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Chen H, Li J, Cao D, Tang H. Construction of a Prognostic Model for Hepatocellular Carcinoma Based on Macrophage Polarization-Related Genes. J Hepatocell Carcinoma 2024; 11:857-878. [PMID: 38751862 PMCID: PMC11095518 DOI: 10.2147/jhc.s453080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Background The progression of hepatocellular carcinoma (HCC) is related to macrophage polarization (MP). Our aim was to identify genes associated with MP in HCC patients and develop a prognostic model based on these genes. Results We successfully developed a prognostic model consisting of six MP-related genes (SCN4A, EBF3, ADGRB2, HOXD9, CLEC1B, and MSC) to calculate the risk score for each patient. Patients were then classified into high- and low-risk groups based on their median risk score. The performance of the MP-related prognostic model was evaluated using Kaplan-Meier and ROC curves, which yielded favorable results. Additionally, the nomogram demonstrated good clinical effectiveness and displayed consistent survival predictions with actual observations. Gene Set Enrichment Analysis (GSEA) revealed enrichment of pathways related to KRAS signaling downregulation, the G2M checkpoint, and E2F targets in the high-risk group. Conversely, pathways associated with fatty acid metabolism, xenobiotic metabolism, bile acid metabolism, and adipogenesis were enriched in the low-risk group. The risk score positively correlated with the number of invasion-related genes. Immune checkpoint expression differed significantly between the two groups. Patients in the high-risk group exhibited increased sensitivity to mitomycin C, cisplatin, gemcitabine, rapamycin, and paclitaxel, while those in the low-risk group showed heightened sensitivity to doxorubicin. These findings suggest that the high-risk group may have more invasive HCC with greater susceptibility to specific drugs. IHC staining revealed higher expression levels of SCN4A in HCC tissues. Furthermore, experiments conducted on HepG2 cells demonstrated that supernatants from cells with reduced SCN4A expression promoted M2 macrophage polarization marker, CD163 in THP-1 cells. Reduced SCN4A expression induced HCC-related genes, while increased SCN4A expression reduced their expression in HepG2 cells. Conclusion The MP-related prognostic model comprising six MPRGs can effectively predict HCC prognosis, infer invasiveness, and guide drug therapy. SCN4A is identified as a suppressor gene in HCC.
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Affiliation(s)
- Han Chen
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
| | - Jianhao Li
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
| | - Dan Cao
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
| | - Hong Tang
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
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Liu Y, Yao Y, Zhang Y, Xu C, Yang T, Qu M, Lu B, Song X, Pan X, Zhou W, Cui X. Identification of prognostic stemness-related genes in kidney renal papillary cell carcinoma. BMC Med Genomics 2024; 17:121. [PMID: 38702698 PMCID: PMC11067181 DOI: 10.1186/s12920-024-01870-2] [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: 08/15/2023] [Accepted: 04/09/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Kidney renal papillary cell carcinoma (KIRP) is the second most prevalent malignant cancer originating from the renal epithelium. Nowadays, cancer stem cells and stemness-related genes (SRGs) are revealed to play important roles in the carcinogenesis and metastasis of various tumors. Consequently, we aim to investigate the underlying mechanisms of SRGs in KIRP. METHODS RNA-seq profiles of 141 KIRP samples were downloaded from the TCGA database, based on which we calculated the mRNA expression-based stemness index (mRNAsi). Next, we selected the differentially expressed genes (DEGs) between low- and high-mRNAsi groups. Then, we utilized weighted gene correlation network analysis (WGCNA) and univariate Cox analysis to identify prognostic SRGs. Afterwards, SRGs were included in the multivariate Cox regression analysis to establish a prognostic model. In addition, a regulatory network was constructed by Pearson correlation analysis, incorporating key genes, upstream transcription factors (TFs), and downstream signaling pathways. Finally, we used Connectivity map analysis to identify the potential inhibitors. RESULTS In total, 1124 genes were characterized as DEGs between low- and high-RNAsi groups. Based on six prognostic SRGs (CCKBR, GPR50, GDNF, SPOCK3, KC877982.1, and MYO15A), a prediction model was established with an area under curve of 0.861. Furthermore, among the TFs, genes, and signaling pathways that had significant correlations, the CBX2-ASPH-Notch signaling pathway was the most significantly correlated. Finally, resveratrol might be a potential inhibitor for KIRP. CONCLUSIONS We suggested that CBX2 could regulate ASPH through activation of the Notch signaling pathway, which might be correlated with the carcinogenesis, development, and unfavorable prognosis of KIRP.
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Affiliation(s)
- Yifan Liu
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Yuntao Yao
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Yu Zhang
- Tongji University School of Medicine, Shanghai, 200092, China
| | - Chengdang Xu
- Tongji University School of Medicine, Shanghai, 200092, China
| | - Tianyue Yang
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Mingyu Qu
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Bingnan Lu
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Xu Song
- Department of Urology, Shanghai Seventh People's Hospital, Shanghai, Shandong, 200137, China.
| | - Xiuwu Pan
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China.
| | - Wang Zhou
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China.
| | - Xingang Cui
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China.
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Hitomi Y, Ueno K, Aiba Y, Nishida N, Kono M, Sugihara M, Kawai Y, Kawashima M, Khor SS, Sugi K, Kouno H, Kohno H, Naganuma A, Iwamoto S, Katsushima S, Furuta K, Nikami T, Mannami T, Yamashita T, Ario K, Komatsu T, Makita F, Shimada M, Hirashima N, Yokohama S, Nishimura H, Sugimoto R, Komura T, Ota H, Kojima M, Nakamuta M, Fujimori N, Yoshizawa K, Mano Y, Takahashi H, Hirooka K, Tsuruta S, Sato T, Yamasaki K, Kugiyama Y, Motoyoshi Y, Suehiro T, Saeki A, Matsumoto K, Nagaoka S, Abiru S, Yatsuhashi H, Ito M, Kawata K, Takaki A, Arai K, Arinaga-Hino T, Abe M, Harada M, Taniai M, Zeniya M, Ohira H, Shimoda S, Komori A, Tanaka A, Ishigaki K, Nagasaki M, Tokunaga K, Nakamura M. A genome-wide association study identified PTPN2 as a population-specific susceptibility gene locus for primary biliary cholangitis. Hepatology 2024:01515467-990000000-00853. [PMID: 38652555 DOI: 10.1097/hep.0000000000000894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/22/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND AND AIMS Previous genome-wide association studies (GWAS) have indicated the involvement of shared (population-nonspecific) and nonshared (population-specific) susceptibility genes in the pathogenesis of primary biliary cholangitis (PBC) among European and East-Asian populations. Although a meta-analysis of these distinct populations has recently identified more than 20 novel PBC susceptibility loci, analyses of population-specific genetic architecture are still needed for a more comprehensive search for genetic factors in PBC. APPROACH AND RESULTS Protein tyrosine phosphatase nonreceptor type 2 ( PTPN2) was identified as a novel PBC susceptibility gene locus through GWAS and subsequent genome-wide meta-analysis involving 2181 cases and 2699 controls from the Japanese population (GWAS-lead variant: rs8098858, p = 2.6 × 10 -8 ). In silico and in vitro functional analyses indicated that the risk allele of rs2292758, which is a primary functional variant, decreases PTPN2 expression by disrupting Sp1 binding to the PTPN2 promoter in T follicular helper cells and plasmacytoid dendritic cells. Infiltration of PTPN2-positive T-cells and plasmacytoid dendritic cells was confirmed in the portal area of the PBC liver by immunohistochemistry. Furthermore, transcriptomic analysis of PBC-liver samples indicated the presence of a compromised negative feedback loop in vivo between PTPN2 and IFNG in patients carrying the risk allele of rs2292758. CONCLUSIONS PTPN2 , a novel susceptibility gene for PBC in the Japanese population, may be involved in the pathogenesis of PBC through an insufficient negative feedback loop caused by the risk allele of rs2292758 in IFN-γ signaling. This suggests that PTPN2 could be a potential molecular target for PBC treatment.
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Affiliation(s)
- Yuki Hitomi
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuko Ueno
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshihiro Aiba
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Nao Nishida
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Michihiro Kono
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mitsuki Sugihara
- Division of Biomedical Information Analysis, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | | | - Seik-Soon Khor
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Kazuhiro Sugi
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hirotaka Kouno
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hiroshi Kohno
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Atsushi Naganuma
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Satoru Iwamoto
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Shinji Katsushima
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kiyoshi Furuta
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Toshiki Nikami
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Tomohiko Mannami
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Tsutomu Yamashita
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Keisuke Ario
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Tatsuji Komatsu
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Fujio Makita
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Masaaki Shimada
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Noboru Hirashima
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Shiro Yokohama
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hideo Nishimura
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Rie Sugimoto
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Takuya Komura
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hajime Ota
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Motoyuki Kojima
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Makoto Nakamuta
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Naoyuki Fujimori
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kaname Yoshizawa
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Yutaka Mano
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hironao Takahashi
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kana Hirooka
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Satoru Tsuruta
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Takeaki Sato
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kazumi Yamasaki
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Yuki Kugiyama
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | | | - Tomoyuki Suehiro
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Akira Saeki
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kosuke Matsumoto
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Shinya Nagaoka
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Seigo Abiru
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | | | - Masahiro Ito
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kazuhito Kawata
- Hepatology Division, Department of Internal Medicine II, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Akinobu Takaki
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kuniaki Arai
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Teruko Arinaga-Hino
- Division of Gastroenterology, Department of Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Masanori Abe
- Department of Gastroenterology and Metabology, Ehime University Graduate School of Medicine, Matsuyama, Japan
| | - Masaru Harada
- The Third Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Makiko Taniai
- Department of Medicine and Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan
| | - Mikio Zeniya
- Department of Gastroenterology and Hepatology, Tokyo Jikei University School of Medicine, Tokyo, Japan
| | - Hiromasa Ohira
- Department of Gastroenterology, Fukushima Medical University, Fukushima, Japan
| | - Shinji Shimoda
- Division of Gastroenterology and Hepatology, Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Atsumasa Komori
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
- Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
| | - Atsushi Tanaka
- Department of Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masao Nagasaki
- Division of Biomedical Information Analysis, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Minoru Nakamura
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
- Division of Biomedical Information Analysis, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
- Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
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Park J, Park SA, Kim YS, Kim D, Shin S, Lee SH, Jeun SS, Chung YJ, Ahn S. Intratumoral IL-12 delivery via mesenchymal stem cells combined with PD-1 blockade leads to long-term antitumor immunity in a mouse glioblastoma model. Biomed Pharmacother 2024; 173:115790. [PMID: 38431436 DOI: 10.1016/j.biopha.2023.115790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Although PD-1 blockade is effective for treating several types of cancer, the efficacy of this agent in glioblastoma is largely limited. To overcome non-responders and the immunosuppressive tumor microenvironment, combinational immunotherapeutic strategies with anti-PD-1 need to be considered. Here, we developed IL-12-secreting mesenchymal stem cells (MSC_IL-12) with glioblastoma tropism and evaluated the therapeutic effects of anti-PD-1, MSC_IL-12, and their combination against glioblastoma. METHODS Therapeutic responses were evaluated using an immunocompetent mouse orthotopic model. Tumor-infiltrating lymphocytes (TILs) were analyzed using immunofluorescent imaging. Single-cell transcriptome was obtained from mouse brains after treatments. RESULTS Anti-PD-1 and MSC_IL-12 showed complete tumor remission in 25.0% (4/16) and 23.1% (3/13) of glioblastoma-implanted mice, respectively, and their combination yielded synergistic antitumor efficacy indicated by 50.0% (6/12) of complete tumor remission. Analyses of TILs revealed that anti-PD-1 increased CD8+ T cells, while MSC_IL-12 led to infiltration of CD4+ T cells and NK cells. Both therapies reduced frequencies of Tregs. All these aspects observed in each monotherapy group were superimposed in the combination group. Notably, no tumor growth was observed upon rechallenge in cured mice, indicating long-term immunity against glioblastoma provoked by the therapies. Single-cell RNA-seq data confirmed these results and revealed that the combined treatment led to immune-favorable tumor microenvironment-CD4+, CD8+ T cells, effector memory T cells, and activated microglia were increased, whereas exhausted T cells, Tregs, and M2 polarized microglia were reduced. CONCLUSION Anti-PD-1 and MSC_IL-12 monotherapies show long-term therapeutic responses, and their combination further enhances antitumor efficacy against glioblastoma via inducing immune-favorable tumor microenvironment.
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Affiliation(s)
- Junseong Park
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Soon A Park
- Department of Bio medicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Department of Neurosurgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yoon-Seob Kim
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dokyeong Kim
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Department of Bio medicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sun Shin
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sug Hyung Lee
- Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sin-Soo Jeun
- Department of Neurosurgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yeun-Jun Chung
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Department of Bio medicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Stephen Ahn
- Department of Neurosurgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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Abunimye DA, Okafor IM, Okorowo H, Obeagu EI. The role of GATA family transcriptional factors in haematological malignancies: A review. Medicine (Baltimore) 2024; 103:e37487. [PMID: 38518015 PMCID: PMC10956995 DOI: 10.1097/md.0000000000037487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 02/13/2024] [Indexed: 03/24/2024] Open
Abstract
GATA transcriptional factors are zinc finger DNA binding proteins that regulate transcription during development and cell differentiation. The 3 important GATA transcription factors GATA1, GATA2 and GATA3 play essential role in the development and maintenance of hematopoietic systems. GATA1 is required for the erythroid and Megakaryocytic commitment during hematopoiesis. GATA2 is crucial for the proliferation and survival of early hematopoietic cells, and is also involved in lineage specific transcriptional regulation as the dynamic partner of GATA1. GATA3 plays an essential role in T lymphoid cell development and immune regulation. As a result, mutations in gene encoding the GATA transcription factor or alteration in the protein expression level or their function have been linked to a variety of human haematological malignancies. This review presents a summary of recent understanding of how the disrupted biological function of GATA may contribute to hematologic diseases.
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Affiliation(s)
- Dennis Akongfe Abunimye
- Department of Haematology and Blood Transfusion Science, University of Calabar, Calabar, Nigeria
| | - Ifeyinwa Maryanne Okafor
- Department of Haematology and Blood Transfusion Science, University of Calabar, Calabar, Nigeria
| | - Henshew Okorowo
- Department of Haematology and Blood Transfusion Science, University of Calabar, Calabar, Nigeria
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Banerjee R, Ajithkumar P, Keestra N, Smith J, Gimenez G, Rodger EJ, Eccles MR, Antony J, Weeks RJ, Chatterjee A. Targeted DNA Methylation Editing Using an All-in-One System Establishes Paradoxical Activation of EBF3. Cancers (Basel) 2024; 16:898. [PMID: 38473261 DOI: 10.3390/cancers16050898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Cutaneous melanoma is rapidly on the rise globally, surpassing the growth rate of other cancers, with metastasis being the primary cause of death in melanoma patients. Consequently, understanding the mechanisms behind this metastatic process and exploring innovative treatments is of paramount importance. Recent research has shown promise in unravelling the role of epigenetic factors in melanoma progression to metastasis. While DNA hypermethylation at gene promoters typically suppresses gene expression, we have contributed to establishing the newly understood mechanism of paradoxical activation of genes via DNA methylation, where high methylation coincides with increased gene activity. This mechanism challenges the conventional paradigm that promoter methylation solely silences genes, suggesting that, for specific genes, it might actually activate them. Traditionally, altering DNA methylation in vitro has involved using global demethylating agents, which is insufficient for studying the mechanism and testing the direct consequence of gene methylation changes. To investigate promoter hypermethylation and its association with gene activation, we employed a novel approach utilising a CRISPR-SunTag All-in-one system. Here, we focused on editing the DNA methylation of a specific gene promoter segment (EBF3) in melanoma cells using the All-in-one system. Using bisulfite sequencing and qPCR with RNA-Seq, we successfully demonstrated highly effective methylation and demethylation of the EBF3 promoter, with subsequent gene expression changes, to establish and validate the paradoxical role of DNA methylation. Further, our study provides novel insights into the function of the EBF3 gene, which remains largely unknown. Overall, this study challenges the conventional view of methylation as solely a gene-silencing mechanism and demonstrates a potential function of EBF3 in IFN pathway signalling, potentially uncovering new insights into epigenetic drivers of malignancy and metastasis.
