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Kadian LK, Arora M, Prasad CP, Pramanik R, Chauhan SS. Signaling pathways and their potential therapeutic utility in esophageal squamous cell carcinoma. Clin Transl Oncol 2022; 24:1014-1032. [PMID: 34990001 DOI: 10.1007/s12094-021-02763-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022]
Abstract
Esophageal cancer is a complex gastrointestinal malignancy with an extremely poor outcome. Approximately 80% of cases of this malignancy in Asian countries including India are of squamous cell origin, termed Esophageal Squamous Cell Carcinoma (ESCC).The five-year survival rate in ESCC patients is less than 20%. Neo-adjuvant chemo-radiotherapy (NACRT) followed by surgical resection remains the major therapeutic strategy for patients with operable ESCC. However, resistance to NACRT and local recurrence after initial treatment are the leading cause of dismal outcomes in these patients. Therefore, an alternative strategy to promote response to the therapy and reduce the post-operative disease recurrence is highly needed. At the molecular level, wide variations have been observed in tumor characteristics among different populations, nevertheless, several common molecular features have been identified which orchestrate disease progression and clinical outcome in the malignancy. Therefore, determination of candidate molecular pathways for targeted therapy remains the mainstream idea of focus in ESCC research. In this review, we have discussed the key signaling pathways associated with ESCC, i.e., Notch, Wnt, and Nrf2 pathways, and their crosstalk during disease progression. We further discuss the recent developments of novel agents to target these pathways in the context of targeted cancer therapy. In-depth research of the signaling pathways, gene signatures, and a combinatorial approach may help in discovering targeted therapy for ESCC.
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Affiliation(s)
- L K Kadian
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - M Arora
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - C P Prasad
- Department of Medical Oncology (Lab), Dr. B. R. Ambedkar-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - R Pramanik
- Department of Medical Oncology, Dr. B. R. Ambedkar-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - S S Chauhan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
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2
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Soares-Lima SC, Mehanna H, Camuzi D, de Souza-Santos PT, Simão TDA, Nicolau-Neto P, Almeida Lopes MDS, Cuenin C, Talukdar FR, Batis N, Costa I, Dias F, Degli Esposti D, Boroni M, Herceg Z, Ribeiro Pinto LF. Upper Aerodigestive Tract Squamous Cell Carcinomas Show Distinct Overall DNA Methylation Profiles and Different Molecular Mechanisms behind WNT Signaling Disruption. Cancers (Basel) 2021; 13:3014. [PMID: 34208581 PMCID: PMC8234055 DOI: 10.3390/cancers13123014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/27/2021] [Accepted: 06/08/2021] [Indexed: 12/28/2022] Open
Abstract
Upper aerodigestive tract (UADT) tumors present different biological behavior and prognosis, suggesting specific molecular mechanisms underlying their development. However, they are rarely considered as single entities (particularly head and neck subsites) and share the most common genetic alterations. Therefore, there is a need for a better understanding of the global DNA methylation differences among UADT tumors. We performed a genome-wide DNA methylation analysis of esophageal (ESCC), laryngeal (LSCC), oral (OSCC) and oropharyngeal (OPSCC) squamous cell carcinomas, and their non-tumor counterparts. The unsupervised analysis showed that non-tumor tissues present markedly distinct DNA methylation profiles, while tumors are highly heterogeneous. Hypomethylation was more frequent in LSCC and OPSCC, while ESCC and OSCC presented mostly hypermethylation, with the latter showing a CpG island overrepresentation. Differentially methylated regions affected genes in 127 signaling pathways, with only 3.1% of these being common among different tumor subsites, but with different genes affected. The WNT signaling pathway, known to be dysregulated in different epithelial tumors, is a frequent hit for DNA methylation and gene expression alterations in ESCC and OPSCC, but mostly for genetic alterations in LSCC and OSCC. UADT tumor subsites present differences in genome-wide methylation regarding their profile, intensity, genomic regions and signaling pathways affected.
