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Zhang Z, Sun X, Liu Y, Zhang Y, Yang Z, Dong J, Wang N, Ying J, Zhou M, Yang L. Spatial Transcriptome-Wide Profiling of Small Cell Lung Cancer Reveals Intra-Tumoral Molecular and Subtype Heterogeneity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402716. [PMID: 38896789 PMCID: PMC11336901 DOI: 10.1002/advs.202402716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/21/2024] [Indexed: 06/21/2024]
Abstract
Small cell lung cancer (SCLC) is a highly aggressive malignancy characterized by rapid growth and early metastasis and is susceptible to treatment resistance and recurrence. Understanding the intra-tumoral spatial heterogeneity in SCLC is crucial for improving patient outcomes and clinically relevant subtyping. In this study, a spatial whole transcriptome-wide analysis of 25 SCLC patients at sub-histological resolution using GeoMx Digital Spatial Profiling technology is performed. This analysis deciphered intra-tumoral multi-regional heterogeneity, characterized by distinct molecular profiles, biological functions, immune features, and molecular subtypes within spatially localized histological regions. Connections between different transcript-defined intra-tumoral phenotypes and their impact on patient survival and therapeutic response are also established. Finally, a gene signature, termed ITHtyper, based on the prevalence of intra-tumoral heterogeneity levels, which enables patient risk stratification from bulk RNA-seq profiles is identified. The prognostic value of ITHtyper is rigorously validated in independent multicenter patient cohorts. This study introduces a preliminary tumor-centric, regionally targeted spatial transcriptome resource that sheds light on previously unexplored intra-tumoral spatial heterogeneity in SCLC. These findings hold promise to improve tumor reclassification and facilitate the development of personalized treatments for SCLC patients.
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Affiliation(s)
- Zicheng Zhang
- School of Biomedical EngineeringNational Clinical Research Center for Ocular DiseasesEye HospitalWenzhou Medical UniversityWenzhou325027P. R. China
- Department of PathologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Xujie Sun
- Department of PathologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Yutao Liu
- Department of Medical OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Yibo Zhang
- School of Biomedical EngineeringNational Clinical Research Center for Ocular DiseasesEye HospitalWenzhou Medical UniversityWenzhou325027P. R. China
| | - Zijian Yang
- School of Biomedical EngineeringNational Clinical Research Center for Ocular DiseasesEye HospitalWenzhou Medical UniversityWenzhou325027P. R. China
| | - Jiyan Dong
- Department of PathologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Nan Wang
- Cosmos Wisdom Biotech Co. LtdBuilding 10thNo. 617 Jiner RoadHangzhou311215P. R. China
| | - Jianming Ying
- Department of PathologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Meng Zhou
- School of Biomedical EngineeringNational Clinical Research Center for Ocular DiseasesEye HospitalWenzhou Medical UniversityWenzhou325027P. R. China
| | - Lin Yang
- Department of PathologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
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Wang Y, Suarez ER, Kastrunes G, de Campos NSP, Abbas R, Pivetta RS, Murugan N, Chalbatani GM, D'Andrea V, Marasco WA. Evolution of cell therapy for renal cell carcinoma. Mol Cancer 2024; 23:8. [PMID: 38195534 PMCID: PMC10775455 DOI: 10.1186/s12943-023-01911-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024] Open
Abstract
Treatment for renal cell carcinoma (RCC) has improved dramatically over the last decade, shifting from high-dose cytokine therapy in combination with surgical resection of tumors to targeted therapy, immunotherapy, and combination therapies. However, curative treatment, particularly for advanced-stage disease, remains rare. Cell therapy as a "living drug" has achieved hematological malignancy cures with a high response rate, and significant research efforts have been made to facilitate its translation to solid tumors. Herein, we overview the cellular therapies for RCC focusing on allogeneic hematopoietic stem cell transplantation, T cell receptor gene-modified T cells, chimeric antigen receptor (CAR) T cells, CAR natural killer (NK) cells, lymphokine-activated killer (LAK) cells, γδ T cells, and dendritic cell vaccination. We have also included perspectives for using other recent approaches, such as CAR macrophages, dendritic cell-cytokine induced killer cells and regulatory CAR-T cells to shed light on preclinical development of cell therapy and advancing cell therapy into clinic to achieve cures for RCC.
