51
|
Trompet E, Temblador A, Gillemot S, Topalis D, Snoeck R, Andrei G. An MHV-68 Mutator Phenotype Mutant Virus, Confirmed by CRISPR/Cas9-Mediated Gene Editing of the Viral DNA Polymerase Gene, Shows Reduced Viral Fitness. Viruses 2021; 13:v13060985. [PMID: 34073189 PMCID: PMC8227558 DOI: 10.3390/v13060985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/11/2021] [Accepted: 05/24/2021] [Indexed: 12/04/2022] Open
Abstract
Drug resistance studies on human γ-herpesviruses are hampered by the absence of an in vitro system that allows efficient lytic viral replication. Therefore, we employed murine γ-herpesvirus-68 (MHV-68) that efficiently replicates in vitro as a model to study the antiviral resistance of γ-herpesviruses. In this study, we investigated the mechanism of resistance to nucleoside (ganciclovir (GCV)), nucleotide (cidofovir (CDV), HPMP-5azaC, HPMPO-DAPy) and pyrophosphate (foscarnet (PFA)) analogues and the impact of these drug resistance mutations on viral fitness. Viral fitness was determined by dual infection competition assays, where MHV-68 drug-resistant viral clones competed with the wild-type virus in the absence and presence of antivirals. Using next-generation sequencing, the composition of the viral populations was determined at the time of infection and after 5 days of growth. Antiviral drug resistance selection resulted in clones harboring mutations in the viral DNA polymerase (DP), denoted Y383SGCV, Q827RHPMP-5azaC, G302WPFA, K442TPFA, G302W+K442TPFA, C297WHPMPO-DAPy and C981YCDV. Without antiviral pressure, viral clones Q827RHPMP-5azaC, G302WPFA, K442TPFA and G302W+K442TPFA grew equal to the wild-type virus. However, in the presence of antivirals, these mutants had a growth advantage over the wild-type virus that was moderately to very strongly correlated with antiviral resistance. The Y383SGCV mutant was more fit than the wild-type virus with and without antivirals, except in the presence of brivudin. The C297W and C981Y changes were associated with a mutator phenotype and had a severely impaired viral fitness in the absence and presence of antivirals. The mutator phenotype caused by C297W in MHV-68 DP was validated by using a CRISPR/Cas9 genome editing approach.
Collapse
|
52
|
Cameselle-García S, Abdulkader-Sande S, Sánchez-Ares M, Rodríguez-Carnero G, Garcia-Gómez J, Gude-Sampedro F, Abdulkader-Nallib I, Cameselle-Teijeiro JM. PD-L1 expression and immune cells in anaplastic carcinoma and poorly differentiated carcinoma of the human thyroid gland: A retrospective study. Oncol Lett 2021; 22:553. [PMID: 34093774 PMCID: PMC8170268 DOI: 10.3892/ol.2021.12814] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/04/2021] [Indexed: 02/07/2023] Open
Abstract
Anaplastic thyroid carcinoma (ATC) and poorly differentiated thyroid carcinoma (PDTC) have limited treatment options, and immune profiling may help select patients for immunotherapy. The prevalence and relevance of programmed death-1 ligand (PD-L1) expression and the presence of immune cells in ATC and PDTC has not yet been well established. The present study investigated PD-L1 expression (clone 22C3) and cells in the tumor microenvironment (TME), including tumor-infiltrating lymphocytes (TILs), tumor-associated macrophages (TAMs) and dendritic cells, in whole tissue sections of 15 cases of ATC and 13 cases of PDTC. Immunohistochemical PD-L1 expression using a tumor proportion score (TPS) with a 1% cut-off was detected in 9/15 (60%) of ATC cases and 1/13 (7.7%) of PDTC cases (P=0.006). PD-L1 expression in TILs was limited to the ATC group (73.3 vs. 0% in ATC and PDTC, respectively). In the ATC group, the TPS for tumor positive PD-L1 expression revealed a non-significant trend towards worse survival, but no difference was observed when investigating PD-L1 expression in TILs and TAMs. In addition to increased PD-L1 expression, all ATC cases exhibited significantly increased CD3+ and CD8+ T cells, CD68+ and CD163+ macrophages, and S100+ dendritic cells compared with the PDTC cases. Loss of mutL homolog 1 and PMS1 homolog 2 expression was observed in one ATC case with the highest PD-L1 expression, as well as in the only PDTC case positive for PD-L1. Notably, the latter was the only PDTC case exhibiting positivity for p53 and a cellular microenvironment similar to ATC. The current results indicated that PD-L1 expression was frequent in ATC, but rare in PDTC. In addition to PD-L1, the present study suggested that microsatellite instability may serve a role in both the TME and the identification of immunotherapy candidates among patients with PDTC.
Collapse
Affiliation(s)
- Soledad Cameselle-García
- Department of Medical Oncology, University Hospital Complex of Ourense, Galician Healthcare Service, 32005 Ourense, Spain
| | - Sámer Abdulkader-Sande
- Department of Pathology, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Galician Healthcare Service, 15706 Santiago de Compostela, Spain
| | - María Sánchez-Ares
- Department of Pathology, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Galician Healthcare Service, 15706 Santiago de Compostela, Spain
| | - Gemma Rodríguez-Carnero
- Department of Endocrinology and Nutrition, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Galician Healthcare Service, 15706 Santiago de Compostela, Spain
| | - Jesús Garcia-Gómez
- Department of Medical Oncology, University Hospital Complex of Ourense, Galician Healthcare Service, 32005 Ourense, Spain
| | - Francisco Gude-Sampedro
- Department of Epidemiology, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Galician Healthcare Service, 15706 Santiago de Compostela, Spain.,School of Medicine, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Ihab Abdulkader-Nallib
- Department of Pathology, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Galician Healthcare Service, 15706 Santiago de Compostela, Spain.,School of Medicine, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José Manuel Cameselle-Teijeiro
- Department of Pathology, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Galician Healthcare Service, 15706 Santiago de Compostela, Spain.,School of Medicine, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| |
Collapse
|
53
|
A Novel Low-Risk Germline Variant in the SH2 Domain of the SRC Gene Affects Multiple Pathways in Familial Colorectal Cancer. J Pers Med 2021; 11:jpm11040262. [PMID: 33916261 PMCID: PMC8066297 DOI: 10.3390/jpm11040262] [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: 02/25/2021] [Revised: 03/24/2021] [Accepted: 03/27/2021] [Indexed: 11/16/2022] Open
Abstract
Colorectal cancer (CRC) shows one of the largest proportions of familial cases among different malignancies, but only 5-10% of all CRC cases are linked to mutations in established predisposition genes. Thus, familial CRC constitutes a promising target for the identification of novel, high- to moderate-penetrance germline variants underlying cancer susceptibility by next generation sequencing. In this study, we performed whole genome sequencing on three members of a family with CRC aggregation. Subsequent integrative in silico analysis using our in-house developed variant prioritization pipeline resulted in the identification of a novel germline missense variant in the SRC gene (V177M), a proto-oncogene highly upregulated in CRC. Functional validation experiments in HT-29 cells showed that introduction of SRCV177M resulted in increased cell proliferation and enhanced protein expression of phospho-SRC (Y419), a potential marker for SRC activity. Upregulation of paxillin, β-Catenin, and STAT3 mRNA levels, increased levels of phospho-ERK, CREB, and CCND1 proteins and downregulation of the tumor suppressor p53 further proposed the activation of several pathways due to the SRCV177M variant. The findings of our pedigree-based study contribute to the exploration of the genetic background of familial CRC and bring insights into the molecular basis of upregulated SRC activity and downstream pathways in colorectal carcinogenesis.
Collapse
|
54
|
Salinas-Vera YM, Gallardo-Rincón D, Ruíz-García E, Silva-Cázares MB, de la Peña-Cruz CS, López-Camarillo C. The role of hypoxia in endometrial cancer. Curr Pharm Biotechnol 2021; 23:221-234. [PMID: 33655827 DOI: 10.2174/1389201022666210224130022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 12/24/2022]
Abstract
Endometrial cancer represents the most frequent neoplasia from the corpus uteri, and comprises the 14th leading cause of death in women worldwide. Risk factors that contribute to the disease include early menarche, late menopause, nulliparity, and menopausal hormone use, as well as hypertension and obesity comorbidities. The clinical effectiveness of chemotherapy is variable, suggesting that novel molecular targeted therapies against specific cellular processes associated with the maintenance of cancer cell survival and therapy resistance urged to ameliorate the rates of success in endometrial cancer treatment. In the course of tumor growth, cancer cells must adapt to decreased oxygen availability in the microenvironment by upregulation of hypoxia-inducible factors, which orchestrate the activation of a transcriptional program leading to cell survival. During this adaptative process, the hypoxic cancer cells may acquire invasive and metastatic properties as well as increased cell proliferation and resistance to chemotherapy, enhanced angiogenesis, vasculogenic mimicry, and maintenance of cancer cell stemness, which contribute to more aggressive cancer phenotypes. Several studies have shown that hypoxia-inducible factor 1 alpha (HIF-1α) protein is aberrantly overexpressed in many solid tumors from breast, prostate, ovarian, bladder, colon, brain, and pancreas. Thus, it has been considered an important therapeutic target. Here, we reviewed the current knowledge of the relevant roles of cellular hypoxia mechanisms and HIF-1α functions in diverse processes associated with endometrial cancer progression. In addition, we also summarize the role of microRNAs in the posttranscriptional regulation of protein-encoding genes involved in the hypoxia response in endometrial cancer. Finally, we pointed out the need for urgent targeted therapies to impair the cellular processes activated by hypoxia in the tumor microenvironment.
Collapse
Affiliation(s)
| | - Dolores Gallardo-Rincón
- Laboratorio de Medicina Traslacional y Departamento de Tumores Gastrointestinales, Instituto Nacional de Cancerología, Ciudad de México. Mexico
| | - Erika Ruíz-García
- Laboratorio de Medicina Traslacional y Departamento de Tumores Gastrointestinales, Instituto Nacional de Cancerología, Ciudad de México. Mexico
| | - Macrina B Silva-Cázares
- Doctorado Institucional en Ingeniería y Ciencia de Materiales, Universidad Autónoma de San Luis Potosí. Mexico
| | | | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México. Mexico
| |
Collapse
|
55
|
Soares de Lima Y, Arnau-Collell C, Díaz-Gay M, Bonjoch L, Franch-Expósito S, Muñoz J, Moreira L, Ocaña T, Cuatrecasas M, Herrera-Pariente C, Carballal S, Moreno L, Díaz de Bustamante A, Castells A, Bujanda L, Cubiella J, Rodríguez-Alcalde D, Balaguer F, Castellví-Bel S. Germline and Somatic Whole-Exome Sequencing Identifies New Candidate Genes Involved in Familial Predisposition to Serrated Polyposis Syndrome. Cancers (Basel) 2021; 13:929. [PMID: 33672345 PMCID: PMC7927050 DOI: 10.3390/cancers13040929] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022] Open
Abstract
The serrated polyposis syndrome (SPS) is the most common and yet underdiagnosed colorectal polyposis syndrome. It is characterized by multiple and/or large colonic serrated polyps and a higher associated risk for colorectal cancer (CRC). The main objective of this study was to identify new candidate genes involved in the germline predisposition to SPS/CRC. Thirty-nine SPS patients from 16 families (≥2 patients per family) were recruited without alterations in well-known hereditary CRC genes, and germline and somatic whole-exome sequencing were performed. Germline rare variants with plausible pathogenicity, located in genes involved in cancer development, senescence and epigenetic regulation were selected. Somatic mutational profiling and signature analysis was pursued in one sample per family, when possible. After data filtering, ANXA10, ASXL1, CFTR, DOT1L, HIC1, INO80, KLF3, MCM3AP, MCM8, PDLIM2, POLD1, TP53BP1, WNK2 and WRN were highlighted as the more promising candidate genes for SPS germline predisposition with potentially pathogenic variants shared within families. Somatic analysis characterized mutational profiles in advanced serrated polyps/tumors, revealing a high proportion of hypermutated samples, with a prevalence of clock-like mutational signatures in most samples and the presence of DNA mismatch repair-defective signatures in some cases. In conclusion, we identified new candidate genes to be involved in familial SPS. Further functional studies and replication in additional cohorts are required to confirm the selected candidates.
Collapse
Affiliation(s)
- Yasmin Soares de Lima
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Coral Arnau-Collell
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Marcos Díaz-Gay
- Moores Cancer Center, Department of Cellular and Molecular Medicine, Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA;
| | - Laia Bonjoch
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Sebastià Franch-Expósito
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Jenifer Muñoz
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Leticia Moreira
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Teresa Ocaña
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Miriam Cuatrecasas
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Pathology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Tumor Bank-Biobank, Hospital Clínic, 08036 Barcelona, Spain;
| | - Cristina Herrera-Pariente
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Sabela Carballal
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Lorena Moreno
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | | | - Antoni Castells
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia-Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Basque Country University (UPV/EHU), 20014 San Sebastián, Spain;
| | - Joaquín Cubiella
- Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 32005 Ourense, Spain;
| | | | - Francesc Balaguer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| | - Sergi Castellví-Bel
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, 08036 Barcelona, Spain; (Y.S.d.L.); (C.A.-C.); (L.B.); (S.F.-E.); (J.M.); (L.M.); (T.O.); (C.H.-P.); (S.C.); (L.M.); (A.C.); (F.B.)
| |
Collapse
|
56
|
Skopelitou D, Miao B, Srivastava A, Kumar A, Kuswick M, Dymerska D, Paramasivam N, Schlesner M, Lubinski J, Hemminki K, Försti A, Bandapalli OR. Whole Exome Sequencing Identifies APCDD1 and HDAC5 Genes as Potentially Cancer Predisposing in Familial Colorectal Cancer. Int J Mol Sci 2021; 22:ijms22041837. [PMID: 33673279 PMCID: PMC7917948 DOI: 10.3390/ijms22041837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/06/2021] [Accepted: 02/07/2021] [Indexed: 01/01/2023] Open
Abstract
Germline mutations in predisposition genes account for only 20% of all familial colorectal cancers (CRC) and the remaining genetic burden may be due to rare high- to moderate-penetrance germline variants that are not explored. With the aim of identifying such potential cancer-predisposing variants, we performed whole exome sequencing on three CRC cases and three unaffected members of a Polish family and identified two novel heterozygous variants: a coding variant in APC downregulated 1 gene (APCDD1, p.R299H) and a non-coding variant in the 5′ untranslated region (UTR) of histone deacetylase 5 gene (HDAC5). Sanger sequencing confirmed the variants segregating with the disease and Taqman assays revealed 8 additional APCDD1 variants in a cohort of 1705 familial CRC patients and no further HDAC5 variants. Proliferation assays indicated an insignificant proliferative impact for the APCDD1 variant. Luciferase reporter assays using the HDAC5 variant resulted in an enhanced promoter activity. Targeting of transcription factor binding sites of SNAI-2 and TCF4 interrupted by the HDAC5 variant showed a significant impact of TCF4 on promoter activity of mutated HDAC5. Our findings contribute not only to the identification of unrecognized genetic causes of familial CRC but also underline the importance of 5’UTR variants affecting transcriptional regulation and the pathogenesis of complex disorders.
