investigate the role of POLE, POLD1, and NTHL1 genetic variants in cancer predisposition, discussing the potential future therapeutic applications and assessing the utility of performing a routine genetic testing for these genes, in order to implement prevention and surveillance strategies in mutation carriers.
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Lam KK, Thean LF, Cheah PY. Advances in colorectal cancer genomics and transcriptomics drive early detection and prevention. Int J Biochem Cell Biol 2021; 137:106032. [PMID: 34182137 DOI: 10.1016/j.biocel.2021.106032] [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: 02/26/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 12/20/2022]
Abstract
Colorectal carcinoma (CRC) is a high incidence cancer and leading cause of cancer mortality worldwide. The advances in genomics and transcriptomics in the past decades have improved the detection and prevention of CRC in familial CRC syndromes. Nevertheless, the ultimate goal of personalized medicine for sporadic CRC is still not within reach due no less to the difficulty in integrating population disparity and clinical data to combat what essentially is a very heterogenous disease. This minireview highlights the achievement of the past decades and present possible direction in the hope of early detection and metastasis prevention for reducing CRC-associated morbidity and mortality.
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Affiliation(s)
- Kuen Kuen Lam
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Lai Fun Thean
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Peh Yean Cheah
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Duke-NUS Medical School, National University of Singapore, Singapore.
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Tomasini PP, Guecheva TN, Leguisamo NM, Péricart S, Brunac AC, Hoffmann JS, Saffi J. Analyzing the Opportunities to Target DNA Double-Strand Breaks Repair and Replicative Stress Responses to Improve Therapeutic Index of Colorectal Cancer. Cancers (Basel) 2021; 13:3130. [PMID: 34201502 PMCID: PMC8268241 DOI: 10.3390/cancers13133130] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/15/2021] [Accepted: 06/18/2021] [Indexed: 12/22/2022] Open
Abstract
Despite the ample improvements of CRC molecular landscape, the therapeutic options still rely on conventional chemotherapy-based regimens for early disease, and few targeted agents are recommended for clinical use in the metastatic setting. Moreover, the impact of cytotoxic, targeted agents, and immunotherapy combinations in the metastatic scenario is not fully satisfactory, especially the outcomes for patients who develop resistance to these treatments need to be improved. Here, we examine the opportunity to consider therapeutic agents targeting DNA repair and DNA replication stress response as strategies to exploit genetic or functional defects in the DNA damage response (DDR) pathways through synthetic lethal mechanisms, still not explored in CRC. These include the multiple actors involved in the repair of DNA double-strand breaks (DSBs) through homologous recombination (HR), classical non-homologous end joining (NHEJ), and microhomology-mediated end-joining (MMEJ), inhibitors of the base excision repair (BER) protein poly (ADP-ribose) polymerase (PARP), as well as inhibitors of the DNA damage kinases ataxia-telangiectasia and Rad3 related (ATR), CHK1, WEE1, and ataxia-telangiectasia mutated (ATM). We also review the biomarkers that guide the use of these agents, and current clinical trials with targeted DDR therapies.
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Affiliation(s)
- Paula Pellenz Tomasini
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre, Avenida Sarmento Leite, 245, Porto Alegre 90050-170, Brazil; (P.P.T.); (N.M.L.)
- Post-Graduation Program in Cell and Molecular Biology, Federal University of Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre 91501-970, Brazil
| | - Temenouga Nikolova Guecheva
- Cardiology Institute of Rio Grande do Sul, University Foundation of Cardiology (IC-FUC), Porto Alegre 90620-000, Brazil;
| | - Natalia Motta Leguisamo
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre, Avenida Sarmento Leite, 245, Porto Alegre 90050-170, Brazil; (P.P.T.); (N.M.L.)
| | - Sarah Péricart
- Laboratoire D’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France; (S.P.); (A.-C.B.); (J.S.H.)
| | - Anne-Cécile Brunac
- Laboratoire D’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France; (S.P.); (A.-C.B.); (J.S.H.)
| | - Jean Sébastien Hoffmann
- Laboratoire D’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France; (S.P.); (A.-C.B.); (J.S.H.)
| | - Jenifer Saffi
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre, Avenida Sarmento Leite, 245, Porto Alegre 90050-170, Brazil; (P.P.T.); (N.M.L.)
- Post-Graduation Program in Cell and Molecular Biology, Federal University of Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre 91501-970, Brazil
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Lengyel CG. Microsatellite Instability as a Predictor of Outcomes in Colorectal Cancer in the Era of Immune-Checkpoint Inhibitors. Curr Drug Targets 2021; 22:968-976. [PMID: 33970843 DOI: 10.2174/1389450122666210325121322] [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: 11/04/2020] [Revised: 12/15/2020] [Accepted: 01/08/2021] [Indexed: 11/22/2022]
Abstract
The microsatellite instable phenotype resulting from errors in DNA mismatch repair proteins accounts for as far as 15 to 20% of non-hereditary colon cancers but is scarce in rectal cancer. It has been shown that the increased existence of tumor-specific neoantigens in hypermutated tumors is correlated with higher tumor-infiltrating lymphocytes (TILs) and overexpression of immune checkpoint receptors and ligands, mainly PD-1 and PD-L1. In particular, the data gained up to now gives evidence that neoantigen recognition constitutes a dominant component in the course of immunotherapies. This review's primary objective is to describe current approvals and summarize present knowledge about the outcomes of immuno-oncology treatment of microsatellite instable colorectal cancer (CRC). The secondary objective is to give a narrative report about testing methodologies, prognostics, and the predictive value of microsatellite instability. For this purpose, a literature review was performed, focusing on published clinical trial results, ongoing clinical trials and timelines, testing methods, and prognostic and predictive value of MSI. Following four recent FDA approvals of immunotherapy of MSI-high CRC, further work should be warranted by pathology societies towards standardization and rising concordance and reproducibility across the IHC/MSI testing landscape in order to facilitate professionals to offer better survival options for patients with CRC.
