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Bouras A, Fabre A, Zattara H, Handallou S, Desseigne F, Kientz C, Prieur F, Peysselon M, Legrand C, Calavas L, Saurin JC, Wang Q. Hereditary Colorectal Cancer and Polyposis Syndromes Caused by Variants in Uncommon Genes. Genes Chromosomes Cancer 2024; 63:e23263. [PMID: 39120161 DOI: 10.1002/gcc.23263] [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: 05/19/2024] [Revised: 07/18/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
A substantial number of hereditary colorectal cancer (CRC) and colonic polyposis cannot be explained by alteration in confirmed predisposition genes, such as mismatch repair (MMR) genes, APC and MUTYH. Recently, a certain number of potential predisposition genes have been suggested, involving each a small number of cases reported so far. Here, we describe the detection of rare variants in the NTLH1, AXIN2, RNF43, BUB1, and TP53 genes in nine unrelated patients who were suspected for inherited CRC and/or colonic polyposis. Seven of them were classified as pathogenic or likely pathogenic variants (PV/LPV). Clinical manifestations of carriers were largely consistent with reported cases with, nevertheless, distinct characteristics. PV/LPV in these uncommon gene can be responsible for up to 2.7% of inherited CRC or colonic polyposis syndromes. Our findings provide supporting evidence for the role of these genes in cancer predisposition, and contribute to the determination of related cancer spectrum and cancer risk for carriers, allowing for the establishment of appropriate screening strategy and genetic counseling in affected families.
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Affiliation(s)
- Ahmed Bouras
- Laboratory of Constitutional Genetics for Frequent Cancer HCL-CLB, Centre Léon Bérard, Lyon, France
- Inserm U1052, Lyon Cancer Research Center, Lyon, France
| | - Aurélie Fabre
- Department of Genetics, Hôpital d'Enfants de La Timone, AP-HM, Marseille, France
| | - Hélène Zattara
- Department of Genetics, Hôpital d'Enfants de La Timone, AP-HM, Marseille, France
| | - Sandrine Handallou
- Cancer Genetics Unit, Department of Public Health, Centre Léon Bérard, Lyon, France
| | | | - Caroline Kientz
- Department of Clinical, Chromosomal and Molecular Genetics, Hôpital Nord, CHU Saint Etienne, Saint Etienne, France
| | - Fabienne Prieur
- Department of Clinical, Chromosomal and Molecular Genetics, Hôpital Nord, CHU Saint Etienne, Saint Etienne, France
| | - Magalie Peysselon
- Genetic Service, Department of Genetics and Procreation, CHU Grenoble Alpes, Grenoble, France
| | - Clémentine Legrand
- Genetic Service, Department of Genetics and Procreation, CHU Grenoble Alpes, Grenoble, France
| | - Laura Calavas
- Department of Gastroenterology and Endoscopy, Edouard Herriot Hospital, Lyon, France
| | | | - Qing Wang
- Laboratory of Constitutional Genetics for Frequent Cancer HCL-CLB, Centre Léon Bérard, Lyon, France
- Inserm U1052, Lyon Cancer Research Center, Lyon, France
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Carballal S, Balaguer F, Bujanda L, Capellá G, González Santiago S, Jover R, Moreira L, Pineda M, Ruiz-Ponte C, Sánchez Heras AB, Serrano Blanch R, Soto JL, Vidal Tocino R, Cubiella J. Use of multi-gene panels in patients at high risk of hereditary digestive cancer: position statement of AEG, SEOM, AEGH and IMPaCT-GENÓMICA consortium. GASTROENTEROLOGIA Y HEPATOLOGIA 2024; 47:293-318. [PMID: 37315767 DOI: 10.1016/j.gastrohep.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/04/2023] [Accepted: 06/07/2023] [Indexed: 06/16/2023]
Abstract
This position statement, sponsored by the Asociación Española de Gastroenterología, the Sociedad Española de Oncología Médica, the Asociación Española de Genética Humana and the IMPaCT-Genómica Consortium aims to establish recommendations for use of multi-gene panel testing in patients at high risk of hereditary gastrointestinal and pancreatic cancer. To rate the quality of the evidence and the levels of recommendation, we used the methodology based on the GRADE system (Grading of Recommendations Assessment, Development and Evaluation). We reached a consensus among experts using a Delphi method. The document includes recommendations on clinical scenarios where multi-gene panel testing is recommended in colorectal cancer, polyposis syndromes, gastric and pancreatic cancer, as well as the genes to be considered in each clinical scenario. Recommendations on the evaluation of mosaicisms, counseling strategies in the absence of an index subject and, finally, constitutional analysis after identification of pathogenic tumor variants are also made.