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Affiliation(s)
- Sheila Coelho Soares-Lima
- Molecular Carcinogenesis Program, Brazilian National Cancer Institute, Rua André Cavalcanti, 37–6° Andar, Bairro de Fátima, Rio de Janeiro 20231-050, Brazil; (S.C.S.-L.); (D.C.); (P.N.-N.); (M.d.S.A.L.)
| | - Hisham Mehanna
- Institute of Head and Neck Studies and Education (InHANSE), Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (H.M.); (N.B.)
| | - Diego Camuzi
- Molecular Carcinogenesis Program, Brazilian National Cancer Institute, Rua André Cavalcanti, 37–6° Andar, Bairro de Fátima, Rio de Janeiro 20231-050, Brazil; (S.C.S.-L.); (D.C.); (P.N.-N.); (M.d.S.A.L.)
| | | | - Tatiana de Almeida Simão
- Departamento de Bioquímica, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Av. 28 de Setembro 87 fundos, Vila Isabel, Rio de Janeiro 20551-013, Brazil;
| | - Pedro Nicolau-Neto
- Molecular Carcinogenesis Program, Brazilian National Cancer Institute, Rua André Cavalcanti, 37–6° Andar, Bairro de Fátima, Rio de Janeiro 20231-050, Brazil; (S.C.S.-L.); (D.C.); (P.N.-N.); (M.d.S.A.L.)
| | - Monique de Souza Almeida Lopes
- Molecular Carcinogenesis Program, Brazilian National Cancer Institute, Rua André Cavalcanti, 37–6° Andar, Bairro de Fátima, Rio de Janeiro 20231-050, Brazil; (S.C.S.-L.); (D.C.); (P.N.-N.); (M.d.S.A.L.)
| | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, CEDEX 08, 69372 Lyon, France; (C.C.); (F.R.T.); (D.D.E.); (Z.H.)
| | - Fazlur Rahman Talukdar
- Epigenetics Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, CEDEX 08, 69372 Lyon, France; (C.C.); (F.R.T.); (D.D.E.); (Z.H.)
| | - Nikolaos Batis
- Institute of Head and Neck Studies and Education (InHANSE), Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (H.M.); (N.B.)
| | - Izabella Costa
- Seção de Cirurgia de Cabeça e Pescoço, Instituto Nacional de Câncer—INCA, Praça da Cruz Vermelha, Rio de Janeiro 20230-130, Brazil; (I.C.); (F.D.)
| | - Fernando Dias
- Seção de Cirurgia de Cabeça e Pescoço, Instituto Nacional de Câncer—INCA, Praça da Cruz Vermelha, Rio de Janeiro 20230-130, Brazil; (I.C.); (F.D.)
| | - Davide Degli Esposti
- Epigenetics Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, CEDEX 08, 69372 Lyon, France; (C.C.); (F.R.T.); (D.D.E.); (Z.H.)
| | - Mariana Boroni
- Bioinformatics and Computational Biology Lab, Brazilian National Cancer Institute, Rua André Cavalcanti, 37–1° Andar, Bairro de Fátima, Rio de Janeiro 20231-050, Brazil;
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, CEDEX 08, 69372 Lyon, France; (C.C.); (F.R.T.); (D.D.E.); (Z.H.)
| | - Luis Felipe Ribeiro Pinto
- Molecular Carcinogenesis Program, Brazilian National Cancer Institute, Rua André Cavalcanti, 37–6° Andar, Bairro de Fátima, Rio de Janeiro 20231-050, Brazil; (S.C.S.-L.); (D.C.); (P.N.-N.); (M.d.S.A.L.)