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Norouzi M, Shafiei M, Abdollahi Z, Miar P, Galehdari H, Emami MH, Zeinalian M, Tabatabaiefar MA. WRN Germline Mutation Is the Likely Inherited Etiology of Various Cancer Types in One Iranian Family. Front Oncol 2021; 11:648649. [PMID: 34164337 PMCID: PMC8215443 DOI: 10.3389/fonc.2021.648649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 05/05/2021] [Indexed: 11/15/2022] Open
Abstract
Background Familial cancers comprise a considerable distribution of colorectal cancers (CRCs), of which only about 5% occurs through well-established hereditary syndromes. It has been demonstrated that deleterious variants at the newly identified cancer-predisposing genes could describe the etiology of undefined familial cancers. Methods The present study aimed to identify the genetic etiology in a 32-year-old man with early onset familial CRC employing several molecular diagnostic techniques. DNA was extracted from tumoral and normal formalin-fixed-paraffin-embedded (FFPE) blocks, and microsatellite instability (MSI) was evaluated. Immunohistochemistry staining of MMR proteins was performed on tumoral FFPE blocks. Next-generation sequencing (NGS), multiplex ligation-dependent amplification (MLPA) assay, and Sanger sequencing were applied on the genomic DNA extracted from peripheral blood. Data analysis was performed using bioinformatics tools. Genetic variants interpretation was based on ACMG. Results MSI analysis indicated MSI-H phenotype, and IHC staining proved no expressions of MSH2 and MSH6 proteins. MLPA and NGS data showed no pathogenic variants in MMR genes. Further analysis of NGS data revealed a candidate WRN frameshift variant (p.R389Efs*3), which was validated with Sanger sequencing. The variant was interpreted as pathogenic since it met the criteria based on the ACMG guideline including very strong (PVS1), strong (PS3), and moderate (PM2). Conclusion WRN is a DNA helicase participating in DNA repair pathways to sustain genomic stability. WRN deficient function may contribute to CRC development that is valuable for further investigation as a candidate gene in hereditary cancer syndrome diagnosis.
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Affiliation(s)
- Mahnaz Norouzi
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohammad Shafiei
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Zeinab Abdollahi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Paniz Miar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohammad Hasan Emami
- Department of Gastroenterology, Poursina Hakim Digestive Disease Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehrdad Zeinalian
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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Stinton C, Jordan M, Fraser H, Auguste P, Court R, Al-Khudairy L, Madan J, Grammatopoulos D, Taylor-Phillips S. Testing strategies for Lynch syndrome in people with endometrial cancer: systematic reviews and economic evaluation. Health Technol Assess 2021; 25:1-216. [PMID: 34169821 PMCID: PMC8273681 DOI: 10.3310/hta25420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Lynch syndrome is an inherited genetic condition that is associated with an increased risk of certain cancers. The National Institute for Health and Care Excellence has recommended that people with colorectal cancer are tested for Lynch syndrome. Routine testing for Lynch syndrome among people with endometrial cancer is not currently conducted. OBJECTIVES To systematically review the evidence on the test accuracy of immunohistochemistry- and microsatellite instability-based strategies to detect Lynch syndrome among people who have endometrial cancer, and the clinical effectiveness and the cost-effectiveness of testing for Lynch syndrome among people who have been diagnosed with endometrial cancer. DATA SOURCES Searches were conducted in the following databases, from inception to August 2019 - MEDLINE ALL, EMBASE (both via Ovid), Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials (both via Wiley Online Library), Database of Abstracts of Reviews of Effects, Health Technology Assessment Database (both via the Centre for Reviews and Dissemination), Science Citation Index, Conference Proceedings Citation Index - Science (both via Web of Science), PROSPERO international prospective register of systematic reviews (via the Centre for Reviews and Dissemination), NHS Economic Evaluation Database, Cost-Effectiveness Analysis Registry, EconPapers (Research Papers in Economics) and School of Health and Related Research Health Utilities Database. The references of included studies and relevant systematic reviews were also checked and experts on the team were consulted. REVIEW METHODS Eligible studies included people with endometrial cancer who were tested for Lynch syndrome using immunohistochemistry- and/or microsatellite instability-based testing [with or without mutL homologue 1 (MLH1) promoter hypermethylation testing], with Lynch syndrome diagnosis being established though germline testing of normal (non-tumour) tissue for constitutional mutations in mismatch repair. The risk of bias in studies was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 tool, the Consolidated Health Economic Reporting Standards and the Philips' checklist. Two reviewers independently conducted each stage of the review. A meta-analysis of test accuracy was not possible because of the number and heterogeneity of studies. A narrative summary of test accuracy results was provided, reporting test accuracy estimates and presenting forest plots. The economic model constituted a decision tree followed by Markov models for the impact of colorectal and endometrial surveillance, and aspirin prophylaxis with a lifetime time horizon. RESULTS The clinical effectiveness search identified 3308 studies; 38 studies of test accuracy were included. (No studies of clinical effectiveness of endometrial cancer surveillance met the inclusion criteria.) Four test accuracy studies compared microsatellite instability with immunohistochemistry. No clear difference in accuracy between immunohistochemistry and microsatellite instability was observed. There was some evidence that specificity of immunohistochemistry could be improved with the addition of methylation testing. There was high concordance between immunohistochemistry and microsatellite instability. The economic model indicated that all testing strategies, compared with no testing, were cost-effective at a willingness-to-pay threshold of £20,000 per quality-adjusted life-year. Immunohistochemistry with MLH1 promoter hypermethylation testing was the most cost-effective strategy, with an incremental cost-effectiveness ratio of £9420 per quality-adjusted life-year. The second most cost-effective strategy was immunohistochemistry testing alone, but incremental analysis produced an incremental cost-effectiveness ratio exceeding £130,000. Results were robust across all scenario analyses. Incremental cost-effectiveness ratios ranged from £5690 to £20,740; only removing the benefits of colorectal cancer surveillance produced an incremental cost-effectiveness ratio in excess of the £20,000 willingness-to-pay threshold. A sensitivity analysis identified the main cost drivers of the incremental cost-effectiveness ratio as percentage of relatives accepting counselling and prevalence of Lynch syndrome in the population. A probabilistic sensitivity analysis showed, at a willingness-to-pay threshold of £20,000 per quality-adjusted life-year, a 0.93 probability that immunohistochemistry with MLH1 promoter hypermethylation testing is cost-effective, compared with no testing. LIMITATIONS The systematic review excluded grey literature, studies written in non-English languages and studies for which the reference standard could not be established. Studies were included when Lynch syndrome was diagnosed by genetic confirmation of constitutional variants in the four mismatch repair genes (i.e. MLH1, mutS homologue 2, mutS homologue 6 and postmeiotic segregation increased 2). Variants of uncertain significance were reported as per the studies. There were limitations in the economic model around uncertainty in the model parameters and a lack of modelling of the potential harms of gynaecological surveillance and specific pathway modelling of genetic testing for somatic mismatch repair mutations. CONCLUSION The economic model suggests that testing women with endometrial cancer for Lynch syndrome is cost-effective, but that results should be treated with caution because of uncertain model inputs. FUTURE WORK Randomised controlled trials could provide evidence on the effect of earlier intervention on outcomes and the balance of benefits and harms of gynaecological cancer surveillance. Follow-up of negative cases through disease registers could be used to determine false negative cases. STUDY REGISTRATION This study is registered as PROSPERO CRD42019147185. FUNDING This project was funded by the National Institute for Health Research (NIHR) Evidence Synthesis programme and will be published in full in Health Technology Assessment; Vol. 25, No. 42. See the NIHR Journals Library website for further project information.