Collapse
Affiliation(s)
- Diamanto Skopelitou
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (D.S.); (B.M.); (A.S.); (A.K.); (K.H.); (A.F.)
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
| | - Beiping Miao
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (D.S.); (B.M.); (A.S.); (A.K.); (K.H.); (A.F.)
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Aayushi Srivastava
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (D.S.); (B.M.); (A.S.); (A.K.); (K.H.); (A.F.)
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
| | - Abhishek Kumar
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (D.S.); (B.M.); (A.S.); (A.K.); (K.H.); (A.F.)
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Magdalena Kuswick
- Department of Genetics and Pathology, Pomeranian Medical University, 71252 Szczecin, Poland; (M.K.); (D.D.); (J.L.)
| | - Dagmara Dymerska
- Department of Genetics and Pathology, Pomeranian Medical University, 71252 Szczecin, Poland; (M.K.); (D.D.); (J.L.)
| | - Nagarajan Paramasivam
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, 71252 Szczecin, Poland; (M.K.); (D.D.); (J.L.)
| | - Kari Hemminki
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (D.S.); (B.M.); (A.S.); (A.K.); (K.H.); (A.F.)
- Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Asta Försti
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (D.S.); (B.M.); (A.S.); (A.K.); (K.H.); (A.F.)
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Obul Reddy Bandapalli
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (D.S.); (B.M.); (A.S.); (A.K.); (K.H.); (A.F.)
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-421809
| |
Collapse
|
57
|
Hildebrand LA, Pierce CJ, Dennis M, Paracha M, Maoz A. Artificial Intelligence for Histology-Based Detection of Microsatellite Instability and Prediction of Response to Immunotherapy in Colorectal Cancer. Cancers (Basel) 2021; 13:391. [PMID: 33494280 PMCID: PMC7864494 DOI: 10.3390/cancers13030391] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 12/14/2022] Open
Abstract
Microsatellite instability (MSI) is a molecular marker of deficient DNA mismatch repair (dMMR) that is found in approximately 15% of colorectal cancer (CRC) patients. Testing all CRC patients for MSI/dMMR is recommended as screening for Lynch Syndrome and, more recently, to determine eligibility for immune checkpoint inhibitors in advanced disease. However, universal testing for MSI/dMMR has not been uniformly implemented because of cost and resource limitations. Artificial intelligence has been used to predict MSI/dMMR directly from hematoxylin and eosin (H&E) stained tissue slides. We review the emerging data regarding the utility of machine learning for MSI classification, focusing on CRC. We also provide the clinician with an introduction to image analysis with machine learning and convolutional neural networks. Machine learning can predict MSI/dMMR with high accuracy in high quality, curated datasets. Accuracy can be significantly decreased when applied to cohorts with different ethnic and/or clinical characteristics, or different tissue preparation protocols. Research is ongoing to determine the optimal machine learning methods for predicting MSI, which will need to be compared to current clinical practices, including next-generation sequencing. Predicting response to immunotherapy remains an unmet need.
Collapse
Affiliation(s)
- Lindsey A. Hildebrand
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA; (L.A.H.); (C.J.P.); (M.D.); (M.P.)
| | - Colin J. Pierce
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA; (L.A.H.); (C.J.P.); (M.D.); (M.P.)
| | - Michael Dennis
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA; (L.A.H.); (C.J.P.); (M.D.); (M.P.)
- Division of Hematology Oncology, Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Munizay Paracha
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA; (L.A.H.); (C.J.P.); (M.D.); (M.P.)
| | - Asaf Maoz
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA; (L.A.H.); (C.J.P.); (M.D.); (M.P.)
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| |
Collapse
|
58
|
Hu H, Cai W, Wu D, Hu W, Dong Wang L, Mao J, Zheng S, Ge W. Ultra-mutated colorectal cancer patients with POLE driver mutations exhibit distinct clinical patterns. Cancer Med 2021; 10:135-142. [PMID: 33125191 PMCID: PMC7826451 DOI: 10.1002/cam4.3579] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 12/15/2022] Open
Abstract
POLE mutations, which lead to an ultramutated phenotype in colorectal cancer (CRC), have been reported as a promising marker in immunotherapy. We performed sequencing of CRC cases in Zhejiang University (ZJU) and extracted obtainable data from recently published results, including The Cancer Genome Atlas (TCGA), Japanese studies and clinical trials, to present clinical patterns of POLE driver-mutated CRC and reveal its heterogeneity. The rate of somatic POLE driver mutations has been reported as 2.60% (ZJU cohort), 1.50% (TCGA cohort), 1.00% (Japan cohort), and 1.00% (Lancet cohort). POLE driver mutations show a clearly increased mutation burden (mean TMB: 217.98 mut/Mb in ZJU; 203.13 mut/Mb in TCGA). Based on pooled data, more than 70.00% of patients with POLE driver mutations were diagnosed before they were 55 years old and at an early disease stage (Stage 0-II >70.00%), and more than 70.00% were male. Among Asian patients, 68.40% developed POLE driver mutations in the left-side colon, whereas 64.00% of non-Asian patients developed them in the right-side colon (p < 0.01). The top three amino acid changes due to POLE driver mutations are P286R, V411L, and S459F. Investigators and physicians should ascertain the heterogeneity and clinical patterns of POLE driver mutations to be better equipped to design clinical trials and analyze the data.
Collapse
Affiliation(s)
- Hanguang Hu
- Department of Medical OncologyThe Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
| | - Wen Cai
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education)The Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Department of GastroenterologySecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
| | - Dehao Wu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education)The Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
| | - Wangxiong Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education)The Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
| | - Li Dong Wang
- Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated HospitalState Key Laboratory for Esophageal Cancer Prevention & TreatmentZhengzhou UniversityZhengzhouHenanChina
| | - Jianshan Mao
- Department of GastroenterologySecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education)The Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
| | - Weiting Ge
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education)The Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
| |
Collapse
|
59
|
Kontizas E, Tastsoglou S, Karamitros T, Karayiannis Y, Kollia P, Hatzigeorgiou AG, Sgouras DN. Impact of Helicobacter pylori Infection and Its Major Virulence Factor CagA on DNA Damage Repair. Microorganisms 2020; 8:microorganisms8122007. [PMID: 33339161 PMCID: PMC7765595 DOI: 10.3390/microorganisms8122007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/10/2023] Open
Abstract
Helicobacter pylori infection induces a plethora of DNA damages. Gastric epithelial cells, in order to maintain genomic integrity, require an integrous DNA damage repair (DDR) machinery, which, however, is reported to be modulated by the infection. CagA is a major H. pylori virulence factor, associated with increased risk for gastric carcinogenesis. Its pathogenic activity is partly regulated by phosphorylation on EPIYA motifs. Our aim was to identify effects of H. pylori infection and CagA on DDR, investigating the transcriptome of AGS cells, infected with wild-type, ΔCagA and EPIYA-phosphorylation-defective strains. Upon RNA-Seq-based transcriptomic analysis, we observed that a notable number of DDR genes were found deregulated during the infection, potentially resulting to base excision repair and mismatch repair compromise and an intricate deregulation of nucleotide excision repair, homologous recombination and non-homologous end-joining. Transcriptome observations were further investigated on the protein expression level, utilizing infections of AGS and GES-1 cells. We observed that CagA contributed to the downregulation of Nth Like DNA Glycosylase 1 (NTHL1), MutY DNA Glycosylase (MUTYH), Flap Structure-Specific Endonuclease 1 (FEN1), RAD51 Recombinase, DNA Polymerase Delta Catalytic Subunit (POLD1), and DNA Ligase 1 (LIG1) and, contrary to transcriptome results, Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APE1) upregulation. Our study accentuates the role of CagA as a significant contributor of H. pylori infection-mediated DDR modulation, potentially disrupting the balance between DNA damage and repair, thus favoring genomic instability and carcinogenesis.
Collapse
Affiliation(s)
- Eleftherios Kontizas
- Laboratory of Medical Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece;
- Correspondence: (E.K.); (D.N.S.); Tel.: +30-210-647-8812 (E.K.); +30-210-647-8824 (D.N.S.)
| | - Spyros Tastsoglou
- Department of Electrical and Computer Engineering, University of Thessaly, 38221 Volos, Greece;
- DIANA-Lab, Hellenic Pasteur Institute, 11521 Athens, Greece;
| | - Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Hellenic Pasteur Institute, 11521 Athens, Greece;
| | - Yiannis Karayiannis
- Laboratory of Medical Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece;
| | - Panagoula Kollia
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece;
| | - Artemis G. Hatzigeorgiou
- DIANA-Lab, Hellenic Pasteur Institute, 11521 Athens, Greece;
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece
| | - Dionyssios N. Sgouras
- Laboratory of Medical Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
- Correspondence: (E.K.); (D.N.S.); Tel.: +30-210-647-8812 (E.K.); +30-210-647-8824 (D.N.S.)
| |
Collapse
|
60
|
Galati MA, Hodel KP, Gams MS, Sudhaman S, Bridge T, Zahurancik WJ, Ungerleider NA, Park VS, Ercan AB, Joksimovic L, Siddiqui I, Siddaway R, Edwards M, de Borja R, Elshaer D, Chung J, Forster VJ, Nunes NM, Aronson M, Wang X, Ramdas J, Seeley A, Sarosiek T, Dunn GP, Byrd JN, Mordechai O, Durno C, Martin A, Shlien A, Bouffet E, Suo Z, Jackson JG, Hawkins CE, Guidos CJ, Pursell ZF, Tabori U. Cancers from Novel Pole-Mutant Mouse Models Provide Insights into Polymerase-Mediated Hypermutagenesis and Immune Checkpoint Blockade. Cancer Res 2020; 80:5606-5618. [PMID: 32938641 PMCID: PMC8218238 DOI: 10.1158/0008-5472.can-20-0624] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/25/2020] [Accepted: 09/11/2020] [Indexed: 12/31/2022]
Abstract
POLE mutations are a major cause of hypermutant cancers, yet questions remain regarding mechanisms of tumorigenesis, genotype-phenotype correlation, and therapeutic considerations. In this study, we establish mouse models harboring cancer-associated POLE mutations P286R and S459F, which cause rapid albeit distinct time to cancer initiation in vivo, independent of their exonuclease activity. Mouse and human correlates enabled novel stratification of POLE mutations into three groups based on clinical phenotype and mutagenicity. Cancers driven by these mutations displayed striking resemblance to the human ultrahypermutation and specific signatures. Furthermore, Pole-driven cancers exhibited a continuous and stochastic mutagenesis mechanism, resulting in intertumoral and intratumoral heterogeneity. Checkpoint blockade did not prevent Pole lymphomas, but rather likely promoted lymphomagenesis as observed in humans. These observations provide insights into the carcinogenesis of POLE-driven tumors and valuable information for genetic counseling, surveillance, and immunotherapy for patients. SIGNIFICANCE: Two mouse models of polymerase exonuclease deficiency shed light on mechanisms of mutation accumulation and considerations for immunotherapy.See related commentary by Wisdom and Kirsch p. 5459.
Collapse
Affiliation(s)
- Melissa A Galati
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Karl P Hodel
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana
| | - Miki S Gams
- Program in Developmental and Stem Cell Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sumedha Sudhaman
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Taylor Bridge
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Cell Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Walter J Zahurancik
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio
| | - Nathan A Ungerleider
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana
| | - Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana
| | - Ayse B Ercan
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lazar Joksimovic
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Iram Siddiqui
- Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Robert Siddaway
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Cell Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Melissa Edwards
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Richard de Borja
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Dana Elshaer
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jiil Chung
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Victoria J Forster
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nuno M Nunes
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Melyssa Aronson
- The Familial Gastrointestinal Cancer Registry at the Zane Cohen Centre for Digestive Disease, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Xia Wang
- H Lee Moffitt Cancer Centre and Research Institute, Tampa, Florida
| | - Jagadeesh Ramdas
- Department of Pediatrics, Geisinger Medical Center, Danville, Pennsylvania
| | - Andrea Seeley
- Department of Pediatrics, Geisinger Medical Center, Danville, Pennsylvania
| | | | - Gavin P Dunn
- Department of Neurological Surgery, Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, Missouri
| | - Jonathan N Byrd
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri
| | - Oz Mordechai
- Department of Pediatric Hematology Oncology, Rambam Health Care Campus, Haifa, Israel
| | - Carol Durno
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alberto Martin
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Eric Bouffet
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Zucai Suo
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida
| | - James G Jackson
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana
| | - Cynthia E Hawkins
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Cell Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Cynthia J Guidos
- Program in Developmental and Stem Cell Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana
| | - Uri Tabori
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada.