- Departamento de Bioquímica, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Av. 28 de Setembro 87 fundos, Vila Isabel, Rio de Janeiro 20551-013, Brazil;
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3
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Nussinov R, Zhang M, Maloney R, Jang H. Drugging multiple same-allele driver mutations in cancer. Expert Opin Drug Discov 2021; 16:823-828. [PMID: 33769165 DOI: 10.1080/17460441.2021.1905628] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunoMetabolism, National Cancer Institute, Frederick U.S.A.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University Israel
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunoMetabolism, National Cancer Institute, Frederick U.S.A
| | - Ryan Maloney
- Computational Structural Biology Section, Laboratory of Cancer ImmunoMetabolism, National Cancer Institute, Frederick USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunoMetabolism, National Cancer Institute, Frederick U.S.A
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Meireles Da Costa N, Palumbo A, De Martino M, Fusco A, Ribeiro Pinto LF, Nasciutti LE. Interplay between HMGA and TP53 in cell cycle control along tumor progression. Cell Mol Life Sci 2021; 78:817-831. [PMID: 32920697 PMCID: PMC11071717 DOI: 10.1007/s00018-020-03634-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/05/2020] [Accepted: 09/03/2020] [Indexed: 01/27/2023]
Abstract
The high mobility group A (HMGA) proteins are found to be aberrantly expressed in several tumors. Studies (in vitro and in vivo) have shown that HMGA protein overexpression has a causative role in carcinogenesis process. HMGA proteins regulate cell cycle progression through distinct mechanisms which strongly influence its normal dynamics along malignant transformation. Tumor protein p53 (TP53) is the most frequently altered gene in cancer. The loss of its activity is recognized as the fall of a barrier that enables neoplastic transformation. Among the different functions, TP53 signaling pathway is tightly involved in control of cell cycle, with cell cycle arrest being the main biological outcome observed upon p53 activation, which prevents accumulation of damaged DNA, as well as genomic instability. Therefore, the interaction and opposing effects of HMGA and p53 proteins on regulation of cell cycle in normal and tumor cells are discussed in this review. HMGA proteins and p53 may reciprocally regulate the expression and/or activity of each other, leading to the counteraction of their regulation mechanisms at different stages of the cell cycle. The existence of a functional crosstalk between these proteins in the control of cell cycle could open the possibility of targeting HMGA and p53 in combination with other therapeutic strategies, particularly those that target cell cycle regulation, to improve the management and prognosis of cancer patients.
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Affiliation(s)
- Nathalia Meireles Da Costa
- Programa de Carcinogênese Molecular, Instituto Nacional de Câncer-INCA, Rua André Cavalcanti, 37-6th floor-Centro, 20231-050, Rio de Janeiro, RJ, Brazil.
| | - Antonio Palumbo
- Laboratório de Interações Celulares, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro Prédio de Ciências da Saúde-Cidade Universitária, Ilha do Fundão, A. Carlos Chagas, 373-Bloco F, Sala 26, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Marco De Martino
- Istituto di Endocrinologia e Oncologia Sperimentale-CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Alfredo Fusco
- Istituto di Endocrinologia e Oncologia Sperimentale-CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Luis Felipe Ribeiro Pinto
- Programa de Carcinogênese Molecular, Instituto Nacional de Câncer-INCA, Rua André Cavalcanti, 37-6th floor-Centro, 20231-050, Rio de Janeiro, RJ, Brazil
| | - Luiz Eurico Nasciutti
- Laboratório de Interações Celulares, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro Prédio de Ciências da Saúde-Cidade Universitária, Ilha do Fundão, A. Carlos Chagas, 373-Bloco F, Sala 26, 21941-902, Rio de Janeiro, RJ, Brazil.