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Affiliation(s)
- Chris Stinton
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Mary Jordan
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Hannah Fraser
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Peter Auguste
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Rachel Court
- Warwick Medical School, University of Warwick, Coventry, UK
| | | | - Jason Madan
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Dimitris Grammatopoulos
- Institute of Precision Diagnostics and Translational Medicine, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, UK
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Lindner AK, Schachtner G, Tulchiner G, Thurnher M, Untergasser G, Obrist P, Pipp I, Steinkohl F, Horninger W, Culig Z, Pichler R. Lynch Syndrome: Its Impact on Urothelial Carcinoma. Int J Mol Sci 2021; 22:E531. [PMID: 33430305 PMCID: PMC7825811 DOI: 10.3390/ijms22020531] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 12/21/2022] Open
Abstract
Lynch syndrome, known as hereditary nonpolyposis colorectal cancer (HNPCC), is an autosomal-dominant familial cancer syndrome with an increased risk for urothelial cancer (UC). Mismatch repair (MMR) deficiency, due to pathogenic variants in MLH1, MSH2, MSH6, and PMS2, and microsatellite instability, are known for development of Lynch syndrome (LS) associated carcinogenesis. UC is the third most common cancer type in LS-associated tumors. The diversity of germline variants in the affected MMR genes and their following subsequent function loss might be responsible for the variation in cancer risk, suggesting an increased risk of developing UC in MSH2 mutation carriers. In this review, we will focus on LS-associated UC of the upper urinary tract (UUT) and bladder, their germline profiles, and outcomes compared to sporadic UC, the impact of genetic testing, as well as urological follow-up strategies in LS. In addition, we present a case of metastatic LS-associated UC of the UUT and bladder, achieving complete response during checkpoint inhibition since more than 2 years.
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Affiliation(s)
- Andrea Katharina Lindner
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (A.K.L.); (G.S.); (G.T.); (M.T.); (W.H.); (Z.C.)
| | - Gert Schachtner
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (A.K.L.); (G.S.); (G.T.); (M.T.); (W.H.); (Z.C.)
| | - Gennadi Tulchiner
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (A.K.L.); (G.S.); (G.T.); (M.T.); (W.H.); (Z.C.)
| | - Martin Thurnher
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (A.K.L.); (G.S.); (G.T.); (M.T.); (W.H.); (Z.C.)
- Immunotherapy Unit, Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Gerold Untergasser
- Department of Internal Medicine V, Medical University Innsbruck, 6020 Innsbruck, Austria;
- Experimental Oncogenomic Group, Tyrolean Cancer Research Institute, 6020 Innsbruck, Austria
| | - Peter Obrist
- Pathology Laboratory Obrist and Brunhuber, 6511 Zams, Austria;
| | - Iris Pipp
- Clinical Pathology and Cytodiagnostics, tirol-kliniken, 6020 Innsbruck, Austria;
| | - Fabian Steinkohl
- Department of Radiology, Medical University Innsbruck, 6020 Innsbruck, Austria;
| | - Wolfgang Horninger
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (A.K.L.); (G.S.); (G.T.); (M.T.); (W.H.); (Z.C.)
| | - Zoran Culig
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (A.K.L.); (G.S.); (G.T.); (M.T.); (W.H.); (Z.C.)
| | - Renate Pichler
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (A.K.L.); (G.S.); (G.T.); (M.T.); (W.H.); (Z.C.)
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Casey L, Singh N. POLE, MMR, and MSI Testing in Endometrial Cancer: Proceedings of the ISGyP Companion Society Session at the USCAP 2020 Annual Meeting. Int J Gynecol Pathol 2021; 40:5-16. [PMID: 33290350 DOI: 10.1097/pgp.0000000000000710] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Subclassification of endometrial carcinoma (EC) based on morphologic features alone has been shown to have suboptimal reproducibility, both in regard to biopsy versus hysterectomy findings, as well as interobserver agreement. This restricts the role of morphologic classification of EC as a tool for risk prediction and therefore treatment planning. A diagnostic algorithm based on The Cancer Genome Atlas (TCGA) classification of EC holds promise for improving accuracy in risk prediction. This classifies EC into 4 groups: those harbouring mutations in the exonuclease domain of DNA polymerase epsilon, POLE (POLEmut), those showing a mismatch repair defect, those showing mutations in TP53 (p53abn) and a heterogenous group showing none of these 3 abnormalities (currently termed no specific molecular profile). These groups can be accurately and reproducibly diagnosed on biopsy samples using a limited panel of tests, namely immunohistochemistry for mismatch repair proteins and p53, and testing for POLE exonuclease domain pathogenic variants. In this article we briefly review the biology, testing and interpretation of POLE and mismatch repair defects in EC.
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Affiliation(s)
- Laura Casey
- Department of Cellular Pathology, Barts Health NHS Trust, London, UK
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Brown GR, Simon M, Wentling C, Spencer DM, Parker AN, Rogers CA. A review of inherited cancer susceptibility syndromes. JAAPA 2020; 33:10-16. [PMID: 33234888 DOI: 10.1097/01.jaa.0000721648.46099.2c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Inherited cancer syndromes are caused by genetic mutations that place patients at an increased risk for developing cancer. Although most cancers are not caused by genetic inheritance, clinicians must understand these syndromes and be able to recognize their common characteristics. A thorough family history and identification of common patterns as well as specific clinical signs and symptoms can help with early recognition. This article describes symptoms of the more common cancer syndromes, including hereditary breast and ovarian cancer, Li-Fraumeni, Lynch, familial adenomatous polyposis, retinoblastoma, multiple endocrine neoplasia, and von Hippel-Lindau. Important patient education regarding genetic testing also is covered.
