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Pudjihartono M, Golovina E, Fadason T, O'Sullivan JM, Schierding W. Links between melanoma germline risk loci, driver genes and comorbidities: insight from a tissue-specific multi-omic analysis. Mol Oncol 2024; 18:1031-1048. [PMID: 38308491 PMCID: PMC10994230 DOI: 10.1002/1878-0261.13599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 11/15/2023] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
Genome-wide association studies (GWAS) have associated 76 loci with the risk of developing melanoma. However, understanding the molecular basis of such associations has remained a challenge because most of these loci are in non-coding regions of the genome. Here, we integrated data on epigenomic markers, three-dimensional (3D) genome organization, and expression quantitative trait loci (eQTL) from melanoma-relevant tissues and cell types to gain novel insights into the mechanisms underlying melanoma risk. This integrative approach revealed a total of 151 target genes, both near and far away from the risk loci in linear sequence, with known and novel roles in the etiology of melanoma. Using protein-protein interaction networks, we identified proteins that interact-directly or indirectly-with the products of the target genes. The interacting proteins were enriched for known melanoma driver genes. Further integration of these target genes into tissue-specific gene regulatory networks revealed patterns of gene regulation that connect melanoma to its comorbidities. Our study provides novel insights into the biological implications of genetic variants associated with melanoma risk.
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Affiliation(s)
| | | | | | - Justin M. O'Sullivan
- Liggins InstituteThe University of AucklandNew Zealand
- The Maurice Wilkins CentreThe University of AucklandNew Zealand
- Australian Parkinson's MissionGarvan Institute of Medical ResearchSydneyAustralia
- MRC Lifecourse Epidemiology UnitUniversity of SouthamptonUK
- Singapore Institute for Clinical SciencesAgency for Science, Technology and Research (A*STAR)Singapore CitySingapore
| | - William Schierding
- Liggins InstituteThe University of AucklandNew Zealand
- The Maurice Wilkins CentreThe University of AucklandNew Zealand
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Lin A, Mou W, Zhu L, Yang T, Zhou C, Zhang J, Luo P. Mutations in the DNA polymerase binding pathway affect the immune microenvironment of patients with small-cell lung cancer and enhance the efficacy of platinum-based chemotherapy. CANCER INNOVATION 2023; 2:500-512. [PMID: 38125769 PMCID: PMC10730006 DOI: 10.1002/cai2.84] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 12/23/2023]
Abstract
Background Small-cell lung cancer (SCLC) is characterized by its high malignancy and is associated with a poor prognosis. In the early stages of the disease, platinum-based chemotherapy is the recommended first-line treatment and has demonstrated efficacy. However, SCLC is prone to recurrence and is generally resistant to chemotherapy in its later stages. Methods Here, we collected samples from SCLC patients who received platinum-based chemotherapy, performed genomic and transcriptomic analyses, and validated our results with publicly available data. Results SCLC patients with DNA polymerase binding pathway mutations had an improved prognosis after platinum chemotherapy compared with patients without such mutations. Patients in the mutant (MT) group had higher infiltration of T cells, B cells, and M1 macrophages compared with patients without DNA polymerase binding pathway mutations. Conclusions DNA polymerase binding pathway mutations can be used as prognostic markers for platinum-based chemotherapy in SCLC.