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| |
Collapse
|
61
|
Newman J, Seetharamu N, Saif MW. Burden of Proof: Evaluating the Efficacy of Tumor Mutational Burden (TMB) in Predicting Response to Immune Checkpoint Inhibitors. CANCER MEDICINE JOURNAL 2020; 3:17-21. [PMID: 33377136 PMCID: PMC7769129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- James Newman
- Northwell Health Cancer Institute, Lake Success, NY, USA
| | | | | |
Collapse
|
62
|
Halbert B, Einstein DJ. Hot or Not: Tumor Mutational Burden (TMB) as a Biomarker of Immunotherapy Response in Genitourinary Cancers. Urology 2020; 147:119-126. [PMID: 33137348 DOI: 10.1016/j.urology.2020.10.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/31/2022]
Abstract
Pembrolizumab was recently approved for treatment of cancers with high tumor mutational burden (TMB). We conduct a focused literature review of TMB as a predictive biomarker. TMB quantifies the sum of nonsynonymous coding mutations (typically single nucleotide substitutions and short insertion-deletions) per megabase of sequenced DNA. As a proxy for expression of immunogenic neoantigens, TMB may be an effective predictive biomarker for response to immune checkpoint inhibitors. However, like other biomarkers in this setting, TMB has many limitations; the effect of this FDA approval in the current management of genitourinary cancers is likely limited to select situations.
Collapse
Affiliation(s)
- Brian Halbert
- Division of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA
| | - David J Einstein
- Division of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA.
| |
Collapse
|
63
|
Zhu Z, Fu H, Wang S, Yu X, You Q, Shi M, Dai C, Wang G, Cha W, Wang W. Whole-exome sequencing identifies prognostic mutational signatures in gastric cancer. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1484. [PMID: 33313229 PMCID: PMC7729362 DOI: 10.21037/atm-20-6620] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background Gastric cancer (GC) is a heterogeneous disease, and is a leading cause of cancer deaths in Eastern Asia. Genomic analysis, such as whole-exome sequencing (WES), can help identify key genetic alterations leading to the malignancy and diversity of GC, and may help identify new drug targets. Methods We identified genomic alterations in a cohort of 38 GC patients, including 26 metastatic and 12 non-metastatic patients. We analyzed the association between novel gene mutations and copy number variations (CNVs) with tumor metastasis and patient survival. Results A number of significantly mutated genes in somatic and germline cells were identified. Among them, ATAD3B somatic mutation, a potential biomarker of immunotherapy in stomach cancers, was associated with better patient survival (P=0.0939) and metastasis (P=0.074). POLE germline variation was correlated with shorter overall survival (OS; P=0.0100). Novel CNVs were also identified and can potentially be used as biomarkers. These included 9p24.1 deletion (P=0.0376) and 16p11.2 amplification (P=0.0066), which were both associated with shorter OS. CNVs of several genes including MMP9, PTPN1, and SS18L1 were found to be significantly related to metastasis (P<0.05). Conclusions We characterized the mutational landscape of 38 GC patients and discovered several potential new predictive markers of survival and metastasis in GC.
Collapse
Affiliation(s)
- Zhenxin Zhu
- Department of Gastro-intestine Surgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hongbing Fu
- Department of Gastro-intestine Surgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | | | - Xinxin Yu
- GenomiCare Biotechnology Co. Ltd., Shanghai, China
| | - Qing You
- Department of Gastro-intestine Surgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Mengyao Shi
- Department of Gastro-intestine Surgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Chun Dai
- GenomiCare Biotechnology Co. Ltd., Shanghai, China
| | - Guan Wang
- GenomiCare Biotechnology Co. Ltd., Shanghai, China
| | - Wei Cha
- Dental Department, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Weimin Wang
- Department of Gastro-intestine Surgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| |
Collapse
|
64
|
Zhou J, Wang C, Lin G, Xiao Y, Jia W, Xiao G, Liu Q, Wu B, Wu A, Qiu H, Zhang F, Hu K, Xue H, Shen Z, Wang Z, Han J, Niu B, Xu Y, Yu Z, Yang L. Serial Circulating Tumor DNA in Predicting and Monitoring the Effect of Neoadjuvant Chemoradiotherapy in Patients with Rectal Cancer: A Prospective Multicenter Study. Clin Cancer Res 2020; 27:301-310. [PMID: 33046514 DOI: 10.1158/1078-0432.ccr-20-2299] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/26/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE We investigated the value of circulating tumor DNA (ctDNA) in predicting tumor response to neoadjuvant chemoradiotherapy (nCRT), monitoring tumor burden, and prognosing survival in patients with locally advanced rectal cancer (LARC). EXPERIMENTAL DESIGN This prospective multicenter trial recruited 106 patients with LARC for treatment with nCRT followed by surgery. Serial ctDNAs were analyzed by next-generation sequencing at four timepoints: at baseline, during nCRT, presurgery, and postsurgery. RESULTS In total, 1,098 mutations were identified in tumor tissues of the 104 patients being analyzed (median, seven mutations/patient). ctDNA was detected in 75%, 15.6%, 10.5%, and 6.7% of cases at the four timepoints, respectively. None of the 29 patients with pathologic complete response (ypCR) had preoperative ctDNA detected. The preoperative ctDNA-positive rate was significantly lower in the well-responded patients with pathologic tumor regression grade of ypCAP 0-1 than ypCAP 2-3 group (P < 0.001), lower in ypCR than non-ypCR group (P = 0.02), and lower in pathologic T stage (ypT) 0-2 than ypT 3-4 group (P = 0.002). With a median follow-up of 18.8 months, 13 patients (12.5%) experienced distant metastasis. ctDNA positivity at all four timepoints was associated with a shorter metastasis-free survival (MFS; P < 0.05). Multivariate analyses showed that the median variant allele frequency (VAF) of mutations in baseline ctDNA was a strong independent predictor of MFS (HR, 1.27; P < 0.001). CONCLUSIONS We show that ctDNA is a real-time monitoring indicator that can accurately reflect the tumor burden. The median VAF of baseline ctDNA is a strong independent predictor of MFS.
Collapse
Affiliation(s)
- Jiaolin Zhou
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | | | - Guole Lin
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China.
| | - Yi Xiao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Wenzhuo Jia
- Department of General Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Gang Xiao
- Department of General Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Qian Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Bin Wu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Aiwen Wu
- Gastrointestinal Cancer Center, Unit III, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P.R. China
| | - Huizhong Qiu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Fuquan Zhang
- Department of Radiotherapy, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Ke Hu
- Department of Radiotherapy, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Huadan Xue
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, P.R. China
| | - Zhenjun Wang
- Department of General Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, P.R. China
| | - Jiagang Han
- Department of General Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, P.R. China
| | - Beizhan Niu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Yaping Xu
- Geneplus-Beijing, Beijing, P.R. China
| | | | - Ling Yang
- Geneplus-Beijing, Beijing, P.R. China.
| |
Collapse
|
65
|
Kiyozumi Y, Matsubayashi H, Higashigawa S, Horiuchi Y, Kado N, Hirashima Y, Shiomi A, Oishi T, Ohnami S, Ohshima K, Urakami K, Nagashima T, Yamaguchi K. Role of Tumor Mutation Burden Analysis in Detecting Lynch Syndrome in Precision Medicine: Analysis of 2,501 Japanese Cancer Patients. Cancer Epidemiol Biomarkers Prev 2020; 30:166-174. [PMID: 33046448 DOI: 10.1158/1055-9965.epi-20-0694] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/23/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Tumor mutation burden (TMB) is the total exonic mutation count per megabase of tumor DNA. Recent advances in precision medicine occasionally detect Lynch syndrome (LS) by germline sequencing for mismatch-repair (g.MMR) genes but not using TMB. The current study analyzes the utility of TMB in detecting LS. METHODS Whole-exome sequencing (ion-semiconductor sequencing) was performed for somatic and germline DNA from 2,501 various cancer patients to detect TMB and g.MMR sequencing. MMR IHC was conducted when high TMB (≥10) was detected in LS-related cancers with an additional condition of wild-type BRAF in colorectal cancers. Target sequencing and multiplex ligation-dependent probe amplification (MLPA) were further performed for g.MMR genes in MMR-deficient cancers (TMB-based g.MMR target sequencing). We compared universal sequencing and TMB-based target sequencing in their sensitivity for detecting LS. RESULTS LS was detected in 16 (0.6%) of the 2,501 patients: 1.1% (9/826) of colorectal cancer patients, 16.2% (6/37) of endometrial cancer patients, and 14.3% (1/7) of small intestine cancer patients. TMB-based g.MMR target sequencing (81.3%) showed superior sensitivity for detecting LS than universal g.MMR sequencing (56.3%; P = 0.127) but missed 3 LS patients (1 with a low-TMB cancer, 1 with a BRAF-mutant colorectal cancer, and 1 with an MMR-proficient cancer). Ion-semiconductor sequencing could detect single-nucleotide substitutions but not large deletions. POL-mutated cancers showed extremely high TMBs (48.4-749.2). CONCLUSIONS g.MMR target sequencing, combined with TMB, somatic BRAF mutation, and MMR IHC is an effective strategy for detecting LS. IMPACT TMB can be a biomarker for detecting LS in precision medicine.
Collapse
Affiliation(s)
- Yoshimi Kiyozumi
- Division of Genetic Medicine Promotion, Shizuoka Cancer Center, Shizuoka, Japan
| | - Hiroyuki Matsubayashi
- Division of Genetic Medicine Promotion, Shizuoka Cancer Center, Shizuoka, Japan.
- Division of Endoscopy, Shizuoka Cancer Center, Shizuoka, Japan
| | - Satomi Higashigawa
- Division of Genetic Medicine Promotion, Shizuoka Cancer Center, Shizuoka, Japan
| | - Yasue Horiuchi
- Division of Genetic Medicine Promotion, Shizuoka Cancer Center, Shizuoka, Japan
- Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Nobuhiro Kado
- Division of Genetic Medicine Promotion, Shizuoka Cancer Center, Shizuoka, Japan
- Division of Gynecology, Shizuoka Cancer Center, Shizuoka, Japan
| | | | - Akio Shiomi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Takuma Oishi
- Division of Pathology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Sumiko Ohnami
- Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | | | | | - Takeshi Nagashima
- Shizuoka Cancer Center Research Institute, Shizuoka, Japan
- SRL Inc., Tokyo, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| |
Collapse
|
66
|
Abstract
Small cell lung cancer (SCLC) is an aggressive malignancy. Until recently the standard of care for newly diagnosed patients with extensive-stage disease was chemotherapy consisting of etoposide plus a platinum (EP). The median overall survival (OS) was only about 10 months with this systemic therapy. Immune checkpoint inhibitors were first evaluated as second or subsequent line treatments in extensive stage disease and later in combination with EP in the first-line setting. Recently two randomized phase III trials have demonstrated statistically improved OS with addition of a programmed death ligand-1 (PD-L1) inhibitor to EP. As a result, the standard of care for newly diagnosed patients with extensive-stage SCLC has changed for the first time in decades. However, many patients do not derive benefit from the addition of a PD-L1 inhibitor to EP. In this review we discuss first-line trials of chemoimmunotherapy in extensive stage SCLC and summarize data on second and subsequent line treatment with immune checkpoint inhibitors in immunotherapy-naïve patients. Additionally, we discuss potential biomarkers that could be utilized to select for which patients derive benefit from addition of a PD-L1 inhibitor to EP and propose ways to improve on first-line chemoimmunotherapy.
Collapse
Affiliation(s)
- Jose M Pacheco
- Division of Medical Oncology, Department of Internal Medicine, University of Colorado Cancer Center, Aurora Colorado, USA
| |
Collapse
|
67
|
Siraj AK, Bu R, Arshad M, Iqbal K, Parvathareddy SK, Masoodi T, Ghazwani LO, Al-Sobhi SS, Al-Dayel F, Al-Kuraya KS. POLE and POLD1 pathogenic variants in the proofreading domain in papillary thyroid cancer. Endocr Connect 2020; 9:923-932. [PMID: 32992294 PMCID: PMC7583138 DOI: 10.1530/ec-20-0258] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 08/25/2020] [Indexed: 12/15/2022]
Abstract
Thyroid cancer is the most frequent endocrine cancer with an increasing incidence rate worldwide and is the second most common malignancy among females in Saudi Arabia. Papillary thyroid cancer (PTC) is the most common subtype. Germline pathogenic variants in the proofreading domain of the POLE and POLD1 genes predispose to several types of cancers. However, the role of pathogenic variants of these two genes in PTC remains unknown. Capture sequencing, Sanger sequencing and immunohistochemistry were performed on 300 PTC cases from the Middle Eastern region. One germline pathogenic variant each of POLE (1/300, 0.33%) and POLD1 (1/300, 0.33%) genes was identified. Low expression of POLD1 was detected in 46.5% (133/286) of cases and was significantly associated with the follicular variant of PTC (P = 0.0006), distant metastasis (P = 0.0033) and stage IV tumours (P = 0.0081). However, no somatic pathogenic variant was detected in POLE gene. Furthermore, low expression of POLE was noted in 61.7% (175/284) of cases with no significant clinicopathological associations. Our study shows that pathogenic variant in the POLE and POLD1 proofreading domain is a cause of PTC and low expression of POLD1 is associated with poor prognostic markers in the Middle Eastern population. Further studies from different geographic populations are needed to determine the frequency and spectrum of proofreading domain pathogenic variants in POLE and POLD1 genes and in PTC from different ethnicities.
Collapse
Affiliation(s)
- Abdul K Siraj
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Rong Bu
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Maham Arshad
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Kaleem Iqbal
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sandeep Kumar Parvathareddy
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Tariq Masoodi
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Laila Omar Ghazwani
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Saif S Al-Sobhi
- Department of Surgery, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Fouad Al-Dayel
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Khawla S Al-Kuraya
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| |
Collapse
|
68
|
Rosa RCA, Yurchenko AA, Chahud F, Ribeiro-Silva A, Brunaldi MO, Silva WA, Kannouche PL, Nikolaev S, Ferraz VEDF. First description of ultramutated endometrial cancer caused by germline loss-of-function and somatic exonuclease domain mutations in POLE gene. Genet Mol Biol 2020; 43:e20200100. [PMID: 33001133 PMCID: PMC7521106 DOI: 10.1590/1678-4685-gmb-2020-0100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/08/2020] [Indexed: 11/22/2022] Open
Abstract
Endometrial cancer (EC) harboring heterozygous POLE proofreading inactivating mutations (POLE-exo*) is associated with an increased number of somatic mutations that result in a distinctive anti-tumor immune response. However, the consequences of such POLE mutations in the context of the missing wild-type allele have not yet been described in endometrial tumors. A 72-year-old woman harboring a germline monoallelic frameshift mutation (p.Pro269fsTer26) in POLE was diagnosed with an EC having a somatic heterozygous mutation in the exonuclease domain of POLE (S459F). Targeted gene sequencing revealed an ultramutated phenotype (381 mutations/Mb) in the tumor and a 2-fold excess of mutations on the DNA leading strand. Additionally, we observed a mutational signature similar to the COSMIC signature 10, a higher mutation rate in this tumor than in endometrial tumors with heterozygous POLE-exo*, and an increased number of T lymphocytes. This is the first report of an ultramutated EC harboring a somatic POLE-exo* mutation in association with a germline loss-of-function mutation in this gene. The absence of a wild type POLE allele led to a particularly high mutational burden.
