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Liffers ST, Godfrey L, Frohn L, Haeberle L, Yavas A, Vesce R, Goering W, Opitz FV, Stoecklein N, Knoefel WT, Schlitter AM, Klöppel G, Espinet E, Trumpp A, Siveke JT, Esposito I. Molecular heterogeneity and commonalities in pancreatic cancer precursors with gastric and intestinal phenotype. Gut 2023; 72:522-534. [PMID: 35944927 PMCID: PMC9933174 DOI: 10.1136/gutjnl-2021-326550] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 07/31/2022] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Due to the limited number of modifiable risk factors, secondary prevention strategies based on early diagnosis represent the preferred route to improve the prognosis of pancreatic ductal adenocarcinoma (PDAC). Here, we provide a comparative morphogenetic analysis of PDAC precursors aiming at dissecting the process of carcinogenesis and tackling the heterogeneity of preinvasive lesions. DESIGN Targeted and whole-genome low-coverage sequencing, genome-wide methylation and transcriptome analyses were applied on a final collective of 122 morphologically well-characterised low-grade and high-grade PDAC precursors, including intestinal and gastric intraductal papillary mucinous neoplasms (IPMN) and pancreatic intraepithelial neoplasias (PanIN). RESULTS Epigenetic regulation of mucin genes determines the phenotype of PDAC precursors. PanIN and gastric IPMN display a ductal molecular profile and numerous similarly regulated pathways, including the Notch pathway, but can be distinguished by recurrent deletions and differential methylation and, in part, by the expression of mucin-like 3. Intestinal IPMN are clearly distinct lesions at the molecular level with a more instable genotype and are possibly related to a different ductal cell compartment. CONCLUSIONS PDAC precursors with gastric and intestinal phenotype are heterogeneous in terms of morphology, genetic and epigenetic profile. This heterogeneity is related to a different cell identity and, possibly, to a different aetiology.
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Affiliation(s)
- Sven-Thorsten Liffers
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Laura Godfrey
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Lisa Frohn
- Institute of Pathology, Heinrich-Heine University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | - Lena Haeberle
- Institute of Pathology, Heinrich-Heine University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | - Aslihan Yavas
- Institute of Pathology, Heinrich-Heine University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | - Rita Vesce
- Institute of Pathology, Heinrich-Heine University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | - Wolfgang Goering
- Institute of Pathology, Heinrich-Heine University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | - Friederike V Opitz
- Institute of Pathology, Heinrich-Heine University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | - Nickolas Stoecklein
- Department of General, Visceral and Pediatric Surgery, Heinrich-Heine-University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | - Wolfram Trudo Knoefel
- Department of General, Visceral and Pediatric Surgery, Heinrich-Heine-University and University Hospital of Dusseldorf, Dusseldorf, Germany
| | | | - Guenter Klöppel
- Institute of Pathology, Technische Universitaet Muenchen, Munich, Germany
| | - Elisa Espinet
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine GmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Centre and DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Consortium, (DKTK), Heidelberg, Germany
| | - Andreas Trumpp
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine GmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Centre and DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Consortium, (DKTK), Heidelberg, Germany
| | - Jens T Siveke
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Irene Esposito
- Institute of Pathology, Heinrich-Heine University and University Hospital of Dusseldorf, Dusseldorf, Germany
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2
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Maurya VK, Szwarc MM, Fernandez-Valdivia R, Lonard DM, Song Y, Joshi N, Fazleabas AT, Lydon JP. Early growth response 1 transcription factor is essential for the pathogenic properties of human endometriotic epithelial cells. Reproduction 2022; 164:41-54. [PMID: 35679138 PMCID: PMC9339520 DOI: 10.1530/rep-22-0123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/09/2022] [Indexed: 01/13/2023]
Abstract
Although a non-malignant gynecological disorder, endometriosis displays some pathogenic features of malignancy, such as cell proliferation, migration, invasion and adaptation to hypoxia. Current treatments of endometriosis include pharmacotherapy and/or surgery, which are of limited efficacy and often associated with adverse side effects. Therefore, to develop more effective therapies to treat this disease, a broader understanding of the underlying molecular mechanisms that underpin endometriosis needs to be attained. Using immortalized human endometriotic epithelial and stromal cell lines, we demonstrate that the early growth response 1 (EGR1) transcription factor is essential for cell proliferation, migration and invasion, which represent some of the pathogenic properties of endometriotic cells. Genome-wide transcriptomics identified an EGR1-dependent transcriptome in human endometriotic epithelial cells that potentially encodes a diverse spectrum of proteins that are known to be involved in tissue pathologies. To underscore the utility of this transcriptomic data set, we demonstrate that carbonic anhydrase 9 (CA9), a homeostatic regulator of intracellular pH, is not only a molecular target of EGR1 but is also important for maintaining many of the cellular properties of human endometriotic epithelial cells that are also ascribed to EGR1. Considering therapeutic intervention strategies are actively being developed for EGR1 and CAIX in the treatment of other pathologies, we believe EGR1 and its transcriptome (which includes CA9) will offer not only a new conceptual framework to advance our understanding of endometriosis but will also furnish new molecular vulnerabilities to be leveraged as potential therapeutic options in the future treatment of endometriosis.