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Affiliation(s)
- Yufei Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02215, USA
| | - Eloah Rabello Suarez
- Center for Natural and Human Sciences, Federal University of ABC, Santo Andre, SP, 09210-580, Brazil
- Graduate Program in Medicine - Hematology and Oncology, Federal University of Sao Paulo, São Paulo, SP, 04023-062, Brazil
| | - Gabriella Kastrunes
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Najla Santos Pacheco de Campos
- Center for Natural and Human Sciences, Federal University of ABC, Santo Andre, SP, 09210-580, Brazil
- Graduate Program in Medicine - Hematology and Oncology, Federal University of Sao Paulo, São Paulo, SP, 04023-062, Brazil
| | - Rabia Abbas
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Renata Schmieder Pivetta
- Center for Natural and Human Sciences, Federal University of ABC, Santo Andre, SP, 09210-580, Brazil
- Graduate Program in Medicine - Hematology and Oncology, Federal University of Sao Paulo, São Paulo, SP, 04023-062, Brazil
| | - Nithyassree Murugan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | | - Vincent D'Andrea
- Department of Surgery, Brigham and Women's Hospital, Boston, MA, 02215, USA
| | - Wayne A Marasco
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Harvard Medical School, Boston, MA, 02215, USA.
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Kemper K, Gielen E, Boross P, Houtkamp M, Plantinga TS, de Poot SAH, Burm SM, Janmaat ML, Koopman LA, van den Brink EN, Rademaker R, Verzijl D, Engelberts PJ, Satijn D, Sasser AK, Breij ECW. Mechanistic and pharmacodynamic studies of DuoBody-CD3x5T4 in preclinical tumor models. Life Sci Alliance 2022; 5:5/11/e202201481. [PMID: 36271507 PMCID: PMC9458754 DOI: 10.26508/lsa.202201481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022] Open
Abstract
CD3 bispecific antibodies (bsAbs) show great promise as anticancer therapeutics. Here, we show in-depth mechanistic studies of a CD3 bsAb in solid cancer, using DuoBody-CD3x5T4. Cross-linking T cells with tumor cells expressing the oncofetal antigen 5T4 was required to induce cytotoxicity. Naive and memory CD4+ and CD8+ T cells were equally effective at mediating cytotoxicity, and DuoBody-CD3x5T4 induced partial differentiation of naive T-cell subsets into memory-like cells. Tumor cell kill was associated with T-cell activation, proliferation, and production of cytokines, granzyme B, and perforin. Genetic knockout of FAS or IFNGR1 in 5T4+ tumor cells abrogated tumor cell kill. In the presence of 5T4+ tumor cells, bystander kill of 5T4− but not of 5T4−IFNGR1− tumor cells was observed. In humanized xenograft models, DuoBody-CD3x5T4 antitumor activity was associated with intratumoral and peripheral blood T-cell activation. Lastly, in dissociated patient-derived tumor samples, DuoBody-CD3x5T4 activated tumor-infiltrating lymphocytes and induced tumor-cell cytotoxicity, even when most tumor-infiltrating lymphocytes expressed PD-1. These data provide an in-depth view on the mechanism of action of a CD3 bsAb in preclinical models of solid cancer.