Collapse
Affiliation(s)
- Reginaldo Cruz Alves Rosa
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão
Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
| | - Andrey A. Yurchenko
- Université Paris Saclay, Inserm U981, Gustave Roussy Cancer
Campus, Villejuif, France
| | - Fernando Chahud
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão
Preto, Departamento de Patologia e Medicina Legal, Ribeirão Preto, SP,
Brazil
| | - Alfredo Ribeiro-Silva
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão
Preto, Departamento de Patologia e Medicina Legal, Ribeirão Preto, SP,
Brazil
| | - Mariângela Ottoboni Brunaldi
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão
Preto, Departamento de Patologia e Medicina Legal, Ribeirão Preto, SP,
Brazil
| | - Wilson Araújo Silva
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão
Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
| | - Patricia L. Kannouche
- Paris-Sud University, CNRS-UMR 8200, Equipe labellisée Ligue
Contre le Cancer, Gustave Roussy Cancer Campus, Villejuif, France
| | - Sergey Nikolaev
- Université Paris Saclay, Inserm U981, Gustave Roussy Cancer
Campus, Villejuif, France
| | - Victor Evangelista de Faria Ferraz
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão
Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
- Universidade de São Paulo, Centro de Genômica Médica, Hospital
das Clínicas, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP,
Brazil
| |
Collapse
|
69
|
Ito T, Nomizu T, Eguchi H, Kamae N, Dechamethakun S, Akama Y, Endo G, Sugano K, Yoshida T, Okazaki Y, Ishida H. The first case report of polymerase proofreading-associated polyposis in POLD1 variant, c.1433G>A p.S478N, in Japan. Jpn J Clin Oncol 2020; 50:1080-1083. [PMID: 32548621 DOI: 10.1093/jjco/hyaa090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/22/2020] [Indexed: 01/15/2023] Open
Abstract
Polymerase proofreading-associated polyposis, caused by germline variants in the exonuclease domains of POLD1 and POLE, is a dominantly inherited rare condition characterized by oligo-adenomatous polyposis and increased risk of colorectal cancer, endometrial cancer and brain tumours. We report the first Japanese case of polymerase proofreading-associated polyposis carrying a POLD1 variant. The proband was a Japanese woman who had undergone resections of early colorectal carcinomas repeatedly and a hysterectomy with bilateral oophorectomy for endometrial cancer, all of which were diagnosed within 2 years after the first colectomy at 49 year old. Colonoscopic examinations demonstrated at least 14 non-cancerous polypoid lesions, some of which were histologically confirmed to be adenoma. Multigene panel sequencing identified a missense variant in POLD1 (c.1433G>A). Although her relatives did not undergo genetic testing, her father and paternal grandfather died of brain tumours at 53 and ~30 years of age, respectively.
Collapse
Affiliation(s)
- Tetsuya Ito
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Kawagoe
| | | | - Hidetaka Eguchi
- Diagnosis and Therapeutics of Intractable Disease, Juntendo University Graduate School of Medicine, Tokyo
| | - Nao Kamae
- Department of Clinical Genetics, Saitama Medical Center, Saitama Medical University, Kawagoe
| | - Sariya Dechamethakun
- Diagnosis and Therapeutics of Intractable Disease, Juntendo University Graduate School of Medicine, Tokyo
| | - Yoshinori Akama
- Department of Genetic Counseling, Hoshi General Hospital, Koriyama
| | - Goichi Endo
- Department of Surgery, Fukushima Red Cross Hospital, Fukushima
| | - Kokichi Sugano
- Oncogene Research Unit/Cancer Prevention Unit, Tochigi Cancer Center Research Institute, Utsunomiya
| | - Teruhiko Yoshida
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Yasushi Okazaki
- Diagnosis and Therapeutics of Intractable Disease, Juntendo University Graduate School of Medicine, Tokyo
| | - Hideyuki Ishida
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Kawagoe
| |
Collapse
|
70
|
Huang F, Tanaka H, Knudsen BS, Rutgers JK. Mutant POLQ and POLZ/REV3L DNA polymerases may contribute to the favorable survival of patients with tumors with POLE mutations outside the exonuclease domain. BMC MEDICAL GENETICS 2020; 21:167. [PMID: 32838755 PMCID: PMC7446057 DOI: 10.1186/s12881-020-01089-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 07/08/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Mutations in the exonuclease domain of POLE, a DNA polymerase associated with DNA replication and repair, lead to cancers with ultra-high mutation rates. Most studies focus on intestinal and uterine cancers with POLE mutations. These cancers exhibit a significant immune cell infiltrate and favorable prognosis. We questioned whether loss of function of other DNA polymerases can cooperate to POLE to generate the ultramutator phenotype. METHODS We used cases and data from 15 cancer types in The Cancer Genome Atlas to investigate mutation frequencies of 14 different DNA polymerases. We tested whether tumor mutation burden, patient outcome (disease-free survival) and immune cell infiltration measured by ESTIMATE can be attributed to mutations in POLQ and POLZ/REV3L. RESULTS Thirty six percent of colorectal, stomach and endometrial cancers with POLE mutations carried additional mutations in POLQ (E/Q), POLZ/REV3L (E/Z) or both DNA polymerases (E/Z/Q). The mutation burden in these tumors was significantly greater compared to POLE-only (E) mutant tumors (p < 0.001). In addition, E/Q, E/Z, and E/Q/Z mutant tumors possessed an increased frequency of mutations in the POLE exonuclease domain (p = 0.013). Colorectal, stomach and endometrial E/Q, E/Z, and E/Q/Z mutant tumors within TCGA demonstrated 100% disease-free survival, even if the POLE mutations occurred outside the exonuclease domain (p = 0.003). However, immune scores in these tumors were related to microsatellite instability (MSI) and not POLE mutation status. This suggests that the host immune response may not be the sole mechanism for prolonged disease-free survival of ultramutated tumors in this cohort. CONCLUSION Results in this study demonstrate that mutations in POLQ and REV3L in POLE mutant tumors should undergo further investigation to determine whether POLQ and REV3L mutations contribute to the ultramutator phenotype and favorable outcome of patients with POLE mutant tumors.
Collapse
Affiliation(s)
- Fangjin Huang
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Hisashi Tanaka
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Samuel Oschin Cancer Research Institute (SOCCI), Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Beatrice S Knudsen
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Samuel Oschin Cancer Research Institute (SOCCI), Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Department of Pathology, University of Utah, Salt Lake City, UT, 84112, USA.
| | - Joanne K Rutgers
- Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| |
Collapse
|
71
|
Role of POLE and POLD1 in familial cancer. Genet Med 2020; 22:2089-2100. [PMID: 32792570 PMCID: PMC7708298 DOI: 10.1038/s41436-020-0922-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023] Open
Abstract
Purpose Germline pathogenic variants in the exonuclease domain (ED) of polymerases POLE and POLD1 predispose to adenomatous polyps, colorectal cancer (CRC), endometrial tumors, and other malignancies, and exhibit increased mutation rate and highly specific associated mutational signatures. The tumor spectrum and prevalence of POLE and POLD1 variants in hereditary cancer are evaluated in this study. Methods POLE and POLD1 were sequenced in 2813 unrelated probands referred for genetic counseling (2309 hereditary cancer patients subjected to a multigene panel, and 504 patients selected based on phenotypic characteristics). Cosegregation and case–control studies, yeast-based functional assays, and tumor mutational analyses were performed for variant interpretation. Results Twelve ED missense variants, 6 loss-of-function, and 23 outside-ED predicted-deleterious missense variants, all with population allele frequencies <1%, were identified. One ED variant (POLE p.Met294Arg) was classified as likely pathogenic, four as likely benign, and seven as variants of unknown significance. The most commonly associated tumor types were colorectal, endometrial and ovarian cancers. Loss-of-function and outside-ED variants are likely not pathogenic for this syndrome. Conclusions Polymerase proofreading–associated syndrome constitutes 0.1–0.4% of familial cancer cases, reaching 0.3–0.7% when only CRC and polyposis are considered. ED variant interpretation is challenging and should include multiple pieces of evidence.
Collapse
|
72
|
Zohud BA, Wang M, Cai X. Germline RAD54L with somatic POLE defect implicated in Hypermutation phenotype: case report. BMC Gastroenterol 2020; 20:255. [PMID: 32758138 PMCID: PMC7409428 DOI: 10.1186/s12876-020-01403-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 07/28/2020] [Indexed: 11/10/2022] Open
Abstract
Background Colorectal cancer is one of the most frequent causes of death among cancer patients. Hypermutated CRC is an extraordinary case of cancer, but curable if detected at early stages. However, the mechanism for developing a hypermutated CRC remains unclear. An association between RAD54L germline mutation and POLE exonuclease domain hypermutated cancer has not been reported before. Case presentation We present a rare case of a 41-year-old Chinese female with a right-sided colon adenocarcinoma who harboured a (p.P286R) POLE somatic mutation. Genomic analysis was performed using the Illumina HiSeq Sequencing platform, which, identified MSS tumour with a (c.1093_1169 + 15dup) germline mutation in RAD54L gene and tumour mutation burden of 377.0 Muts/Mb. Based on our report a new mechanism for developing hypermutated colon cancer has been conjectured through a novel RAD54L_POLE DSBR pathway. Conclusion This report highlights the clinical importance of next-generation sequencing technology in diagnosing rare tumours and investigating novel mechanisms for developing exceptional genetic diseases.
Collapse
Affiliation(s)
- Bisan Abdalfatah Zohud
- Department of Oncology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, China
| | - Meiling Wang
- Department of Oncology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, China
| | - Xin Cai
- Department of Oncology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, China.
| |
Collapse
|
73
|
Silvestri R, Landi S. DNA polymerases in the risk and prognosis of colorectal and pancreatic cancers. Mutagenesis 2020; 34:363-374. [PMID: 31647559 DOI: 10.1093/mutage/gez031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/17/2019] [Indexed: 12/30/2022] Open
Abstract
Human cancers arise from the alteration of genes involved in important pathways that mainly affect cell growth and proliferation. DNA replication and DNA damages recognition and repair are among these pathways and DNA polymerases that take part in these processes are frequently involved in cancer onset and progression. For example, damaging alterations within the proofreading domain of replicative polymerases, often reported in patients affected by colorectal cancer (CRC), are considered risk factors and drivers of carcinogenesis as they can lead to the accumulation of several mutations throughout the genome. Thus, replicative polymerases can be involved in cancer when losses of their physiological functions occur. On the contrary, reparative polymerases are often involved in cancer precisely because of their physiological role. In fact, their ability to repair and bypass DNA damages, which confers genome stability, can also counteract the effect of most anticancer drugs. In addition, the altered expression can characterise some type of cancers, which exacerbates this aspect. For example, all of the DNA polymerases involved a damage bypass mechanism, known as translesion synthesis, with the only exception of polymerase theta, are downregulated in CRC. Conversely, in pancreatic ductal adenocarcinoma (PDAC), most of these polymerase result upregulated. This suggests that different types of cancer can rely on different reparative polymerases to acquire drug resistance. Here we will examine all of the aspects that link DNA polymerases with CRC and PDAC.
Collapse
Affiliation(s)
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| |
Collapse
|
74
|
Hodel KP, Sun MJS, Ungerleider N, Park VS, Williams LG, Bauer DL, Immethun VE, Wang J, Suo Z, Lu H, McLachlan JB, Pursell ZF. POLE Mutation Spectra Are Shaped by the Mutant Allele Identity, Its Abundance, and Mismatch Repair Status. Mol Cell 2020; 78:1166-1177.e6. [PMID: 32497495 PMCID: PMC8177757 DOI: 10.1016/j.molcel.2020.05.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/10/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
Human tumors with exonuclease domain mutations in the gene encoding DNA polymerase ε (POLE) have incredibly high mutation burdens. These errors arise in four unique mutation signatures occurring in different relative amounts, the etiologies of which remain poorly understood. We used CRISPR-Cas9 to engineer human cell lines expressing POLE tumor variants, with and without mismatch repair (MMR). Whole-exome sequencing of these cells after defined numbers of population doublings permitted analysis of nascent mutation accumulation. Unlike an exonuclease active site mutant that we previously characterized, POLE cancer mutants readily drive signature mutagenesis in the presence of functional MMR. Comparison of cell line and human patient data suggests that the relative abundance of mutation signatures partitions POLE tumors into distinct subgroups dependent on the nature of the POLE allele, its expression level, and MMR status. These results suggest that different POLE mutants have previously unappreciated differences in replication fidelity and mutagenesis.
Collapse
Affiliation(s)
- Karl P Hodel
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Meijuan J S Sun
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Leonard G Williams
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA; BioInnovation Program, Tulane University, New Orleans, LA 70112, USA
| | - David L Bauer
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Victoria E Immethun
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jieqiong Wang
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Zucai Suo
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Hua Lu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - James B McLachlan
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA.
| |
Collapse
|
75
|
Metastatic Mixed Adenoneuroendocrine Carcinoma of the Colon with Response to Immunotherapy with Pembrolizumab: A Case Report. J Immunother 2020; 42:274-277. [PMID: 31219972 DOI: 10.1097/cji.0000000000000279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mixed adenoneuroendocrine carcinoma (MANEC) is a rare, aggressive tumor arising from different localizations along the gastrointestinal tract with generally poor prognosis. We present the case of a 51-year-old female patient with histopathologically confirmed diagnosis of a MANEC of the descending colon. At presentation, the tumor had already spread to the liver causing extensive hepatic metastases. Immunohistochemical examination showed 5%-10% of tumor cells to express the programmed cell death receptor ligand 1 and FoundationOne testing revealed a high mutational tumor burden with 149 Muts/Mb. The patient responded very well clinically and radiologically to anti-programmed death 1 receptor monoclonal antibody pembrolizumab therapy after having undergone 3 previous systemic treatment regimens as well as selective internal radiation therapy of her hepatic metastases. Clinical improvement was evident after the first infusion already and is ongoing for 10 months so far with very little side effects including initial and short lived skin irritation as well as muscle pain. To our knowledge, this is the first published case where a MANEC was successfully treated with immunotherapy targeting the programmed death 1 receptor.