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Affiliation(s)
- Gina R Brown
- Gina R. Brown is an associate professor at Wichita (Kan.) State University. Madeline Simon practices at Midwest Orthopaedics at Rush in Chicago, Ill. Chris Wentling is a hospitalist at Southwest Medical Center in Liberal, Kan. Danielle M. Spencer practices in trauma and general surgery at Stormont Vail Hospital in Topeka, Kan. Ashley N. Parker practices at Freeman Orthopaedics and Sports Medicine in Joplin, Mo. Corey A. Rogers is an assistant clinical professor at Wichita State University. The authors have disclosed no potential conflicts of interest, financial or otherwise
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Oldfield LE, Li T, Tone A, Aronson M, Edwards M, Holter S, Quevedo R, Van de Laar E, Lerner-Ellis J, Pollett A, Clarke B, Tabori U, Gallinger S, Ferguson SE, Pugh TJ. An Integrative DNA Sequencing and Methylation Panel to Assess Mismatch Repair Deficiency. J Mol Diagn 2020; 23:242-252. [PMID: 33259954 DOI: 10.1016/j.jmoldx.2020.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/09/2020] [Accepted: 11/09/2020] [Indexed: 12/30/2022] Open
Abstract
Clinical testing for mismatch repair (MMR) deficiency often entails serial testing of tumor and constitutional DNA using multiple assays. To minimize cost and specimen requirements of MMR testing, we developed an integrated targeted sequencing protocol (termed MultiMMR) that tests for promoter methylation, mutations, copy number alterations, copy neutral loss of heterozygosity, and microsatellite instability from a single aliquot of DNA. Hybrid capture of DNA-sequencing libraries constructed with methylated adapters was performed on 142 samples (60 tumors and 82 constitutional samples) from 82 patients with MMR-associated colorectal, endometrial, and brain cancers as well as a synthetic DNA mix with 11 known mutations. The captured material was split to enable parallel bisulfite and conventional sequence analysis. The panel targeted microsatellite regions and 13 genes associated with MMR, hypermutation, and hereditary colorectal cancer. MultiMMR recapitulated clinical testing results in 23 of 24 cases, was able to explain MMR loss in an additional 29 of 48 patients with incomplete or inconclusive testing, and identified all 11 MMR variants within the synthetic DNA mix. Promoter methylation and microsatellite instability analysis found 95% and 97% concordance with clinical testing, respectively. We report the feasibility for amalgamation of the current stepwise and complex clinical testing workflow into an integrated test for hereditary and somatic causes of MMR deficiency.
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Affiliation(s)
- Leslie E Oldfield
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tiantian Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alicia Tone
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Spring Holter
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Rene Quevedo
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Emily Van de Laar
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Aaron Pollett
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Blaise Clarke
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Uri Tabori
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sarah E Ferguson
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
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Kim SR, Tone A, Kim RH, Cesari M, Clarke BA, Eiriksson L, Hart T, Aronson M, Holter S, Lytwyn A, Maganti M, Oldfield L, Gallinger S, Bernardini MQ, Oza AM, Djordjevic B, Lerner‐Ellis J, Van de Laar E, Vicus D, Pugh TJ, Pollett A, Ferguson SE. Performance characteristics of screening strategies to identify Lynch syndrome in women with ovarian cancer. Cancer 2020; 126:4886-4894. [PMID: 32809219 PMCID: PMC7693219 DOI: 10.1002/cncr.33144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND For women with ovarian cancer (OC), the optimal screening strategy to identify Lynch syndrome (LS) has not been determined. In the current study, the authors compared the performance characteristics of various strategies combining mismatch repair (MMR) immunohistochemistry (IHC), microsatellite instability testing (MSI), and family history for the detection of LS. METHODS Women with nonserous and/or nonmucinous ovarian cancer were recruited prospectively from 3 cancer centers in Ontario, Canada. All underwent germline testing for LS and completed a family history assessment. Tumors were assessed using MMR IHC and MSI. The sensitivity, specificity, and positive and negative predictive values of screening strategies were compared with the gold standard of a germline result. RESULTS Of 215 women, germline data were available for 189 (88%); 13 women (7%) had pathogenic germline variants with 7 women with mutS homolog 6 (MSH6); 3 women with mutL homolog 1 (MLH1); 2 women with PMS1 homolog 2, mismatch repair system component (PMS2); and 1 woman with mutS homolog 2 (MSH2). A total of 28 women had MMR-deficient tumors (13%); of these, 11 had pathogenic variants (39%). Sequential IHC (with MLH1 promoter methylation analysis on MLH1-deficient tumors) followed by MSI for nonmethylated and/or MMR-intact patients was the most sensitive (92.3%; 95% confidence interval, 64%-99.8%) and specific (97.7%; 95% confidence interval, 94.2%-99.4%) approach, missing 1 case of LS. IHC with MLH1 promoter methylation analysis missed 2 patients of LS. Family history was found to have the lowest sensitivity at 55%. CONCLUSIONS Sequential IHC (with MLH1 promoter methylation analysis) followed by MSI was found to be most sensitive. However, IHC with MLH1 promoter methylation analysis also performed well and is likely more cost-effective and efficient in the clinical setting. The pretest probability of LS is high in patients with MMR deficiency and warrants universal screening for LS.