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Chengcheng L, Haidar Abbas Raza S, Shengchen Y, Mohammedsaleh ZM, Shater AF, Saleh FM, Alamoudi MO, Aloufi BH, Mohajja Alshammari A, Schreurs NM, Zan L. Bioinformatics role of the WGCNA analysis and Co-expression network identifies of prognostic marker in lung cancer. Saudi J Biol Sci 2022; 29:3519-3527. [PMID: 35844396 PMCID: PMC9280221 DOI: 10.1016/j.sjbs.2022.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/25/2022] [Accepted: 02/13/2022] [Indexed: 12/09/2022] Open
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Beeraka NM, Gu H, Xue N, Liu Y, Yu H, Liu J, Chen K, Nikolenko VN, Fan R. Testing lncRNAs signature as clinical stage–related prognostic markers in gastric cancer progression using TCGA database. Exp Biol Med (Maywood) 2022; 247:658-671. [PMID: 35068210 DOI: 10.1177/15353702211067173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
LncRNA expression can be conducive to gastric cancer (GC) prognosis. The objective of this study is to ascertain five specific lncRNAs involved in tumor progression of GC and their role as prognostic markers to diagnose clinical stage-wise GC. High-throughput RNA sequencing data were obtained from The Cancer Genome Atlas (TCGA) database and performed genome-wide lncRNA expression analysis using edgeR package, Bioconductor.org , and R-statistical computing to analyze differentially expressed lncRNA analysis. Cutoff parameters were FDR < 0.05 and |Log2FC| > 2. Total 351 tumor samples with differentially expressed lncRNAs were divided into group-1 lncRNAs such as AC019117.2 and LINC00941, and group-2 lncRNAs such as LINC02410, AC012317.2, and AC141273.1 by 2:1. The Spearman correlation coefficients ( p < 0.05) and correlation test function (cor.test ()) were performed for lncRNAs as per clinical stage. Cytoscape software was used to construct lncRNA–mRNA interaction networks. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway ( p < 0.05) analysis were conducted using the clusterProfiler package. Kaplan–Meier survival analysis was performed to determine the overall survival of patients based on the expression of five lncRNAs in different clinical stages of GC. AC019117.2 and LINC00941 of group 1 inferred a positive correlation with clinical stages of stage I to stage IV, and their expressions were higher in tumor tissues than normal tissues. On the contrary, LINC02410, AC012317.2, and AC141273.1 of group 2 exhibited a negative correlation with clinical stage, and they exhibited more expression in normal tissues compared to tumor tissues. GO and KEGG pathway analysis reported that AC019117.2 may interact with LINC00941 via ITGA3 and trophoblast glycoprotein (TPBG) to foster tumor progression. Tumor-specific group-1 lncRNAs were conducive to the poor overall survival and exhibited a positive correlation with the clinical stages of stage I to stage IV in GC as per the lncRNA–mRNA networking analysis. These five lncRNAs could be considered as clinically useful lncRNA-based prognostic markers to predict clinical stage-wise GC progression.
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Affiliation(s)
- Narasimha M Beeraka
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Human Anatomy, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119991, Russia
| | - Hao Gu
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Nannan Xue
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yang Liu
- Department of Radiotherapy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou 450052, China
| | - Huiming Yu
- Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing 450052, China
| | - Junqi Liu
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Kuo Chen
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Vladimir N Nikolenko
- Department of Human Anatomy, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119991, Russia
- M.V. Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ruitai Fan
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
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Ghaffari S, Hanson C, Schmidt RE, Bouchonville KJ, Offer SM, Sinha S. An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes. Genome Biol 2021; 22:19. [PMID: 33413550 PMCID: PMC7789593 DOI: 10.1186/s13059-020-02213-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 11/25/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Metastatic progress is the primary cause of death in most cancers, yet the regulatory dynamics driving the cellular changes necessary for metastasis remain poorly understood. Multi-omics approaches hold great promise for addressing this challenge; however, current analysis tools have limited capabilities to systematically integrate transcriptomic, epigenomic, and cistromic information to accurately define the regulatory networks critical for metastasis. RESULTS To address this limitation, we use a purposefully generated cellular model of colon cancer invasiveness to generate multi-omics data, including expression, accessibility, and selected histone modification profiles, for increasing levels of invasiveness. We then adopt a rigorous probabilistic framework for joint inference from the resulting heterogeneous data, along with transcription factor binding profiles. Our approach uses probabilistic graphical models to leverage the functional information provided by specific epigenomic changes, models the influence of multiple transcription factors simultaneously, and automatically learns the activating or repressive roles of cis-regulatory events. Global analysis of these relationships reveals key transcription factors driving invasiveness, as well as their likely target genes. Disrupting the expression of one of the highly ranked transcription factors JunD, an AP-1 complex protein, confirms functional relevance to colon cancer cell migration and invasion. Transcriptomic profiling confirms key regulatory targets of JunD, and a gene signature derived from the model demonstrates strong prognostic potential in TCGA colorectal cancer data. CONCLUSIONS Our work sheds new light into the complex molecular processes driving colon cancer metastasis and presents a statistically sound integrative approach to analyze multi-omics profiles of a dynamic biological process.