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Affiliation(s)
- Rakesh Banerjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Priyadarshana Ajithkumar
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Nicholas Keestra
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Jim Smith
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Gregory Gimenez
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Euan J Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Jisha Antony
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Robert J Weeks
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
- School of Health Sciences and Technology, UPES University, Dehradun 248007, India
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7
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Lavogina D, Krõlov MK, Vellama H, Modhukur V, Di Nisio V, Lust H, Eskla KL, Salumets A, Jaal J. Inhibition of epigenetic and cell cycle-related targets in glioblastoma cell lines reveals that onametostat reduces proliferation and viability in both normoxic and hypoxic conditions. Sci Rep 2024; 14:4303. [PMID: 38383756 PMCID: PMC10881536 DOI: 10.1038/s41598-024-54707-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/15/2024] [Indexed: 02/23/2024] Open
Abstract
The choice of targeted therapies for treatment of glioblastoma patients is currently limited, and most glioblastoma patients die from the disease recurrence. Thus, systematic studies in simplified model systems are required to pinpoint the choice of targets for further exploration in clinical settings. Here, we report screening of 5 compounds targeting epigenetic writers or erasers and 6 compounds targeting cell cycle-regulating protein kinases against 3 glioblastoma cell lines following incubation under normoxic or hypoxic conditions. The viability/proliferation assay indicated that PRMT5 inhibitor onametostat was endowed with high potency under both normoxic and hypoxic conditions in cell lines that are strongly MGMT-positive (T98-G), weakly MGMT-positive (U-251 MG), or MGMT-negative (U-87 MG). In U-251 MG and U-87 MG cells, onametostat also affected the spheroid formation at concentrations lower than the currently used chemotherapeutic drug lomustine. In T98-G cell line, treatment with onametostat led to dramatic changes in the transcriptome profile by inducing the cell cycle arrest, suppressing RNA splicing, and down-regulating several major glioblastoma cell survival pathways. Further validation by immunostaining in three cell lines confirmed that onametostat affects cell cycle and causes reduction in nucleolar protein levels. In this way, inhibition of epigenetic targets might represent a viable strategy for glioblastoma treatment even in the case of decreased chemo- and radiation sensitivity, although further studies in clinically more relevant models are required.
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Affiliation(s)
- Darja Lavogina
- Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, 50406, Tartu, Estonia.
- Chair of Bioorganic Chemistry, Institute of Chemistry, University of Tartu, Tartu, Estonia.
- Competence Centre on Health Technologies, Tartu, Estonia.
| | - Mattias Kaspar Krõlov
- Chair of Bioorganic Chemistry, Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Hans Vellama
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Centre of Excellence for Genomics and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Vijayachitra Modhukur
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Valentina Di Nisio
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Huddinge, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Helen Lust
- Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, 50406, Tartu, Estonia
| | - Kattri-Liis Eskla
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Centre of Excellence for Genomics and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Huddinge, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Jana Jaal
- Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, 50406, Tartu, Estonia.
- Department of Radiotherapy and Oncological Therapy, Tartu University Hospital, Tartu, Estonia.
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8
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Zhang Y, Liu F, Zheng J, Jiang K, Ai H, Liu L, Mao D. MAPRE3 as an epigenetic target of EZH2 restricts ovarian cancer proliferation in vitro and in vivo. Exp Cell Res 2024; 435:113913. [PMID: 38199479 DOI: 10.1016/j.yexcr.2024.113913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/12/2024]
Abstract
Ovarian cancer (OC) is a lethal gynecologic cancer and the common cause of death within women worldwide. The polycomb group protein enhancer of zeste homolog 2 (EZH2) is a histone methyltransferase highly expressed in various tumors, including OC. However, the mechanistic basis of EZH2 oncogenic activity in OC remain incompletely understood. Bioinformatics analysis showed that the expression of MAPRE3 was lower in OC tissues than in normal tissues, and was positively correlated with the overall survival. MAPRE3 overexpression decreased cell growth, inducing cell cycle arrest and apoptosis in OC cells, whereas MAPRE3 silencing promoted proliferation and accelerated cell cycle progression of OC cells. The in vivo study validated that overexpression of MAPRE3 impeded tumor formation and growth of OC xenografts in nude mice. In addition, knockdown of EZH2 in OC cells downregulated H3K27me3 expression and increased MAPRE3 expression. Inhibiting EZH2 in OC cells reduced the enrichment of H3K27me3 on the promoter of MAPRE3. Furthermore, MAPRE3 silencing significantly reversed changes in the expression of cell cycle and apoptosis-related markers and cell growth mediated by EZH2 knockdown in OC cells. MAPRE3 functions as a suppressor of OC and is epigenetic repressed by EZH2, suggesting a potential therapeutic strategy for OC by targeting EZH2/MAPRE3 axis.
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Affiliation(s)
- Yun Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China; Liaoning Key Laboratory of Follicular Development and Reproductive Health, Jinzhou, Liaoning, China.
| | - Fanglin Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
| | - Jindan Zheng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
| | - Keping Jiang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
| | - Hao Ai
- Liaoning Key Laboratory of Follicular Development and Reproductive Health, Jinzhou, Liaoning, China; Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
| | - Lili Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
| | - Dong Mao
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
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Li L, Zhang D, Cao X. EBF1, PAX5, and MYC: regulation on B cell development and association with hematologic neoplasms. Front Immunol 2024; 15:1320689. [PMID: 38318177 PMCID: PMC10839018 DOI: 10.3389/fimmu.2024.1320689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
During lymphocyte development, a diverse repertoire of lymphocyte antigen receptors is produced to battle against pathogens, which is the basis of adaptive immunity. The diversity of the lymphocyte antigen receptors arises primarily from recombination-activated gene (RAG) protein-mediated V(D)J rearrangement in early lymphocytes. Furthermore, transcription factors (TFs), such as early B cell factor 1 (EBF1), paired box gene 5 (PAX5), and proto-oncogene myelocytomatosis oncogene (MYC), play critical roles in regulating recombination and maintaining normal B cell development. Therefore, the aberrant expression of these TFs may lead to hematologic neoplasms.
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Affiliation(s)
- Li Li
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Daiquan Zhang
- Department of Traditional Chinese Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xinmei Cao
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
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Yuan X, Yu T, Zhao J, Jiang H, Hao Y, Lei W, Liang Y, Li B, Qian W. Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing in Chinese patients. Front Med 2023; 17:889-906. [PMID: 37418076 DOI: 10.1007/s11684-023-0994-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/06/2023] [Indexed: 07/08/2023]
Abstract
Primary central nervous system lymphoma (PCNSL) is an uncommon non-Hodgkin's lymphoma with poor prognosis. This study aimed to depict the genetic landscape of Chinese PCNSLs. Whole-genome sequencing was performed on 68 newly diagnosed Chinese PCNSL samples, whose genomic characteristics and clinicopathologic features were also analyzed. Structural variations were identified in all patients with a mean of 349, which did not significantly influence prognosis. Copy loss occurred in all samples, while gains were detected in 77.9% of the samples. The high level of copy number variations was significantly associated with poor progression-free survival (PFS) and overall survival (OS). A total of 263 genes mutated in coding regions were identified, including 6 newly discovered genes (ROBO2, KMT2C, CXCR4, MYOM2, BCLAF1, and NRXN3) detected in ⩾ 10% of the cases. CD79B mutation was significantly associated with lower PFS, TMSB4X mutation and high expression of TMSB4X protein was associated with lower OS. A prognostic risk scoring system was also established for PCNSL, which included Karnofsky performance status and six mutated genes (BRD4, EBF1, BTG1, CCND3, STAG2, and TMSB4X). Collectively, this study comprehensively reveals the genomic landscape of newly diagnosed Chinese PCNSLs, thereby enriching the present understanding of the genetic mechanisms of PCNSL.
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Affiliation(s)
- Xianggui Yuan
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Teng Yu
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Jianzhi Zhao
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Huawei Jiang
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Yuanyuan Hao
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Wen Lei
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Yun Liang
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Baizhou Li
- Department of Pathology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China.
| | - Wenbin Qian
- Department of Hematology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China.
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11
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Ciaccio C, Pantaleoni C, Moscatelli M, Chiapparini L, Nigro V, Valente EM, Sciacca F, Canafoglia L, Bulgheroni S, D'Arrigo S. Neurologic, Neuropsychologic, and Neuroradiologic Features of EBF3-Related Syndrome. NEUROLOGY GENETICS 2023; 9:e200049. [PMID: 37090941 PMCID: PMC10117703 DOI: 10.1212/nxg.0000000000200049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/25/2022] [Indexed: 01/24/2023]
Abstract
Background and ObjectivesHeterozygous mutations or deletions of theEBF3gene are known to cause a syndrome characterized by intellectual disability, neurodevelopmental disorders, facial dysmorphisms, hypotonia, and ataxia; the latter is quite common despite in most patients brain MRI is reported to be normal. Despite the predominant neurologic involvement ofEBF3-related syndrome, a systematic definition of neurologic, cognitive/behavioral, and neuroradiologic features is lacking.MethodsWe report on 6 patients (2 females and 4 males, age range 2–12 years), of whom 4 carrying a heterozygous point mutation of theEBF3gene and 2 with 10q26 deletion encompassing the gene, diagnosed at Carlo Besta Neurologic Institute of Milan, Italy. Clinical evaluation was performed by a pediatric neurologist and pediatric dysmorphologist; ataxia severity was rated by Scale for the Assessment and Rating of Ataxia (SARA); brain MRIs were reviewed by expert neuroradiologists; general quotient levels were obtained through standardized Griffiths Mental Development Scales. Patients carrying a 10q26.3 deletion were diagnosed by array-CGH, whereasEBF3variants were detected by whole exome sequencing.ResultsPhenotype was consistent in all patients, but with wide variability in severity. Developmental milestones were invariably delayed and resulted in an extremely variable cognitive impairment. All patients showed ataxic signs, as confirmed by SARA scores, often associated with hypotonia. Brain MRI revealed in all children a cerebellar malformation with vermis hypoplasia and a peculiar foliation anomaly characterized by a radial disposition of cerebellar folia (dandelion sign). Neurophysiologic examinations were unremarkable.DiscussionEBF3-related syndrome has been so far described as a neurodevelopmental condition with dysmorphic traits, with limited emphasis on the neurologic features; we highlight the predominant neurologic involvement of these patients, which can be explained at least in part by the underlying cerebellar malformation. We therefore propose thatEBF3-related syndrome should be classified and treated as a congenital, nonprogressive ataxia.
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Affiliation(s)
- Claudia Ciaccio
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Chiara Pantaleoni
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Marco Moscatelli
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Luisa Chiapparini
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Vincenzo Nigro
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Enza Maria Valente
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Francesca Sciacca
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Laura Canafoglia
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Sara Bulgheroni
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Stefano D'Arrigo
- Department of Pediatric Neurosciences (C.C., C.P., S.B., S.D.A.), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Neuroradiology Unit (M.M., Luisa Chiapparini), Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano; Department of Biomedical Sciences for Health (M.M.), University of Milan; Neuroradiology Unit (Luisa Chiapparini), Fondazione IRCCS Policlinico San Matteo, Pavia; Telethon Institute of Genetics and Medicine (TIGEM) (V.N.), Pozzuoli; Department of Precision Medicine (V.N.), Università Della Campania Luigi Vanvitelli, Naples; Department of Molecular Medicine (E.M.V.), University of Pavia, Pavia; Molecular Genetics and Cytogenetics Lab-Neurogenetics Research Center (E.M.V.), IRCCS Mondino Foundation, Pavia; Laboratory of Cytogenetics (F.S.), Unit of Neurological Biochemistry and Neuropharmacology, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan; and Integrated Diagnostics for Epilepsy (Laura Canafoglia), Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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12
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Floy ME, Shabnam F, Givens SE, Patil VA, Ding Y, Li G, Roy S, Raval AN, Schmuck EG, Masters KS, Ogle BM, Palecek SP. Identifying molecular and functional similarities and differences between human primary cardiac valve interstitial cells and ventricular fibroblasts. Front Bioeng Biotechnol 2023; 11:1102487. [PMID: 37051268 PMCID: PMC10083504 DOI: 10.3389/fbioe.2023.1102487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/06/2023] [Indexed: 03/29/2023] Open
Abstract
Introduction: Fibroblasts are mesenchymal cells that predominantly produce and maintain the extracellular matrix (ECM) and are critical mediators of injury response. In the heart, valve interstitial cells (VICs) are a population of fibroblasts responsible for maintaining the structure and function of heart valves. These cells are regionally distinct from myocardial fibroblasts, including left ventricular cardiac fibroblasts (LVCFBs), which are located in the myocardium in close vicinity to cardiomyocytes. Here, we hypothesize these subpopulations of fibroblasts are transcriptionally and functionally distinct. Methods: To compare these fibroblast subtypes, we collected patient-matched samples of human primary VICs and LVCFBs and performed bulk RNA sequencing, extracellular matrix profiling, and functional contraction and calcification assays. Results: Here, we identified combined expression of SUSD2 on a protein-level, and MEOX2, EBF2 and RHOU at a transcript-level to be differentially expressed in VICs compared to LVCFBs and demonstrated that expression of these genes can be used to distinguish between the two subpopulations. We found both VICs and LVCFBs expressed similar activation and contraction potential in vitro, but VICs showed an increase in ALP activity when activated and higher expression in matricellular proteins, including cartilage oligomeric protein and alpha 2-Heremans-Schmid glycoprotein, both of which are reported to be linked to calcification, compared to LVCFBs. Conclusion: These comparative transcriptomic, proteomic, and functional studies shed novel insight into the similarities and differences between valve interstitial cells and left ventricular cardiac fibroblasts and will aid in understanding region-specific cardiac pathologies, distinguishing between primary subpopulations of fibroblasts, and generating region-specific stem-cell derived cardiac fibroblasts.
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Affiliation(s)
- Martha E. Floy
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Fathima Shabnam
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Sophie E. Givens
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, United States
| | - Vaidehi A. Patil
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Yunfeng Ding
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Grace Li
- Department of Chemical Engineering, University of Florida, Gainesville, FL, United States
| | - Sushmita Roy
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Amish N. Raval
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Eric G. Schmuck
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Kristyn S. Masters
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Brenda M. Ogle
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, United States
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, United States
| | - Sean P. Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States
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13
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Dong L, Sun Q, Song F, Song X, Lu C, Li Y, Song X. Identification and verification of eight cancer-associated fibroblasts related genes as a prognostic signature for head and neck squamous cell carcinoma. Heliyon 2023; 9:e14003. [PMID: 36938461 PMCID: PMC10018481 DOI: 10.1016/j.heliyon.2023.e14003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
Cancer-associated fibroblasts (CAFs) can exert their immunosuppressive effects by secreting various effectors that are involved in the regulation of tumor-infiltrating immune cells as well as other immune components in the tumor immune microenvironment (TIME), thereby promoting tumorigenesis, progression, metastasis, and drug resistance. Although a large number of studies suggest that CAFs play a key regulatory role in the development of head and neck squamous cell carcinoma (HNSCC), there are limited studies on the relevance of CAFs to the prognosis of HNSCC. In this study, we identified a prognostic signature containing eight CAF-related genes for HNSCC by univariate Cox analysis, lasso regression, stepwise regression, and multivariate Cox analysis. Our validation in primary cultures of CAFs from human HNSCC and four human HNSCC cell lines confirmed that these eight genes are indeed characteristic markers of CAFs. Immune cell infiltration differences analysis between high-risk and low-risk groups according to the eight CAF-related genes signature hinted at CAFs regulatory roles in the TIME, further revealing its potential role on prognosis. The signature of the eight CAF-related genes was validated in different independent validation cohorts and all showed that it was a valid marker for prognosis. The significantly higher overall survival (OS) in the low-risk group compared to the high-risk group was confirmed by Kaplan-Meier (K-M) analysis, suggesting that the signature of CAF-related genes can be used as a non-invasive predictive tool for HNSCC prognosis. The low-risk group had significantly higher levels of tumor-killing immune cell infiltration, as confirmed by CIBERSORT analysis, such as CD8+ T cells, follicular helper T cells, and Dendritic cells (DCs) in the low-risk group. In contrast, the level of infiltration of pro-tumor cells such as M0 macrophages and activated Mast cells (MCs) was lower. It is crucial to delve into the complex mechanisms between CAFs and immune cells to find potential regulatory targets and may provide new evidence for subsequently targeted immunotherapy. These results suggest that the signature of the eight CAF-related genes is a powerful indicator for the assessment of the TIME of HNSCC. It may provide a new and reliable potential indicator for clinicians to predict the prognosis of HNSCC, which may be used to guide treatment and clinical decision-making in HNSCC patients. Meanwhile, CAF-related genes are expected to become tumor biomarkers and effective targets for HNSCC.