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5
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Barros LRC, Souza-Santos PTD, Pretti MAM, Vieira GF, Bragatte MADS, Mendes MFDA, De Freitas MV, Scherer NDM, De Oliveira IM, Rapozo DCM, Fernandes PV, Simão TDA, Soares-Lima SC, Boroni M, Ribeiro Pinto LF, Bonamino MH. High infiltration of B cells in tertiary lymphoid structures, TCR oligoclonality, and neoantigens are part of esophageal squamous cell carcinoma microenvironment. J Leukoc Biol 2020; 108:1307-1318. [PMID: 32827331 DOI: 10.1002/jlb.5ma0720-710rrr] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 12/16/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCA) exhibits high intratumoral molecular heterogeneity posing a challenge to cancer therapy. Immune checkpoint blockade therapy has been approved for this disease, but with modest results. RNA-Seq data from paired tumor and surrounding nonmalignant tissue from 14 patients diagnosed with ESCA without previous treatment and from The Cancer Genome Atlas-ESCA cohort were analyzed. Herein, we investigated ESCA immune landscape including mutation-derived neoantigens and immune cell subpopulations. Tumor-associated antigen expression was determined by in silico analyses and confirmed by immunohistochemistry showing that PRAME, CEACAM4, and MAGEA11 proteins are expressed on tumors. Immune checkpoint molecules gene expression was higher in the tumor compared with surrounding nonmalignant tissue, but its expression varies greatly among patients. TCR repertoire and BCR transcripts analysis evidenced low clonal diversity with one TCR clone predicted to be specific for a MAGEA11-derived peptide. A high number of B-cell clones infiltrating the tumors and the abundance of these cells in tertiary lymphoid structures observed in ESCA tumors support B cells as a potential immune modulator in this tumor.
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Affiliation(s)
| | | | - Marco Antonio Marques Pretti
- Programa de Carcinogênese Molecular, Instituto Nacional de Câncer-INCA, Rio de Janeiro, Brazil.,Laboratório de Bioinformática e Biologia Computacional, Instituto Nacional de Câncer, INCA
| | - Gustavo Fioravanti Vieira
- Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Canoas, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Marcelo Alves De Souza Bragatte
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Marcus Fabiano De Almeida Mendes
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Martiela Vaz De Freitas
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | | | | | | | - Tatiana De Almeida Simão
- Departamento de Bioquímica, IBRAG, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Mariana Boroni
- Laboratório de Bioinformática e Biologia Computacional, Instituto Nacional de Câncer, INCA
| | - Luis Felipe Ribeiro Pinto
- Programa de Carcinogênese Molecular, Instituto Nacional de Câncer-INCA, Rio de Janeiro, Brazil.,Departamento de Bioquímica, IBRAG, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Martin Hernan Bonamino
- Programa de Carcinogênese Molecular, Instituto Nacional de Câncer-INCA, Rio de Janeiro, Brazil.,Vice-Presidência de Pesquisa e Coleções Biológicas (VPPCB), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
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Song G, Xu J, He L, Sun X, Xiong R, Luo Y, Hu X, Zhang R, Yue Q, Liu K, Feng G. Systematic profiling identifies PDLIM2 as a novel prognostic predictor for oesophageal squamous cell carcinoma (ESCC). J Cell Mol Med 2019; 23:5751-5761. [PMID: 31222932 PMCID: PMC6653303 DOI: 10.1111/jcmm.14491] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/29/2019] [Accepted: 05/26/2019] [Indexed: 02/06/2023] Open
Abstract
Till now, no appropriate biomarkers for high‐risk population screening and prognosis prediction have been identified for patients with oesophageal squamous cell carcinoma (ESCC). In this study, by the combined use of data from the Gene Expression Omnibus (GEO) datasets and The Cancer Genome Atlas (TCGA)‐oesophageal carcinoma (ESCA), we aimed to screen dysregulated genes with prognostic value in ESCC and the genetic and epigenetic alterations underlying the dysregulation. About 222 genes that had at least fourfold change in ESCC compared with adjacent normal tissues were identified using the microarray data in GDS3838. Among these genes, only PDLIM2 was associated with nodal invasion and overall survival (OS) at the same time. The high PDLIM2 expression group had significantly longer OS and its expression was independently associated with better OS (HR: 0.64, 95% CI: 0.43‐0.95, P = 0.03), after adjustment for gender and pathologic stages. The expression of its exon 7/8/9/10 had the highest AUC value (0.724) and better prognostic value (HR: 0.43, 95% CI: 0.22‐0.83, P = 0.01) than total PDLIM2 expression. PDLIM2 DNA copy deletion was common in ESCC and was associated with decreased gene expression. The methylation status of two CpG sites (cg23696886 and cg20449614) in the proximal promoter region of PDLIM2 showed a moderate negative correlation with the gene expression in PDLIM2 copy neutral/amplification group. In conclusion, we infer that PDLIM2 expression might be a novel prognostic indicator for ESCC patients. Its exon 7/8/9/10 expression had the best prognostic value. Its down‐regulation might be associated with gene‐level copy deletion and promoter hypermethylation.