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Affiliation(s)
- Soyoun Rachel Kim
- Division of Gynecologic OncologyPrincess Margaret Cancer Centre, University Health NetworkSinai Health SystemsTorontoOntarioCanada
- Department of Obstetrics and GynaecologyUniversity of TorontoTorontoOntarioCanada
| | - Alicia Tone
- Division of Gynecologic OncologyPrincess Margaret Cancer Centre, University Health NetworkSinai Health SystemsTorontoOntarioCanada
| | - Raymond H. Kim
- Fred A. Litwin Family Centre for Genetic MedicineUniversity Health NetworkTorontoOntarioCanada
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer RegistryMount Sinai HospitalTorontoOntarioCanada
- Division of Medical Oncology and HematologyPrincess Margaret Cancer Centre, University Health NetworkSinai Health SystemsTorontoOntarioCanada
| | - Matthew Cesari
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Blaise A. Clarke
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Lua Eiriksson
- Division of Gynecologic OncologyDepartment of Obstetrics and GynecologyJuravinski Cancer Centre, McMaster UniversityHamiltonOntarioCanada
| | - Tae Hart
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer RegistryMount Sinai HospitalTorontoOntarioCanada
- Department of PsychologyRyerson UniversityTorontoOntarioCanada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer RegistryMount Sinai HospitalTorontoOntarioCanada
| | - Spring Holter
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer RegistryMount Sinai HospitalTorontoOntarioCanada
| | - Alice Lytwyn
- Division of Anatomical PathologyDepartment of Pathology and Molecular MedicineMcMaster UniversityHamiltonOntarioCanada
| | - Manjula Maganti
- Department of BiostatisticsPrincess Margaret Cancer Centre, University Health NetworkUniversity of TorontoTorontoOntarioCanada
| | - Leslie Oldfield
- Department of Medical BiophysicsUniversity of TorontoTorontoOntarioCanada
| | - Steven Gallinger
- Division of General SurgeryPrincess Margaret Cancer Centre, University Health NetworkSinai Health SystemsTorontoOntarioCanada
| | - Marcus Q. Bernardini
- Division of Gynecologic OncologyPrincess Margaret Cancer Centre, University Health NetworkSinai Health SystemsTorontoOntarioCanada
- Department of Obstetrics and GynaecologyUniversity of TorontoTorontoOntarioCanada
| | - Amit M. Oza
- Division of Medical Oncology and HematologyPrincess Margaret Cancer Centre, University Health NetworkSinai Health SystemsTorontoOntarioCanada
| | - Bojana Djordjevic
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Jordan Lerner‐Ellis
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Emily Van de Laar
- Division of Gynecologic OncologyPrincess Margaret Cancer Centre, University Health NetworkSinai Health SystemsTorontoOntarioCanada
| | - Danielle Vicus
- Department of Obstetrics and GynaecologyUniversity of TorontoTorontoOntarioCanada
- Division of Gynecologic OncologyDepartment of Obstetrics and GynecologySunnybrook Health Sciences Centre, University of TorontoTorontoOntarioCanada
| | - Trevor J. Pugh
- Department of Medical BiophysicsUniversity of TorontoTorontoOntarioCanada
- Ontario Institute for Cancer ResearchUniversity Health NetworkTorontoOntarioCanada
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoOntarioCanada
| | - Aaron Pollett
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
- Pathology and Laboratory MedicineMount Sinai HospitalTorontoOntarioCanada
| | - Sarah E. Ferguson
- Division of Gynecologic OncologyPrincess Margaret Cancer Centre, University Health NetworkSinai Health SystemsTorontoOntarioCanada
- Department of Obstetrics and GynaecologyUniversity of TorontoTorontoOntarioCanada
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer RegistryMount Sinai HospitalTorontoOntarioCanada
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Lang GT, Shi JX, Huang L, Cao AY, Zhang CH, Song CG, Zhuang ZG, Hu X, Huang W, Shao ZM. Multiple cancer susceptible genes sequencing in BRCA-negative breast cancer with high hereditary risk. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1417. [PMID: 33313162 PMCID: PMC7723566 DOI: 10.21037/atm-20-2999] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Hereditary factors contributed to breast cancer susceptibility. Low BRCA mutation prevalence was demonstrated in previous BRCA mutation screening in Chinese breast cancer patients. Multiple-gene sequencing may assist in discovering detrimental germline mutation in BRCA negative breast cancers. Methods A total of 384 Chinese subjects with any two of high-risk factors were recruited and screened by next-generation sequencing (NGS) for 30 cancer susceptible genes. Variants with a truncating, initiation codon or splice donor/acceptor effect, or with pathogenicity demonstrated in published literature were classified into pathogenic/likely-pathogenic mutations. Results In total, we acquired 39 (10.2%) patients with pathogenic/likely-pathogenic germline mutations, including one carrying two distinct mutations. Major mutant non-BRCA genes were MUTYH (n=11, 2.9%), PTCH1 (n=7, 1.8%), RET (n=6, 1.6%) and PALB2 (n=5, 1.3%). Other mutant genes included TP53 (n=3, 0.8%), RAD51D (n=2, 0.5%), CHEK2 (n=1, 0.3%), BRIP1 (n=1, 0.3%), CDH1 (n=1, 0.3%), MRE11 (n=1, 0.3%), RAD50 (n=1, 0.3%) and PALLD (n=1, 0.3%). A splicing germline mutation, MUTYH c.934-2A>G, was a hotspot (9/384, 2.3%) in Chinese breast cancer. Conclusions Among BRCA-negative breast cancer patients with high hereditary risk in China, 10.2% carried mutations in cancer associated susceptibility genes. MUTYH and PTCH1 had relatively high mutation rates (2.9% and 1.8%). Multigene testing contributes to understand genetic background of BRCA-negative breast cancer patients with high hereditary risk.
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Affiliation(s)
- Guan-Tian Lang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jin-Xiu Shi
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Industrial Technology Institute (SITI), Shanghai, China
| | - Liang Huang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - A-Yong Cao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chen-Hui Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Industrial Technology Institute (SITI), Shanghai, China
| | - Chuan-Gui Song
- Department of Breast Surgery, Affiliated Union Hospital, Fujian Medical University, Fuzhou, China
| | - Zhi-Gang Zhuang
- Department of Breast Surgery, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xin Hu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Huang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Industrial Technology Institute (SITI), Shanghai, China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Cavaillé M, Uhrhammer N, Privat M, Ponelle-Chachuat F, Gay-Bellile M, Lepage M, Viala S, Bidet Y, Bignon YJ. Feedback of extended panel sequencing in 1530 patients referred for suspicion of hereditary predisposition to adult cancers. Clin Genet 2020; 99:166-175. [PMID: 33047316 PMCID: PMC7821123 DOI: 10.1111/cge.13864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/09/2020] [Accepted: 10/10/2020] [Indexed: 12/12/2022]
Abstract
High‐throughput sequencing analysis represented both a medical diagnosis and technological revolution. Gene panel analysis is now routinely performed in the exploration of hereditary predisposition to cancer, which is becoming increasingly heterogeneous, both clinically and molecularly. We present 1530 patients with suspicion of hereditary predisposition to cancer, for which two types of analyses were performed: a) oriented according to the clinical presentation (n = 417), or b) extended to genes involved in hereditary predisposition to adult cancer (n = 1113). Extended panel analysis had a higher detection rate compared to oriented analysis in hereditary predisposition to breast / ovarian cancer (P < .001) and in digestive cancers (P < .094) (respectively 15% vs 5% and 19.3%, vs 12.5%). This higher detection is explained by the inclusion of moderate penetrance genes, as well as the identification of incident mutations and double mutations. Our study underscores the utility of proposing extended gene panel analysis to patients with suspicion of hereditary predisposition to adult cancer.