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Key Words
- CAFs, Cancer-associated fibroblasts
- CSCs, cancer stem cells
- Cancer-associated fibroblasts
- DCs, Dendritic cells
- EMT, epithelial mesenchymal transition
- GEO, Gene Expression Omnibus
- GEPIA, Gene Expression Profiling Interactive Analysis
- GO, Gene Ontology
- GSEA, Gene Set Enrichment Analysis
- HNSCC, head and neck squamous cell carcinoma
- HR, Hazard Ratio
- Head and neck squamous cell carcinoma
- Immune cell infiltration
- K-M, Kaplan-Meier
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MCs, Mast cells
- NFs, normal fibroblasts
- OS, overall survival
- OSCC, oral squamous cell carcinomas
- Prognostic signature
- ROC, receiver operating characteristic
- TAMs, tumor-associated macrophages
- TCGA, The Cancer Genome Atlas
- TIME, tumor immune microenvironment
- TME, tumor microenvironment
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Affiliation(s)
- Lei Dong
- Department of Otorhinolaryngology Head and Neck Surgery, Yantai Yuhuangding Hospital, Shandong University, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases
| | - Qi Sun
- Department of Otorhinolaryngology Head and Neck Surgery, Yantai Yuhuangding Hospital, Shandong University, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases
| | - Fei Song
- Department of Otorhinolaryngology Head and Neck Surgery, Yantai Yuhuangding Hospital, Shandong University, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases
| | - Xiaoyu Song
- Department of Otorhinolaryngology Head and Neck Surgery, Yantai Yuhuangding Hospital, Shandong University, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases
| | - Congxian Lu
- Department of Otorhinolaryngology Head and Neck Surgery, Yantai Yuhuangding Hospital, Shandong University, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases
| | - Yumei Li
- Department of Otorhinolaryngology Head and Neck Surgery, Yantai Yuhuangding Hospital, Shandong University, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases
- Corresponding author. Yumei Li: Department of Otorhinolaryngology Head and Neck Surgery. Yantai Yuhuangding Hospital, No.20, Yuhuangding East Road, Zhifu District, Yantai, Shandong, 264000, China.
| | - Xicheng Song
- Department of Otorhinolaryngology Head and Neck Surgery, Yantai Yuhuangding Hospital, Shandong University, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases
- Corresponding author. Xicheng Song: Department of Otorhinolaryngology Head and Neck Surgery. Yantai Yuhuangding Hospital, No.20, Yuhuangding East Road, Zhifu District, Yantai, Shandong, 264000, China.
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14
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Cheng Y, Ni YJ, Tang LM. ZNF521/EBF1 axis regulates AKR1B1 to promote the proliferation, migration, and invasion of gastric cancer cells. Kaohsiung J Med Sci 2023; 39:244-253. [PMID: 36397644 DOI: 10.1002/kjm2.12624] [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: 07/21/2022] [Revised: 10/09/2022] [Accepted: 11/02/2022] [Indexed: 11/20/2022] Open
Abstract
Although the incidence and death rates of gastric cancer (GC) are decreasing, approximately one million new cases and 800,000 GC-related deaths were reported worldwide in 2018. Currently, the oncogenesis of GC remains unclear, and the demand for novel treatment options are unmet. Here, we explored the role of aldo-keto reductase family 1 member B (AKR1B1) in the progression of GC. The proliferation, migration, and invasion of GC cells were evaluated by CCK-8 assay, wound healing assay, and transwell assay, respectively. The interaction between EBF transcription factor 1 (EBF1) and the promoter region of AKR1B1 was determined by luciferase reporter assay and chromatin immunoprecipitation (ChIP). Gene expression levels were measured by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting assay. The expression of AKR1B1 was elevated in GC cells, resulting in increased cell proliferation, migration, and invasion. Meanwhile, EBF1 was a negative regulator of AKR1B1; its overexpression suppressed AKR1B1 expression and GC progression. Furthermore, knockdown of ZNF521 induced EBF1 expression, thus suppressing AKR1B1 expression and resulting in attenuated GC growth and invasiveness. Notably, knockdown of ZNF521 attenuated GC progression and was rescued by overexpression of AKR1B1. Our current study revealed a novel ZNF521/EBF1/AKR1B1 axis in GC and elaborated its important role in promoting GC progression, providing potential therapeutic targets for anti-GC treatments.
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Affiliation(s)
- Yu Cheng
- Department of Gastrointestinal Surgery, Changzhou No. 2 People's Hospital (Affiliated Hospital of Nanjing Medical University), Changzhou, Jiangsu, People's Republic of China
| | - Yi-Jiang Ni
- Department of Gastrointestinal Surgery, Changzhou No. 2 People's Hospital (Affiliated Hospital of Nanjing Medical University), Changzhou, Jiangsu, People's Republic of China
| | - Li-Ming Tang
- Department of Gastrointestinal Surgery, Changzhou No. 2 People's Hospital (Affiliated Hospital of Nanjing Medical University), Changzhou, Jiangsu, People's Republic of China
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15
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Yadav V, Sharma K, Bhattacharya S, Talwar P, Purohit PK, Saini N. RETRACTED: hsa-miR-23a~27a~24-2 cluster members inhibit aggressiveness of breast cancer cells by commonly targeting NCOA1, NLK and RAP1B. Life Sci 2022; 307:120906. [PMID: 36007610 DOI: 10.1016/j.lfs.2022.120906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/10/2022] [Accepted: 08/18/2022] [Indexed: 11/28/2022]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editor-in-Chief. The corresponding author notified the journal of three examples of image duplication within the published article (two in Figure 3D and one in Figure 4A), and requested a corrigendum. As per journal policy when considering corrigendum requests, the journal requested the authors to provide source data relating to these affected figures. The editorial team noticed 12 additional suspected image duplications within the supplied source data and the corresponding author was informed. Upon submission of revised source data, the editorial team noticed two new suspected image duplications. The editorial team have concerns about the provenance of the data and therefore the Editor-in-Chief decided to retract the article.
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Affiliation(s)
- Vikas Yadav
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology (IGIB), Mall Road, 110007, Delhi, India
| | - Kritika Sharma
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology (IGIB), Mall Road, 110007, Delhi, India
| | - Sushant Bhattacharya
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology (IGIB), Mall Road, 110007, Delhi, India
| | - Puneet Talwar
- Institute of Human Behaviour & Allied Sciences (IHBAS), Delhi, India
| | - Paresh Kumar Purohit
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology (IGIB), Mall Road, 110007, Delhi, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Neeru Saini
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology (IGIB), Mall Road, 110007, Delhi, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
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16
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Early B cell factor 4 modulates FAS-mediated apoptosis and promotes cytotoxic function in human immune cells. Proc Natl Acad Sci U S A 2022; 119:e2208522119. [PMID: 35939714 PMCID: PMC9388157 DOI: 10.1073/pnas.2208522119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Apoptosis is a genetically regulated program of cell death that plays a key role in immune disease processes. We identified EBF4, a little-studied member of the early B cell factor (EBF) family of transcription factors, in a whole-genome CRISPR screen for regulators of Fas/APO-1/CD95-mediated T cell death. Loss of EBF4 increases the half-life of the c-FLIP protein, and its presence in the Fas signaling complex impairs caspase-8 cleavage and apoptosis. Transcriptome analysis revealed that EBF4 regulates molecules such as TBX21, EOMES, granzyme, and perforin that are important for human natural killer (NK) and CD8+ T cell functions. Proximity-dependent biotin identification (Bio-ID) mass spectrometry analyses showed EBF4 binding to STAT3, STAT5, and MAP kinase 3 and a strong pathway relationship to interleukin-2 regulated genes, which are known to govern cytotoxicity pathways. Chromatin immunoprecipitation and DNA sequencing analysis defined a canonical EBF4 binding motif, 5'-CCCNNGG/AG-3', closely related to the EBF1 binding site; using a luciferase-based reporter, we found a dose-dependent transcriptional response of this motif to EBF4. We also conducted assay for transposase-accessible chromatin sequencing in EBF4-overexpressing cells and found increased chromatin accessibility upstream of granzyme and perforin and in topologically associated domains in human lymphocytes. Finally, we discovered that the EBF4 has basal expression in human but not mouse NK cells and CD8+ T cells and vanishes following activating stimulation. Together, our data reveal key features of a previously unknown transcriptional regulator of human cytotoxic immune function.
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17
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Identifying General Tumor and Specific Lung Cancer Biomarkers by Transcriptomic Analysis. BIOLOGY 2022; 11:biology11071082. [PMID: 36101460 PMCID: PMC9313083 DOI: 10.3390/biology11071082] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/25/2022] [Accepted: 07/03/2022] [Indexed: 11/17/2022]
Abstract
The bioinformatic pipeline previously developed in our research laboratory is used to identify potential general and specific deregulated tumor genes and transcription factors related to the establishment and progression of tumoral diseases, now comparing lung cancer with other two types of cancer. Twenty microarray datasets were selected and analyzed separately to identify hub differentiated expressed genes and compared to identify all the deregulated genes and transcription factors in common between the three types of cancer and those unique to lung cancer. The winning DEGs analysis allowed to identify an important number of TFs deregulated in the majority of microarray datasets, which can become key biomarkers of general tumors and specific to lung cancer. A coexpression network was constructed for every dataset with all deregulated genes associated with lung cancer, according to DAVID’s tool enrichment analysis, and transcription factors capable of regulating them, according to oPOSSUM´s tool. Several genes and transcription factors are coexpressed in the networks, suggesting that they could be related to the establishment or progression of the tumoral pathology in any tissue and specifically in the lung. The comparison of the coexpression networks of lung cancer and other types of cancer allowed the identification of common connectivity patterns with deregulated genes and transcription factors correlated to important tumoral processes and signaling pathways that have not been studied yet to experimentally validate their role in lung cancer. The Kaplan–Meier estimator determined the association of thirteen deregulated top winning transcription factors with the survival of lung cancer patients. The coregulatory analysis identified two top winning transcription factors networks related to the regulatory control of gene expression in lung and breast cancer. Our transcriptomic analysis suggests that cancer has an important coregulatory network of transcription factors related to the acquisition of the hallmarks of cancer. Moreover, lung cancer has a group of genes and transcription factors unique to pulmonary tissue that are coexpressed during tumorigenesis and must be studied experimentally to fully understand their role in the pathogenesis within its very complex transcriptomic scenario. Therefore, the downstream bioinformatic analysis developed was able to identify a coregulatory metafirm of cancer in general and specific to lung cancer taking into account the great heterogeneity of the tumoral process at cellular and population levels.
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18
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Shafi O, Siddiqui G. Tracing the origins of glioblastoma by investigating the role of gliogenic and related neurogenic genes/signaling pathways in GBM development: a systematic review. World J Surg Oncol 2022; 20:146. [PMID: 35538578 PMCID: PMC9087910 DOI: 10.1186/s12957-022-02602-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/15/2022] [Indexed: 02/16/2023] Open
Abstract
Background Glioblastoma is one of the most aggressive tumors. The etiology and the factors determining its onset are not yet entirely known. This study investigates the origins of GBM, and for this purpose, it focuses primarily on developmental gliogenic processes. It also focuses on the impact of the related neurogenic developmental processes in glioblastoma oncogenesis. It also addresses why glial cells are at more risk of tumor development compared to neurons. Methods Databases including PubMed, MEDLINE, and Google Scholar were searched for published articles without any date restrictions, involving glioblastoma, gliogenesis, neurogenesis, stemness, neural stem cells, gliogenic signaling and pathways, neurogenic signaling and pathways, and astrocytogenic genes. Results The origin of GBM is dependent on dysregulation in multiple genes and pathways that accumulatively converge the cells towards oncogenesis. There are multiple layers of steps in glioblastoma oncogenesis including the failure of cell fate-specific genes to keep the cells differentiated in their specific cell types such as p300, BMP, HOPX, and NRSF/REST. There are genes and signaling pathways that are involved in differentiation and also contribute to GBM such as FGFR3, JAK-STAT, and hey1. The genes that contribute to differentiation processes but also contribute to stemness in GBM include notch, Sox9, Sox4, c-myc gene overrides p300, and then GFAP, leading to upregulation of nestin, SHH, NF-κB, and others. GBM mutations pathologically impact the cell circuitry such as the interaction between Sox2 and JAK-STAT pathway, resulting in GBM development and progression. Conclusion Glioblastoma originates when the gene expression of key gliogenic genes and signaling pathways become dysregulated. This study identifies key gliogenic genes having the ability to control oncogenesis in glioblastoma cells, including p300, BMP, PAX6, HOPX, NRSF/REST, LIF, and TGF beta. It also identifies key neurogenic genes having the ability to control oncogenesis including PAX6, neurogenins including Ngn1, NeuroD1, NeuroD4, Numb, NKX6-1 Ebf, Myt1, and ASCL1. This study also postulates how aging contributes to the onset of glioblastoma by dysregulating the gene expression of NF-κB, REST/NRSF, ERK, AKT, EGFR, and others.
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Affiliation(s)
- Ovais Shafi
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan.
| | - Ghazia Siddiqui
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan
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19
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Puhka M, Thierens L, Nicorici D, Forsman T, Mirtti T, af Hällström T, Serkkola E, Rannikko A. Exploration of Extracellular Vesicle miRNAs, Targeted mRNAs and Pathways in Prostate Cancer: Relation to Disease Status and Progression. Cancers (Basel) 2022; 14:cancers14030532. [PMID: 35158801 PMCID: PMC8833493 DOI: 10.3390/cancers14030532] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/10/2022] [Accepted: 01/17/2022] [Indexed: 02/08/2023] Open
Abstract
Simple Summary Prostate cancer lacks non-invasive specific biomarkers for aggressive disease. Urinary extracellular vesicles (uEV) could provide such markers; however, due to technical challenges, little is known regarding the pathogenesis pathways reflected in uEV. We performed a miRNA, target mRNA and pathway study focused on uEV, exploring the differences between cancer (1) status groups (Gleason score) and (2) progression groups. The uEV provided a surprisingly comprehensive presentation of differentially expressed miRNAs, target mRNAs and pathogenesis pathways. The miRNAs associated with prostate cancer status or progression were mostly unique, but still targeted overlapping sets of signalling, resistance, hormonal and immune pathways. Interestingly, mRNA targets of the key miRNAs (miR-892a, miR-223-3p, miR-146a-5p) were widely expressed in both uEV and plasma EV from PCa patients. The study thus suggests that uEV carry a vast presentation of PCa status and progression-linked RNAs that are worth further exploration in large personalized medicine trials. Abstract Background: Prostate cancer (PCa) lacks non-invasive specific biomarkers for aggressive disease. We studied the potential of urinary extracellular vesicles (uEV) as a liquid PCa biopsy by focusing on the micro RNA (miRNA) cargo, target messenger RNA (mRNA) and pathway analysis. Methods: We subjected uEV samples from 31 PCa patients (pre-prostatectomy) to miRNA sequencing and matched uEV and plasma EV (pEV) from three PCa patients to mRNA sequencing. EV quality control was performed by electron microscopy, Western blotting and particle and RNA analysis. We compared miRNA expression based on PCa status (Gleason Score) and progression (post-prostatectomy follow-up) and confirmed selected miRNAs by quantitative PCR. Expression of target mRNAs was mapped in matched EV. Results: Quality control showed typical small uEV, pEV, RNA and EV-protein marker enriched samples. Comparisons between PCa groups revealed mostly unique differentially expressed miRNAs. However, they targeted comprehensive and largely overlapping sets of cancer and progression-associated signalling, resistance, hormonal and immune pathways. Quantitative PCR confirmed changes in miR-892a (Gleason Score 7 vs. ≥8), miR-223-3p (progression vs. no progression) and miR-146a-5p (both comparisons). Their target mRNAs were expressed widely in PCa EV. Conclusions: PCa status and progression-linked RNAs in uEV are worth exploration in large personalized medicine trials.