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Affiliation(s)
- Guiqin Song
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China.,Department of Biology, North Sichuan Medical College, Nanchong, China
| | - Jun Xu
- Department of Thoracic Surgery, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China
| | - Lang He
- Department of Oncology, The Fifth People's Hospital of Chengdu, The Second Clinical Medical School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiao Sun
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China.,Precision Medicine Center, Nanchong Central Hospital, Nanchong, China
| | - Rong Xiong
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China.,Precision Medicine Center, Nanchong Central Hospital, Nanchong, China
| | - Yuxi Luo
- The First Clinical College of Anhui Medical University, Hefei, China
| | - Xin Hu
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China.,Precision Medicine Center, Nanchong Central Hospital, Nanchong, China
| | - Ruolan Zhang
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China.,Precision Medicine Center, Nanchong Central Hospital, Nanchong, China
| | - Qiuju Yue
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China.,Precision Medicine Center, Nanchong Central Hospital, Nanchong, China
| | - Kang Liu
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China.,Precision Medicine Center, Nanchong Central Hospital, Nanchong, China
| | - Gang Feng
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China.,Precision Medicine Center, Nanchong Central Hospital, Nanchong, China
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Krimpenfort P, Snoek M, Lambooij JP, Song JY, van der Weide R, Bhaskaran R, Teunissen H, Adams DJ, de Wit E, Berns A. A natural WNT signaling variant potently synergizes with Cdkn2ab loss in skin carcinogenesis. Nat Commun 2019; 10:1425. [PMID: 30926782 PMCID: PMC6441055 DOI: 10.1038/s41467-019-09321-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 02/13/2019] [Indexed: 12/15/2022] Open
Abstract
Cdkn2ab knockout mice, generated from 129P2 ES cells develop skin carcinomas. Here we show that the incidence of these carcinomas drops gradually in the course of backcrossing to the FVB/N background. Microsatellite analyses indicate that this cancer phenotype is linked to a 20 Mb region of 129P2 chromosome 15 harboring the Wnt7b gene, which is preferentially expressed from the 129P2 allele in skin carcinomas and derived cell lines. ChIPseq analysis shows enrichment of H3K27-Ac, a mark for active enhancers, in the 5' region of the Wnt7b 129P2 gene. The Wnt7b 129P2 allele appears sufficient to cause in vitro transformation of Cdkn2ab-deficient cell lines primarily through CDK6 activation. These results point to a critical role of the Cdkn2ab locus in keeping the oncogenic potential of physiological levels of WNT signaling in check and illustrate that GWAS-based searches for cancer predisposing allelic variants can be enhanced by including defined somatically acquired lesions as an additional input.
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Affiliation(s)
- Paul Krimpenfort
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Margriet Snoek
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jan-Paul Lambooij
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Ji-Ying Song
- Department of Experimental Animal Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Robin van der Weide
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Rajith Bhaskaran
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Hans Teunissen
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Elzo de Wit
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Anton Berns
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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