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Affiliation(s)
- Mathias Cavaillé
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
| | - Nancy Uhrhammer
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
| | - Maud Privat
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
| | - Flora Ponelle-Chachuat
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
| | - Mathilde Gay-Bellile
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
| | - Mathis Lepage
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Sandrine Viala
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
| | - Yannick Bidet
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
| | - Yves-Jean Bignon
- Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France.,Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies, Clermont Ferrand, France
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Sobocińska J, Kolenda T, Teresiak A, Badziąg-Leśniak N, Kopczyńska M, Guglas K, Przybyła A, Filas V, Bogajewska-Ryłko E, Lamperska K, Mackiewicz A. Diagnostics of Mutations in MMR/ EPCAM Genes and Their Role in the Treatment and Care of Patients with Lynch Syndrome. Diagnostics (Basel) 2020; 10:diagnostics10100786. [PMID: 33027913 PMCID: PMC7600989 DOI: 10.3390/diagnostics10100786] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 02/07/2023] Open
Abstract
Lynch syndrome (LS), also known as hereditary nonpolyposis colorectal cancer (HNPCC), is a disorder caused by an autosomal dominant heterozygous germline mutation in one of the DNA mismatch repair (MMR) genes. Individuals with LS are at an increased risk of developing colorectal and extracolonic cancers, such as endometrial, small bowel, or ovarian. In this review, the mutations involved with LS and their diagnostic methods are described and compared, as are their current uses in clinical decision making. Nowadays, LS diagnosis is based on a review of family medical history, and when necessary, microsatellite instability (MSI) or/and immunohistochemistry (IHC) analyses should be performed. In the case of a lack of MMR protein expression (dMMR) or MSI-H (MSI-High) detection in tumor tissue, molecular genetic testing can be undertaken. More and more genetic testing for LS is based mainly on next-generation sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA), which provide better and quicker information about the molecular profile of patients as well as individuals at risk. Testing based on these two methods should be the standard and commonly used. The identification of individuals with mutations provides opportunities for the detection of cancer at an early stage as well as the introduction of proper, more effective treatment, which will result in increased patient survival and reduced costs of medical care.
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Affiliation(s)
- Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (T.K.); (M.K.); (A.P.); (A.M.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland
- Correspondence:
| | - Tomasz Kolenda
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (T.K.); (M.K.); (A.P.); (A.M.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland; (A.T.); (K.G.); (K.L.)
| | - Natalia Badziąg-Leśniak
- Oncological Genetics Clinic, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland;
| | - Magda Kopczyńska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (T.K.); (M.K.); (A.P.); (A.M.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland; (A.T.); (K.G.); (K.L.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Anna Przybyła
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (T.K.); (M.K.); (A.P.); (A.M.)
| | - Violetta Filas
- Department of Tumor Pathology and Prophylaxis, Poznan University of Medical Sciences, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland; (V.F.); (E.B.-R.)
- Department of Cancer Pathology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland
| | - Elżbieta Bogajewska-Ryłko
- Department of Tumor Pathology and Prophylaxis, Poznan University of Medical Sciences, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland; (V.F.); (E.B.-R.)
- Department of Cancer Pathology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland; (A.T.); (K.G.); (K.L.)
| | - Andrzej Mackiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (T.K.); (M.K.); (A.P.); (A.M.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland
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Schupmann W, Jamal L, Berkman BE. Re-examining the Ethics of Genetic Counselling in the Genomic Era. JOURNAL OF BIOETHICAL INQUIRY 2020; 17:325-335. [PMID: 32557217 PMCID: PMC10084396 DOI: 10.1007/s11673-020-09983-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 05/17/2020] [Indexed: 05/06/2023]
Abstract
Respect for patient autonomy has served as the dominant ethical principle of genetic counselling, but as we move into a genomic era, it is time to actively re-examine the role that this principle plays in genetic counselling practice. In this paper, we argue that the field of genetic counselling should move away from its emphasis on patient autonomy and toward the incorporation of a more balanced set of principles that allows counsellors to offer clear guidance about how best to obtain or use genetic information. We begin with a brief history of how respect for patient autonomy gained such emphasis in the field and how it has taken on various manifestations over time, including the problematic concept of nondirectiveness. After acknowledging the field's preliminary move away from nondirectiveness, we turn to a series of arguments about why the continued dominance of patient autonomy has become untenable given the arrival of the genomic era. To conclude, we describe how a more complete set of bioethical principles can be adapted and used by genetic counsellors to strengthen their practice without undermining patient autonomy.
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Affiliation(s)
- Will Schupmann
- Department of Bioethics, Clinical Center, National Institutes of Health, 10 Center Dr., Bldg. 10/Room 1C118, Bethesda, MD, 20892, USA.
| | - Leila Jamal
- Department of Bioethics, Clinical Center, National Institutes of Health; National Institute of Allergy and Infectious Diseases, NIH, 10 Center Dr., Bldg. 10/Room 1C118, Bethesda, MD, 20892, USA
| | - Benjamin E Berkman
- Department of Bioethics, Clinical Center, National Institutes of Health; Bioethics Core, National Human Genome Research Institute, NIH, 10 Center Dr., Bldg. 10/Room 1C118, Bethesda, MD, 20892, USA
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43
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Sun BL. Current Microsatellite Instability Testing in Management of Colorectal Cancer. Clin Colorectal Cancer 2020; 20:e12-e20. [PMID: 32888812 DOI: 10.1016/j.clcc.2020.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. In the past decade, mismatch repair deficiency (dMMR), manifested as microsatellite instability-high (MSI-H), has been recognized as a distinct mechanism promoting tumorigenesis in 15% of CRCs including 3% Lynch syndrome and 12% sporadic CRCs. As the molecular classifications of CRCs are continuously evolving, MSI-H CRCs appear to be the most homogeneous CRCs with distinct molecular, morphologic, and clinical features. MSI-H CRCs have dMMR causing MSI-H and genetic hypermutation but with diploid chromosomes. Morphologically, MSI-H CRCs appear as poorly differentiated or mucinous adenocarcinoma with characteristic lymphocytic infiltration. Most importantly, MSI-H CRCs have better stage-adjusted survival, do not respond well to standard 5-fluorouracil-based adjuvant chemotherapy, but do respond to immunotherapy. The United States Food and Drug Administration granted accelerated approval to immune checkpoint inhibitors, anti-programmed cell death protein-1 antibodies pembrolizumab and nivolumab, and the combination of nivolumab with anti-CTLA4 antibody ipilimumab for the second-line treatment of patients with stage IV MSI-H CRCs in 2017. There are still ongoing phase III clinical trials evaluating pembrolizumab and anti-programmed death-ligand 1 antibody atezolizumab as the first-line treatment in stage IV MSI-H CRCs and a phase I study on the combination of nivolumab and ipilimumab in patients with early stage CRC. These ongoing clinical studies on immunotherapy may lead to practice-changing results in the management of MSI-H CRCs. The National Comprehensive Cancer Network 2018 guidelines recommended MSI to be tested in all newly diagnosed CRCs. The MSI test will become increasingly vital in guiding adjuvant chemotherapy and immunotherapy in the management of CRCs.