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Affiliation(s)
- Saba Ghaffari
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Casey Hanson
- Department of Genetics, Stanford University, Stanford, USA
| | - Remington E Schmidt
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St SW, Rochester, MN, 55905, USA
| | - Kelly J Bouchonville
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St SW, Rochester, MN, 55905, USA
| | - Steven M Offer
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St SW, Rochester, MN, 55905, USA.
| | - Saurabh Sinha
- Department of Computer Science, Carl R. Woese Institute of Genomic Biology, and Cancer Center of Illinois, University of Illinois at Urbana-Champaign, 2122, Siebel Center, 201 N. Goodwin Ave., Urbana, IL, 61801, USA.
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7
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Ríos-Castro E, Souza GHMF, Delgadillo-Álvarez DM, Ramírez-Reyes L, Torres-Huerta AL, Velasco-Suárez A, Cruz-Cruz C, Hernández-Hernández JM, Tapia-Ramírez J. Quantitative Proteomic Analysis of MARC-145 Cells Infected with a Mexican Porcine Reproductive and Respiratory Syndrome Virus Strain Using a Label-Free Based DIA approach. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1302-1312. [PMID: 32379441 DOI: 10.1021/jasms.0c00134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is an infectious disease characterized by severe reproductive failure in sows, acute respiratory disorders in growing pigs, and high mortality in piglets. The causative agent of this syndrome is the PRRS virus (PRRSV), an RNA virus belonging to the Arteriviridae family. To date, several quantitative approaches of proteomics have been applied to analyze the gene expression profiles during PRRSV infection in PAMs and MARC-145 cells, and few proteins have been consistent among independent studies, probably due to the differences in the levels of virulence of different PRRSV strains used and/or due to analytical conditions. In this study, total proteins isolated from noninfected and infected MARC-145 cells with a Mexican PRRSV strain were relatively quantified using label-free based DIA approach in combination with ion-mobility separation. As a result, 1456 quantified proteins were found to be shared between the control and infected samples. Afterward, these proteins were filtered, and 699 of them were considered without change. Also, 17 proteins were up-regulated and 19 proteins were down-regulated during the PRSSV infection. Bioinformatic analysis revealed that many of the differentially expressed proteins are involved in processes like antigen processing, presentation of antigens, response to viruses, response to IFNs, and innate immune response, among others. The present work is the first one which provides a detailed proteomic analysis through label-free based DIA approach in MARC-145 cells during the infection with a Mexican PRRSV strain.