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Affiliation(s)
- Sabela Carballal
- Servicio de Gastroenterología, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, España.
| | - Francesc Balaguer
- Servicio de Gastroenterología, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, España
| | - Luis Bujanda
- Servicio de Aparato Digestivo, Hospital Universitario Donostia, Instituto Biodonostia. Universidad del País Vasco (UPV/EHU), CIBEREHD, San Sebastián, Guipúzcoa, España
| | - Gabriel Capellá
- Programa de Cáncer Hereditario, Instituto Catalán de Oncología, Programa ONCOBELL, IDIBELL, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), L'Hospitalet de Llobregat, Barcelona, España
| | | | - Rodrigo Jover
- Servicio de Medicina Digestiva, Hospital General Universitario Dr. Balmis, Instituto de Investigación Sanitaria de Alicante (ISABIAL), Departamento de Medicina Clínica, Universidad Miguel Hernández, Alicante, España
| | - Leticia Moreira
- Servicio de Gastroenterología, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, España
| | - Marta Pineda
- Programa de Cáncer Hereditario, Instituto Catalán de Oncología, Programa ONCOBELL, IDIBELL, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), L'Hospitalet de Llobregat, Barcelona, España
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica (SERGAS), Instituto de Investigación Sanitaria de Santiago (IDIS), Grupo de Medicina Xenomica (USC), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERer), Santiago de Compostela, La Coruña, España
| | - Ana Beatriz Sánchez Heras
- Unidad de Consejo Genético en Cáncer, Servicio de Oncología Médica, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Elche, Alicante, España
| | - Raquel Serrano Blanch
- Unidad de Consejo Genético en Cáncer, Unidad de Gestión Clínica de Oncología Médica, H.U. Reina Sofía de Córdoba. Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), CIBERONC, Universidad de Córdoba (UCO), Córdoba, España
| | - José Luis Soto
- Unidad de Genética Molecular, Hospital General Universitario de Elche, FISABIO, Elche, Alicante, España
| | - Rosario Vidal Tocino
- Servicio de Oncología Médica, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, España
| | - Joaquín Cubiella
- Servicio de Aparato Digestivo, Hospital Universitario de Ourense, Grupo de Investigación en Oncología Digestiva-Ourense (GIODO), CIBEREHD, Ourense, España.
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3
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Fortuno C, Feng BJ, Carroll C, Innella G, Kohlmann W, Lázaro C, Brunet J, Feliubadaló L, Iglesias S, Menéndez M, Teulé A, Ballinger ML, Thomas DM, Campbell A, Field M, Harris M, Kirk J, Pachter N, Poplawski N, Susman R, Tucker K, Wallis M, Williams R, Cops E, Goldgar D, James PA, Spurdle AB. Cancer Risks Associated With TP53 Pathogenic Variants: Maximum Likelihood Analysis of Extended Pedigrees for Diagnosis of First Cancers Beyond the Li-Fraumeni Syndrome Spectrum. JCO Precis Oncol 2024; 8:e2300453. [PMID: 38412388 PMCID: PMC10914239 DOI: 10.1200/po.23.00453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/23/2023] [Accepted: 12/21/2023] [Indexed: 02/29/2024] Open
Abstract
PURPOSE Establishing accurate age-related penetrance figures for the broad range of cancer types that occur in individuals harboring a pathogenic germline variant in the TP53 gene is essential to determine the most effective clinical management strategies. These figures also permit optimal use of cosegregation data for classification of TP53 variants of unknown significance. Penetrance estimation can easily be affected by bias from ascertainment criteria, an issue not commonly addressed by previous studies. MATERIALS AND METHODS We performed a maximum likelihood penetrance estimation using full pedigree data from a multicenter study of 146 TP53-positive families, incorporating adjustment for the effect of ascertainment and population-specific background cancer risks. The analysis included pedigrees from Australia, Spain, and United States, with phenotypic information for 4,028 individuals. RESULTS Core Li-Fraumeni syndrome (LFS) cancers (breast cancer, adrenocortical carcinoma, brain cancer, osteosarcoma, and soft tissue sarcoma) had the highest hazard ratios of all cancers analyzed in this study. The analysis also detected a significantly increased lifetime risk for a range of cancers not previously formally associated with TP53 pathogenic variant status, including colorectal, gastric, lung, pancreatic, and ovarian cancers. The cumulative risk of any cancer type by age 50 years was 92.4% (95% CI, 82.2 to 98.3) for females and 59.7% (95% CI, 39.9 to 81.3) for males. Females had a 63.3% (95% CI, 35.6 to 90.1) cumulative risk of developing breast cancer by age 50 years. CONCLUSION The results from maximum likelihood analysis confirm the known high lifetime risk for the core LFS-associated cancer types providing new risk estimates and indicate significantly increased lifetime risks for several additional cancer types. Accurate cancer risk estimates will help refine clinical recommendations for TP53 pathogenic variant carriers and improve TP53 variant classification.