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Affiliation(s)
- Maija Puhka
- HiPrep and EV Core, Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00290 Helsinki, Finland;
- Correspondence: (M.P.); (A.R.)
| | - Lisse Thierens
- HiPrep and EV Core, Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00290 Helsinki, Finland;
| | - Daniel Nicorici
- Orion Pharma, Orion Corporation, 02200 Espoo, Finland; (D.N.); (T.F.); (E.S.)
| | - Tarja Forsman
- Orion Pharma, Orion Corporation, 02200 Espoo, Finland; (D.N.); (T.F.); (E.S.)
| | - Tuomas Mirtti
- Department of Pathology, HUS Diagnostic Centre, Helsinki University Hospital, 00290 Helsinki, Finland;
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | | | - Elina Serkkola
- Orion Pharma, Orion Corporation, 02200 Espoo, Finland; (D.N.); (T.F.); (E.S.)
| | - Antti Rannikko
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Urology, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
- Correspondence: (M.P.); (A.R.)
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20
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Liu Y, Chen H, Heine J, Lindstrom S, Turman C, Warner ET, Winham SJ, Vachon CM, Tamimi RM, Kraft P, Jiang X. A genome-wide association study of mammographic texture variation. Breast Cancer Res 2022; 24:76. [PMCID: PMC9639267 DOI: 10.1186/s13058-022-01570-8] [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: 05/13/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022] Open
Abstract
Background Breast parenchymal texture features, including grayscale variation (V), capture the patterns of texture variation on a mammogram and are associated with breast cancer risk, independent of mammographic density (MD). However, our knowledge on the genetic basis of these texture features is limited. Methods We conducted a genome-wide association study of V in 7040 European-ancestry women. V assessments were generated from digitized film mammograms. We used linear regression to test the single-nucleotide polymorphism (SNP)-phenotype associations adjusting for age, body mass index (BMI), MD phenotypes, and the top four genetic principal components. We further calculated genetic correlations and performed SNP-set tests of V with MD, breast cancer risk, and other breast cancer risk factors. Results We identified three genome-wide significant loci associated with V: rs138141444 (6q24.1) in ECT2L, rs79670367 (8q24.22) in LINC01591, and rs113174754 (12q22) near PGAM1P5. 6q24.1 and 8q24.22 have not previously been associated with MD phenotypes or breast cancer risk, while 12q22 is a known locus for both MD and breast cancer risk. Among known MD and breast cancer risk SNPs, we identified four variants that were associated with V at the Bonferroni-corrected thresholds accounting for the number of SNPs tested: rs335189 (5q23.2) in PRDM6, rs13256025 (8p21.2) in EBF2, rs11836164 (12p12.1) near SSPN, and rs17817449 (16q12.2) in FTO. We observed significant genetic correlations between V and mammographic dense area (rg = 0.79, P = 5.91 × 10−5), percent density (rg = 0.73, P = 1.00 × 10−4), and adult BMI (rg = − 0.36, P = 3.88 × 10−7). Additional significant relationships were observed for non-dense area (z = − 4.14, P = 3.42 × 10−5), estrogen receptor-positive breast cancer (z = 3.41, P = 6.41 × 10−4), and childhood body fatness (z = − 4.91, P = 9.05 × 10−7) from the SNP-set tests. Conclusions These findings provide new insights into the genetic basis of mammographic texture variation and their associations with MD, breast cancer risk, and other breast cancer risk factors. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-022-01570-8.
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Affiliation(s)
- Yuxi Liu
- grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA ,grid.38142.3c000000041936754XProgram in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2-249A, Boston, MA 02115 USA
| | - Hongjie Chen
- grid.34477.330000000122986657Department of Epidemiology, University of Washington, Seattle, WA USA
| | - John Heine
- grid.468198.a0000 0000 9891 5233Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL USA
| | - Sara Lindstrom
- grid.34477.330000000122986657Department of Epidemiology, University of Washington, Seattle, WA USA ,grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Constance Turman
- grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Erica T. Warner
- grid.38142.3c000000041936754XClinical and Translational Epidemiology Unit, Department of Medicine, Mongan Institute, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
| | - Stacey J. Winham
- grid.66875.3a0000 0004 0459 167XBiomedical Statistics and Informatics, Mayo Clinic, Rochester, MN USA
| | - Celine M. Vachon
- grid.66875.3a0000 0004 0459 167XDivision of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN USA
| | - Rulla M. Tamimi
- grid.38142.3c000000041936754XChanning Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA ,grid.5386.8000000041936877XDepartment of Population Health Sciences, Weill Cornell Medicine, New York, NY USA
| | - Peter Kraft
- grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA ,grid.38142.3c000000041936754XProgram in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2-249A, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Xia Jiang
- grid.465198.7Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Visionsgatan 18, 171 77 Solna, Stockholm Sweden ,grid.13291.380000 0001 0807 1581West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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Ding S, Wang X, Lv D, Tao Y, Liu S, Chen C, Huang Z, Zheng S, Wei Y, Kang T, Xia Y. EBF3 reactivation by inhibiting the EGR1/EZH2/HDAC9 complex promotes metastasis via transcriptionally enhancing vimentin in nasopharyngeal carcinoma. Cancer Lett 2021; 527:49-65. [PMID: 34906623 DOI: 10.1016/j.canlet.2021.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/18/2021] [Accepted: 12/08/2021] [Indexed: 01/31/2023]
Abstract
Metastasis is the major reason for treatment failure and accounts for cancer-related death in patients with nasopharyngeal carcinoma. However, the genetic alterations and molecular mechanisms that cause nasopharyngeal carcinoma metastasis are elusive. Herein, we performed RNA sequencing in patients with or without metastasis, and found that the early B-cell factor 3 (EBF3) was significantly elevated in the samples with metastasis. Mechanistically, EBF3 promoted metastasis by directly combining with the promoter of Vimentin and transcriptionally upregulating it. In addition, EBF3 was epigenetically silenced by EGR1/EZH2/HDAC9 complexes via sustaining the high level of H3K27-Me3 at its promoter. Clinically, there was a positive correlation between EBF3 and Vimentin in nasopharyngeal carcinoma tissues. Moreover, high expression of EBF3 or Vimentin was correlated with poor overall survival, while the combination of high EBF3 and Vimentin expression was associated with more significant poor prognosis. Therefore, specific agents targeting EBF3 or stabilizing the EGR1/EZH2/HDAC9 complex could be novel therapeutic strategies for cancer metastasis.
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Affiliation(s)
- Shirong Ding
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Xin Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; The Department of Liver Surgery, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Dongming Lv
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yalan Tao
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Songran Liu
- Department of Pathology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Chen Chen
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Zilu Huang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Shuohan Zheng
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Yinghong Wei
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Yunfei Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China.
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22
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Pagani F, Tratta E, Dell'Era P, Cominelli M, Poliani PL. EBF1 is expressed in pericytes and contributes to pericyte cell commitment. Histochem Cell Biol 2021; 156:333-347. [PMID: 34272603 PMCID: PMC8550016 DOI: 10.1007/s00418-021-02015-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 01/27/2023]
Abstract
Early B-cell factor-1 (EBF1) is a transcription factor with an important role in cell lineage specification and commitment during the early stage of cell maturation. Originally described during B-cell maturation, EBF1 was subsequently identified as a crucial molecule for proper cell fate commitment of mesenchymal stem cells into adipocytes, osteoblasts and muscle cells. In vessels, EBF1 expression and function have never been documented. Our data indicate that EBF1 is highly expressed in peri-endothelial cells in both tumor vessels and in physiological conditions. Immunohistochemistry, quantitative reverse transcription polymerase chain reaction (RT-qPCR) and fluorescence-activated cell sorting (FACS) analysis suggest that EBF1-expressing peri-endothelial cells represent bona fide pericytes and selectively express well-recognized markers employed in the identification of the pericyte phenotype (SMA, PDGFRβ, CD146, NG2). This observation was also confirmed in vitro in human placenta-derived pericytes and in human brain vascular pericytes (HBVP). Of note, in accord with the key role of EBF1 in the cell lineage commitment of mesenchymal stem cells, EBF1-silenced HBVP cells showed a significant reduction in PDGFRβ and CD146, but not CD90, a marker mostly associated with a prominent mesenchymal phenotype. Moreover, the expression levels of VEGF, angiopoietin-1, NG2 and TGF-β, cytokines produced by pericytes during angiogenesis and linked to their differentiation and activation, were also significantly reduced. Overall, the data suggest a functional role of EBF1 in the cell fate commitment toward the pericyte phenotype.
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Affiliation(s)
- Francesca Pagani
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia Medical School, P.le Spedali Civili 1, 25125, Brescia, BS, Italy
| | - Elisa Tratta
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia Medical School, P.le Spedali Civili 1, 25125, Brescia, BS, Italy
| | - Patrizia Dell'Era
- Cellular Fate Reprogramming Unit, Department of Molecular and Translational Medicine, University of Brescia, Brescia, BS, Italy
| | - Manuela Cominelli
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia Medical School, P.le Spedali Civili 1, 25125, Brescia, BS, Italy
| | - Pietro Luigi Poliani
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia Medical School, P.le Spedali Civili 1, 25125, Brescia, BS, Italy.
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23
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Kim MH, Yang GE, Jeong MS, Mun JY, Lee SY, Nam JK, Choi YH, Kim TN, Leem SH. VNTR polymorphism in the breakpoint region of ABL1 and susceptibility to bladder cancer. BMC Med Genomics 2021; 14:121. [PMID: 33952249 PMCID: PMC8097952 DOI: 10.1186/s12920-021-00968-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND ABL1 is primarily known as a leukemia-related oncogene due to translocation, but about 2.2% of ABL1 mutations have been identified in bladder cancer, and high expression in solid cancer has also been detected. METHODS Here, we used the NCBI database, UCSC genome browser gateway and Tandem repeat finder program to investigate the structural characterization of the ABL1 breakpoint region and to identify the variable number of tandem repeats (VNTR). To investigate the relationship between ABL1-MS1 and bladder cancer, a case-controlled study was conducted in 207 controls and 197 bladder cancer patients. We also examined the level of transcription of the reporter gene driven by the ABL1 promoter to determine if the VNTR region affects gene expression. RESULTS In our study, one VNTR was identified in the breakpoint region, the intron 1 region of ABL1, and was named ABL1-MS1. In the control group, only two common alleles (TR13, TR15) were detected, but an additional two rare alleles (TR14, TR16) were detected in bladder cancer. A statistically significant association was identified between the rare ABL1-MS1 allele and bladder cancer risk: P = 0.013. Investigating the level of transcription of the reporter gene driven by the ABL1 promoter, VNTR showed inhibition of ABL1 expression in non-cancer cells 293 T, but not in bladder cancer cells. In addition, ABL1-MS1 was accurately passed on to offspring according to Mendelian inheritance through meiosis. CONCLUSIONS Therefore, the ABL1-MS1 region can affect ABL1 expression of bladder cancer. This study provides that ABL1-MS1 can be used as a DNA fingerprinting marker. In addition, rare allele detection can predict susceptibility to bladder cancer.
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Affiliation(s)
- Min-Hye Kim
- Department of Biomedical Sciences, Dong-A University, Busan, 49315 Korea
| | - Gi-Eun Yang
- Department of Biomedical Sciences, Dong-A University, Busan, 49315 Korea
- Department of Health Sciences, The Graduated of Dong-A University, Busan, 49315 Korea
| | - Mi-So Jeong
- Department of Biomedical Sciences, Dong-A University, Busan, 49315 Korea
| | - Jeong-Yeon Mun
- Department of Biomedical Sciences, Dong-A University, Busan, 49315 Korea
| | - Sang-Yeop Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, 28119 Korea
| | - Jong-Kil Nam
- Department of Urology, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, 50612 Korea
| | - Yung Hyun Choi
- Department of Biochemistry, College of Oriental Medicine, Anti-Aging Research Center, Dong-Eui University, Busan, 47227 Korea
| | - Tae Nam Kim
- Department of Urology, Medical Research Institute, Pusan National University Hospital, Busan, 49241 Korea
| | - Sun-Hee Leem
- Department of Biomedical Sciences, Dong-A University, Busan, 49315 Korea
- Department of Health Sciences, The Graduated of Dong-A University, Busan, 49315 Korea
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24
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Jiménez de la Peña M, Jiménez de Domingo A, Tirado P, Calleja-Pérez B, Alcaraz LA, Álvarez S, Williams J, Hagman JR, Németh AH, Fernández-Jaén A. Neuroimaging Findings in Patients with EBF3 Mutations: Report of Two Cases. Mol Syndromol 2021; 12:186-193. [PMID: 34177436 DOI: 10.1159/000513583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 12/03/2020] [Indexed: 12/27/2022] Open
Abstract
Early B cell factor 3 (EBF3) is a transcription factor involved in brain development. Heterozygous, loss-of-function mutations in EBF3 have been reported in an autosomal dominant neurodevelopmental syndrome characterized by hypotonia, ataxia, and developmental delay (sometimes described as "HADD"s). We report 2 unrelated cases with novel de novo EBF3 mutations: c.455G>T (p.Arg152Leu) and c.962dup (p.Tyr321*) to expand the genotype/phenotype correlations of this disorder; clinical, neuropsychological, and MRI studies were used to define the phenotype. IQ was in the normal range and diffusion tensor imaging revealed asymmetric alterations of the longitudinal fasciculus in both cases. Our results demonstrate that EBF3 mutations can underlie neurodevelopmental disorders without intellectual disability. Long tract abnormalities have not been previously recognized and suggest that they may be an unrecognized and characteristic feature in this syndrome.
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Affiliation(s)
| | | | - Pilar Tirado
- Department of Pediatric Neurology, Hospital Universitario La Paz, Madrid, Spain
| | | | | | - Sara Álvarez
- Genomics and Medicine, NIMGenetics, Madrid, Spain
| | - Jonathan Williams
- Oxford Medical Genetics Laboratories, Churchill Hospital, Oxford, United Kingdom
| | - James R Hagman
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.,Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Alberto Fernández-Jaén
- Department of Pediatric Neurology, Hospital Universitario Quirónsalud, and Medicine School, Universidad Europea de Madrid, Madrid, Spain
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25
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Armartmuntree N, Jusakul A, Sakonsinsiri C, Loilome W, Pinlaor S, Ungarreevittaya P, Yong CH, Techasen A, Imtawil K, Kraiklang R, Suwannakul N, Kaewlert W, Chaiprasert T, Thanan R, Murata M. Promoter hypermethylation of early B cell factor 1 (EBF1) is associated with cholangiocarcinoma progression. J Cancer 2021; 12:2673-2686. [PMID: 33854627 PMCID: PMC8040704 DOI: 10.7150/jca.52378] [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: 08/25/2020] [Accepted: 02/14/2021] [Indexed: 01/20/2023] Open
Abstract
DNA hypermethylation in a promoter region causes gene silencing via epigenetic changes. We have previously reported that early B cell factor 1 (EBF1) was down-regulated in cholangiocarcinoma (CCA) tissues and related to tumor progression. Thus, we hypothesized that the DNA hypermethylation of EBF1 promoter would suppress EBF1 expression in CCA and induce its progression. In this study, the DNA methylation status of EBF1 and mRNA expression levels were analyzed in CCA and normal bile duct (NBD) tissues using a publicly available database of genome-wide association data. The results showed that the DNA methylation of EBF1 promoter region was significantly increased in CCA tissues compared with those of NBD. The degree of methylation was negatively correlated with EBF1 mRNA expression levels. Using methylation-specific PCR technique, the DNA methylation rates of EBF1 promoter region were investigated in CCA tissues (n=72). CCA patients with high methylation rates of EBF1 promoter region in the tumor tissues (54/72) had a poor prognosis. Higher methylation rates of EBF1 promoter region have shown in all CCA cell lines than that of an immortal cholangiocyte cell line (MMNK1). Upon treatment with the DNA methyltransferase inhibitor 5-Aza-dC, increased EBF1 expression levels and reduced DNA methylation rates were observed in CCA cells. Moreover, restoration of EBF1 expression in CCA cells led to inhibition of cell growth, migration and invasion. In addition, RNA sequencing analysis suggested that EBF1 is involved in suppression of numerous pathways in cancer. Taken together, DNA hypermethylation in the EBF1 promoter region suppresses EBF1 expression and induces CCA progression with aggressive clinical outcomes.