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Affiliation(s)
- Vineet K. Maurya
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Maria M. Szwarc
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | | | - David M. Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Yong Song
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University, Grand Rapids, Michigan
| | - Niraj Joshi
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University, Grand Rapids, Michigan
| | - Asgerally T. Fazleabas
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University, Grand Rapids, Michigan
| | - John P. Lydon
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA,Correspondence should be addressed to JP Lydon;
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Zhang R, Cao L, Chen W, Ge H, Hu X, Li Z, Wang Y, Fan W, Yong L, Yu Y, Mao Y, Zhen Q, Liu H, Zhang F, Sun L. Fine-Mapping of the Major Histocompatibility Complex Region Linked to Leprosy in Northern China. Front Genet 2022; 12:768259. [PMID: 34976012 PMCID: PMC8716717 DOI: 10.3389/fgene.2021.768259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/29/2021] [Indexed: 01/31/2023] Open
Abstract
Background: Leprosy is a chronic infectious skin and neurological disease, and genetic background is considered to be one of the major factors of risk. The major histocompatibility complex (MHC) region not only affects susceptibility to leprosy but also its development and outcome. Given the complex traits of the MHC region, variants and the potential mechanism by which HLA influences leprosy development need to be further explored. Methods: We extracted previous genome-wide association study data from the Northern Han Chinese population to perform HLA fine-mapping. Using the 1,000 Genome Project Phase 3 dataset as the reference panel, single-nucleotide polymorphisms (SNP), insertion and deletion (INDEL) and copy number variant (CNV) imputation were carried out. HLA classical alleles and amino acids in the MHC region were imputed using the HAN-MHC database. Further stepwise regression analysis was conducted to analyze independent signals of variants related to leprosy. Results: We identified four independent variants: esv3608598, rs7754498, rs3130781 and rs144388449. Among them, esv3608598 is a CNV and the first HLA CNV associated with leprosy risk. SNP annotation using RegulomeDB, HaploReg, and rVarBase showed that three SNPs are likely to affect the pathogenesis of leprosy. Conclusion: In summary, this is the first study to assess the association between HLA CNV and leprosy susceptibility in a Northern Han Chinese population. By fine mapping of the MHC region in this population, our findings provide evidence for the contribution of HLA to leprosy susceptibility.
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Affiliation(s)
- Ruixue Zhang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Lu Cao
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Weiwei Chen
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Huiyao Ge
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Xia Hu
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Zhuo Li
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Yirui Wang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Wencheng Fan
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Liang Yong
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Yafen Yu
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Yiwen Mao
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Qi Zhen
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Hong Liu
- Shandong Provincial Hospital for Skin Diseases and Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Furen Zhang
- Shandong Provincial Hospital for Skin Diseases and Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Liangdan Sun
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
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Halo JV, Pendleton AL, Jarosz AS, Gifford RJ, Day ML, Kidd JM. Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids. Retrovirology 2019; 16:6. [PMID: 30845962 PMCID: PMC6407205 DOI: 10.1186/s12977-019-0468-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 02/28/2019] [Indexed: 01/20/2023] Open
Abstract
Background Vertebrate genomes contain a record of retroviruses that invaded the germlines of ancestral hosts and are passed to offspring as endogenous retroviruses (ERVs). ERVs can impact host function since they contain the necessary sequences for expression within the host. Dogs are an important system for the study of disease and evolution, yet no substantiated reports of infectious retroviruses in dogs exist. Here, we utilized Illumina whole genome sequence data to assess the origin and evolution of a recently active gammaretroviral lineage in domestic and wild canids. Results We identified numerous recently integrated loci of a canid-specific ERV-Fc sublineage within Canis, including 58 insertions that were absent from the reference assembly. Insertions were found throughout the dog genome including within and near gene models. By comparison of orthologous occupied sites, we characterized element prevalence across 332 genomes including all nine extant canid species, revealing evolutionary patterns of ERV-Fc segregation among species as well as subpopulations. Conclusions Sequence analysis revealed common disruptive mutations, suggesting a predominant form of ERV-Fc spread by trans complementation of defective proviruses. ERV-Fc activity included multiple circulating variants that infected canid ancestors from the last 20 million to within 1.6 million years, with recent bursts of germline invasion in the sublineage leading to wolves and dogs. Electronic supplementary material The online version of this article (10.1186/s12977-019-0468-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julia V Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
| | - Amanda L Pendleton
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Abigail S Jarosz
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Robert J Gifford
- Centre for Virus Research, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Malika L Day
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Ave., Ann Arbor, MI, 48109, USA
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