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Affiliation(s)
- Cristina Fortuno
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Bing-Jian Feng
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Courtney Carroll
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Giovanni Innella
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Wendy Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
- Hereditary Cancer Program, ONCOBELL, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
- Hereditary Cancer Program, ONCOBELL, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
- Precision Oncology in Girona, IDIBGI, Girona, Spain
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
- Hereditary Cancer Program, ONCOBELL, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Silvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Mireia Menéndez
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Alex Teulé
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
- Hereditary Cancer Program, ONCOBELL, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Mandy L. Ballinger
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, New South Wales, Australia
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - David M. Thomas
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Centre for Molecular Oncology, Faculty of Medicine, University of New South Wales, New South Wales, Australia
| | - Ainsley Campbell
- Department of Clinical Genetics, Austin Health, Melbourne, Victoria, Australia
| | - Mike Field
- Familial Cancer Service, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Marion Harris
- Monash Health Familial Cancer Service, Melbourne, Victoria, Australia
| | - Judy Kirk
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Westmead, New South Wales, Australia
| | - Nicholas Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia, Australia
| | - Nicola Poplawski
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Rachel Susman
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Kathy Tucker
- Hereditary Cancer Clinic, Prince of Wales Hospital, Randwick, New South Wales, Australia
- Prince of Wales Clinical School, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Royal Hobart Hospital, Hobart, Tasmania, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Rachel Williams
- Prince of Wales Clinical School, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- Prince of Wales Hereditary Cancer Centre, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Elisa Cops
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - David Goldgar
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - kConFab Investigators
- kConFab, Research Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Paul A. James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Amanda B. Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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4
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Butz H, Bozsik A, Grolmusz V, Szőcs E, Papp J, Patócs A. Challenging interpretation of germline TP53 variants based on the experience of a national comprehensive cancer centre. Sci Rep 2023; 13:14259. [PMID: 37653074 PMCID: PMC10471726 DOI: 10.1038/s41598-023-41481-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 08/27/2023] [Indexed: 09/02/2023] Open
Abstract
TP53 variant interpretation is still challenging, especially in patients with attenuated Li-Fraumeni syndrome (LFS). We investigated the prevalence of pathogenic/likely pathogenic (P/LP) variants and LFS disease in the Hungarian population of cancer patients. By testing 893 patients with multiplex or familial cancer, we identified and functionally characterized novel splice variants of TP53 helping accurate variant classification. The differences among various semi-automated interpretation platforms without manual curation highlight the importance of focused interpretation as the automatic classification systems do not apply the TP53-specific criteria. The predicted frequency of the TP53 P/LP variants in Hungary is 0.3 per million which most likely underestimates the real prevalence. The higher detection rate of disease-causing variants in patients with attenuated LFS phenotype compared to the control population (OR 12.5; p < 0.0001) may raise the potential benefit of the TP53 genetic testing as part of the hereditary cancer panels of patients with multiple or familial cancer even when they do not meet Chompret criteria. Tumours developed at an earlier age in phenotypic LFS patients compared to the attenuated LFS patients which complicates genetic counselling as currently there are no different recommendations in surveillance protocols for LFS, phenotypic LFS, and attenuated LFS patients.
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Affiliation(s)
- Henriett Butz
- Department of Molecular Genetics and the National Tumour Biology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, Budapest, Hungary.
- Department of Oncology Biobank, National Institute of Oncology, Comprehensive Cancer Center, Budapest, Hungary.
- Hereditary Tumours Research Group, Eötvös Loránd Research Network, Budapest, Hungary.
- Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary.
| | - Anikó Bozsik
- Department of Molecular Genetics and the National Tumour Biology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, Budapest, Hungary
- Hereditary Tumours Research Group, Eötvös Loránd Research Network, Budapest, Hungary
| | - Vince Grolmusz
- Department of Molecular Genetics and the National Tumour Biology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, Budapest, Hungary
- Hereditary Tumours Research Group, Eötvös Loránd Research Network, Budapest, Hungary
| | - Erika Szőcs
- Department of Oncology Biobank, National Institute of Oncology, Comprehensive Cancer Center, Budapest, Hungary
| | - János Papp
- Department of Molecular Genetics and the National Tumour Biology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, Budapest, Hungary
- Hereditary Tumours Research Group, Eötvös Loránd Research Network, Budapest, Hungary
| | - Attila Patócs
- Department of Molecular Genetics and the National Tumour Biology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, Budapest, Hungary
- Hereditary Tumours Research Group, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
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5
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Butz H, Nagy P, Papp J, Bozsik A, Grolmusz VK, Pócza T, Oláh E, Patócs A. PALB2 Variants Extend the Mutational Profile of Hungarian Patients with Breast and Ovarian Cancer. Cancers (Basel) 2023; 15:4350. [PMID: 37686625 PMCID: PMC10487218 DOI: 10.3390/cancers15174350] [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: 07/26/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND The pathogenic/likely pathogenic (P/LP) variant detection rate and profile of PALB2, the third most important breast cancer gene, may vary between different populations. METHODS PALB2 was analyzed in peripheral blood samples of three independent cohorts: prospectively between September 2021 and March 2023 (i) in 1280 consecutive patients with breast and/or ovarian cancer (HBOC), (ii) in 568 patients with other cancers (controls), and retrospectively, (iii) in 191 young breast cancer (<33 years, yBC) patients. These data were compared with data of 134,187 non-cancer individuals retrieved from the Genome Aggregation Database. RESULTS Altogether, 235 cases (235/1280; 18.3%) carried at least one P/LP variant in one of the HBOC susceptibility genes. P/LP PALB2 variants were identified in 18 patients (1.4%; 18/1280) in the HBOC and 3 cases (1.5%; 3/191) in the yBC group. In the control group, only one patient had a disease-causing PALB2 variant (0.17%; 1/568) as a secondary finding not related to the disease, which was similar (0.15%; 205/134,187) in the non-cancer control group. The NM_024675.4:c.509_510delGA variant was the most common among our patients (33%; 6/18). We did not find a significant difference in the incidence of PALB2 disease-causing variants according to age; however, the median age of tumor onset was lower in PALB2 P/LP carriers versus wild-type patients (44 vs. 48 years). In our cohort, the odds ratio for breast cancer risk in women with PALB2 P/LP variants was between 8.1 and 9.3 compared to non-HBOC cancer patients and the non-cancer population, respectively. CONCLUSIONS PALB2 P/LP variants are not uncommon among breast and/or ovarian cancer patients. Their incidence was the same in the two breast cancer cohorts studied but may occur rarely in patients with non-breast/ovarian cancer. The c.509_510delGA variant is particularly common in the studied Hungarian patient population.
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Affiliation(s)
- Henriett Butz
- Department of Molecular Genetics, The National Tumor Biology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary (A.B.); (V.K.G.); (T.P.); (E.O.); (A.P.)
- Department of Oncology Biobank, National Institute of Oncology, 1122 Budapest, Hungary
- Hereditary Tumours Research Group, Eötvös Loránd Research Network, 1089 Budapest, Hungary
- Department of Laboratory Medicine, Semmelweis University, 1092 Budapest, Hungary
| | - Petra Nagy
- Department of Molecular Genetics, The National Tumor Biology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary (A.B.); (V.K.G.); (T.P.); (E.O.); (A.P.)
| | - János Papp
- Department of Molecular Genetics, The National Tumor Biology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary (A.B.); (V.K.G.); (T.P.); (E.O.); (A.P.)
- Hereditary Tumours Research Group, Eötvös Loránd Research Network, 1089 Budapest, Hungary
| | - Anikó Bozsik
- Department of Molecular Genetics, The National Tumor Biology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary (A.B.); (V.K.G.); (T.P.); (E.O.); (A.P.)
- Hereditary Tumours Research Group, Eötvös Loránd Research Network, 1089 Budapest, Hungary
| | - Vince Kornél Grolmusz
- Department of Molecular Genetics, The National Tumor Biology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary (A.B.); (V.K.G.); (T.P.); (E.O.); (A.P.)