Collapse
|
76
|
Hühns M, Nürnberg S, Kandashwamy KK, Maletzki C, Bauer P, Prall F. High mutational burden in colorectal carcinomas with monoallelic POLE mutations: absence of allelic loss and gene promoter methylation. Mod Pathol 2020; 33:1220-1231. [PMID: 31857678 DOI: 10.1038/s41379-019-0430-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/28/2019] [Accepted: 11/11/2019] [Indexed: 01/09/2023]
Abstract
Hypermutator-type colorectal carcinomas are microsatellite-stable and have point mutations of the exonuclease domain of the DNA polymerase ε or δ genes (POLE and POLD1, respectively), and an ultrahigh tumor mutational burden (TMB). These tumors may be associated with enhanced antitumor immunity and preferentially afflict younger patients, but this notion awaits validation by accrual of further cases for detailed correlative phenotypic and molecular study. We performed POLE and POLD1 exonuclease domain Sanger sequencing of 271 unselected colorectal carcinomas. We identified two microsatellite-stable tumors with somatic POLE p.P286R variants, both with ultrahigh TMBs as demonstrated by whole exome sequencing. A POLE p.V411L was found in another two microsatellite-stable tumors with ultrahigh TMBs. Two of these four tumors were from young patients (<50 years old, nonsyndromic), and there was seen a prominent T-cell infiltration in three of them. Furthermore, a somatic POLE p.A465T was found in a Lynch-associated tumor, which, hypothetically, might have enhanced TMB (which was the highest of all). In two tumors, a somatic POLE p.V411L and a POLD1 p.E279K, respectively, were found only focally, and TMBs were low. It is commonly assumed that compromise of one allele is sufficient, but this has not been specifically addressed. Therefore, resequencing of the POLE or POLD1 mutations was done with DNA from tumor cells isolated by laser-capture microdissection. This demonstrated that the mutations were monoallelic, and there was no evidence of a "second hit", neither by allelic loss (allelotyping with polymorphic microsatellite markers), nor by promoter methylation (Pyromark CpG assays). Taken together, including at least the more common DNA polymerase mutations in NGS panels allows for straightforward identification of hypermutator-type colorectal carcinomas which often may be "immunoreactive". This is important at least in young patients or when a metastasizing stage of disease has been reached and immune-checkpoint therapy enters deliberation.
Collapse
Affiliation(s)
- Maja Hühns
- Institute of Pathology, University Medicine of Rostock, Strempelstraße 14, 18057, Rostock, Germany
| | | | | | - Claudia Maletzki
- Clinic for Hematology, Oncology and Palliative Care, University Medical Center Rostock, University of Rostock, Ernst-Heydemann-Strasse 6, 18057, Rostock, Germany
| | - Peter Bauer
- Centogene AG, Am Strande 7, 18055, Rostock, Germany
| | - Friedrich Prall
- Institute of Pathology, University Medicine of Rostock, Strempelstraße 14, 18057, Rostock, Germany.
| |
Collapse
|
77
|
Salem ME, Battaglin F, Goldberg RM, Puccini A, Shields AF, Arguello D, Korn WM, Marshall JL, Grothey A, Lenz H. Molecular Analyses of Left- and Right-Sided Tumors in Adolescents and Young Adults with Colorectal Cancer. Oncologist 2020; 25:404-413. [PMID: 31848314 PMCID: PMC7216442 DOI: 10.1634/theoncologist.2019-0552] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/13/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The incidence of colorectal cancer (CRC), particularly left-sided tumors (LT), in adolescents and young adults (AYA) is rising. Epigenetic events appear to play an important role in tumorigenesis and cancer progression, especially in younger patients. We compared molecular features of LT to right-sided tumors (RT) in AYA. MATERIALS AND METHODS A total of 246 LT and 56 RT were identified in a cohort of 612 AYA with primary CRC. Tumors were examined by next-generation sequencing (NGS), protein expression, and gene amplification. Tumor mutational burden (TMB) and microsatellite instability (MSI) were determined based on NGS data. RESULTS RT showed higher mutation rates compared with LT in several genes including BRAF (10.3% vs. 2.8%), KRAS (64.1% vs. 45.5%), PIK3CA (27% vs. 11.2%), and RNF43 (24.2% vs. 2.9%). Notably, additional mutations in distinct genes involved in histone modification and chromatin remodeling, as well as genes associated with DNA repair and cancer-predisposing syndromes, were characteristic of RT; most frequently KMT2D (27.8% vs. 3.4%), ARID1A (53.3% vs. 21.4%), MSH6 (11.1% vs. 2.3%), MLH1 (10.5% vs. 2.3%), MSH2 (10.5% vs. 1.2%), POLE (5.9% vs. 0.6%), PTEN (10.8% vs. 2.3%), and BRCA1 (5.4% vs. 0.6%). MSI was seen in 20.8% of RT versus 4.8% of LT. RT had a higher frequency of TMB-high regardless of MSI status. CONCLUSION Molecular profiling of AYA CRC revealed different molecular characteristics in RT versus LT. Epigenetic mechanisms and alteration in DNA repair genes warrant further investigation and may be a promising treatment target for CRC in AYA. IMPLICATIONS FOR PRACTICE Colorectal cancer (CRC) in adolescents and young adults (AYA) comprises a distinct entity with different clinicopathologic features and prognosis compared with older patients. Molecular profiling of right- and left-sided tumors in AYA is needed to gain novel insight into CRC biology and to tailor targeted treatment in this age group. This study found that right- and left-sided CRC show distinct molecular features in AYA, overall and in subgroups based on microsatellite instability status. Alterations in DNA double-strand break repair and homologous recombination repair, as well as epigenetic mechanisms, appear to play a critical role. The present molecular profiling data may support the development of personalized treatment strategies in the AYA population.
Collapse
Affiliation(s)
- Mohamed E. Salem
- Department of Medical Oncology, Levine Cancer Institute, Atrium HealthCharlotteNorth CarolinaUSA
| | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern CaliforniaLos AngelesCaliforniaUSA
| | | | - Alberto Puccini
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern CaliforniaLos AngelesCaliforniaUSA
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, University of GenoaItaly
| | - Anthony F. Shields
- Department of Oncology, Karmanos Cancer Institute, Wayne State UniversityDetroitMichiganUSA
| | | | - W. Michael Korn
- Caris Life SciencesPhoenixArizonaUSA
- University of California at San FranciscoSan FranciscoCaliforniaUSA
| | - John L. Marshall
- The Ruesch Center and Georgetown Lombardi Comprehensive Cancer CenterWashingtonDCUSA
| | | | - Heinz‐Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern CaliforniaLos AngelesCaliforniaUSA
| |
Collapse
|
78
|
Pedigree analysis of a POLD1 germline mutation in urothelial carcinoma shows a close association between different mutation burdens and overall survival. Cell Mol Immunol 2020; 18:767-769. [PMID: 32265515 DOI: 10.1038/s41423-020-0425-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 03/18/2020] [Indexed: 12/11/2022] Open
|
79
|
De Pasquale MD, Crocoli A, Caldaro T, Rinelli M, Spinelli GP, Francalanci P, Cozza R, Inserra A, Miele E. Targeting Epidermal Growth Factor Receptor (EGFR) in Pediatric Colorectal Cancer. Cancers (Basel) 2020; 12:E414. [PMID: 32053874 PMCID: PMC7072611 DOI: 10.3390/cancers12020414] [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: 12/31/2019] [Revised: 01/30/2020] [Accepted: 02/04/2020] [Indexed: 11/17/2022] Open
Abstract
Background: Colorectal carcinoma (CRC) is very rare in the pediatric and adolescent age range and clinical management is performed according to adult protocols. We report, for the first time in the literature, a case of a child with metastatic CRC successfully treated with panitumumab associated to chemotherapy. Methods: A twelve-year-old male was diagnosed with CRC with nodal metastasis and peritoneal neoplastic effusion. After performing a genetic evaluation, in light of the absence of mutations in RAS family genes, anti-Epidermal Growth Factor Receptor (EGFR) monoclonal antibody, panitumumab, was added to chemotherapy FOLFOXIRI. Results: The child successfully responded to therapy with normalization of the Carbohydrate Antigen (CA) 19.9 value after the third cycle of treatment. After the sixth cycle, he underwent surgery that consisted in sigmoid resection with complete D3 lymphadenectomy. At histological evaluation, no residual neoplastic cells were detectable in the surgical specimen. He completed 12 cycles of chemotherapy plus panitumomab and he is alive without disease 14 months from diagnosis. Conclusions: Our results suggest performing mutational screening for colorectal cancer also in the pediatric setting, in order to orient treatment that should include targeted therapies.
Collapse
Affiliation(s)
- Maria Debora De Pasquale
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (M.D.D.P.); (R.C.)
| | - Alessandro Crocoli
- Surgical Oncology Unit, Department of Surgery, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (A.C.); (A.I.)
| | - Tamara Caldaro
- Digestive Endoscopy and Surgery Unit, Department of Surgery, Bambino Gesù Children’s Hospital-IRCCS, 00165 Rome, Italy;
| | - Martina Rinelli
- Department of Laboratories, Genetic Unit, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy;
| | - Gian Paolo Spinelli
- Oncology Unit, Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Via Giustiniano, 04011 Aprilia, Italy;
| | - Paola Francalanci
- Department of Laboratories, Pathology Unit, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy;
| | - Raffaele Cozza
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (M.D.D.P.); (R.C.)
| | - Alessandro Inserra
- Surgical Oncology Unit, Department of Surgery, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (A.C.); (A.I.)
| | - Evelina Miele
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (M.D.D.P.); (R.C.)
| |
Collapse
|
80
|
Fang H, Barbour JA, Poulos RC, Katainen R, Aaltonen LA, Wong JWH. Mutational processes of distinct POLE exonuclease domain mutants drive an enrichment of a specific TP53 mutation in colorectal cancer. PLoS Genet 2020; 16:e1008572. [PMID: 32012149 PMCID: PMC7018097 DOI: 10.1371/journal.pgen.1008572] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 02/13/2020] [Accepted: 12/17/2019] [Indexed: 01/16/2023] Open
Abstract
Cancer genomes with mutations in the exonuclease domain of Polymerase Epsilon (POLE) present with an extraordinarily high somatic mutation burden. In vitro studies have shown that distinct POLE mutants exhibit different polymerase activity. Yet, genome-wide mutation patterns and driver mutation formation arising from different POLE mutants remains unclear. Here, we curated somatic mutation calls from 7,345 colorectal cancer samples from published studies and publicly available databases. These include 44 POLE mutant samples including 9 with whole genome sequencing data available. The POLE mutant samples were categorized based on the specific POLE mutation present. Mutation spectrum, associations of somatic mutations with epigenomics features and co-occurrence with specific driver mutations were examined across different POLE mutants. We found that different POLE mutants exhibit distinct mutation spectrum with significantly higher relative frequency of C>T mutations in POLE V411L mutants. Our analysis showed that this increase frequency in C>T mutations is not dependent on DNA methylation and not associated with other genomic features and is thus specifically due to DNA sequence context alone. Notably, we found strong association of the TP53 R213* mutation specifically with POLE P286R mutants. This truncation mutation occurs within the TT[C>T]GA context. For C>T mutations, this sequence context is significantly more likely to be mutated in POLE P286R mutants compared with other POLE exonuclease domain mutants. This study refines our understanding of DNA polymerase fidelity and underscores genome-wide mutation spectrum and specific cancer driver mutation formation observed in POLE mutant cancers. Cancer arises through the accumulation of somatic mutations. The way that these somatic mutations form can vary greatly in different cancers. One of the most mutagenic processes that have been identified is caused by mutations within a replicative DNA polymerase known as Polymerase Epsilon (POLE). Cancers with such mutations present with hundreds of thousands of somatic mutations in their genome. Previous cancer genomics studies have identified a number of mutation hotspots in POLE, however how these different POLE mutants behave in affecting mutation distribution has not been studied. Here, we describe the genome-wide mutation profiles of distinct POLE mutant cancers. We find that different mutants indeed result in different mutation profiles and that this can be explained by the different fidelities of these mutants in replicating specific DNA sequences. Significantly, these differences have important implications in cancer formation as we found that a POLE mutation is strongly associated with a specific truncation of the TP53 cancer driver gene. This study furthers our understanding of the POLE mutagenic process in cancer and provide important insights into carcinogenesis in cancers with such mutations.
Collapse
Affiliation(s)
- Hu Fang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Jayne A. Barbour
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
- Prince of Wales Clinical School, UNSW Medicine, UNSW Sydney, New South Wales, Australia
| | - Rebecca C. Poulos
- Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Riku Katainen
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Lauri A. Aaltonen
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Jason W. H. Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
- Prince of Wales Clinical School, UNSW Medicine, UNSW Sydney, New South Wales, Australia
- * E-mail:
| |
Collapse
|
81
|
Characterizations of Gene Alterations in Melanoma Patients from Chinese Population. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6096814. [PMID: 32083130 PMCID: PMC7011309 DOI: 10.1155/2020/6096814] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/23/2019] [Accepted: 09/01/2019] [Indexed: 12/29/2022]
Abstract
Melanoma is a human skin malignant tumor with high invasion and poor prognosis. The limited understanding of genomic alterations in melanomas in China impedes the diagnosis and therapeutic strategy selection. We conducted comprehensive genomic profiling of melanomas from 39 primary and metastatic formalin-fixed paraffin-embedded (FFPE) samples from 27 patients in China based on an NGS panel of 223 genes. No significant difference in gene alterations was found between primary and metastasis melanomas. The status of germline mutation, CNV, and somatic mutation in our cohort was quite different from that reported in Western populations. We further delineated the mutation patterns of 4 molecular subgroups (BRAF, RAS, NF1, and Triple-WT) of melanoma in our cohort. BRAF mutations were more frequently identified in melanomas without chromic sun-induced damage (non-CSD), while RAS mutations were more likely observed in acral melanomas. NF1 and Triple-WT subgroups were unbiased between melanomas arising in non-CSD and acral skin. BRAF, RAS, and NF1 mutations were significantly associated with lymph node metastasis or presence of ulceration, implying that these cancer driver genes were independent prognostic factors. In summary, our results suggest that mutational profiles of malignant melanomas in China are significantly different from Western countries, and both gene mutation and amplification play an important role in the development and progression of melanomas.