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Affiliation(s)
- Anqi Lin
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Weiming Mou
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
- The First Clinical Medical SchoolSouthern Medical UniversityGuangzhouGuangdongChina
- Department of Urology, Shanghai General HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Lingxuan Zhu
- The First Clinical Medical SchoolSouthern Medical UniversityGuangzhouGuangdongChina
- Department of Etiology and CarcinogenesisNational Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Tao Yang
- The First Clinical Medical SchoolSouthern Medical UniversityGuangzhouGuangdongChina
- Department of Medical OncologyNational Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Chaozheng Zhou
- The First Clinical Medical SchoolSouthern Medical UniversityGuangzhouGuangdongChina
| | - Jian Zhang
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Peng Luo
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
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Azzarito G, Kurmann L, Leeners B, Dubey RK. Micro-RNA193a-3p Inhibits Breast Cancer Cell Driven Growth of Vascular Endothelial Cells by Altering Secretome and Inhibiting Mitogenesis: Transcriptomic and Functional Evidence. Cells 2022; 11:cells11192967. [PMID: 36230929 PMCID: PMC9562882 DOI: 10.3390/cells11192967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/12/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022] Open
Abstract
Breast cancer (BC) cell secretome in the tumor microenvironment (TME) facilitates neo-angiogenesis by promoting vascular endothelial cell (VEC) growth. Drugs that block BC cell growth or angiogenesis can restrict tumor growth and are of clinical relevance. Molecules that can target both BC cell and VEC growth as well as BC secretome may be more effective in treating BC. Since small non-coding microRNAs (miRs) regulate cell growth and miR193a-3p has onco-suppressor activity, we investigated whether miR193a-3p inhibits MCF-7-driven growth (proliferation, migration, capillary formation, signal transduction) of VECs. Using BC cells and VECs grown in monolayers or 3D spheroids and gene microarrays, we demonstrate that: pro-growth effects of MCF-7 and MDA-MB231 conditioned medium (CM) are lost in CM collected from MCF-7/MDA-MB231 cells pre-transfected with miR193a-3p (miR193a-CM). Moreover, miR193a-CM inhibited MAPK and Akt phosphorylation in VECs. In microarray gene expression studies, miR193a-CM upregulated 553 genes and downregulated 543 genes in VECs. Transcriptomic and pathway enrichment analysis of differentially regulated genes revealed downregulation of interferon-associated genes and pathways that induce angiogenesis and BC/tumor growth. An angiogenesis proteome array confirmed the downregulation of 20 pro-angiogenesis proteins by miR193a-CM in VECs. Additionally, in MCF-7 cells and VECs, estradiol (E2) downregulated miR193a-3p expression and induced growth. Ectopic expression of miR193a-3p abrogated the growth stimulatory effects of estradiol E2 and serum in MCF-7 cells and VECs, as well as in MCF-7 and MCF-7+VEC 3D spheroids. Immunostaining of MCF-7+VEC spheroid sections with ki67 showed miR193a-3p inhibits cell proliferation. Taken together, our findings provide first evidence that miR193a-3p abrogates MCF-7-driven growth of VECs by altering MCF-7 secretome and downregulating pro-growth interferon signals and proangiogenic proteins. Additionally, miR193a-3p inhibits serum and E2-induced growth of MCF-7, VECs, and MCF-7+VEC spheroids. In conclusion, miRNA193a-3p can potentially target/inhibit BC tumor angiogenesis via a dual mechanism: (1) altering proangiogenic BC secretome/TME and (2) inhibiting VEC growth. It may represent a therapeutic molecule to target breast tumor growth.
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Affiliation(s)
- Giovanna Azzarito
- Department of Reproductive Endocrinology, University Hospital Zurich, 8952 Schlieren, Switzerland
| | - Lisa Kurmann
- Department of Reproductive Endocrinology, University Hospital Zurich, 8952 Schlieren, Switzerland
| | - Brigitte Leeners
- Department of Reproductive Endocrinology, University Hospital Zurich, 8952 Schlieren, Switzerland
| | - Raghvendra K. Dubey
- Department of Reproductive Endocrinology, University Hospital Zurich, 8952 Schlieren, Switzerland
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Correspondence:
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Wang Z, Wang J, Zhao H, Zhao T, Chen Y, Jiang M, Zhang S, Wei Y, Zhang J, Zhou Y, Shi S, Fu Z, Yang Y, Zhang Y, Yang L, Que J, Liu K. Targeting the SOX2/PARP1 complex to intervene in the growth of esophageal squamous cell carcinoma. Biomed Pharmacother 2022; 153:113309. [PMID: 35738180 DOI: 10.1016/j.biopha.2022.113309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022] Open
Abstract
Elevated SOX2 protein levels are closely correlated with the increased incidence of esophageal squamous cell carcinoma (ESCC). However, establishing effective target measures for ESCC treatments continue to be researched. It has been previously proposed that SOX2 represents a potential therapeutic target for ESCC. Here, we found that the enzyme Poly(ADP-Ribose) polymerase 1 (PARP1) enriched in ESCCs interact with SOX2. Inhibition of PARP1 with 3-aminobenzamide (3-ABA) or shRNA knockdown reduced the proliferation of ESCCs, accompanied by decreased protein levels of SOX2. RNA sequencing demonstrated that PARP1 inhibition affected multiple signaling pathways involved in cancer cell proliferation. Additionally, 3-ABA synergistically suppressed the growth of ESCC cells when combined with cisplatin, and metformin potentiated the suppressive effect of 3-ABA on ESCC cell growth. Together these findings suggest that targeting SOX2 binding partner PARP1 provides a possible avenue to treat patients with high levels of SOX2.