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Affiliation(s)
- Belinda L Sun
- Department of Pathology, Banner-University Medical Center, University of Arizona, Tucson, AZ.
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44
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Bademci R, Bollo J, Ramón Y Cajal T, Martínez MC, Hernández MP, Targarona EM. Presentation and Follow-up of Familial Adenomatous Polyposis: Differences Between APC and MUTYH Mutations. Cir Esp 2020; 98:465-471. [PMID: 32505560 DOI: 10.1016/j.ciresp.2020.04.033] [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: 01/24/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 01/15/2023]
Abstract
BACKGROUND Familial adenomatous polyposis is described as one of the common two types of genetic disorders: APC and MUTYH gene associated polyposis syndrome and the clinical differences between the two can sometimes be unclear. MATERIALS AND METHODS A retrospective analysis and comparison was made of clinical, surgical, and histological criteria, mutation types and the long-term results of patients who underwent genetic analysis which resulted in the diagnosis of Familial Adenomatous Polyposis between 1984 and 2018. RESULTS Of the total 71 patients included in the study, 14 were identified with the MUTYH gene, and 57 with the APC mutation. In patients with the APC mutation, 63% had duodenal adenoma, 61% gastric polyp and 54% had desmoid tumor. Of the patients with the MUTYH mutation, 21% had duodenal adenoma and 21% were diagnosed with gastric polyps. In 21% of the patients with APC mutation, the polyp count was <100, and 64% of those with the MUTYH mutation had >100 polyps in the colon No statistical difference was determined between the groups in respect of the proportion of patients with >100 polyps. CONCLUSION The pre-operative genetic testing of patients with polyposis coli will be useful in determining the future clinical outcome and helpful in guiding an informed decision as to whether to apply surgical treatment. It is useful to determine the colonic and extra-colonic involvement of genetic mutation diseases in patients with Familial adenomatous polyposis.
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Affiliation(s)
- Refik Bademci
- Servicio de Cirugía General, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, España
| | - Jesús Bollo
- Servicio de Cirugía General, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, España.
| | - Teresa Ramón Y Cajal
- Servicio de Oncología Médica, Hospital de la Santa Creu i Sant Pau, Barcelona, España
| | - M Carmen Martínez
- Servicio de Cirugía General, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, España
| | - María Pilar Hernández
- Servicio de Cirugía General, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, España
| | - Eduard Maria Targarona
- Servicio de Cirugía General, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, España
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Bai H, Wang R, Cheng W, Shen Y, Li H, Xia W, Ding Z, Zhang Y. Evaluation of Concordance Between Deficient Mismatch Repair and Microsatellite Instability Testing and Their Association with Clinicopathological Features in Colorectal Cancer. Cancer Manag Res 2020; 12:2863-2873. [PMID: 32425600 PMCID: PMC7187941 DOI: 10.2147/cmar.s248069] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/08/2020] [Indexed: 12/20/2022] Open
Abstract
Background Microsatellite instability (MSI) is one of the most important molecular characteristics of colorectal cancer (CRC), which mainly results from defective DNA mismatch repair (MMR). This study was performed to investigate the concordance between deficient MMR and MSI testing, and to evaluate the association of these two results with clinicopathological characteristics in Chinese CRC patients. Methods A total of 738 CRC patients were included. Tumor tissues and paired peripheral blood specimens were obtained. Screening for MMR was investigated using immunohistochemical (IHC) technique, and multiple polymerase chain reaction-capillary electrophoresis (PCR-CE) method was performed to detect the MSI status. All clinicopathological data, immunohistochemistry and microsatellite instability analyses were then statistically analyzed. Results Of the 738 (17.75%) CRC patients, 131 expressed as deficient mismatch repair (dMMR) status, and postmeiotic segregation increased 2 (PMS2) deficiency was the most frequent deficiency among these four MMR proteins. MSI-high (MSI-H) status occurred in 74 of the 738 (10.03%) CRC patients, 55 of whom showed instability at all six mononucleotides repeat markers. dMMR was significantly associated with MSI-H and moderate concordance was observed between IHC and PCR-CE in evaluating deficient MMR/MSI through Kappa test. Statistically, dMMR was significantly associated with younger age, right-sided colon and poor differentiation. MSI-H was associated with younger age, right-sided colon, poor differentiation, mucinous type and tumor, node, metastasis (TNM) stage II. Conclusion A moderate concordance between deficient MMR and MSI testing indicates that both IHC and PCR-CE methods should be routinely tested to provide reliable data for clinical treatment decisions.