Collapse
|
82
|
Kreidieh M, Mukherji D, Temraz S, Shamseddine A. Expanding the Scope of Immunotherapy in Colorectal Cancer: Current Clinical Approaches and Future Directions. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9037217. [PMID: 32090113 PMCID: PMC7008242 DOI: 10.1155/2020/9037217] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/16/2019] [Indexed: 12/14/2022]
Abstract
The success of immune checkpoint inhibitors (ICIs) in an increasing range of heavily mutated tumor types such as melanoma has culminated in their exploration in different subsets of patients with metastatic colorectal cancer (mCRC). As a result of their dramatic and durable response rates in patients with chemorefractory, mismatch repair-deficient-microsatellite instability-high (dMMR-MSI-H) mCRC, ICIs have become potential alternatives to classical systemic therapies. The anti-programmed death-1 (PD-1) agents, Pembrolizumab and Nivolumab, have been granted FDA approval for this subset of patients. Unfortunately, however, not all CRC cases with the dMMR-MSI-H phenotype respond well to ICIs, and ongoing studies are currently exploring biomarkers that can predict good response to them. Another challenge lies in developing novel treatment strategies for the subset of patients with the mismatch repair-proficient-microsatellite instability-low (pMMR-MSI-L) phenotype that comprises 95% of all mCRC cases in whom treatment with currently approved ICIs has been largely unsuccessful. Approaches aiming at overcoming the resistance of tumors in this subset of patients are being developed including combining different checkpoint inhibitors with either chemotherapy, anti-angiogenic agents, cancer vaccines, adoptive cell transfer (ACT), or bispecific T-cell (BTC) antibodies. This review describes the rationale behind using immunotherapeutics in CRC. It sheds light on the progress made in the use of immunotherapy in the treatment of patients with dMMR-MSI-H CRC. It also discusses emerging approaches and proposes potential strategies for targeting the immune microenvironment in patients with pMMR-MSI-L CRC tumors in an attempt to complement immune checkpoint inhibition.
Collapse
Affiliation(s)
- Malek Kreidieh
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut, Beirut, Lebanon
| | - Deborah Mukherji
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut, Beirut, Lebanon
| | - Sally Temraz
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut, Beirut, Lebanon
| | - Ali Shamseddine
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut, Beirut, Lebanon
| |
Collapse
|
83
|
Al-Shaheri FN, Al-Shami KM, Gamal EH, Mahasneh AA, Ayoub NM. Association of DNA repair gene polymorphisms with colorectal cancer risk and treatment outcomes. Exp Mol Pathol 2019; 113:104364. [PMID: 31881200 DOI: 10.1016/j.yexmp.2019.104364] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/16/2019] [Accepted: 12/24/2019] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is the third most common carcinoma worldwide. Despite the progress in screening and treatment, CRC remains a leading cause of cancer-related mortality. Alterations to normal nucleic acid processing may drive neoplastic transformation of colorectal epithelium. DNA repair machinery performs an essential function in the protection of genome by reducing the number of genetic polymorphisms/variations that may drive carcinogenicity. Four essential DNA repair systems are known which include nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), and double-strand break repair (DSBR). Polymorphisms of DNA repair genes have been shown to influence the risk of cancer development as well as outcomes of treatment. Several studies demonstrated the association between genetic polymorphism of DNA repair genes and increased risk of CRC in different populations. In this review, we have summarized the impact of DNA repair gene polymorphisms on risk of CRC development and treatment outcomes. Advancements of the current understanding for the impact of DNA repair gene polymorphisms on the risk and treatment of CRC may support diagnostic and predictive roles in patients with CRC.
Collapse
Affiliation(s)
- Fawaz N Al-Shaheri
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), ImNeuenheimer Feld 580, 69120 Heidelberg, Germany; Medical Faculty Heidelberg, University of Heidelberg, ImNeuenheimer Feld 672, 69120 Heidelberg, Germany; Faculty of Applied Medical Sciences, Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Kamal M Al-Shami
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, 720 South Donahue Drive, Auburn, Alabama 36849, United States of America; Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Eshrak H Gamal
- Department of Oncology, Collage of Medicine, Bonn University, Germany; Faculty of Applied Medical Sciences, Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Amjad A Mahasneh
- Department of Applied Biological Sciences, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Nehad M Ayoub
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan.
| |
Collapse
|
84
|
Li Y, Bian Y, Wang K, Wan XP. POLE mutations improve the prognosis of endometrial cancer via regulating cellular metabolism through AMF/AMFR signal transduction. BMC MEDICAL GENETICS 2019; 20:202. [PMID: 31864301 PMCID: PMC6925869 DOI: 10.1186/s12881-019-0936-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/08/2019] [Indexed: 02/07/2023]
Abstract
Background The morbidity and mortality of endometrial tumors, a common type of malignant cancer in women, have increased in recent years. POLE encodes the DNA polymerase ε, which is responsible for the leading strand DNA replication. Somatic mutations of POLE have been acknowledged in numerous cancers, resulting in the accumulation of DNA errors, leading to ultra-mutated tumors. Mutations in the exonuclease domain of POLE have been reported to improve progression-free survival in endometrial cancer. However, the potential relationship and underlying mechanism between POLE mutations and the prognosis of endometrial cancer patients remains unclear. Methods The whole exome sequencing data, RNA sequencing data, and clinical information were obtained from the TCGA database and employed for the analyses in this study. The detailed mutational information was analyzed using whole exome sequencing data and the mutated genes were shown with OncoPlot. The survival curves and cox proportional hazards regression analysis were used to accessed patient prognosis, the association of clinical characteristics and prognosis. Differentially expressed genes were analyzed by the edgeR R/Bioconductor package, then the GSEA Pre-ranked tool was used for Gene Set Enrichment Analysis (GSEA) to estimate the function of genes. Expression values were clustered using hierarchical clustering with Euclidean distance and ward linkage by the dendextend R package. Results POLE mutational status was proven to be an independent prognostic factor for endometrial cancer patients. Patients with somatic POLE mutations presented a favorable prognosis. POLE mutations regulated glycolysis and cytokine secretion, affecting cell metabolism and immune response. Autocrine motility factor (AMF)/PGI and AMFR/gp78 exhibited higher expression levels in POLE mutant patients. The comprehensive high expressions of AMFR/gp78 and low expression of POLE were associated with the favorable prognosis of endometrial cancer patients. Conclusions This study showed the POLE mutations a vital factor in endometrial cancer patients, leading to a higher expression of AMF/PGI and AMFR/gp78. These results suggested comprehensive consideration of the POLE mutations, expression of AMF/PGI and AMFR/gp78 may provide a more feasible and effective approach for the treatment of endometrial cancer, which might improve the prognosis.
Collapse
Affiliation(s)
- Yiran Li
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 2699 Gaoke West Road, Shanghai, China
| | - Yiding Bian
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 2699 Gaoke West Road, Shanghai, China
| | - Kai Wang
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiao-Ping Wan
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 2699 Gaoke West Road, Shanghai, China.
| |
Collapse
|
85
|
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.
Collapse
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
| |
Collapse
|
86
|
Siraj AK, Parvathareddy SK, Bu R, Iqbal K, Siraj S, Masoodi T, Concepcion RM, Ghazwani LO, AlBadawi I, Al-Dayel F, Al-Kuraya KS. Germline POLE and POLD1 proofreading domain mutations in endometrial carcinoma from Middle Eastern region. Cancer Cell Int 2019; 19:334. [PMID: 31866764 PMCID: PMC6907229 DOI: 10.1186/s12935-019-1058-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/04/2019] [Indexed: 12/24/2022] Open
Abstract
Background Endometrial carcinoma (EC) accounts for 5.8% of all cancers in Saudi females. Although most ECs are sporadic, 2–5% tend to be familial, being associated with Lynch syndrome and Cowden syndrome. In this study, we attempted to uncover the frequency, spectrum and phenotype of germline mutations in the proofreading domain of POLE and POLD1 genes in a large cohort of ECs from Middle Eastern region. Methods We performed Capture sequencing and Sanger sequencing to screen for proofreading domains of POLE and POLD1 genes in 432 EC cases, followed by evaluation of protein expression using immunohistochemistry. Variant interpretation was performed using PolyPhen-2, MutationAssessor, SIFT, CADD and Mutation Taster. Results In our cohort, four mutations (0.93%) were identified in 432 EC cases, two each in POLE and POLD1 proofreading domains. Furthermore, low expression of POLE and POLD1 was noted in 41.1% (170/1414) and 59.9% (251/419) of cases, respectively. Both the cases harboring POLE mutation showed high nuclear expression of POLE protein, whereas, of the two POLD1 mutant cases, one case showed high expression and another case showed low expression of POLD1 protein. Conclusions Our study shows that germline mutations in POLE and POLD1 proofreading region are a rare cause of EC in Middle Eastern population. However, it is still feasible to screen multiple cancer related genes in EC patients from Middle Eastern region using multigene panels including POLE and POLD1.
Collapse
Affiliation(s)
- Abdul K Siraj
- 1Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211 Saudi Arabia
| | - Sandeep Kumar Parvathareddy
- 1Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211 Saudi Arabia
| | - Rong Bu
- 1Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211 Saudi Arabia
| | - Kaleem Iqbal
- 1Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211 Saudi Arabia
| | - Sarah Siraj
- 1Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211 Saudi Arabia
| | - Tariq Masoodi
- 1Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211 Saudi Arabia
| | - Rica Micaela Concepcion
- 1Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211 Saudi Arabia
| | - Laila Omar Ghazwani
- 1Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211 Saudi Arabia
| | - Ismail AlBadawi
- 2Department of Obstetrics-Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fouad Al-Dayel
- 3Department of Pathology, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh, 11211 Saudi Arabia
| | - Khawla S Al-Kuraya
- 1Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211 Saudi Arabia
| |
Collapse
|
87
|
Ben Sghaier R, Jansen AML, Bdioui A, Van Wezel T, Ksiaa M, Elgolli L, Ben Fatma L, Ben Ahmed S, Azzouz MM, Hellara O, Elghali A, Darbel F, Skandrani K, Mokkni M, Gdissa A, Ltaief R, Saad A, Hmila F, Gribaa M, Morreau H. Targeted next generation sequencing screening of Lynch syndrome in Tunisian population. Fam Cancer 2019; 18:343-348. [PMID: 31114938 DOI: 10.1007/s10689-019-00130-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A high colorectal cancer (CRC) incidence is observed in Tunisia, with a relatively high proportion of patients developing CRC before the age of 40. While this suggests a genetic susceptibility, only a few Tunisian Lynch Syndrome families have been described. In this study we aimed to identify the underlying genetic cause in 32 patients with early onset CRC and/or a positive family history. Of twenty-four patients' tumor or biopsies could be analyzed with immunohistochemical staining to detect loss of expression of one of the MMR proteins. Ten tumors showed loss of expression, of which one tumor was from a patient where a germline pathogenic MSH2 variant was detected previously with Sanger sequencing. Next generation sequencing of the MMR, POLE and POLD1 genes was performed in leukocyte and tumor DNA of the remaining nine patients, as well as in two patients with MMR-proficient tumors, but with severe family history. In six of 11 patients a germline variant was detected in MLH1 (n = 5) or MSH2 (n = 1). Two of six patients were from the same family and both were found to carry a novel in-frame MLH1 deletion, predicted to affect MLH1 function. All MLH1 variant carriers had loss of heterozygosity with retention of the variant in the tumors, while a somatic pathogenic variant was detected in the patient with the germline MSH2 variant.