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Affiliation(s)
- Zhuo Wang
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China; School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Junkai Wang
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Hongzhou Zhao
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China; School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Tingting Zhao
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China; School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Yunyun Chen
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China; School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Ming Jiang
- Department of Gastroenterology of The Children's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Shihui Zhang
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Yuxuan Wei
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China; School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Jiaying Zhang
- School of Life Science, Xiamen University, Xiamen, Fujian 361102, China
| | - Yijian Zhou
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China; School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Songlin Shi
- School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Zhichao Fu
- Department of radiotherapy, 900 Hospital of the Joint Logistics Team (Dongfang Hospital, Xiamen University), Fuzhou, Fujian 350025, China
| | - Yaxin Yang
- Department of Biology, University of Rochester, NY 14627, USA
| | - Yujun Zhang
- School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Ling Yang
- School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Jianwen Que
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA.
| | - Kuancan Liu
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China; School of Medicine, Xiamen University, Xiamen, Fujian 361102, China.
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Association of Melanoma-Risk Variants with Primary Melanoma Tumor Prognostic Characteristics and Melanoma-Specific Survival in the GEM Study. Curr Oncol 2021; 28:4756-4771. [PMID: 34898573 PMCID: PMC8628692 DOI: 10.3390/curroncol28060401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/11/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
Genome-wide association studies (GWAS) and candidate pathway studies have identified low-penetrant genetic variants associated with cutaneous melanoma. We investigated the association of melanoma-risk variants with primary melanoma tumor prognostic characteristics and melanoma-specific survival. The Genes, Environment, and Melanoma Study enrolled 3285 European origin participants with incident invasive primary melanoma. For each of 47 melanoma-risk single nucleotide polymorphisms (SNPs), we used linear and logistic regression modeling to estimate, respectively, the per allele mean changes in log of Breslow thickness and odds ratios for presence of ulceration, mitoses, and tumor-infiltrating lymphocytes (TILs). We also used Cox proportional hazards regression modeling to estimate the per allele hazard ratios for melanoma-specific survival. Passing the false discovery threshold (p = 0.0026) were associations of IRF4 rs12203592 and CCND1 rs1485993 with log of Breslow thickness, and association of TERT rs2242652 with presence of mitoses. IRF4 rs12203592 also had nominal associations (p < 0.05) with presence of mitoses and melanoma-specific survival, as well as a borderline association (p = 0.07) with ulceration. CCND1 rs1485993 also had a borderline association with presence of mitoses (p = 0.06). MX2 rs45430 had nominal associations with log of Breslow thickness, presence of mitoses, and melanoma-specific survival. Our study indicates that further research investigating the associations of these genetic variants with underlying biologic pathways related to tumor progression is warranted.