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Affiliation(s)
- Emmanuel Ríos-Castro
- Unidad de Genómica, Proteómica y Metabolómica (UGPM), LaNSE, Cinvestav-IPN, Ciudad de México C.P. 07360, México
| | | | | | - Lorena Ramírez-Reyes
- Unidad de Genómica, Proteómica y Metabolómica (UGPM), LaNSE, Cinvestav-IPN, Ciudad de México C.P. 07360, México
| | - Ana Laura Torres-Huerta
- Unidad de Desarrollo e Innovación (UDI), LaNSE, Cinvestav-IPN, Ciudad de México, C.P. 07360, México
| | - Andrea Velasco-Suárez
- Unidad de Genómica, Proteómica y Metabolómica (UGPM), LaNSE, Cinvestav-IPN, Ciudad de México C.P. 07360, México
| | - Carlos Cruz-Cruz
- Departamento de Genética y Biologı́a Molecular, Cinvestav-IPN, Ciudad de México, C.P. 07360, México
| | | | - José Tapia-Ramírez
- Departamento de Genética y Biologı́a Molecular, Cinvestav-IPN, Ciudad de México, C.P. 07360, México
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Koroknai V, Szász I, Hernandez-Vargas H, Fernandez-Jimenez N, Cuenin C, Herceg Z, Vízkeleti L, Ádány R, Ecsedi S, Balázs M. DNA hypermethylation is associated with invasive phenotype of malignant melanoma. Exp Dermatol 2020; 29:39-50. [PMID: 31602702 DOI: 10.1111/exd.14047] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 08/29/2019] [Accepted: 10/06/2019] [Indexed: 01/01/2023]
Abstract
Tumor cell invasion is one of the key processes during cancer progression, leading to life-threatening metastatic lesions in melanoma. As methylation of cancer-related genes plays a fundamental role during tumorigenesis and may lead to cellular plasticity which promotes invasion, our aim was to identify novel epigenetic markers on selected invasive melanoma cells. Using Illumina BeadChip assays and Affymetrix Human Gene 1.0 microarrays, we explored the DNA methylation landscape of selected invasive melanoma cells and examined the impact of DNA methylation on gene expression patterns. Our data revealed predominantly hypermethylated genes in the invasive cells affecting the neural crest differentiation pathway and regulation of the actin cytoskeleton. Integrative analysis of the methylation and gene expression profiles resulted in a cohort of hypermethylated genes (IL12RB2, LYPD6B, CHL1, SLC9A3, BAALC, FAM213A, SORCS1, GPR158, FBN1 and ADORA2B) with decreased expression. On the other hand, hypermethylation in the gene body of the EGFR and RBP4 genes was positively correlated with overexpression of the genes. We identified several methylation changes that can have role during melanoma progression, including hypermethylation of the promoter regions of the ARHGAP22 and NAV2 genes that are commonly altered in locally invasive primary melanomas as well as during metastasis. Interestingly, the down-regulation of the methylcytosine dioxygenase TET2 gene, which regulates DNA methylation, was associated with hypermethylated promoter region of the gene. This can probably lead to the observed global hypermethylation pattern of invasive cells and might be one of the key changes during the development of malignant melanoma cells.