- Hereditary Tumours Research Group, Eötvös Loránd Research Network, 1089 Budapest, Hungary
| | - Tímea Pócza
- Department of Molecular Genetics, The National Tumor Biology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary (A.B.); (V.K.G.); (T.P.); (E.O.); (A.P.)
| | - Edit Oláh
- Department of Molecular Genetics, The National Tumor Biology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary (A.B.); (V.K.G.); (T.P.); (E.O.); (A.P.)
| | - Attila Patócs
- Department of Molecular Genetics, The National Tumor Biology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary (A.B.); (V.K.G.); (T.P.); (E.O.); (A.P.)
- Hereditary Tumours Research Group, Eötvös Loránd Research Network, 1089 Budapest, Hungary
- Department of Laboratory Medicine, Semmelweis University, 1092 Budapest, Hungary
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Zhang Z, Zhang Y, Lao S, Qiu J, Pan Z, Feng X. The clinicopathological and prognostic significances of IGF-1R and Livin expression in patients with colorectal cancer. BMC Cancer 2022; 22:855. [PMID: 35931997 PMCID: PMC9354317 DOI: 10.1186/s12885-022-09961-y] [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: 04/02/2022] [Accepted: 07/31/2022] [Indexed: 11/12/2022] Open
Abstract
Background Colorectal cancer (CRC) is the third most common cancer worldwide. However, limited effective biomarkers are associated with the tumorigenesis and prognosis of CRC. Methods The present study identified potential signatures from The Cancer Genome Atlas (TCGA) database and further validated the identified biomarkers in CRC tissues by immunohistochemistry (IHC). Results The expression of insulin-like growth factor 1 receptor (IGF-1R) and Livin gene was significantly upregulated in CRC samples compared to the adjacent normal samples in the TCGA dataset. IHC indicated that IGF-1R and Livin protein levels are increased in CRC and adenoma tissues compared to normal tissues. Notably, the IGF-1R protein levels differed significantly between adenoma and CRC. The elevated IGF-1R and Livin expression was associated with CRC clinicopathological features, including age, gender, histological subtype, individual cancer stages, nodal metastasis, and TP53-mutant in TCGA. Additionally, the IGF-1R promoter methylation level was closely related to CRC. Consistent with the TCGA study, IHC indicated that overexpressed IGF-1R and Livin proteins were independent risk factors for stage and metastasis. A marked correlation was established between IGF-1R and Livin expression in CRC, while the survival map showed no significant correlation with CRC. Kaplan–Meier survival curves showed that CRC patients with high IGF-1R or Livin expression had a prolonged overall disease-free survival than those with low expression in TCGA. Conclusion IGF-1R and Livin are associated with CRC tumorigenesis and might be valuable for novel biomarker identification and targeted therapeutic strategy development. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09961-y.
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Affiliation(s)
- Zhenling Zhang
- Department of Gastroenterology, the Second Hospital of Dalian Medical University, Dalian, 116023, China
| | - Yuxin Zhang
- Department of Gastroenterology, the Second Hospital of Dalian Medical University, Dalian, 116023, China
| | - Si Lao
- Department of Gastroenterology, the Second Hospital of Dalian Medical University, Dalian, 116023, China
| | - Jian Qiu
- Department of Gastroenterology, the Second Hospital of Dalian Medical University, Dalian, 116023, China
| | - Ziang Pan
- Department of Pathology, the Second Hospital of Dalian Medical University, Dalian, 116023, China
| | - Xiaoying Feng
- Department of Gastroenterology, the Second Hospital of Dalian Medical University, Dalian, 116023, China.
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7
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Opportunities and challenges for the use of common controls in sequencing studies. Nat Rev Genet 2022; 23:665-679. [PMID: 35581355 DOI: 10.1038/s41576-022-00487-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2022] [Indexed: 01/02/2023]
Abstract
Genome-wide association studies using large-scale genome and exome sequencing data have become increasingly valuable in identifying associations between genetic variants and disease, transforming basic research and translational medicine. However, this progress has not been equally shared across all people and conditions, in part due to limited resources. Leveraging publicly available sequencing data as external common controls, rather than sequencing new controls for every study, can better allocate resources by augmenting control sample sizes or providing controls where none existed. However, common control studies must be carefully planned and executed as even small differences in sample ascertainment and processing can result in substantial bias. Here, we discuss challenges and opportunities for the robust use of common controls in high-throughput sequencing studies, including study design, quality control and statistical approaches. Thoughtful generation and use of large and valuable genetic sequencing data sets will enable investigation of a broader and more representative set of conditions, environments and genetic ancestries than otherwise possible.