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Nain Z, Barman SK, Sheam MM, Syed SB, Samad A, Quinn JMW, Karim MM, Himel MK, Roy RK, Moni MA, Biswas SK. Transcriptomic studies revealed pathophysiological impact of COVID-19 to predominant health conditions. Brief Bioinform 2021; 22:bbab197. [PMID: 34076249 PMCID: PMC8194991 DOI: 10.1093/bib/bbab197] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/10/2021] [Accepted: 04/30/2021] [Indexed: 12/16/2022] Open
Abstract
Despite the association of prevalent health conditions with coronavirus disease 2019 (COVID-19) severity, the disease-modifying biomolecules and their pathogenetic mechanisms remain unclear. This study aimed to understand the influences of COVID-19 on different comorbidities and vice versa through network-based gene expression analyses. Using the shared dysregulated genes, we identified key genetic determinants and signaling pathways that may involve in their shared pathogenesis. The COVID-19 showed significant upregulation of 93 genes and downregulation of 15 genes. Interestingly, it shares 28, 17, 6 and 7 genes with diabetes mellitus (DM), lung cancer (LC), myocardial infarction and hypertension, respectively. Importantly, COVID-19 shared three upregulated genes (i.e. MX2, IRF7 and ADAM8) with DM and LC. Conversely, downregulation of two genes (i.e. PPARGC1A and METTL7A) was found in COVID-19 and LC. Besides, most of the shared pathways were related to inflammatory responses. Furthermore, we identified six potential biomarkers and several important regulatory factors, e.g. transcription factors and microRNAs, while notable drug candidates included captopril, rilonacept and canakinumab. Moreover, prognostic analysis suggests concomitant COVID-19 may result in poor outcome of LC patients. This study provides the molecular basis and routes of the COVID-19 progression due to comorbidities. We believe these findings might be useful to further understand the intricate association of these diseases as well as for the therapeutic development.
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Affiliation(s)
- Zulkar Nain
- Department of Biotechnology and Genetic Engineering, Islamic University, Bangladesh
| | | | - Md Moinuddin Sheam
- Department of Biotechnology and Genetic Engineering, Islamic University, Bangladesh
| | - Shifath Bin Syed
- Department of Biotechnology and Genetic Engineering, Islamic University, Bangladesh
| | - Abdus Samad
- Department of Genetic Engineering and Biotechnology at the Jashore University of Science and Technology, Bangladesh
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Corrigendum. Pigment Cell Melanoma Res 2021; 34:994. [PMID: 34487428 DOI: 10.1111/pcmr.13001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wei Y, Chen X, Ren X, Wang B, Zhang Q, Bu H, Qian J, Shao P. Identification of MX2 as a Novel Prognostic Biomarker for Sunitinib Resistance in Clear Cell Renal Cell Carcinoma. Front Genet 2021; 12:680369. [PMID: 34306023 PMCID: PMC8299280 DOI: 10.3389/fgene.2021.680369] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 05/21/2021] [Indexed: 11/13/2022] Open
Abstract
Background Antiangiogenic agents that specifically target vascular endothelial growth factor receptor (VEGFR), such as sunitinib, have been utilized as the standard therapy for metastatic clear cell renal cell carcinoma (ccRCC) patients. However, most patients eventually show no responses to the targeted drugs, and the mechanisms for the resistance remain unclear. This study is aimed to identify pivotal molecules and to uncover their potential functions involved in this adverse event in ccRCC treatment. Methods Two datasets, GSE64052 and GSE76068, were obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using the limma package in R software. The gene set enrichment analysis (GSEA) was conducted using clusterProfiler package. A protein-protein interaction (PPI) network was built using the STRING database and Cytoscape software. Kaplan-Meier survival curves were plotted using R software. qRT-PCR and Western blotting were used to detect the MX2 and pathway expression in RCC cell lines. Sunitinib-resistant cell lines were constructed, and loss-of-function experiments were conducted by knocking down MX2. All statistical analyses were performed using R version 3.6.1 and SPSS 23.0. Results A total of 760 DEGs were derived from two datasets in GEO database, and five hub genes were identified, among which high-level MX2 exhibited a pronounced correlation with poor overall survival (OS) in sunitinib-resistant ccRCC patients. Clinical correlation analysis and Gene Set Variation Analysis (GSVA) on MX2 showed that the upregulation of MX2 was significantly related to the malignant phenotype of ccRCC, and it was involved in several pathways and biological processes associated with anticancer drug resistance. qRT-PCR and Western blotting revealed that MX2 was distinctly upregulated in sunitinib-resistant RCC cell lines. Colony formation assay and Cell Counting Kit-8 (CCK8) assay showed that MX2 strongly promoted resistant capability to sunitinib of ccRCC cells. Conclusion MX2 is a potent indicator for sunitinib resistance and a therapeutic target in ccRCC patients.