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Affiliation(s)
- Napat Armartmuntree
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Apinya Jusakul
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand.,Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chadamas Sakonsinsiri
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Watcharin Loilome
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Somchai Pinlaor
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand.,Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Piti Ungarreevittaya
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand.,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chern Han Yong
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Anchalee Techasen
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand.,Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Kanokwan Imtawil
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | | | - Nattawan Suwannakul
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Mie 514-8507, Japan
| | - Waleeporn Kaewlert
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Timpika Chaiprasert
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Raynoo Thanan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Mariko Murata
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Mie 514-8507, Japan
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26
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Genomic Space of MGMT in Human Glioma Revisited: Novel Motifs, Regulatory RNAs, NRF1, 2, and CTCF Involvement in Gene Expression. Int J Mol Sci 2021; 22:ijms22052492. [PMID: 33801310 PMCID: PMC7958331 DOI: 10.3390/ijms22052492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/18/2021] [Accepted: 02/25/2021] [Indexed: 01/08/2023] Open
Abstract
Background: The molecular regulation of increased MGMT expression in human brain tumors, the associated regulatory elements, and linkages of these to its epigenetic silencing are not understood. Because the heightened expression or non-expression of MGMT plays a pivotal role in glioma therapeutics, we applied bioinformatics and experimental tools to identify the regulatory elements in the MGMT and neighboring EBF3 gene loci. Results: Extensive genome database analyses showed that the MGMT genomic space was rich in and harbored many undescribed RNA regulatory sequences and recognition motifs. We extended the MGMT’s exon-1 promoter to 2019 bp to include five overlapping alternate promoters. Consensus sequences in the revised promoter for (a) the transcriptional factors CTCF, NRF1/NRF2, GAF, (b) the genetic switch MYC/MAX/MAD, and (c) two well-defined p53 response elements in MGMT intron-1, were identified. A putative protein-coding or non-coding RNA sequence was located in the extended 3′ UTR of the MGMT transcript. Eleven non-coding RNA loci coding for miRNAs, antisense RNA, and lncRNAs were identified in the MGMT-EBF3 region and six of these showed validated potential for curtailing the expression of both MGMT and EBF3 genes. ChIP analysis verified the binding site in MGMT promoter for CTCF which regulates the genomic methylation and chromatin looping. CTCF depletion by a pool of specific siRNA and shRNAs led to a significant attenuation of MGMT expression in human GBM cell lines. Computational analysis of the ChIP sequence data in ENCODE showed the presence of NRF1 in the MGMT promoter and this occurred only in MGMT-proficient cell lines. Further, an enforced NRF2 expression markedly augmented the MGMT mRNA and protein levels in glioma cells. Conclusions: We provide the first evidence for several new regulatory components in the MGMT gene locus which predict complex transcriptional and posttranscriptional controls with potential for new therapeutic avenues.
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27
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Xing M, Ooi WF, Tan J, Qamra A, Lee PH, Li Z, Xu C, Padmanabhan N, Lim JQ, Guo YA, Yao X, Amit M, Ng LM, Sheng T, Wang J, Huang KK, Anene-Nzelu CG, Ho SWT, Ray M, Ma L, Fazzi G, Lim KJ, Wijaya GC, Zhang S, Nandi T, Yan T, Chang MM, Das K, Isa ZFA, Wu J, Poon PSY, Lam YN, Lin JS, Tay ST, Lee MH, Tan ALK, Ong X, White K, Rozen SG, Beer M, Foo RSY, Grabsch HI, Skanderup AJ, Li S, Teh BT, Tan P. Genomic and epigenomic EBF1 alterations modulate TERT expression in gastric cancer. J Clin Invest 2021; 130:3005-3020. [PMID: 32364535 DOI: 10.1172/jci126726] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Transcriptional reactivation of telomerase catalytic subunit (TERT) is a frequent hallmark of cancer, occurring in 90% of human malignancies. However, specific mechanisms driving TERT reactivation remain obscure for many tumor types and in particular gastric cancer (GC), a leading cause of global cancer mortality. Here, through comprehensive genomic and epigenomic analysis of primary GCs and GC cell lines, we identified the transcription factor early B cell factor 1 (EBF1) as a TERT transcriptional repressor and inactivation of EBF1 function as a major cause of TERT upregulation. Abolishment of EBF1 function occurs through 3 distinct (epi)genomic mechanisms. First, EBF1 is epigenetically silenced via DNA methyltransferase, polycomb-repressive complex 2 (PRC2), and histone deacetylase activity in GCs. Second, recurrent, somatic, and heterozygous EBF1 DNA-binding domain mutations result in the production of dominant-negative EBF1 isoforms. Third, more rarely, genomic deletions and rearrangements proximal to the TERT promoter remobilize or abolish EBF1-binding sites, derepressing TERT and leading to high TERT expression. EBF1 is also functionally required for various malignant phenotypes in vitro and in vivo, highlighting its importance for GC development. These results indicate that multimodal genomic and epigenomic alterations underpin TERT reactivation in GC, converging on transcriptional repressors such as EBF1.
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Affiliation(s)
- Manjie Xing
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Wen Fong Ooi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Jing Tan
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre, Singapore
| | - Aditi Qamra
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Po-Hsien Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Zhimei Li
- Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre, Singapore
| | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Nisha Padmanabhan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | - Yu Amanda Guo
- Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore
| | - Xiaosai Yao
- Institute of Molecular and Cell Biology, Singapore
| | - Mandoli Amit
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Ley Moy Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Taotao Sheng
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Department of Biochemistry, National University of Singapore, Singapore
| | - Jing Wang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University Health System, Singapore.,Human Genetics, Genome Institute of Singapore, Singapore
| | - Shamaine Wei Ting Ho
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Mohana Ray
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Lijia Ma
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Gregorio Fazzi
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Kevin Junliang Lim
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Giovani Claresta Wijaya
- Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre, Singapore
| | - Shenli Zhang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Tannistha Nandi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Tingdong Yan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Mei Mei Chang
- Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore
| | - Kakoli Das
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Zul Fazreen Adam Isa
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Jeanie Wu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Polly Suk Yean Poon
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Yue Ning Lam
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Joyce Suling Lin
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Su Ting Tay
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Ming Hui Lee
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Kevin White
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA.,Tempus Labs, Chicago, Illinois, USA
| | - Steven George Rozen
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore
| | - Michael Beer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins Medicine, and.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Roger Sik Yin Foo
- Cardiovascular Research Institute, National University Health System, Singapore.,Human Genetics, Genome Institute of Singapore, Singapore
| | - Heike Irmgard Grabsch
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands.,Pathology and Data Analyticis, Leeds Institute of Medical Research at St. James's, University of Leeds, Leeds, United Kingdom
| | - Anders Jacobsen Skanderup
- Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bin Tean Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Institute of Molecular and Cell Biology, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore.,Cellular and Molecular Research, National Cancer Centre, Singapore.,Singapore Gastric Cancer Consortium, Singapore.,Biomedical Research Council, Agency for Science, Technology and Research, Singapore
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28
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Bi H, Zhang M, Wang J, Long G. The mRNA landscape profiling reveals potential biomarkers associated with acute kidney injury AKI after kidney transplantation. PeerJ 2020; 8:e10441. [PMID: 33312771 PMCID: PMC7703406 DOI: 10.7717/peerj.10441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/06/2020] [Indexed: 12/22/2022] Open
Abstract
Background This study aims to identify potential biomarkers associated with acute kidney injury (AKI) post kidney transplantation. Material and Methods Two mRNA expression profiles from Gene Expression Omnibus repertory were downloaded, including 20 delayed graft function (DGF) and 68 immediate graft function (IGF) samples. Differentially expressed genes (DEGs) were identified between DGF and IGF group. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis of DEGs were performed. Then, a protein-protein interaction analysis was performed to extract hub genes. The key genes were searched by literature retrieval and cross-validated based on the training dataset. An external dataset was used to validate the expression levels of key genes. Receiver operating characteristic curve analyses were performed to evaluate diagnostic performance of key genes for AKI. Results A total of 330 DEGs were identified between DGF and IGF samples, including 179 up-regulated and 151 down-regulated genes. Of these, OLIG3, EBF3 and ETV1 were transcription factor genes. Moreover, LEP, EIF4A3, WDR3, MC4R, PPP2CB, DDX21 and GPT served as hub genes in PPI network. EBF3 was significantly up-regulated in validation GSE139061 dataset, which was consistently with our initial gene differential expression analysis. Finally, we found that LEP had a great diagnostic value for AKI (AUC = 0.740). Conclusion EBF3 may be associated with the development of AKI following kidney transplantation. Furthermore, LEP had a good diagnostic value for AKI. These findings provide deeper insights into the diagnosis and management of AKI post renal transplantation.
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Affiliation(s)
- Hui Bi
- Department of Nephrology, Tianjin Union Medical Center, Tianjin, China
| | - Min Zhang
- Department of Nephrology, Tianjin Union Medical Center, Tianjin, China
| | - Jialin Wang
- Department of Nephrology, Tianjin Union Medical Center, Tianjin, China
| | - Gang Long
- Department of Nephrology, Tianjin Union Medical Center, Tianjin, China
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29
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Hodkinson BP, Schaffer M, Brody JD, Jurczak W, Carpio C, Ben-Yehuda D, Avivi I, Forslund A, Özcan M, Alvarez J, Ceulemans R, Fourneau N, Younes A, Balasubramanian S. Biomarkers of response to ibrutinib plus nivolumab in relapsed diffuse large B-cell lymphoma, follicular lymphoma, or Richter's transformation. Transl Oncol 2020; 14:100977. [PMID: 33395752 PMCID: PMC7723809 DOI: 10.1016/j.tranon.2020.100977] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/11/2020] [Accepted: 11/25/2020] [Indexed: 12/30/2022] Open
Abstract
Biomarkers of response to ibrutinib + nivolumab were analyzed in diffuse large B-cell lymphoma (DLBCL), follicular lymphoma and Richter transformation. DLBCL patients with elevated PD-L1 by immunohistochemistry tended to have better response and survival. Whole exome sequencing identified gene mutations in alternate B-cell receptor pathways linked to response in DLBCL. Enriched pathways by gene expression profiling were related to immune activation in responders and proliferation/replication in nonresponders. This preliminary work may help to generate hypotheses on genetically defined subsets of patients most likely to benefit from ibrutinib + nivolumab.
We analyzed potential biomarkers of response to ibrutinib plus nivolumab in biopsies from patients with diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), and Richter's transformation (RT) from the LYM1002 phase I/IIa study, using programmed death ligand 1 (PD-L1) immunohistochemistry, whole exome sequencing (WES), and gene expression profiling (GEP). In DLBCL, PD-L1 elevation was more frequent in responders versus nonresponders (5/8 [62.5%] vs. 3/16 [18.8%]; p = 0.065; complete response 37.5% vs. 0%; p = 0.028). Overall response rates for patients with WES and GEP data, respectively, were: DLBCL (38.5% and 29.6%); FL (46.2% and 43.5%); RT (76.5% and 81.3%). In DLBCL, WES analyses demonstrated that mutations in RNF213 (40.0% vs. 6.2%; p = 0.055), KLHL14 (30.0% vs. 0%; p = 0.046), and LRP1B (30.0% vs. 6.2%; p = 0.264) were more frequent in responders. No responders had mutations in EBF1, ADAMTS20, AKAP9, TP53, MYD88, or TNFRSF14, while the frequency of these mutations in nonresponders ranged from 12.5% to 18.8%. In FL and RT, genes with different mutation frequencies in responders versus nonresponders were: BCL2 (75.0% vs. 28.6%; p = 0.047) and ROS1 (0% vs. 50.0%; p = 0.044), respectively. Per GEP, the most upregulated genes in responders were LEF1 and BTLA (overall), and CRTAM (germinal center B-cell–like DLBCL). Enriched pathways were related to immune activation in responders and resistance-associated proliferation/replication in nonresponders. This preliminary work may help to generate hypotheses regarding genetically defined subsets of DLBCL, FL, and RT patients most likely to benefit from ibrutinib plus nivolumab.
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Affiliation(s)
- Brendan P Hodkinson
- Oncology Translational Research, Janssen Research & Development, Spring House, PA 19477, United States
| | - Michael Schaffer
- Oncology Translational Research, Janssen Research & Development, Spring House, PA 19477, United States
| | - Joshua D Brody
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Wojciech Jurczak
- Department of Clinical Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Krakow, 31-115, Poland
| | - Cecilia Carpio
- Department of Hematology, University Hospital Vall d'Hebron, Department of Medicine. Universitat Autònoma de Barcelona (UAB), Vall d'Hebron Institut of Oncology (VHIO), Barcelona, Spain
| | - Dina Ben-Yehuda
- Department of Hematology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Irit Avivi
- Department of Hematology and Bone Marrow Transplantation, Tel Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel Aviv 6997801, Israel
| | - Ann Forslund
- Oncology Biomarkers, Bristol-Myers Squibb, Lawrenceville, NJ 08543, United States
| | - Muhit Özcan
- Department of Hematology, Ankara University School of Medicine, Ankara 06100, Turkey
| | - John Alvarez
- Oncology Translational Research, Janssen Research & Development, Spring House, PA 19477, United States
| | - Rob Ceulemans
- Translational Medicine, Janssen Research & Development, Beerse 2340, Belgium
| | - Nele Fourneau
- Translational Medicine, Janssen Research & Development, Beerse 2340, Belgium
| | - Anas Younes
- Lymphoma Department, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - Sriram Balasubramanian
- Oncology Translational Research, Janssen Research & Development, Spring House, PA 19477, United States.
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Xin J, Chai Z, Zhang C, Zhang Q, Zhu Y, Cao H, Yangji C, Chen X, Jiang H, Zhong J, Ji Q. Methylome and transcriptome profiles in three yak tissues revealed that DNA methylation and the transcription factor ZGPAT co-regulate milk production. BMC Genomics 2020; 21:731. [PMID: 33081725 PMCID: PMC7576800 DOI: 10.1186/s12864-020-07151-3] [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: 01/21/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
Background Domestic yaks play an indispensable role in sustaining the livelihood of Tibetans and other ethnic groups on the Qinghai-Tibetan Plateau (QTP), by providing milk and meat. They have evolved numerous physiological adaptations to high-altitude environment, including strong blood oxygen transportation capabilities and high metabolism. The roles of DNA methylation and gene expression in milk production and high-altitudes adaptation need further exploration. Results We performed genome-wide DNA methylome and transcriptome analyses of breast, lung, and biceps brachii muscle tissues from yaks of different ages. We identified 432,350 differentially methylated regions (DMRs) across the age groups within each tissue. The post-mature breast tissue had considerably more differentially methylated regions (155,957) than that from the three younger age groups. Hypomethylated genes with high expression levels might regulate milk production by influencing protein processing in the endoplasmic reticulum. According to weighted gene correlation network analysis, the “hub” gene ZGPAT was highly expressed in the post-mature breast tissue, indicating that it potentially regulates the transcription of 280 genes that influence protein synthesis, processing, and secretion. The tissue network analysis indicated that high expression of HIF1A regulates energy metabolism in the lung. Conclusions This study provides a basis for understanding the epigenetic mechanisms underlying milk production in yaks, and the results offer insight to breeding programs aimed at improving milk production. Supplementary information Supplementary information accompanies this paper at 10.1186/s12864-020-07151-3.