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8
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MC1R Is a Prognostic Marker and Its Expression Is Correlated with MSI in Colorectal Cancer. Curr Issues Mol Biol 2021; 43:1529-1547. [PMID: 34698109 PMCID: PMC8929037 DOI: 10.3390/cimb43030108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/29/2021] [Accepted: 10/06/2021] [Indexed: 12/16/2022] Open
Abstract
Melanocortin 1 receptor (MC1R) is thought to be a marker of poor prognosis and a potential target for the treatment of melanoma. Studies have found that MC1R promotes several tumor behaviors, including cell proliferation and differentiation, pigment formation, and genome damage repair. Some single-nucleotide polymorphisms (SNPs) of MC1R are involved in the occurrence and development of melanoma. A few studies have reported a relationship between MC1R and colorectal cancer (CRC). In this research, our objective was to examine MC1R expression and MC1R SNPs and investigate their correlation with the clinicopathological features of human CRC tissues. We evaluated MC1R mRNA expression by performing bioinformatic analyses on human CRC expression datasets. We used Western blotting and RT-qPCR to compare MC1R expression in CRC tissues with that in normal tissues, and MC1R SNPs in CRC tissues were detected by PCR-direct sequencing (DS). The expression of MC1R was significantly decreased in CRC tissues compared with normal tissue, and its expression was negatively associated with P53 expression, MLH1 expression, and PMS2 expression, and high MC1R expression was significantly associated with microsatellite instability (MSI). MC1R SNPs were also associated with the clinicopathological characteristics of CRC; for example, the rs2228479 locus genotype was correlated with Ki67 status, and the rs885479 locus genotype was correlated with age and T stage. In conclusion, MC1R plays a crucial role in the progression of CRC and may be a marker of poor prognosis in CRC.
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Daca Alvarez M, Quintana I, Terradas M, Mur P, Balaguer F, Valle L. The Inherited and Familial Component of Early-Onset Colorectal Cancer. Cells 2021; 10:cells10030710. [PMID: 33806975 PMCID: PMC8005051 DOI: 10.3390/cells10030710] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 02/07/2023] Open
Abstract
Early-onset colorectal cancer (EOCRC), defined as that diagnosed before the age of 50, accounts for 10–12% of all new colorectal cancer (CRC) diagnoses. Epidemiological data indicate that EOCRC incidence is increasing, despite the observed heterogeneity among countries. Although the cause for such increase remains obscure, ≈13% (range: 9–26%) of EOCRC patients carry pathogenic germline variants in known cancer predisposition genes, including 2.5% of patients with germline pathogenic variants in hereditary cancer genes traditionally not associated with CRC predisposition. Approximately 28% of EOCRC patients have family history of the disease. This article recapitulates current evidence on the inherited syndromes that predispose to EOCRC and its familial component. The evidence gathered support that all patients diagnosed with an EOCRC should be referred to a specialized genetic counseling service and offered somatic and germline pancancer multigene panel testing. The identification of a germline pathogenic variant in a known hereditary cancer gene has relevant implications for the clinical management of the patient and his/her relatives, and it may guide surgical and therapeutic decisions. The relative high prevalence of hereditary cancer syndromes and familial component among EOCRC patients supports further research that helps understand the genetic background, either monogenic or polygenic, behind this increasingly common disease.
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Affiliation(s)
- Maria Daca Alvarez
- Department of Gastroenterology, Hospital Clínic de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain;
| | - Isabel Quintana
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain; (I.Q.); (M.T.); (P.M.)
| | - Mariona Terradas
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain; (I.Q.); (M.T.); (P.M.)
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain; (I.Q.); (M.T.); (P.M.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Francesc Balaguer
- Department of Gastroenterology, Hospital Clínic de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029 Madrid, Spain
- Correspondence: (F.B.); (L.V.); Tel.: +34-932275400 (ext. 5418) (F.B.); +34-93-260-7145 (L.V.)
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain; (I.Q.); (M.T.); (P.M.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Correspondence: (F.B.); (L.V.); Tel.: +34-932275400 (ext. 5418) (F.B.); +34-93-260-7145 (L.V.)
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