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Affiliation(s)
- Yuang Wei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xinglin Chen
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaohan Ren
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Bao Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qian Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hengtao Bu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jian Qian
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pengfei Shao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Kushima H, Tsunoda T, Matsumoto T, Kinoshita Y, Izumikawa K, Shirasawa S, Fujita M, Ishii H. Effects of Aspergillus fumigatus Conidia on Apoptosis and Proliferation in an In Vitro Model of the Lung Microenvironment. Microorganisms 2021; 9:microorganisms9071435. [PMID: 34361872 PMCID: PMC8304463 DOI: 10.3390/microorganisms9071435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 01/19/2023] Open
Abstract
Background/Aim: Aspergillus is often detected in respiratory samples from patients with chronic respiratory diseases, including pulmonary fibrosis, suggesting that it can easily colonize the airways. To determine the role of Aspergillus colonization in pulmonary fibrosis, we cultured human lung epithelial A549 cells or murine embryo fibroblast NIH/3T3 cells with Aspergillus conidia in 3D floating culture representing the microenvironment. Materials and Methods: Cells were cultured in two-dimensional (2D) and three-dimensional floating (3DF) culture with heat-inactivated Aspergillus fumigatus (AF) 293 conidia at an effector-to-target cell ratio of 1:10 (early-phase model) and 1:100 (colonization model), and RNA-sequencing and Western blots (WB) were performed. Results: AF293 conidia reduced A549 cell growth in 2D and 3DF cultures and induced apoptosis in A549 spheroids in 3DF culture. RNA-sequencing revealed the increased expression of genes associated with interferon-mediated antiviral responses including MX dymamin-like GTPase 1 (MX1). Interestingly, the decreased expression of genes associated with the cell cycle was observed with a high concentration of AF293 conidia. WB revealed that epithelial-mesenchymal transition was not involved. Notably, AF293 conidia increased NIH/3T3 growth only in 3DF culture without inducing an apoptotic reaction. RNA-sequencing revealed the increased expression of genes associated with interferon signalling, including MX2; however, the decreased expression of genes associated with the cell cycle was not observed. Conclusions: AF affects both apoptosis of epithelial cells and the growth of fibroblasts. A deeper understanding of the detailed mechanisms underlying Aspergillus-mediated signaling pathway in epithelial cells and fibroblasts will help us to understand the lung microenvironment.
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Affiliation(s)
- Hisako Kushima
- Department of Respiratory Medicine, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan;
- Department of Respiratory Medicine, Fukuoka University Chikushi Hospital, Fukuoka 818-8502, Japan; (Y.K.); (H.I.)
- Correspondence: ; Tel.: +81-92-921-1011; Fax: +81-92-928-3890
| | - Toshiyuki Tsunoda
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan; (T.T.); (S.S.)
- Department of Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan
| | - Taichi Matsumoto
- Department of Pharmaceutical Sciences, Faculty of Drug Informatics and Translational Research, Fukuoka University, Fukuoka 814-0180, Japan;
| | - Yoshiaki Kinoshita
- Department of Respiratory Medicine, Fukuoka University Chikushi Hospital, Fukuoka 818-8502, Japan; (Y.K.); (H.I.)
| | - Koichi Izumikawa
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan;
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan; (T.T.); (S.S.)
- Department of Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan
| | - Masaki Fujita
- Department of Respiratory Medicine, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan;
| | - Hiroshi Ishii
- Department of Respiratory Medicine, Fukuoka University Chikushi Hospital, Fukuoka 818-8502, Japan; (Y.K.); (H.I.)