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Affiliation(s)
- Huili Bai
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Rong Wang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.,Department of Laboratory Medicine, Guangyuan Central Hospital, Guangyuan, Sichuan, People's Republic of China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Yifan Shen
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Haijun Li
- Department of Laboratory Medicine, Guangyuan Central Hospital, Guangyuan, Sichuan, People's Republic of China
| | - Wei Xia
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Zhenglin Ding
- Department of Laboratory Medicine, The People's Hospital of Nanchuan, Chongqing, People's Republic of China
| | - Yuhong Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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Points to consider for reporting of germline variation in patients undergoing tumor testing: a statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2020; 22:1142-1148. [PMID: 32321997 DOI: 10.1038/s41436-020-0783-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 02/08/2023] Open
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47
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Zarrinpar A, Kim UB, Boominathan V. Phenotypic Response and Personalized Medicine in Liver Cancer and Transplantation: Approaches to Complex Systems. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.201900167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ali Zarrinpar
- Department of Surgery, College of MedicineUniversity of Florida Gainesville FL 32610 USA
- Department of Biochemistry and Molecular Biology, College of MedicineUniversity of Florida Gainesville FL 32610 USA
- Department of Bioengineering, Herbert Wertheim College of EngineeringUniversity of Florida Gainesville FL 32610 USA
| | - Un Bi Kim
- Department of Surgery, College of MedicineUniversity of Florida Gainesville FL 32610 USA
| | - Vijay Boominathan
- Department of Surgery, College of MedicineUniversity of Florida Gainesville FL 32610 USA
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Li L, Feng Q, Wang X. PreMSIm: An R package for predicting microsatellite instability from the expression profiling of a gene panel in cancer. Comput Struct Biotechnol J 2020; 18:668-675. [PMID: 32257050 PMCID: PMC7113609 DOI: 10.1016/j.csbj.2020.03.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/06/2020] [Accepted: 03/08/2020] [Indexed: 01/10/2023] Open
Abstract
Microsatellite instability (MSI) is a genomic property of the cancers with defective DNA mismatch repair and is a useful marker for cancer diagnosis and treatment in diverse cancer types. In particular, MSI has been associated with the active immune checkpoint blockade therapy response in cancer. Most of computational methods for predicting MSI are based on DNA sequencing data and a few are based on mRNA expression data. Using the RNA-Seq pan-cancer datasets for three cancer cohorts (colon, gastric, and endometrial cancers) from The Cancer Genome Atlas (TCGA) program, we developed an algorithm (PreMSIm) for predicting MSI from the expression profiling of a 15-gene panel in cancer. We demonstrated that PreMSIm had high prediction performance in predicting MSI in most cases using both RNA-Seq and microarray gene expression datasets. Moreover, PreMSIm displayed superior or comparable performance versus other DNA or mRNA-based methods. We conclude that PreMSIm has the potential to provide an alternative approach for identifying MSI in cancer.
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Key Words
- ACC, adrenocortical carcinoma
- AUC, area under the curve
- Algorithm
- BLCA, bladder urothelial carcinoma
- BRCA, breast invasive carcinoma
- CESC, cervical squamous cell carcinoma and endocervical adenocarcinoma
- CHOL, cholangiocarcinoma
- COAD, colon adenocarcinoma
- CV, cross validation
- Cancer
- Classification
- DLBC, lymphoid neoplasm diffuse large B-cell lymphoma
- ESCA, esophageal carcinoma
- GBM, glioblastoma multiforme
- GEO, Gene Expression Omnibus
- GO, gene ontology
- Gene expression profiling
- HNSC, head and neck squamous cell carcinoma
- KICH, kidney chromophobe
- KIRC, kidney renal clear cell carcinoma
- KIRP, kidney renal papillary cell carcinoma
- LAML, acute myeloid leukemia
- LGG, brain lower grade glioma
- LIHC, liver hepatocellular carcinoma
- LUAD, lung adenocarcinoma
- LUSC, lung squamous cell carcinoma
- MESO, mesothelioma
- MSI, microsatellite instability
- MSS, microsatellite stability
- Machine learning
- Microsatellite instability
- OV, ovarian serous cystadenocarcinoma
- PAAD, pancreatic adenocarcinoma
- PCPG, pheochromocytoma and paraganglioma
- PPI, protein-protein interaction
- PRAD, prostate adenocarcinoma
- READ, rectum adenocarcinoma
- RF, random forest
- ROC, receiver operating characteristic
- SARC, sarcoma
- SKCM, skin cutaneous melanoma
- STAD, stomach adenocarcinoma
- SVM, support vector machine
- TCGA, The Cancer Genome Atlas
- TGCT, testicular germ cell tumors
- THCA, thyroid carcinoma
- THYM, thymoma
- UCEC, uterine corpus endometrial carcinoma
- UCS, uterine carcinosarcoma
- UVM, uveal melanoma
- XGBoost, extreme gradient boosting
- k-NN, k-nearest neighbor
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Affiliation(s)
- Lin Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Qiushi Feng
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
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Hujová P, Souček P, Grodecká L, Grombiříková H, Ravčuková B, Kuklínek P, Hakl R, Litzman J, Freiberger T. Deep Intronic Mutation in SERPING1 Caused Hereditary Angioedema Through Pseudoexon Activation. J Clin Immunol 2020; 40:435-446. [PMID: 31982983 DOI: 10.1007/s10875-020-00753-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/17/2020] [Indexed: 01/26/2023]
Abstract
PURPOSE Hereditary angioedema (HAE) is a rare autosomal dominant life-threatening disease characterized by low levels of C1 inhibitor (type I HAE) or normal levels of ineffective C1 inhibitor (type II HAE), typically occurring as a consequence of a SERPING1 mutation. In some cases, a causal mutation remains undetected after using a standard molecular genetic analysis. RESULTS Here we show a long methodological way to the final discovery of c.1029 + 384A > G, a novel deep intronic mutation in intron 6 which is responsible for HAE type I in a large family and has not been identified by a conventional diagnostic approach. This mutation results in de novo donor splice site creation and subsequent pseudoexon inclusion, the mechanism firstly described to occur in SERPING1 in this study. We additionally discovered that the proximal part of intron 6 is a region potentially prone to pseudoexon-activating mutations, since natural alternative exons and additional cryptic sites occur therein. Indeed, we confirmed the existence of at least two different alternative exons in this region not described previously. CONCLUSIONS In conclusion, our results suggest that detecting aberrant transcripts, which are often low abundant because of nonsense-mediated decay, requires a modified methodological approach. We suggest SERPING1 intron 6 sequencing and/or tailored mRNA analysis to be routinely used in HAE patients with no mutation identified in the coding sequence.
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Affiliation(s)
- Pavla Hujová
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic.,Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Přemysl Souček
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lucie Grodecká
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Hana Grombiříková
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic.,Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Barbora Ravčuková
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Pavel Kuklínek
- Department of Allergology and Clinical Immunology, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Roman Hakl
- Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Allergology and Clinical Immunology, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Jiří Litzman
- Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Allergology and Clinical Immunology, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic. .,Faculty of Medicine, Masaryk University, Brno, Czech Republic. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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50
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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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