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Affiliation(s)
- Viktória Koroknai
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | - István Szász
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | | | | | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Laura Vízkeleti
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | - Róza Ádány
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | - Szilvia Ecsedi
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Margit Balázs
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
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Pancreatic duct-like cell line derived from pig embryonic stem cells: expression of uroplakin genes in pig pancreatic tissue. In Vitro Cell Dev Biol Anim 2019; 55:285-301. [PMID: 30868438 DOI: 10.1007/s11626-019-00336-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 02/12/2019] [Indexed: 02/04/2023]
Abstract
The isolation of a cell line, PICM-31D, with phenotypic characteristics like pancreatic duct cells is described. The PICM-31D cell line was derived from the previously described pig embryonic stem cell-derived exocrine pancreatic cell line, PICM-31. The PICM-31D cell line was morphologically distinct from the parental cells in growing as a monolayer rather than self-assembling into multicellular acinar-like structures. The PICM-31D cells were propagated for over a year at split ratios of 1:3 to 1:10 at each passage without change in phenotype or growth rate. Electron microscopy showed the cells to be a polarized epithelium of cuboidal cells joined by tight junction-like adhesions at their apical/lateral aspect. The cells contained numerous mucus-like secretory vesicles under their apical cell membrane. Proteomic analysis of the PICM-31D's cellular proteins detected MUC1 and MUC4, consistent with mucus vesicle morphology. Gene expression analysis showed the cells expressed pancreatic ductal cell-related transcription factors such as GATA4, GATA6, HES1, HNF1A, HNF1B, ONECUT1 (HNF6), PDX1, and SOX9, but little or no pancreas progenitor cell markers such as PTF1A, NKX6-1, SOX2, or NGN3. Pancreas ductal cell-associated genes including CA2, CFTR, MUC1, MUC5B, MUC13, SHH, TFF1, KRT8, and KRT19 were expressed by the PICM-31D cells, but the exocrine pancreas marker genes, CPA1 and PLA2G1B, were not expressed by the cells. However, the exocrine marker, AMY2A, was still expressed by the cells. Surprisingly, uroplakin proteins were prominent in the PICM-31D cell proteome, particularly UPK1A. Annexin A1 and A2 proteins were also relatively abundant in the cells. The expression of the uroplakin and annexin genes was detected in the cells, although only UPK1B, UPK3B, ANXA2, and ANXA4 were detected in fetal pig pancreatic duct tissue. In conclusion, the PICM-31D cell line models the mucus-secreting ductal cells of the fetal pig pancreas.
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Chen F, Szymanski EP, Olivier KN, Liu X, Tettelin H, Holland SM, Duggal P. Whole-Exome Sequencing Identifies the 6q12-q16 Linkage Region and a Candidate Gene, TTK, for Pulmonary Nontuberculous Mycobacterial Disease. Am J Respir Crit Care Med 2017; 196:1599-1604. [PMID: 28777004 DOI: 10.1164/rccm.201612-2479oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
RATIONALE Pulmonary nontuberculous mycobacterial disease (PNTM) often affects white postmenopausal women, with a tall and lean body habitus and higher rates of scoliosis, pectus excavatum, mitral valve prolapse, and mutations in the CFTR gene. These clinical features and the familial clustering of the disease suggest an underlying genetic mechanism. OBJECTIVES To map the genes associated with PNTM, whole-exome sequencing was conducted in 12 PNTM families and 57 sporadic cases recruited at the National Institutes of Health Clinical Center during 2001-2013. METHODS We performed a variant-level and a gene-level parametric linkage analysis on nine PNTM families (16 affected and 20 unaffected) as well as a gene-level association analysis on nine PNTM families and 55 sporadic cases. MEASUREMENTS AND MAIN RESULTS The genome-wide variant-level linkage analysis using 4,328 independent common variants identified a 20-cM region on chromosome 6q12-6q16 (heterogeneity logarithm of odds score = 3.9), under a recessive disease model with 100% penetrance and a risk allele frequency of 5%. All genes on chromosome 6 were then tested in the gene-level linkage analysis, using the collapsed haplotype pattern method. The TTK protein kinase gene (TTK) on chromosome 6q14.1 was the most significant (heterogeneity logarithm of odds score = 3.38). In addition, the genes MAP2K4, RCOR3, KRT83, IFNLR1, and SLC29A1 were associated with PNTM in our gene-level association analysis. CONCLUSIONS The TTK gene encodes a protein kinase that is essential for mitotic checkpoints and the DNA damage response. TTK and other genetic loci identified in our study may contribute to the increased susceptibility to NTM infection and its progression to pulmonary disease.
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Affiliation(s)
- Fei Chen
- 1 Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Eva P Szymanski
- 2 Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland
| | - Kenneth N Olivier
- 3 Cardiovascular and Pulmonary Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland; and
| | - Xinyue Liu
- 4 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland
| | - Hervé Tettelin
- 4 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland
| | - Steven M Holland
- 2 Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland
| | - Priya Duggal
- 1 Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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