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Juraleviciute M, Nsengimana J, Newton-Bishop J, Hendriks GJ, Slipicevic A. MX2 mediates establishment of interferon response profile, regulates XAF1, and can sensitize melanoma cells to targeted therapy. Cancer Med 2021; 10:2840-2854. [PMID: 33734579 PMCID: PMC8026919 DOI: 10.1002/cam4.3846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 02/02/2021] [Accepted: 02/23/2021] [Indexed: 01/05/2023] Open
Abstract
MX2 is an interferon inducible gene that is mostly known for its antiviral activity. We have previously demonstrated that MX2 is also associated with the tumorigenesis process in melanoma. However, it remains unknown which molecular mechanisms are regulated by MX2 in response to interferon signaling in this disease. Here, we report that MX2 is necessary for the establishment of an interferon‐induced transcriptional profile partially through regulation of STAT1 phosphorylation and other interferon‐related downstream factors, including proapoptotic tumor suppressor XAF1. MX2 and XAF1 expression tightly correlate in both cultured melanoma cell lines and in patient‐derived primary and metastatic tumors, where they also are significantly related with survival. MX2 mediates IFN growth‐inhibitory signals in both XAF1 dependent and independent ways and in a cell type and context‐dependent manner. Higher MX2 expression renders melanoma cells more sensitive to targeted therapy drugs such as vemurafenib and trametinib; however, this effect is XAF1 independent. In summary, we uncovered a new mechanism in the complex regulation of interferon signaling in melanoma that can influence both survival and response to therapy.
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Affiliation(s)
- Marina Juraleviciute
- Department of Pathology, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jérémie Nsengimana
- Faculty of Medical Sciences, Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Julia Newton-Bishop
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Gert J Hendriks
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ana Slipicevic
- Department of Pathology, Oslo University Hospital, Oslo, Norway
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Choi J, Zhang T, Vu A, Ablain J, Makowski MM, Colli LM, Xu M, Hennessey RC, Yin J, Rothschild H, Gräwe C, Kovacs MA, Funderburk KM, Brossard M, Taylor J, Pasaniuc B, Chari R, Chanock SJ, Hoggart CJ, Demenais F, Barrett JH, Law MH, Iles MM, Yu K, Vermeulen M, Zon LI, Brown KM. Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma. Nat Commun 2020; 11:2718. [PMID: 32483191 PMCID: PMC7264232 DOI: 10.1038/s41467-020-16590-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 05/12/2020] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified ~20 melanoma susceptibility loci, most of which are not functionally characterized. Here we report an approach integrating massively-parallel reporter assays (MPRA) with cell-type-specific epigenome and expression quantitative trait loci (eQTL) to identify susceptibility genes/variants from multiple GWAS loci. From 832 high-LD variants, we identify 39 candidate functional variants from 14 loci displaying allelic transcriptional activity, a subset of which corroborates four colocalizing melanocyte cis-eQTL genes. Among these, we further characterize the locus encompassing the HIV-1 restriction gene, MX2 (Chr21q22.3), and validate a functional intronic variant, rs398206. rs398206 mediates the binding of the transcription factor, YY1, to increase MX2 levels, consistent with the cis-eQTL of MX2 in primary human melanocytes. Melanocyte-specific expression of human MX2 in a zebrafish model demonstrates accelerated melanoma formation in a BRAFV600E background. Our integrative approach streamlines GWAS follow-up studies and highlights a pleiotropic function of MX2 in melanoma susceptibility. There are more than 20 known melanoma susceptibility genes. Here, using a massively parallel reporter assay, the authors identify risk-associated variants that alter gene transcription, and demonstrate that expression of one such gene, MX2, leads to the promotion of melanoma in a zebrafish model.
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Affiliation(s)
- Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Andrew Vu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Julien Ablain
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Matthew M Makowski
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 XZ, Nijmegen, The Netherlands
| | - Leandro M Colli
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Mai Xu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Rebecca C Hennessey
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Jinhu Yin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Harriet Rothschild
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 XZ, Nijmegen, The Netherlands
| | - Michael A Kovacs
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Karen M Funderburk
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Myriam Brossard
- Université de Paris, UMRS-1124, Institut National de la Santé et de la Recherche Médicale (INSERM), F-75006, Paris, France
| | - John Taylor
- Leeds Institute for Data Analytics, School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90024, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Lab for Cancer Research, National Cancer Institute, Frederick, MD, 21701, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Clive J Hoggart
- Department of Medicine, Imperial College London, London, SW7 2BU, UK
| | - Florence Demenais
- Université de Paris, UMRS-1124, Institut National de la Santé et de la Recherche Médicale (INSERM), F-75006, Paris, France
| | - Jennifer H Barrett
- Leeds Institute for Data Analytics, School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Mark M Iles
- Leeds Institute for Data Analytics, School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 XZ, Nijmegen, The Netherlands
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA.
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