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Affiliation(s)
- Jinwei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, China
| | - Chengfu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Qiang Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Yong Zhu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Hanwen Cao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Cidan Yangji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Xiaoying Chen
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Hui Jiang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, China.
| | - Qiumei Ji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China. .,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China.
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Barone C, Buccarelli M, Alessandrini F, Pagin M, Rigoldi L, Sambruni I, Favaro R, Ottolenghi S, Pallini R, Ricci-Vitiani L, Malatesta P, Nicolis SK. Sox2-dependent maintenance of mouse oligodendroglioma involves the Sox2-mediated downregulation of Cdkn2b, Ebf1, Zfp423, and Hey2. Glia 2020; 69:579-593. [PMID: 32975900 DOI: 10.1002/glia.23914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 01/06/2023]
Abstract
Cancer stem cells (CSC) are essential for tumorigenesis. The transcription factor Sox2 is overexpressed in brain gliomas, and is essential to maintain CSC. In mouse high-grade glioma pHGG cells in culture, Sox2 deletion causes cell proliferation arrest and inability to reform tumors after transplantation in vivo; in Sox2-deleted cells, 134 genes are derepressed. To identify genes mediating Sox2 deletion effects, we overexpressed into pHGG cells nine among the most derepressed genes, and identified four genes, Ebf1, Hey2, Zfp423, and Cdkn2b, that strongly reduced cell proliferation in vitro and brain tumorigenesis in vivo. CRISPR/Cas9 mutagenesis of each gene, individually or in combination (Ebf1 + Cdkn2b), significantly antagonized the proliferation arrest caused by Sox2 deletion. The same genes also repressed clonogenicity in primary human glioblastoma-derived CSC-like lines. These experiments identify a network of critical tumor suppressive Sox2-targets whose inhibition by Sox2 is involved in glioma CSC maintenance, defining new potential therapeutic targets.
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Affiliation(s)
- Cristiana Barone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Mariachiara Buccarelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Francesco Alessandrini
- Dipartimento di Medicina Sperimentale, Università di Genova, and Ospedale Policlinico San Martino, IRCCS, Genoa, Italy
| | - Miriam Pagin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Laura Rigoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Irene Sambruni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Rebecca Favaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Sergio Ottolenghi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Roberto Pallini
- Institute of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Lucia Ricci-Vitiani
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Paolo Malatesta
- Dipartimento di Medicina Sperimentale, Università di Genova, and Ospedale Policlinico San Martino, IRCCS, Genoa, Italy
| | - Silvia K Nicolis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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32
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Kothari C, Diorio C, Durocher F. The Importance of Breast Adipose Tissue in Breast Cancer. Int J Mol Sci 2020; 21:ijms21165760. [PMID: 32796696 PMCID: PMC7460846 DOI: 10.3390/ijms21165760] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
Adipose tissue is a complex endocrine organ, with a role in obesity and cancer. Adipose tissue is generally linked to excessive body fat, and it is well known that the female breast is rich in adipose tissue. Hence, one can wonder: what is the role of adipose tissue in the breast and why is it required? Adipose tissue as an organ consists of adipocytes, an extracellular matrix (ECM) and immune cells, with a significant role in the dynamics of breast changes throughout the life span of a female breast from puberty, pregnancy, lactation and involution. In this review, we will discuss the importance of breast adipose tissue in breast development and its involvement in breast changes happening during pregnancy, lactation and involution. We will focus on understanding the biology of breast adipose tissue, with an overview on its involvement in the various steps of breast cancer development and progression. The interaction between the breast adipose tissue surrounding cancer cells and vice-versa modifies the tumor microenvironment in favor of cancer. Understanding this mutual interaction and the role of breast adipose tissue in the tumor microenvironment could potentially raise the possibility of overcoming breast adipose tissue mediated resistance to therapies and finding novel candidates to target breast cancer.
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Affiliation(s)
- Charu Kothari
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, QC G1T 1C2, Canada;
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada;
| | - Caroline Diorio
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada;
- Department of Preventive and Social Medicine, Faculty of Medicine, Laval University, Quebec, QC G1T 1C2, Canada
| | - Francine Durocher
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, QC G1T 1C2, Canada;
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada;
- Correspondence: ; Tel.: +1-(418)-525-4444 (ext. 48508)
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33
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Belrose JL, Prasad A, Sammons MA, Gibbs KM, Szaro BG. Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons. BMC Genomics 2020; 21:540. [PMID: 32758133 PMCID: PMC7430912 DOI: 10.1186/s12864-020-06954-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The South African claw-toed frog, Xenopus laevis, is uniquely suited for studying differences between regenerative and non-regenerative responses to CNS injury within the same organism, because some CNS neurons (e.g., retinal ganglion cells after optic nerve crush (ONC)) regenerate axons throughout life, whereas others (e.g., hindbrain neurons after spinal cord injury (SCI)) lose this capacity as tadpoles metamorphose into frogs. Tissues from these CNS regions (frog ONC eye, tadpole SCI hindbrain, frog SCI hindbrain) were used in a three-way RNA-seq study of axotomized CNS axons to identify potential core gene expression programs for successful CNS axon regeneration. RESULTS Despite tissue-specific changes in expression dominating the injury responses of each tissue, injury-induced changes in gene expression were nonetheless shared between the two axon-regenerative CNS regions that were not shared with the non-regenerative region. These included similar temporal patterns of gene expression and over 300 injury-responsive genes. Many of these genes and their associated cellular functions had previously been associated with injury responses of multiple tissues, both neural and non-neural, from different species, thereby demonstrating deep phylogenetically conserved commonalities between successful CNS axon regeneration and tissue regeneration in general. Further analyses implicated the KEGG adipocytokine signaling pathway, which links leptin with metabolic and gene regulatory pathways, and a novel gene regulatory network with genes regulating chromatin accessibility at its core, as important hubs in the larger network of injury response genes involved in successful CNS axon regeneration. CONCLUSIONS This study identifies deep, phylogenetically conserved commonalities between CNS axon regeneration and other examples of successful tissue regeneration and provides new targets for studying the molecular underpinnings of successful CNS axon regeneration, as well as a guide for distinguishing pro-regenerative injury-induced changes in gene expression from detrimental ones in mammals.
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Affiliation(s)
- Jamie L Belrose
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Aparna Prasad
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Morgan A Sammons
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Kurt M Gibbs
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, 40351, USA
| | - Ben G Szaro
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.
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34
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Qiu K, Zheng Z, Huang Y. Long intergenic noncoding RNA 00844 promotes apoptosis and represses proliferation of prostate cancer cells through upregulating GSTP1 by recruiting EBF1. J Cell Physiol 2020; 235:8472-8485. [PMID: 32329523 DOI: 10.1002/jcp.29690] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/03/2020] [Accepted: 03/24/2020] [Indexed: 12/24/2022]
Abstract
Accumulating evidence have suggested the function of long noncoding RNAs as crucial players in the pathogenesis of prostate cancer (PC), a urologic tumor in male with poor prognosis. This study was designed to explore the functions of long intergenic noncoding RNA 00844 (LINC00844) in PC progression. The expression of LINC00844 and glutathione S-transferase P1-1 (GSTP1) was detected by reverse transcription quantitative polymerase chain reaction, followed by the identification of the relationship among LINC00844, GSTP1, and early B cell factor 1 (EBF1) by dual luciferase reporter gene assay, RNA immunoprecipitation assay, electrophoretic mobility shift assay, and chromatin immunoprecipitation assay. Using loss- and gain-of-function assays, the effects of LINC00844, GSTP1, and EBF1 on the biological characteristics of PC cells were assessed by cell counting kit-8 assay, 5-ethynyl-2'-deoxyuridine assay, and flow cytometry. Lastly, the results from in vitro experiments were verified in vivo by establishing a xenograft tumor model in nude mice. LINC00844 and GSTP1 both displayed low expression in PC tissues and cells. LINC00844 positively regulated the expression of GSTP1 via recruiting EBF1. Overexpression of LINC00844 reduced proliferation and elevated apoptosis of PC cells through recruiting EBF1, which subsequently upregulated GSTP1. In vivo experiments confirmed that LINC00844 or GSTP1 upregulation attenuated tumor growth. LINC00844 elevated GSTP1 expression by recruiting EBF1 to the promoter region of GSTP1, thereby suppressing PC progression. Hence, LINC00844 is a novel therapeutic target for the development of new treatment protocols for PC.
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Affiliation(s)
- Kaiyan Qiu
- Department of Urology, Quanzhou First Hospital Affiliated Fujian Medical University, Quanzhou, P.R. China
| | - Zhixiong Zheng
- Department of Urology, Quanzhou First Hospital Affiliated Fujian Medical University, Quanzhou, P.R. China
| | - Yingfu Huang
- Department of Urology, Quanzhou First Hospital Affiliated Fujian Medical University, Quanzhou, P.R. China
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35
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Camponeschi I, Damasco A, Uversky VN, Giuliani A, Bianchi MM. Phenotypic suppression caused by resonance with light-dark cycles indicates the presence of a 24-hours oscillator in yeast and suggests a new role of intrinsically disordered protein regions as internal mediators. J Biomol Struct Dyn 2020; 39:2490-2501. [PMID: 32223547 DOI: 10.1080/07391102.2020.1749133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The mutual interaction between environment and life is a main topic of biological sciences. An interesting aspect of this interaction is the existence of biological rhythms spanning all the levels of organisms from bacteria to humans. On the other hand, the existence of a coupling between external oscillatory stimuli and adaptation and evolution rate of biological systems is a still unexplored issue. Here we give the demonstration of a substantial increase of heritable phenotypic changes in yeast, an organism lacking a photoreception system, when growing at 12 h light/dark cycles, with respect to both stable dark (or light) or non-12 + 12 h cycling. The model system was a yeast strain lacking a gene whose product is at the crossroad of many different physiological regulations, so ruling out any simple explanation in terms of increase in reverse gene mutations. The abundance of intrinsically disordered protein regions (IDPRs) in both deleted gene product and in its vast ensemble of interactors supports the hypothesis that resonance with the environmental cycle might be mediated by intrinsic disorder-driven interactions of protein molecules. This result opens to the speculation of the effect of environment/biological resonance phenomena in evolution and of the role of protein intrinsically disordered regions as internal mediators.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ilaria Camponeschi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza Università di Roma, Roma, Italy
| | - Achille Damasco
- Department of Physics 'Ettore Pancini', Università di Napoli Federico II, Napoli, Italy
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Russia
| | - Alessandro Giuliani
- Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy
| | - Michele M Bianchi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza Università di Roma, Roma, Italy
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Dai JY, Wang X, Wang B, Sun W, Jordahl KM, Kolb S, Nyame YA, Wright JL, Ostrander EA, Feng Z, Stanford JL. DNA methylation and cis-regulation of gene expression by prostate cancer risk SNPs. PLoS Genet 2020; 16:e1008667. [PMID: 32226005 PMCID: PMC7145271 DOI: 10.1371/journal.pgen.1008667] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 04/09/2020] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies have identified more than 100 SNPs that increase the risk of prostate cancer (PrCa). We identify and compare expression quantitative trait loci (eQTLs) and CpG methylation quantitative trait loci (meQTLs) among 147 established PrCa risk SNPs in primary prostate tumors (n = 355 from a Seattle-based study and n = 495 from The Cancer Genome Atlas, TCGA) and tumor-adjacent, histologically benign samples (n = 471 from a Mayo Clinic study). The role of DNA methylation in eQTL regulation of gene expression was investigated by data triangulation using several causal inference approaches, including a proposed adaptation of the Causal Inference Test (CIT) for causal direction. Comparing eQTLs between tumors and benign samples, we show that 98 of the 147 risk SNPs were identified as eQTLs in the tumor-adjacent benign samples, and almost all 34 eQTL identified in tumor sets were also eQTLs in the benign samples. Three lines of results support the causal role of DNA methylation. First, nearly 100 of the 147 risk SNPs were identified as meQTLs in one tumor set, and almost all eQTLs in tumors were meQTLs. Second, the loss of eQTLs in tumors relative to benign samples was associated with altered DNA methylation. Third, among risk SNPs identified as both eQTLs and meQTLs, mediation analyses suggest that over two-thirds have evidence of a causal role for DNA methylation, mostly mediating genetic influence on gene expression. In summary, we provide a comprehensive catalog of eQTLs, meQTLs and putative cancer genes for known PrCa risk SNPs. We observe that a substantial portion of germline eQTL regulatory mechanisms are maintained in the tumor development, despite somatic alterations in tumor genome. Finally, our mediation analyses illuminate the likely intermediary role of CpG methylation in eQTL regulation of gene expression.
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Affiliation(s)
- James Y. Dai
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Xiaoyu Wang
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
| | - Bo Wang
- Department of Laboratory Medicine, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Sun
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Kristina M. Jordahl
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
| | - Yaw A. Nyame
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Urology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Jonathan L. Wright
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Urology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Ziding Feng
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, United States of America
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Zhu H, Uusküla-Reimand L, Isaev K, Wadi L, Alizada A, Shuai S, Huang V, Aduluso-Nwaobasi D, Paczkowska M, Abd-Rabbo D, Ocsenas O, Liang M, Thompson JD, Li Y, Ruan L, Krassowski M, Dzneladze I, Simpson JT, Lupien M, Stein LD, Boutros PC, Wilson MD, Reimand J. Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks. Mol Cell 2020; 77:1307-1321.e10. [PMID: 31954095 DOI: 10.1016/j.molcel.2019.12.027] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 06/04/2019] [Accepted: 12/24/2019] [Indexed: 12/17/2022]
Abstract
A comprehensive catalog of cancer driver mutations is essential for understanding tumorigenesis and developing therapies. Exome-sequencing studies have mapped many protein-coding drivers, yet few non-coding drivers are known because genome-wide discovery is challenging. We developed a driver discovery method, ActiveDriverWGS, and analyzed 120,788 cis-regulatory modules (CRMs) across 1,844 whole tumor genomes from the ICGC-TCGA PCAWG project. We found 30 CRMs with enriched SNVs and indels (FDR < 0.05). These frequently mutated regulatory elements (FMREs) were ubiquitously active in human tissues, showed long-range chromatin interactions and mRNA abundance associations with target genes, and were enriched in motif-rewiring mutations and structural variants. Genomic deletion of one FMRE in human cells caused proliferative deficiencies and transcriptional deregulation of cancer genes CCNB1IP1, CDH1, and CDKN2B, validating observations in FMRE-mutated tumors. Pathway analysis revealed further sub-significant FMREs at cancer genes and processes, indicating an unexplored landscape of infrequent driver mutations in the non-coding genome.