Collapse
Affiliation(s)
- Rihab Ben Sghaier
- Cytogenetic, Molecular Genetics and Human Reproduction Biology - Farhat, HACHED Hospital, Sousse, Tunisia.
| | | | - Ahlem Bdioui
- Cytology and Anatomopathology Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Tom Van Wezel
- Pathology Department, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
| | - Mehdi Ksiaa
- Gastroenterology Department, Sahloul Hospital, Sousse, Tunisia
| | | | - Leila Ben Fatma
- Carcinology Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Slim Ben Ahmed
- Carcinology Department, Farhat HACHED Hospital, Sousse, Tunisia
| | | | - Olfa Hellara
- Gastroenterology Department, Fatouma Bourguiba Hospital, Monastir, Tunisia
| | - Amine Elghali
- General Surgery Department, Farhat HACHED Hospital, Sousse, Tunisia
| | | | | | - Moncef Mokkni
- Cytology and Anatomopathology Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Ameni Gdissa
- Cytogenetic, Molecular Genetics and Human Reproduction Biology - Farhat, HACHED Hospital, Sousse, Tunisia
| | - Rached Ltaief
- General Surgery Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Ali Saad
- Cytogenetic, Molecular Genetics and Human Reproduction Biology - Farhat, HACHED Hospital, Sousse, Tunisia
| | - Fahmi Hmila
- General Surgery Department, Farhat HACHED Hospital, Sousse, Tunisia
| | - Moez Gribaa
- Cytogenetic, Molecular Genetics and Human Reproduction Biology - Farhat, HACHED Hospital, Sousse, Tunisia
| | - Hans Morreau
- Pathology Department, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
| |
Collapse
|
88
|
Nuñez-Olvera SI, Gallardo-Rincón D, Puente-Rivera J, Salinas-Vera YM, Marchat LA, Morales-Villegas R, López-Camarillo C. Autophagy Machinery as a Promising Therapeutic Target in Endometrial Cancer. Front Oncol 2019; 9:1326. [PMID: 31850214 PMCID: PMC6896250 DOI: 10.3389/fonc.2019.01326] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/13/2019] [Indexed: 01/01/2023] Open
Abstract
Endometrial cancer is the fourth most frequent neoplasia for women worldwide, and over the past two decades it incidence has increased. The most common histological type of endometrial cancer is endometrioid adenocarcinoma, also known as type 1 endometrial cancer. Endometrioid endometrial cancer is associated with diverse epidemiological risk factors including estrogen use, obesity, diabetes, cigarette smoking, null parity, early menarche, and late menopause. Clinical effectiveness of chemotherapy is variable, indicating that novel molecular therapies against specific cellular processes associated to cell survival and resistance to therapy, such as autophagy, urged to ameliorate the rates of success in endometrial cancer treatment. Autophagy (also known as macroautophagy) is a specialized mechanism that maintains cell homeostasis which is activated in response to cellular stressors including nutrients deprivation, amino acids starvation, hypoxia, and metabolic stress to prolong cell survival via lysosomal degradation of cytoplasmic macromolecules and organelles. However, in human cancer cells, autophagy has a controversial function due to its dual role as self-protective or apoptotic. Conventional antitumor therapies including hormones, chemotherapy and ionizing radiation, may activate autophagy as a pro-survival tumor response contributing to treatment resistance. Intriguingly, if autophagy continues above reversibility of cell viability, autophagy can result in apoptosis of tumor cells. Here, we have reviewed the mechanisms of autophagy described in endometrial cancers, including the role of PI3K/AKT/mTOR, AMPK-mTOR, and p53 signaling pathways that trigger or inhibit the process and thus representing potential molecular targets in therapeutic clinical approaches. In addition, we discussed the recent findings indicating that autophagy can be modulated using repurposing drugs which may leads to faster experimentation and validation, as well as more easy access of the medications to patients. Finally, the promising role of dietary compounds and microRNAs in autophagy modulation is also discussed. In conclusion, although the research about autophagy is scarce but ongoing in endometrial cancer, the actual findings highlight the promising usefulness of novel molecules for directing targeted therapies.
Collapse
Affiliation(s)
- Stephanie I Nuñez-Olvera
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Dolores Gallardo-Rincón
- Laboratorio de Medicina Translacional, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Jonathan Puente-Rivera
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Yarely M Salinas-Vera
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Laurence A Marchat
- Programa en Biomedicina Molecular y Red de Biotecnología, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Raúl Morales-Villegas
- Coordinación Académica Huasteca del Sur, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| |
Collapse
|
89
|
Chen W, Pearlman R, Hampel H, Pritchard CC, Markow M, Arnold C, Knight D, Frankel WL. MSH6 immunohistochemical heterogeneity in colorectal cancer: comparative sequencing from different tumor areas. Hum Pathol 2019; 96:104-111. [PMID: 31783044 DOI: 10.1016/j.humpath.2019.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/19/2019] [Accepted: 11/19/2019] [Indexed: 01/01/2023]
Abstract
Mismatch repair protein (MMR) immunohistochemistry is an important tool in screening for Lynch syndrome in colorectal cancer patients. Unusual staining patterns such as heterogeneous MSH6 staining have been reported in colorectal and endometrial cancers. We aim to better understand MSH6 staining heterogeneity in colorectal cancer by comparative sequencing of different tumor areas for MMR and DNA polymerase mutations. Whole-section slides of 1754 colorectal cancers were reviewed for heterogeneous MSH6 staining, defined as discrete tumor areas with abrupt loss of staining juxtaposed to tumor areas with retained staining. Nine cases (0.05%) demonstrated heterogeneous MSH6 staining; none received neoadjuvant therapy prior to the specimen collection. The area of tumor with loss of MSH6 expression ranged from 5% to 60% (average 22%). Four cases had enough tissue remaining in both retained and lost MSH6 areas to perform tumor sequencing on both areas. All 9 cases were negative for MSH6 germline mutation; MSH6 heterogeneous staining was seen in tumors with MLH1 or PMS2 abnormalities (6 cases of MLH1 methylation, 2 PMS2 germline mutation, 1 MLH1 germline mutation). In addition, case 1 also had a somatic POLD1 exonuclease domain mutation (p.Y405C) in the MSH6 loss area but not in the intact area. We recommend reporting MSH6 heterogeneous pattern as MSH6 staining is present with a comment stating that the heterogeneous pattern typically does not indicate germline mutation in MSH6 but is commonly associated with abnormality in another MMR gene such as MLH1 or PMS2, or even other DNA repair genes such as DNA polymerase.
Collapse
Affiliation(s)
- Wei Chen
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210
| | - Rachel Pearlman
- Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210
| | - Heather Hampel
- Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington WA 98195
| | - Michael Markow
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210
| | - Christina Arnold
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210
| | - Deborah Knight
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210
| | - Wendy L Frankel
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210.
| |
Collapse
|
90
|
Matsutani T, Ueno Y, Fukunaga T, Hamada M. Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference. Bioinformatics 2019; 35:4543-4552. [PMID: 30993319 PMCID: PMC6853711 DOI: 10.1093/bioinformatics/btz266] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 12/18/2022] Open
Abstract
MOTIVATION A cancer genome includes many mutations derived from various mutagens and mutational processes, leading to specific mutation patterns. It is known that each mutational process leads to characteristic mutations, and when a mutational process has preferences for mutations, this situation is called a 'mutation signature.' Identification of mutation signatures is an important task for elucidation of carcinogenic mechanisms. In previous studies, analyses with statistical approaches (e.g. non-negative matrix factorization and latent Dirichlet allocation) revealed a number of mutation signatures. Nonetheless, strictly speaking, these existing approaches employ an ad hoc method or incorrect approximation to estimate the number of mutation signatures, and the whole picture of mutation signatures is unclear. RESULTS In this study, we present a novel method for estimating the number of mutation signatures-latent Dirichlet allocation with variational Bayes inference (VB-LDA)-where variational lower bounds are utilized for finding a plausible number of mutation patterns. In addition, we performed cluster analyses for estimated mutation signatures to extract novel mutation signatures that appear in multiple primary lesions. In a simulation with artificial data, we confirmed that our method estimated the correct number of mutation signatures. Furthermore, applying our method in combination with clustering procedures for real mutation data revealed many interesting mutation signatures that have not been previously reported. AVAILABILITY AND IMPLEMENTATION All the predicted mutation signatures with clustering results are freely available at http://www.f.waseda.jp/mhamada/MS/index.html. All the C++ source code and python scripts utilized in this study can be downloaded on the Internet (https://github.com/qkirikigaku/MS_LDA). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Taro Matsutani
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan
| | - Yuki Ueno
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan
| | - Tsukasa Fukunaga
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
- Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Michiaki Hamada
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| |
Collapse
|
91
|
Germline POLE mutation in a child with hypermutated medulloblastoma and features of constitutional mismatch repair deficiency. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004499. [PMID: 31624068 PMCID: PMC6824253 DOI: 10.1101/mcs.a004499] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/15/2019] [Indexed: 01/02/2023] Open
Abstract
Ultra-hypermutation (>100 mutations/Mb) is rare in childhood cancer genomes and has been primarily reported in patients with constitutional mismatch repair deficiency (CMMRD) caused by biallelic germline mismatch repair (MMR) gene mutations. We report a 5-yr-old child with classic clinical features of CMMRD and an ultra-hypermutated medulloblastoma with retained MMR protein expression and absence of germline MMR mutations. Mutational signature analysis of tumor panel sequencing data revealed a canonical DNA polymerase-deficiency-associated signature, prompting further genetic testing that uncovered a germline POLE p.A456P missense variant, which has previously been reported as a recurrent somatic driver mutation in cancers. This represents the earliest known onset of malignancy in a patient with a germline mutation in the POLE proofreading polymerase. The clinical features in this child, virtually indistinguishable from those of CMMRD, suggest that polymerase-proofreading deficiency should be considered in the differential diagnosis of CMMRD patients with retained MMR function.
Collapse
|
92
|
Johansen AFB, Kassentoft CG, Knudsen M, Laursen MB, Madsen AH, Iversen LH, Sunesen KG, Rasmussen MH, Andersen CL. Validation of computational determination of microsatellite status using whole exome sequencing data from colorectal cancer patients. BMC Cancer 2019; 19:971. [PMID: 31638937 PMCID: PMC6802299 DOI: 10.1186/s12885-019-6227-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/09/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Microsatellite instability (MSI), resulting from a defective mismatch repair system, occurs in approximately 15% of sporadic colorectal cancers (CRC). Since MSI is associated with a poor response to 5-fluorouracile based chemotherapy and is a positive predictive marker of immunotherapy, it is routine practice to evaluate the MSI status of resected tumors in CRC patients. MSIsensor is a novel computational tool for determining MSI status using Next Generation Sequencing. However, it is not widely used in the clinic and has not been independently validated in exome data from CRC. To facilitate clinical implementation of computational determination of MSI status, we compared MSIsensor to current gold standard methods for MSI testing. METHODS MSI status was determined for 130 CRC patients (UICC stage I-IV) using immunohistochemistry, PCR based microsatellite stability testing and by applying MSIsensor to exome sequenced tumors and paired germline DNA. Furthermore, we investigated correlation between MSI status, mutational load and mutational signatures. RESULTS Eighteen out of 130 (13.8%) patients were microsatellite instable. We found a 100% agreement between MSIsensor and gold standard methods for MSI testing. All MSI tumors were hypermutated. In addition, two microsatellite stable (MSS) tumors were hypermutated, which was explained by a dominant POLE signature and pathogenic POLE mutations (p.Pro286Arg and p.Ser459Phe). CONCLUSION MSIsensor is a robust tool, which can be used to determine MSI status of tumor samples from exome sequenced CRC patients.
Collapse
Affiliation(s)
| | - Christine Gaasdal Kassentoft
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200, Aarhus N, Denmark
| | - Michael Knudsen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200, Aarhus N, Denmark
| | - Maria Bach Laursen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200, Aarhus N, Denmark
| | | | | | | | - Mads Heilskov Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200, Aarhus N, Denmark
| | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200, Aarhus N, Denmark.
| |
Collapse
|
93
|
Jansen AML, Ghosh P, Dakal TC, Slavin TP, Boland CR, Goel A. Novel candidates in early-onset familial colorectal cancer. Fam Cancer 2019; 19:1-10. [PMID: 31555933 DOI: 10.1007/s10689-019-00145-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/15/2019] [Indexed: 12/12/2022]
Abstract
In 20-30% of patients suspected of a familial colorectal cancer (CRC) syndrome, no underlying genetic cause is detected. Recent advances in whole exome sequencing have generated evidence for new CRC-susceptibility genes including POLE, POLD1 and NTHL1¸ but many patients remain unexplained. Whole exome sequencing was performed on DNA from nine patients from five different families with familial clusters of CRC in which traditional genetic testing failed to yield a diagnosis. Variants were filtered by minor allele frequencies, followed by prioritization based on in silico prediction tools, and the presence in cancer susceptibility genes or genes in cancer-associated pathways. Effects of frameshift variants on protein structure were modeled using I-Tasser. One known pathogenic variant in POLD1 was detected (p.S478N), together with variants in 17 candidate genes not previously associated with CRC. Additional in silico analysis using SIFT, PROVEAN and PolyPhen on the 14 missense variants indicated a possible damaging effect in nine of 14 variants. Modeling of the insertions/deletions showed a damaging effect of two variants in NOTCH2 and CYP1B1. One family was explained by a mutation in a known familial CRC gene. In the remaining four families, the most promising candidates found are a frameshift NOTCH2 and a missense RAB25 variant. This study provides potential novel candidate variants in unexplained familial CRC patients, however, functional validation is imperative to confirm the role of these variants in CRC tumorigenesis. Additionally, while whole exome sequencing enables detection of variants throughout the exome, other causes explaining the familial phenotype such as multiple single nucleotide polymorphisms accumulating to a polygenic risk or epigenetic events, might be missed with this approach.
Collapse
Affiliation(s)
- Anne M L Jansen
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Dallas, TX, USA
| | - Pradipta Ghosh
- Departments of Medicine and Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tikam C Dakal
- Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India
| | - Thomas P Slavin
- Division of Clinical Cancer Genomics City of Hope, Department of Medical Oncology, National Medical Center, Duarte, CA, USA
| | - C Richard Boland
- Departments of Medicine and Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Dallas, TX, USA.
- Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, 91016, USA.
| |
Collapse
|
94
|
DeLeonardis K, Hogan L, Cannistra SA, Rangachari D, Tung N. When Should Tumor Genomic Profiling Prompt Consideration of Germline Testing? J Oncol Pract 2019; 15:465-473. [DOI: 10.1200/jop.19.00201] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Somatic genomic testing is rapidly becoming an integral part of care for patients with metastatic cancer. Extrapolation of these results beyond personalized cancer therapy is a skill being demanded of practicing oncologists without prior specialty in genetics. Up to 12% of tumor genomic profiling reports will reveal a germline pathogenic variant. Recognition of these germline variants is essential not only for optimal care of the patient with cancer but also to initiate cascade genetic testing in at-risk family members who also may carry the familial mutation. This article provides a concise and methodical, evidence-based strategy to guide oncology providers about how to identify genes associated with an inherited predisposition for cancer, determine the pathogenicity of variants reported within those genes, and understand the likelihood that these variants are of germline origin in a particular patient with cancer. Case examples are provided to illustrate clinical scenarios and facilitate application of the proposed approach.