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Affiliation(s)
- Helen Zhu
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON M5G 1L7, Canada
| | - Liis Uusküla-Reimand
- Program in Genetics and Genome Biology, SickKids Research Institute, Peter Gilgan Centre for Research and Learning (PGCRL), 686 Bay Street, Toronto, ON M5G 0A4, Canada; Division of Gene Technology, Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| | - Keren Isaev
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON M5G 1L7, Canada
| | - Lina Wadi
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Azad Alizada
- Program in Genetics and Genome Biology, SickKids Research Institute, Peter Gilgan Centre for Research and Learning (PGCRL), 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Shimin Shuai
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Vincent Huang
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Dike Aduluso-Nwaobasi
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Marta Paczkowska
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Diala Abd-Rabbo
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Oliver Ocsenas
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON M5G 1L7, Canada
| | - Minggao Liang
- Program in Genetics and Genome Biology, SickKids Research Institute, Peter Gilgan Centre for Research and Learning (PGCRL), 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - J Drew Thompson
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Yao Li
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Luyao Ruan
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Michal Krassowski
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Irakli Dzneladze
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Jared T Simpson
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada; Department of Computer Science, University of Toronto, 214 College Street, Toronto, ON M5T 3A1, Canada
| | - Mathieu Lupien
- Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 0A3, Canada
| | - Lincoln D Stein
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON M5G 1L7, Canada; Department of Human Genetics, University of California Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA; Department of Urology, University of California Los Angeles, 200 Medical Plaza Driveway #140, Los Angeles, CA 90024, USA; Institute of Precision Health, University of California Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90024, USA; Jonsson Comprehensive Cancer Centre, University of California Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90024, USA
| | - Michael D Wilson
- Program in Genetics and Genome Biology, SickKids Research Institute, Peter Gilgan Centre for Research and Learning (PGCRL), 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Jüri Reimand
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON M5G 1L7, Canada.
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Mahmud I, Liao D. DAXX in cancer: phenomena, processes, mechanisms and regulation. Nucleic Acids Res 2019; 47:7734-7752. [PMID: 31350900 PMCID: PMC6735914 DOI: 10.1093/nar/gkz634] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022] Open
Abstract
DAXX displays complex biological functions. Remarkably, DAXX overexpression is a common feature in diverse cancers, which correlates with tumorigenesis, disease progression and treatment resistance. Structurally, DAXX is modular with an N-terminal helical bundle, a docking site for many DAXX interactors (e.g. p53 and ATRX). DAXX's central region folds with the H3.3/H4 dimer, providing a H3.3-specific chaperoning function. DAXX has two functionally critical SUMO-interacting motifs. These modules are connected by disordered regions. DAXX's structural features provide a framework for deciphering how DAXX mechanistically imparts its functions and how its activity is regulated. DAXX modulates transcription through binding to transcription factors, epigenetic modifiers, and chromatin remodelers. DAXX's localization in the PML nuclear bodies also plays roles in transcriptional regulation. DAXX-regulated genes are likely important effectors of its biological functions. Deposition of H3.3 and its interactions with epigenetic modifiers are likely key events for DAXX to regulate transcription, DNA repair, and viral infection. Interactions between DAXX and its partners directly impact apoptosis and cell signaling. DAXX's activity is regulated by posttranslational modifications and ubiquitin-dependent degradation. Notably, the tumor suppressor SPOP promotes DAXX degradation in phase-separated droplets. We summarize here our current understanding of DAXX's complex functions with a focus on how it promotes oncogenesis.
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Affiliation(s)
- Iqbal Mahmud
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, 1333 Center Drive, Gainesville, FL 32610-0235, USA
| | - Daiqing Liao
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, 1333 Center Drive, Gainesville, FL 32610-0235, USA
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Ohkubo N, Aoto M, Kon K, Mitsuda N. Lack of zinc finger protein 521 upregulates dopamine β-hydroxylase expression in the mouse brain, leading to abnormal behavior. Life Sci 2019; 231:116559. [PMID: 31200001 DOI: 10.1016/j.lfs.2019.116559] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/22/2019] [Accepted: 06/10/2019] [Indexed: 10/26/2022]
Abstract
AIM Previously, we reported that mice deficient in most of the Zfp521 coding region (Zfp521Δ/Δ mice) displayed abnormal behaviors, including hyperlocomotion and lower anxiety. In this study, we aimed to elucidate the involvement and mechanisms of monoamine variation. MAIN METHODS First, we compared the levels of dopamine (DA), noradrenaline (NA), and serotonin in the brains of Zfp521Δ/Δ and Zfp521+/+ mice using enzyme-linked immunosorbent assay. Next, we elucidated the mechanisms using quantitative PCR and Western Blotting. Additionally, we administered inhibitory drug to the mice and performed behavioral tests. KEY FINDINGS Our results showed that the DA level decreased and the NA level increased in Zfp521Δ/Δ mice. We found that ZFP521 suppresses the expression of dopamine β-hydroxylase (DBH), which converts DA into NA. We also demonstrated that paired homeodomain transcription factor 2 and early growth response protein-1, which are the transcription factors for Dbh, were involved in the upregulation of Dbh by ZFP521. The administration of nepicastat, a specific inhibitor of DBH, attenuated the abnormal behaviors of Zfp521Δ/Δ mice. SIGNIFICANCE These results suggest that the lack of ZFP521 upregulates the expression of DBH, which leads to a decrease in the DA level and an increase in the NA level in the brain, resulting in abnormal behaviors.
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Affiliation(s)
- Nobutaka Ohkubo
- Department of Circulatory Physiology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan..
| | - Mamoru Aoto
- Department of Circulatory Physiology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Kazunori Kon
- Department of Circulatory Physiology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Noriaki Mitsuda
- Department of Circulatory Physiology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
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Martinez-Gutierrez AD, Catalan OM, Vázquez-Romo R, Porras Reyes FI, Alvarado-Miranda A, Lara Medina F, Bargallo-Rocha JE, Orozco Moreno LT, Cantú De León D, Herrera LA, López-Camarillo C, Pérez-Plasencia C, Campos-Parra AD. miRNA profile obtained by next‑generation sequencing in metastatic breast cancer patients is able to predict the response to systemic treatments. Int J Mol Med 2019; 44:1267-1280. [PMID: 31364724 PMCID: PMC6713405 DOI: 10.3892/ijmm.2019.4292] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/03/2019] [Indexed: 12/20/2022] Open
Abstract
Metastatic breast cancer (MBC) is a challenge for oncologists, and public efforts should focus on identifying additional molecular markers and therapeutic management to improve clinical outcomes. Among all diagnosed cases of breast cancer (BC; approximately 10%) involve metastatic disease; notably, approximately 40% of patients with early-stage BC develop metastasis within 5 years. The management of MBC consists of systemic therapy. Despite different treatment options, the 5-year survival rate is <20%, which may be due to a lack of response with de novo or acquired resistance. MicroRNAs (miRNAs or miRs) are promising biomarkers as they are readily detectable and have a broad spectrum and potential clinical applications. The aim of this study was to identify a miRNA profile for distinguishing patients with MBC who respond to systemic treatment. Patients with MBC were treated according to the National Comprehensive Cancer Network guidelines. We performed miRNA-Seq on 9 primary tumors using the Thermo Fisher Scientific Ion S5 system. To obtain global miRNA profiles, we carried out differentially expressed gene elimination strategy (DEGES) analysis between the responsive and non-responsive patients. The results identified a profile of 12 miRNAs associated with the response to systemic treatment. The data were validated in an independent cohort (TCGA database). Based on the results, the upregulation of miR-342-3p and miR-187-3p was associated with the response to systemic treatment, and with an increased progression-free survival (PFS) and overall survival (OS); by contrast, the downregulation of miR-301a-3p was associated with a higher PFS and OS. On the whole, the findings of this study indicate that these miRNAs may serve as biomarkers for the response to systemic treatment or the prognosis of patients with MBC. However, these data should be validated experimentally in other robust cohorts and using different specimens before implementing these miRNAs as biomarkers in clinical practice to benefit this group of patients.
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Affiliation(s)
| | - Oliver Millan Catalan
- Laboratorio de Genómica, Instituto Nacional de Cancerología (INCan), UNAM, Mexico City 14080, Mexico
| | - Rafael Vázquez-Romo
- Departamento de Cirugía de Tumores Mamarios, Instituto Nacional de Cancerología (INCan), UNAM, Mexico City 14080, Mexico
| | - Fany Iris Porras Reyes
- Servicio de Anatomía Patológica, Instituto Nacional de Cancerología (INCan), UNAM, Mexico City 14080, Mexico
| | - Alberto Alvarado-Miranda
- Unidad de Cáncer de Mama, Instituto Nacional de Cancerología (INCan), UNAM, Mexico City 14080, Mexico
| | - Fernando Lara Medina
- Unidad de Cáncer de Mama, Instituto Nacional de Cancerología (INCan), UNAM, Mexico City 14080, Mexico
| | - Juan E Bargallo-Rocha
- Unidad de Cáncer de Mama, Instituto Nacional de Cancerología (INCan), UNAM, Mexico City 14080, Mexico
| | | | - David Cantú De León
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)‑Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico
| | - Luis Alonso Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)‑Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, CDMX, Mexico City 03100, Mexico
| | - Carlos Pérez-Plasencia
- Laboratorio de Genómica, Instituto Nacional de Cancerología (INCan), UNAM, Mexico City 14080, Mexico
| | - Alma D Campos-Parra
- Laboratorio de Genómica, Instituto Nacional de Cancerología (INCan), UNAM, Mexico City 14080, Mexico
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41
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Badaloni A, Casoni F, Croci L, Chiara F, Bizzoca A, Gennarini G, Cremona O, Hawkes R, Consalez GG. Dynamic Expression and New Functions of Early B Cell Factor 2 in Cerebellar Development. THE CEREBELLUM 2019; 18:999-1010. [DOI: 10.1007/s12311-019-01051-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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42
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Shen A, Chen Y, Liu L, Huang Y, Chen H, Qi F, Lin J, Shen Z, Wu X, Wu M, Li Q, Qiu L, Yu N, Sferra TJ, Peng J. EBF1-Mediated Upregulation of Ribosome Assembly Factor PNO1 Contributes to Cancer Progression by Negatively Regulating the p53 Signaling Pathway. Cancer Res 2019; 79:2257-2270. [PMID: 30862720 DOI: 10.1158/0008-5472.can-18-3238] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/31/2019] [Accepted: 03/08/2019] [Indexed: 11/16/2022]
Abstract
The RNA-binding protein PNO1 is critical for ribosome biogenesis, but its potential role in cancer remains unknown. In this study, online data mining, cDNA, and tissue microarrays indicated that PNO1 expression was higher in colorectal cancer tissue than in noncancerous tissue, and its overexpression was associated with worse patient survival. Gain-of-function and loss-of-function studies demonstrated that PNO1 knockdown suppressed growth of colorectal cancer cells in vitro and in vivo, while PNO1 overexpression promoted colorectal cancer cell proliferation in vitro. In colorectal cancer cells expressing wild-type p53, PNO1 knockdown enhanced expression of p53 and its downstream gene p21, and reduced cell viability; these effects were prevented by p53 knockout and attenuated by the p53 inhibitor PFT-α. Moreover, PNO1 knockdown in HCT116 cells decreased levels of 18S rRNA, of 40S and 60S ribosomal subunits, and of the 80S ribosome. It also reduced global protein synthesis, increasing nuclear stress and inhibiting MDM2-mediated ubiquitination and p53 degradation. Overexpressing EBF1 suppressed PNO1 promoter activity and decreased PNO1 mRNA and protein, inhibiting cell proliferation and inducing cell apoptosis through the p53/p21 pathway. In colorectal cancer tissues, the expression of EBF1 correlated inversely with PNO1. Data mining of online breast and lung cancer databases showed increased PNO1 expression and association with poor patient survival; PNO1 knockdown reduced cell viability of cultured breast and lung cancer cells. Taken together, these findings indicate that PNO1 is overexpressed in colorectal cancer and correlates with poor patient survival, and that PNO1 exerts oncogenic effects, at least, in part, by altering ribosome biogenesis. SIGNIFICANCE: This study identifies the ribosome assembly factor PNO1 as a potential oncogene involved in tumor growth and progression of colorectal cancer.
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Affiliation(s)
- Aling Shen
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China.,Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fujian, China
| | - Youqin Chen
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China.,Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fujian, China.,Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Liya Liu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China.,Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fujian, China.,Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Yue Huang
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China.,Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fujian, China
| | - Hongwei Chen
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China.,Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fujian, China
| | - Fei Qi
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China.,Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fujian, China
| | - Jiumao Lin
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China.,Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fujian, China
| | - Zhiqing Shen
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China.,Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fujian, China
| | - Xiangyan Wu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China.,Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fujian, China
| | - Meizhu Wu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China.,Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fujian, China
| | - Qiongyu Li
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China.,Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fujian, China
| | - Liman Qiu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China.,Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fujian, China
| | - Na Yu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China.,Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fujian, China
| | - Thomas J Sferra
- Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Jun Peng
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China. .,Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fujian, China
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Zhang J, Zhang Y, Tan X, Zhang Q, Liu C, Zhang Y. MiR-23b-3p induces the proliferation and metastasis of esophageal squamous cell carcinomas cells through the inhibition of EBF3. Acta Biochim Biophys Sin (Shanghai) 2018; 50:605-614. [PMID: 29750239 DOI: 10.1093/abbs/gmy049] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs (miRNAs), some small non-coding RNAs that regulate gene expression at the posttranscriptional level, are always aberrantly expressed in carcinomas. In this study, we found that miR-23b-3p was remarkably up-regulated in human esophageal squamous cell carcinoma cells and tissues. Moreover, miR-23b-3p could induce the proliferation, invasion, and metastasis in vitro. EBF3 was identified as the direct downstream target gene of miR-23b-3p and ectogenic EBF3 could strongly inhibit the proliferation, invasion, and metastasis in vitro. Furthermore, it was found that miR-23b-3p could regulate epithelial-to-mesenchymal transition progress by blocking EBF3. Therefore, it was concluded that miR-23b-3p targeted EBF3 to accelerate the proliferation, invasion, and metastasis in ESCC.
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Affiliation(s)
- Jing Zhang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Medical School of Yangtze University, Jingzhou 434023, China
| | - Yan Zhang
- Department of Gastroenterology, No. 1 Hospital Affiliated to Yangtze University, Jingzhou 434000, China
| | - Xiaoping Tan
- Department of Gastroenterology, No. 1 Hospital Affiliated to Yangtze University, Jingzhou 434000, China
| | - Qing Zhang
- Department of Gastroenterology, No. 1 Hospital Affiliated to Yangtze University, Jingzhou 434000, China
| | - Chaoyong Liu
- Department of Gastroenterology, No. 1 Hospital Affiliated to Yangtze University, Jingzhou 434000, China
| | - Yali Zhang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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44
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Li D, Yang W, Zhang J, Yang JY, Guan R, Yang MQ. Transcription Factor and lncRNA Regulatory Networks Identify Key Elements in Lung Adenocarcinoma. Genes (Basel) 2018; 9:E12. [PMID: 29303984 PMCID: PMC5793165 DOI: 10.3390/genes9010012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/15/2017] [Accepted: 12/21/2017] [Indexed: 12/20/2022] Open
Abstract
Lung cancer is the second most commonly diagnosed carcinoma and is the leading cause of cancer death. Although significant progress has been made towards its understanding and treatment, unraveling the complexities of lung cancer is still hampered by a lack of comprehensive knowledge on the mechanisms underlying the disease. High-throughput and multidimensional genomic data have shed new light on cancer biology. In this study, we developed a network-based approach integrating somatic mutations, the transcriptome, DNA methylation, and protein-DNA interactions to reveal the key regulators in lung adenocarcinoma (LUAD). By combining Bayesian network analysis with tissue-specific transcription factor (TF) and targeted gene interactions, we inferred 15 disease-related core regulatory networks in co-expression gene modules associated with LUAD. Through target gene set enrichment analysis, we identified a set of key TFs, including known cancer genes that potentially regulate the disease networks. These TFs were significantly enriched in multiple cancer-related pathways. Specifically, our results suggest that hepatitis viruses may contribute to lung carcinogenesis, highlighting the need for further investigations into the roles that viruses play in treating lung cancer. Additionally, 13 putative regulatory long non-coding RNAs (lncRNAs), including three that are known to be associated with lung cancer, and nine novel lncRNAs were revealed by our study. These lncRNAs and their target genes exhibited high interaction potentials and demonstrated significant expression correlations between normal lung and LUAD tissues. We further extended our study to include 16 solid-tissue tumor types and determined that the majority of these lncRNAs have putative regulatory roles in multiple cancers, with a few showing lung-cancer specific regulations. Our study provides a comprehensive investigation of transcription factor and lncRNA regulation in the context of LUAD regulatory networks and yields new insights into the regulatory mechanisms underlying LUAD. The novel key regulatory elements discovered by our research offer new targets for rational drug design and accompanying therapeutic strategies.
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Affiliation(s)
- Dan Li
- Joint Bioinformatics Graduate Program, Department of Information Science, George W. Donaghey College of Engineering and Information Technology, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, 2801 S. University Ave, Little Rock, AR 72204, USA.
| | - William Yang
- School of Computer Science, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213, USA.
| | - Jialing Zhang
- Department of Genetics, Yale University, New Haven, CT 06520, USA.
| | - Jack Y Yang
- Joint Bioinformatics Graduate Program, Department of Information Science, George W. Donaghey College of Engineering and Information Technology, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, 2801 S. University Ave, Little Rock, AR 72204, USA.
| | - Renchu Guan
- Joint Bioinformatics Graduate Program, Department of Information Science, George W. Donaghey College of Engineering and Information Technology, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, 2801 S. University Ave, Little Rock, AR 72204, USA.
| | - Mary Qu Yang
- Joint Bioinformatics Graduate Program, Department of Information Science, George W. Donaghey College of Engineering and Information Technology, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, 2801 S. University Ave, Little Rock, AR 72204, USA.
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45
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Bond HM, Scicchitano S, Chiarella E, Amodio N, Lucchino V, Aloisio A, Montalcini Y, Mesuraca M, Morrone G. ZNF423: A New Player in Estrogen Receptor-Positive Breast Cancer. Front Endocrinol (Lausanne) 2018; 9:255. [PMID: 29867779 PMCID: PMC5968090 DOI: 10.3389/fendo.2018.00255] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/03/2018] [Indexed: 01/13/2023] Open
Abstract
Preventive therapy can target hormone-responsive breast cancer (BC) by treatment with selective estrogen receptor modulators (SERMs) and reduce the incidence of BC. Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) with relevant predictive values, SNPs in the ZNF423 gene were associated with decreased risk of BC during SERM therapy, and SNPs in the Cathepsin O gene with an increased risk. ZNF423, which was not previously associated with BC is a multifunctional transcription factor known to have a role in development, neurogenesis, and adipogenesis and is implicated in other types of cancer. ZNF423 is transcriptionally controlled by the homolog ZNF521, early B cell factor transcription factor, epigenetic silencing of the promoter by CpG island hyper-methylation, and also by ZNF423 itself in an auto-regulatory loop. In BC cells, ZNF423 expression is found to be induced by estrogen, dependent on the binding of the estrogen receptor and calmodulin-like 3 to SNPs in ZNP423 intronic sites in proximity to consensus estrogen response elements. ZNF423 has also been shown to play a mechanistic role by trans-activating the tumor suppressor BRCA1 and thus modulating the DNA damage response. Even though recent extensive trial studies did not classify these SNPs with the highest predictive values, for inclusion in polygenic SNP analysis, the mechanism unveiled in these studies has introduced ZNF423 as a factor important in the control of the estrogen response. Here, we aim at providing an overview of ZNF423 expression and functional role in human malignancies, with a specific focus on its implication in hormone-responsive BC.
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Affiliation(s)
- Heather M. Bond
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
- *Correspondence: Heather M. Bond, ; Maria Mesuraca, ; Giovanni Morrone,
| | - Stefania Scicchitano
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Emanuela Chiarella
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Nicola Amodio
- Laboratory of Medical Oncology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Valeria Lucchino
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Annamaria Aloisio
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Ylenia Montalcini
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Maria Mesuraca
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
- *Correspondence: Heather M. Bond, ; Maria Mesuraca, ; Giovanni Morrone,
| | - Giovanni Morrone
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro, Italy
- *Correspondence: Heather M. Bond, ; Maria Mesuraca, ; Giovanni Morrone,
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Artomov M, Stratigos AJ, Kim I, Kumar R, Lauss M, Reddy BY, Miao B, Daniela Robles-Espinoza C, Sankar A, Njauw CN, Shannon K, Gragoudas ES, Marie Lane A, Iyer V, Newton-Bishop JA, Timothy Bishop D, Holland EA, Mann GJ, Singh T, Daly MJ, Tsao H. Rare Variant, Gene-Based Association Study of Hereditary Melanoma Using Whole-Exome Sequencing. J Natl Cancer Inst 2017; 109:3861235. [PMID: 29522175 PMCID: PMC5939858 DOI: 10.1093/jnci/djx083] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 02/03/2017] [Accepted: 04/04/2017] [Indexed: 12/29/2022] Open
Abstract
Background Extraordinary progress has been made in our understanding of common variants in many diseases, including melanoma. Because the contribution of rare coding variants is not as well characterized, we performed an exome-wide, gene-based association study of familial cutaneous melanoma (CM) and ocular melanoma (OM). Methods Using 11 990 jointly processed individual DNA samples, whole-exome sequencing was performed, followed by large-scale joint variant calling using GATK (Genome Analysis ToolKit). PLINK/SEQ was used for statistical analysis of genetic variation. Four models were used to estimate the association among different types of variants. In vitro functional validation was performed using three human melanoma cell lines in 2D and 3D proliferation assays. In vivo tumor growth was assessed using xenografts of human melanoma A375 melanoma cells in nude mice (eight mice per group). All statistical tests were two-sided. Results Strong signals were detected for CDKN2A (Pmin = 6.16 × 10-8) in the CM cohort (n = 273) and BAP1 (Pmin = 3.83 × 10-6) in the OM (n = 99) cohort. Eleven genes that exhibited borderline association (P < 10-4) were independently validated using The Cancer Genome Atlas melanoma cohort (379 CM, 47 OM) and a matched set of 3563 European controls with CDKN2A (P = .009), BAP1 (P = .03), and EBF3 (P = 4.75 × 10-4), a candidate risk locus, all showing evidence of replication. EBF3 was then evaluated using germline data from a set of 132 familial melanoma cases and 4769 controls of UK origin (joint P = 1.37 × 10-5). Somatically, loss of EBF3 expression correlated with progression, poorer outcome, and high MITF tumors. Functionally, induction of EBF3 in melanoma cells reduced cell growth in vitro, retarded tumor formation in vivo, and reduced MITF levels. Conclusions The results of this large rare variant germline association study further define the mutational landscape of hereditary melanoma and implicate EBF3 as a possible CM predisposition gene.
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Affiliation(s)
- Mykyta Artomov
- MGH Analytic and Translational Genetics Unit, MGH and Broad Institute, Boston, MA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
| | - Alexander J Stratigos
- 1st Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Ivana Kim
- Retina Service, Massachusetts Eye and Ear Infirmary, Boston, MA
| | - Raj Kumar
- Department of Dermatology, Wellman Center for Photomedicine, MGH, Boston, MA
| | - Martin Lauss
- Retina Service, Massachusetts Eye and Ear Infirmary, Boston, MA
- Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden
| | - Bobby Y Reddy
- Department of Dermatology, Wellman Center for Photomedicine, MGH, Boston, MA
| | - Benchun Miao
- Department of Dermatology, Wellman Center for Photomedicine, MGH, Boston, MA
| | - Carla Daniela Robles-Espinoza
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro, Mexico
| | - Aravind Sankar
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Ching-Ni Njauw
- Department of Dermatology, Wellman Center for Photomedicine, MGH, Boston, MA
| | - Kristen Shannon
- Melanoma Genetics Program, MGH Cancer Center, MGH, Boston, MA
| | | | - Anne Marie Lane
- Retina Service, Massachusetts Eye and Ear Infirmary, Boston, MA
| | - Vivek Iyer
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Julia A Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - D Timothy Bishop
- Department of Dermatology, Wellman Center for Photomedicine, MGH, Boston, MA
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Elizabeth A Holland
- Centre for Cancer Research, Westmead Institute for Medical Research, University of Sydney, Westmead, Australia
| | - Graham J Mann
- Centre for Cancer Research, Westmead Institute for Medical Research, University of Sydney, Westmead, Australia
- Melanoma Institute Australia, University of Sydney, North Sydney, NSW, Australia
| | - Tarjinder Singh
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Mark J Daly
- MGH Analytic and Translational Genetics Unit, MGH and Broad Institute, Boston, MA
| | - Hensin Tsao
- Melanoma Genetics Program, MGH Cancer Center, MGH, Boston, MA
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47
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Armartmuntree N, Murata M, Techasen A, Yongvanit P, Loilome W, Namwat N, Pairojkul C, Sakonsinsiri C, Pinlaor S, Thanan R. Prolonged oxidative stress down-regulates Early B cell factor 1 with inhibition of its tumor suppressive function against cholangiocarcinoma genesis. Redox Biol 2017; 14:637-644. [PMID: 29169115 PMCID: PMC5701798 DOI: 10.1016/j.redox.2017.11.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/31/2017] [Accepted: 11/12/2017] [Indexed: 02/07/2023] Open
Abstract
Early B cell factor 1 (EBF1) is a transcription factor involved in the differentiation of several stem cell lineages and it is a negative regulator of estrogen receptors. EBF1 is down-regulated in many tumors, and is believed to play suppressive roles in cancer promotion and progression. However, the functional roles of EBF1 in carcinogenesis are unclear. Liver fluke-infection-associated cholangiocarcinoma (CCA) is an oxidative stress-driven cancer of bile duct epithelium. In this study, we investigated EBF1 expression in tissues from CCA patients, CCA cell lines (KKU-213, KKU-214 and KKU-156), cholangiocyte (MMNK1) and its oxidative stress-resistant (ox-MMNK1-L) cell lines. The formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) was used as an oxidative stress marker. Our results revealed that EBF1 expression was suppressed in cancer cells compared with the individual normal bile duct cells at tumor adjacent areas of CCA tissues. CCA patients with low EBF1 expression and high formation of 8-oxodG were shown to correlate with poor survival. Moreover, EBF1 was suppressed in the oxidative stress-resistant cell line and all of CCA cell lines compared to the cholangiocyte cell line. This suggests that prolonged oxidative stress suppressed EBF1 expression and the reduced EBF1 level may facilitate CCA genesis. To elucidate the significance of EBF1 suppression in CCA genesis, EBF1 expression of the MMNK1 cell line was down-regulated by siRNA technique, and its effects on stem cell properties (CD133 and Oct3/4 expressions), tumorigenic properties (cell proliferation, wound healing and cell migration), estrogen responsive gene (TFF1), estrogen-stimulated wound healing, and cell migration were examined. The results showed that CD133, Oct3/4 and TFF1 expression levels, wound healing, and cell migration of EBF1 knockdown-MMNK1 cells were significantly increased. Also, cell migration of EBF1-knockdown cells was significantly enhanced after 17β-estradiol treatment. Our findings suggest that EBF1 down-regulation via oxidative stress induces stem cell properties, tumorigenic properties and estrogen responses of cholangiocytes leading to CCA genesis with aggressive clinical outcomes.
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Affiliation(s)
- Napat Armartmuntree
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Mariko Murata
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Mie 514-8507, Japan
| | - Anchalee Techasen
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; Faculty of Associated Medical Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Puangrat Yongvanit
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Watcharin Loilome
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Nisana Namwat
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chawalit Pairojkul
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chadamas Sakonsinsiri
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Somchai Pinlaor
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Raynoo Thanan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand.
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48
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Kurtsdotter I, Topcic D, Karlén A, Singla B, Hagey DW, Bergsland M, Siesjö P, Nistér M, Carlson JW, Lefebvre V, Persson O, Holmberg J, Muhr J. SOX5/6/21 Prevent Oncogene-Driven Transformation of Brain Stem Cells. Cancer Res 2017; 77:4985-4997. [PMID: 28687615 DOI: 10.1158/0008-5472.can-17-0704] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/19/2017] [Accepted: 06/29/2017] [Indexed: 11/16/2022]
Abstract
Molecular mechanisms preventing self-renewing brain stem cells from oncogenic transformation are poorly defined. We show that the expression levels of SOX5, SOX6, and SOX21 (SOX5/6/21) transcription factors increase in stem cells of the subventricular zone (SVZ) upon oncogenic stress, whereas their expression in human glioma decreases during malignant progression. Elevated levels of SOX5/6/21 promoted SVZ cells to exit the cell cycle, whereas genetic ablation of SOX5/6/21 dramatically increased the capacity of these cells to form glioma-like tumors in an oncogene-driven mouse brain tumor model. Loss-of-function experiments revealed that SOX5/6/21 prevent detrimental hyperproliferation of oncogene expressing SVZ cells by facilitating an antiproliferative expression profile. Consistently, restoring high levels of SOX5/6/21 in human primary glioblastoma cells enabled expression of CDK inhibitors and decreased p53 protein turnover, which blocked their tumorigenic capacity through cellular senescence and apoptosis. Altogether, these results provide evidence that SOX5/6/21 play a central role in driving a tumor suppressor response in brain stem cells upon oncogenic insult. Cancer Res; 77(18); 4985-97. ©2017 AACR.
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Affiliation(s)
- Idha Kurtsdotter
- Ludwig Institute for Cancer Research, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Danijal Topcic
- Ludwig Institute for Cancer Research, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alexandra Karlén
- Ludwig Institute for Cancer Research, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Daniel W Hagey
- Ludwig Institute for Cancer Research, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Peter Siesjö
- Department of Clinical Sciences Lund, Glioma Immunotherapy Group, Division of Neurosurgery, Lund University, Lund, Sweden
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Joseph W Carlson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Veronique Lefebvre
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Oscar Persson
- Department of Neurosurgery, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Holmberg
- Ludwig Institute for Cancer Research, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jonas Muhr
- Ludwig Institute for Cancer Research, Stockholm, Sweden.
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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49
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Genomic analysis of adult B-ALL identifies potential markers of shorter survival. Leuk Res 2017; 56:44-51. [DOI: 10.1016/j.leukres.2017.01.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/02/2017] [Accepted: 01/29/2017] [Indexed: 11/17/2022]
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50
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Chatterjee A, Stockwell PA, Ahn A, Rodger EJ, Leichter AL, Eccles MR. Genome-wide methylation sequencing of paired primary and metastatic cell lines identifies common DNA methylation changes and a role for EBF3 as a candidate epigenetic driver of melanoma metastasis. Oncotarget 2017; 8:6085-6101. [PMID: 28030832 PMCID: PMC5351615 DOI: 10.18632/oncotarget.14042] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 12/12/2016] [Indexed: 12/15/2022] Open
Abstract
Epigenetic alterations are increasingly implicated in metastasis, whereas very few genetic mutations have been identified as authentic drivers of cancer metastasis. Yet, to date, few studies have identified metastasis-related epigenetic drivers, in part because a framework for identifying driver epigenetic changes in metastasis has not been established. Using reduced representation bisulfite sequencing (RRBS), we mapped genome-wide DNA methylation patterns in three cutaneous primary and metastatic melanoma cell line pairs to identify metastasis-related epigenetic drivers. Globally, metastatic melanoma cell lines were hypomethylated compared to the matched primary melanoma cell lines. Using whole genome RRBS we identified 75 shared (10 hyper- and 65 hypomethylated) differentially methylated fragments (DMFs), which were associated with 68 genes showing significant methylation differences. One gene, Early B Cell Factor 3 (EBF3), exhibited promoter hypermethylation in metastatic cell lines, and was validated with bisulfite sequencing and in two publicly available independent melanoma cohorts (n = 40 and 458 melanomas, respectively). We found that hypermethylation of the EBF3 promoter was associated with increased EBF3 mRNA levels in metastatic melanomas and subsequent inhibition of DNA methylation reduced EBF3 expression. RNAi-mediated knockdown of EBF3 mRNA levels decreased proliferation, migration and invasion in primary and metastatic melanoma cell lines. Overall, we have identified numerous epigenetic changes characterising metastatic melanoma cell lines, including EBF3-induced aggressive phenotypic behaviour with elevated EBF3 expression in metastatic melanoma, suggesting that EBF3 promoter hypermethylation may be a candidate epigenetic driver of metastasis.
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Affiliation(s)
- Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Peter A Stockwell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Antonio Ahn
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Euan J Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Anna L Leichter
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
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