Collapse
Affiliation(s)
| | - Lauren Hogan
- Beth Israel Deaconess Medical Center, Boston, MA
| | | | | | - Nadine Tung
- Beth Israel Deaconess Medical Center, Boston, MA
| |
Collapse
|
95
|
Natali F, Rancati G. The Mutator Phenotype: Adapting Microbial Evolution to Cancer Biology. Front Genet 2019; 10:713. [PMID: 31447882 PMCID: PMC6691094 DOI: 10.3389/fgene.2019.00713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 07/05/2019] [Indexed: 01/07/2023] Open
Abstract
The mutator phenotype hypothesis was postulated almost 40 years ago to reconcile the observation that while cancer cells display widespread mutational burden, acquisition of mutations in non-transformed cells is a rare event. Moreover, it also suggested that cancer evolution could be fostered by increased genome instability. Given the evolutionary conservation throughout the tree of life and the genetic tractability of model organisms, yeast and bacterial species pioneered studies to dissect the functions of genes required for genome maintenance (caretaker genes) or for cell growth control (gatekeeper genes). In this review, we first provide an overview of what we learned from model organisms about the roles of these genes and the genome instability that arises as a consequence of their dysregulation. We then discuss our current understanding of how mutator phenotypes shape the evolution of bacteria and yeast species. We end by bringing clinical evidence that lessons learned from single-cell organisms can be applied to tumor evolution.
Collapse
Affiliation(s)
- Federica Natali
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Giulia Rancati
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| |
Collapse
|
96
|
Hino H, Shiomi A, Kusuhara M, Kagawa H, Yamakawa Y, Hatakeyama K, Kawabata T, Oishi T, Urakami K, Nagashima T, Kinugasa Y, Yamaguchi K. Clinicopathological and mutational analyses of colorectal cancer with mutations in the POLE gene. Cancer Med 2019; 8:4587-4597. [PMID: 31240875 PMCID: PMC6712448 DOI: 10.1002/cam4.2344] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 05/28/2019] [Accepted: 05/31/2019] [Indexed: 01/03/2023] Open
Abstract
Here, we investigated the clinicopathological and mutation profiles of colorectal cancer (CRC) with POLE mutations. Whole‐exome sequencing was performed in 910 surgically resected primary CRCs. Tumors exceeding 500 counts of nonsynonymous single nucleotide variants (SNVs) were classified as hypermutators, whereas the remaining were classified as nonhypermutators. The hypermutators were subdivided into 2 groups. CRCs harboring more than 20% C‐to‐A and less than 3% C‐to‐G transversions were classified as POLE category tumors, whereas the remaining were classified as common‐hypermutators. Gene expression profiling (GEP) analysis was performed in 892 (98.0%) tumors. Fifty‐seven (6.3%) and 10 (1.1%) tumors were classified common‐hypermutators and POLE category tumors, respectively. POLE category tumors harbored a significantly higher SNV count than common‐hypermutators, and all POLE category tumors were associated with exonuclease domain mutations, such as P286R, F367C, V411L, and S297Y, in the POLE gene. Patients with POLE category tumors were significantly younger than those with nonhypermutators and common‐hypermutators. All POLE mutations in the early‐onset (age of onset ≤50 years old) POLE category (7 tumors) were P286R mutations. GEP analysis revealed that PD‐L1 and PD‐1 gene expression levels were significantly increased in both common‐hypermutators and POLE category tumors compared with those in nonhypermutators. CD8A expression was significantly upregulated in POLE category tumors compared with that in nonhypermutators. Thus, we concluded that CRCs with POLE proofreading deficiency had characteristics distinct from those of other CRCs. Analysis of POLE proofreading deficiency may be clinically significant for personalized management of CRCs.
Collapse
Affiliation(s)
- Hitoshi Hino
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Akio Shiomi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Masatoshi Kusuhara
- Regional Resources Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Hiroyasu Kagawa
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Yushi Yamakawa
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Keiichi Hatakeyama
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Takanori Kawabata
- Clinical Research Promotion Unit, Clinical Research Center, Shizuoka Cancer Center, Shizuoka, Japan
| | - Takuma Oishi
- Division of Pathology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | | | - Yusuke Kinugasa
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan.,Department of Gastrointestinal Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center Hospital and Research Institute, Shizuoka, Japan
| |
Collapse
|
97
|
Van Esch H, Colnaghi R, Freson K, Starokadomskyy P, Zankl A, Backx L, Abramowicz I, Outwin E, Rohena L, Faulkner C, Leong GM, Newbury-Ecob RA, Challis RC, Õunap K, Jaeken J, Seuntjens E, Devriendt K, Burstein E, Low KJ, O'Driscoll M. Defective DNA Polymerase α-Primase Leads to X-Linked Intellectual Disability Associated with Severe Growth Retardation, Microcephaly, and Hypogonadism. Am J Hum Genet 2019; 104:957-967. [PMID: 31006512 PMCID: PMC6506757 DOI: 10.1016/j.ajhg.2019.03.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/04/2019] [Indexed: 12/26/2022] Open
Abstract
Replicating the human genome efficiently and accurately is a daunting challenge involving the duplication of upward of three billion base pairs. At the core of the complex machinery that achieves this task are three members of the B family of DNA polymerases: DNA polymerases α, δ, and ε. Collectively these multimeric polymerases ensure DNA replication proceeds at optimal rates approaching 2 × 103 nucleotides/min with an error rate of less than one per million nucleotides polymerized. The majority of DNA replication of undamaged DNA is conducted by DNA polymerases δ and ε. The DNA polymerase α-primase complex performs limited synthesis to initiate the replication process, along with Okazaki-fragment synthesis on the discontinuous lagging strand. An increasing number of human disorders caused by defects in different components of the DNA-replication apparatus have been described to date. These are clinically diverse and involve a wide range of features, including variable combinations of growth delay, immunodeficiency, endocrine insufficiencies, lipodystrophy, and cancer predisposition. Here, by using various complementary approaches, including classical linkage analysis, targeted next-generation sequencing, and whole-exome sequencing, we describe distinct missense and splice-impacting mutations in POLA1 in five unrelated families presenting with an X-linked syndrome involving intellectual disability, proportionate short stature, microcephaly, and hypogonadism. POLA1 encodes the p180 catalytic subunit of DNA polymerase α-primase. A range of replicative impairments could be demonstrated in lymphoblastoid cell lines derived from affected individuals. Our findings describe the presentation of pathogenic mutations in a catalytic component of a B family DNA polymerase member, DNA polymerase α.
Collapse
Affiliation(s)
- Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium; Laboratory for the Genetics of Cognition, Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
| | - Rita Colnaghi
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Sussex, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Petro Starokadomskyy
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andreas Zankl
- Department of Clinical Genetics, the Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Hospital Westmead Clinical School, Sydney Medical School, the University of Sydney, Westmead, NSW 2145, Australia; Bone Biology Division and Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Liesbeth Backx
- Laboratory for the Genetics of Cognition, Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Iga Abramowicz
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Sussex, UK
| | - Emily Outwin
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Sussex, UK
| | - Luis Rohena
- Division of Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, TX 78234, USA
| | - Claire Faulkner
- Bristol Genetics Laboratory, Southmead Hospital, BS10 5NB Bristol, UK
| | - Gary M Leong
- Department of Paediatrics, Nepean Hospital, Nepean Clinical School, the University of Sydney, Kingswood, NSW 2747, Australia
| | - Ruth A Newbury-Ecob
- Clinical Genetics, St. Michael's Hospital, University Hospitals NHS Trust, BS2 8HW Bristol, UK
| | - Rachel C Challis
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, UK
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Jacques Jaeken
- Center for Metabolic Diseases, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Eve Seuntjens
- Developmental Neurobiology, Department of Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Ezra Burstein
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390 Texas, USA
| | - Karen J Low
- Clinical Genetics, St. Michael's Hospital, University Hospitals NHS Trust, BS2 8HW Bristol, UK
| | - Mark O'Driscoll
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Sussex, UK.
| |
Collapse
|
98
|
Bonjoch L, Mur P, Arnau-Collell C, Vargas-Parra G, Shamloo B, Franch-Expósito S, Pineda M, Capellà G, Erman B, Castellví-Bel S. Approaches to functionally validate candidate genetic variants involved in colorectal cancer predisposition. Mol Aspects Med 2019; 69:27-40. [PMID: 30935834 DOI: 10.1016/j.mam.2019.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 02/07/2023]
Abstract
Most next generation sequencing (NGS) studies identified candidate genetic variants predisposing to colorectal cancer (CRC) but do not tackle its functional interpretation to unequivocally recognize a new hereditary CRC gene. Besides, germline variants in already established hereditary CRC-predisposing genes or somatic variants share the same need when trying to categorize those with relevant significance. Functional genomics approaches have an important role in identifying the causal links between genetic architecture and phenotypes, in order to decipher cellular function in health and disease. Therefore, functional interpretation of identified genetic variants by NGS platforms is now essential. Available approaches nowadays include bioinformatics, cell and molecular biology and animal models. Recent advances, such as the CRISPR-Cas9, ZFN and TALEN systems, have been already used as a powerful tool with this objective. However, the use of cell lines is of limited value due to the CRC heterogeneity and its close interaction with microenvironment. Access to tridimensional cultures or organoids and xenograft models that mimic the in vivo tissue architecture could revolutionize functional analysis. This review will focus on the application of state-of-the-art functional studies to better tackle new genes involved in germline predisposition to this neoplasm.
Collapse
Affiliation(s)
- Laia Bonjoch
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Coral Arnau-Collell
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Gardenia Vargas-Parra
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Bahar Shamloo
- Molecular Biology, Genetics, and Bioengineering Department, Legacy Research Institute, Portland, OR, USA
| | - Sebastià Franch-Expósito
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Gabriel Capellà
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Batu Erman
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain.
| |
Collapse
|
99
|
Alldredge J, Randall L. Germline and Somatic Tumor Testing in Gynecologic Cancer Care. Obstet Gynecol Clin North Am 2019; 46:37-53. [PMID: 30683265 DOI: 10.1016/j.ogc.2018.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
New technologies have advanced the science of tumor biology and genomics. Commercially available germline and somatic testing modalities have the downstream benefits of enabling prevention strategies in women with hereditary cancers and their family members in addition to identifying women who benefit most from novel targeted therapeutics. The matrix of available testing is complex and evolving. Women's health providers need to be versed in benefits and limitations of available testing. Genetic counselors play a pivotal role in interpretation of relevant mutations, and in avoiding common pitfalls, but their skill set is not sufficient to optimally integrate cancer genomics into clinical practice.
Collapse
Affiliation(s)
- Jill Alldredge
- University of California, Irvine, 333 The City Boulevard, Suite 1400, Orange, CA 92868, USA.
| | - Leslie Randall
- University of California, Irvine, 333 The City Boulevard, Suite 1400, Orange, CA 92868, USA
| |
Collapse
|
100
|
Puccini A, Lenz HJ, Marshall JL, Arguello D, Raghavan D, Korn WM, Weinberg BA, Poorman K, Heeke AL, Philip PA, Shields AF, Goldberg RM, Salem ME. Impact of Patient Age on Molecular Alterations of Left-Sided Colorectal Tumors. Oncologist 2019; 24:319-326. [PMID: 30018131 PMCID: PMC6519749 DOI: 10.1634/theoncologist.2018-0117] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/27/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The incidence of colorectal cancer (CRC) in younger patients is rising, mostly due to tumors in the descending colon and rectum. Therefore, we aimed to explore the molecular differences of left-sided CRC between younger (≤45 years) and older patients (≥65). SUBJECTS, MATERIALS, AND METHODS In total, 1,126 CRC tumor samples from the splenic flexure to (and including) the rectum were examined by next-generation sequencing (NGS), immunohistochemistry, and in situ hybridization. Microsatellite instability (MSI) and tumor mutational burden (TMB) were assessed by NGS. RESULTS Younger patients (n = 350), when compared with older patients (n = 776), showed higher mutation rates in genes associated with cancer-predisposing syndromes (e.g., Lynch syndrome), such as MSH6 (4.8% vs. 1.2%, p = .005), MSH2 (2.7% vs. 0.0%, p = .004), POLE (1.6% vs. 0.0%, p = .008), NF1 (5.9% vs. 0.5%, p < .001), SMAD4 (14.3% vs. 8.3%, p = .024), and BRCA2 (3.7% vs. 0.5%, p = .002). Genes involved in histone modification were also significantly more mutated: KDM5C (1.9% vs. 0%, p = .036), KMT2A (1.1% vs. 0%, p = .033), KMT2C (1.6% vs. 0%, p = .031), KMT2D (3.8% vs. 0.7%, p = .005), and SETD2 (3.2% vs. 0.9%, p = .039). Finally, TMB-high (9.7% vs. 2.8%, p < .001) and MSI-high (MSI-H; 8.1% vs. 1.9%, p = .009) were more frequent in younger patients. CONCLUSION Our findings highlight the importance of genetic counseling and screening in younger CRC patients. MSI-H and TMB-high tumors could benefit from immune-checkpoint inhibitors, now approved for the treatment of MSI-H/deficient mismatch repair metastatic CRC patients. Finally, histone modifiers could serve as a new promising therapeutic target. With confirmatory studies, these results may influence our approach to younger adults with CRC. IMPLICATIONS FOR PRACTICE The increasing rate of colorectal cancers (CRC), primarily distal tumors, among young adults poses a global health issue. This study investigates the molecular differences between younger (≤45 years old) and older (≥65) adults with left-sided CRCs. Younger patients more frequently harbor mutations in genes associated with cancer-predisposing syndromes. Higher rates of microsatellite instability-high and tumor mutational burden-high tumors occur in younger patients, who could benefit from immune-checkpoint inhibitors. Finally, histone modifiers are more frequently mutated in younger patients and could serve as a new promising therapeutic target. This study provides new insights into mutations that may guide development of novel tailored therapy in younger CRC patients.
Collapse
Affiliation(s)
- Alberto Puccini
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Department of Medical Oncology, Ospedale Policlinico San Martino, Genova, Italy
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - John L Marshall
- Ruesch Center for The Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | | | - Derek Raghavan
- Levine Cancer Institute, Carolinas HealthCare System, Charlotte, North Carolina, USA
| | | | - Benjamin A Weinberg
- Ruesch Center for The Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | | | - Arielle L Heeke
- Ruesch Center for The Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Philip A Philip
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, Michigan, USA
| | - Anthony F Shields
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, Michigan, USA
| | - Richard M Goldberg
- West Virginia University Cancer Institute, Morgantown, West Virginia, USA
| | - Mohamed E Salem
- Levine Cancer Institute, Carolinas HealthCare System, Charlotte, North Carolina, USA
| |
Collapse
|