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Sato Y, Habara M, Hanaki S, Sharif J, Tomiyasu H, Miki Y, Shimada M. Calcineurin/NFATc1 pathway represses cellular cytotoxicity by modulating histone H3 expression. Sci Rep 2024; 14:14732. [PMID: 38926604 PMCID: PMC11208570 DOI: 10.1038/s41598-024-65769-9] [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: 12/31/2023] [Accepted: 06/24/2024] [Indexed: 06/28/2024] Open
Abstract
Excess amounts of histones in the cell induce mitotic chromosome loss and genomic instability, and are therefore detrimental to cell survival. In yeast, excess histones are degraded by the proteasome mediated via the DNA damage response factor Rad53. Histone expression, therefore, is tightly regulated at the protein level. Our understanding of the transcriptional regulation of histone genes is far from complete. In this study, we found that calcineurin inhibitor treatment increased histone protein levels, and that the transcription factor NFATc1 (nuclear factor of activated T cells 1) repressed histone transcription and acts downstream of the calcineurin. We further revealed that NFATc1 binds to the promoter regions of many histone genes and that histone transcription is downregulated in a manner dependent on intracellular calcium levels. Indeed, overexpression of histone H3 markedly inhibited cell proliferation. Taken together, these findings suggest that NFATc1 prevents the detrimental effects of histone H3 accumulation by inhibiting expression of histone at the transcriptional level.
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Affiliation(s)
- Yuki Sato
- Department of Veterinary Biochemistry, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8511, Japan
| | - Makoto Habara
- Department of Veterinary Biochemistry, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8511, Japan
| | - Shunsuke Hanaki
- Department of Veterinary Biochemistry, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8511, Japan
| | - Jafar Sharif
- Developmental Genetics Group, Center for Integrative Medical Sciences (IMS), RIKEN, 1-7-22 Suehiro, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Haruki Tomiyasu
- Department of Veterinary Biochemistry, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8511, Japan
| | - Yosei Miki
- Department of Veterinary Biochemistry, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8511, Japan
| | - Midori Shimada
- Department of Veterinary Biochemistry, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8511, Japan.
- Department of Molecular Biology, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
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Zheng K, Zhang XX, Yu X, Yu B, Yang YF. Identification and validation of a prognostic anoikis-related gene signature in papillary thyroid carcinoma by integrated analysis of single-cell and bulk RNA-sequencing. Medicine (Baltimore) 2024; 103:e38144. [PMID: 38728457 PMCID: PMC11081552 DOI: 10.1097/md.0000000000038144] [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: 12/12/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Papillary thyroid carcinoma (PTC) prognosis may be deteriorated due to the metastases, and anoikis palys an essential role in the tumor metastasis. However, the potential effect of anoikis-related genes on the prognosis of PTC was unclear. The mRNA and clinical information were obtained from the cancer genome atlas database. Hub genes were identified and risk model was constructed using Cox regression analysis. Kaplan-Meier (K-M) curve was applied for the survival analysis. Immune infiltration and immune therapy response were calculated using CIBERSORT and TIDE. The identification of cell types and cell interaction was performed by Seurat, SingleR and CellChat packages. GO, KEGG, and GSVA were applied for the enrichment analysis. Protein-protein interaction network was constructed in STRING and Cytoscape. Drug sensitivity was assessed in GSCA. Based on bulk RNA data, we identified 4 anoikis-related risk signatures, which were oncogenes, and constructed a risk model. The enrichment analysis found high risk group was enriched in some immune-related pathways. High risk group had higher infiltration of Tregs, higher TIDE score and lower levels of monocytes and CD8 T cells. Based on scRNA data, we found that 4 hub genes were mainly expressed in monocytes and macrophages, and they interacted with T cells. Hub genes were significantly related to immune escape-related genes. Drug sensitivity analysis suggested that cyclin dependent kinase inhibitor 2A may be a better chemotherapy target. We constructed a risk model which could effectively and steadily predict the prognosis of PTC. We inferred that the immune escape may be involved in the development of PTC.
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Affiliation(s)
- Ke Zheng
- Department of Thyroid and Breast Surgery, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xiu-Xia Zhang
- Department of Thyroid and Breast Surgery, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xin Yu
- Department of Thyroid and Breast Surgery, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Bin Yu
- Department of Thyroid and Breast Surgery, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yi-Fei Yang
- Department of Thyroid and Breast Surgery, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
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Wu Q, Fu X, He X, Liu J, Li Y, Ou C. Experimental prognostic model integrating N6-methyladenosine-related programmed cell death genes in colorectal cancer. iScience 2024; 27:108720. [PMID: 38299031 PMCID: PMC10829884 DOI: 10.1016/j.isci.2023.108720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/30/2023] [Accepted: 12/11/2023] [Indexed: 02/02/2024] Open
Abstract
Colorectal cancer (CRC) intricacies, involving dysregulated cellular processes and programmed cell death (PCD), are explored in the context of N6-methyladenosine (m6A) RNA modification. Utilizing the TCGA-COADREAD/CRC cohort, 854 m6A-related PCD genes are identified, forming the basis for a robust 10-gene risk model (CDRS) established through LASSO Cox regression. qPCR experiments using CRC cell lines and fresh tissues was performed for validation. The CDRS served as an independent risk factor for CRC and showed significant associations with clinical features, molecular subtypes, and overall survival in multiple datasets. Moreover, CDRS surpasses other predictors, unveiling distinct genomic profiles, pathway activations, and associations with the tumor microenvironment. Notably, CDRS exhibits predictive potential for drug sensitivity, presenting a novel paradigm for CRC risk stratification and personalized treatment avenues.
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Affiliation(s)
- Qihui Wu
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xiaodan Fu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jiaxin Liu
- Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha 410078, China
| | - Yimin Li
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha 410008, China
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Hajebi Khaniki S, Shokoohi F, Esmaily H, Kerachian MA. Analyzing aberrant DNA methylation in colorectal cancer uncovered intangible heterogeneity of gene effects in the survival time of patients. Sci Rep 2023; 13:22104. [PMID: 38092774 PMCID: PMC10719305 DOI: 10.1038/s41598-023-47377-1] [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: 05/19/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
Colorectal cancer (CRC) involves epigenetic alterations. Irregular gene-methylation alteration causes and advances CRC tumor growth. Detecting differentially methylated genes (DMGs) in CRC and patient survival time paves the way to early cancer detection and prognosis. However, CRC data including survival times are heterogeneous. Almost all studies tend to ignore the heterogeneity of DMG effects on survival. To this end, we utilized a sparse estimation method in the finite mixture of accelerated failure time (AFT) regression models to capture such heterogeneity. We analyzed a dataset of CRC and normal colon tissues and identified 3406 DMGs. Analysis of overlapped DMGs with several Gene Expression Omnibus datasets led to 917 hypo- and 654 hyper-methylated DMGs. CRC pathways were revealed via gene ontology enrichment. Hub genes were selected based on Protein-Protein-Interaction network including SEMA7A, GATA4, LHX2, SOST, and CTLA4, regulating the Wnt signaling pathway. The relationship between identified DMGs/hub genes and patient survival time uncovered a two-component mixture of AFT regression model. The genes NMNAT2, ZFP42, NPAS2, MYLK3, NUDT13, KIRREL3, and FKBP6 and hub genes SOST, NFATC1, and TLE4 were associated with survival time in the most aggressive form of the disease that can serve as potential diagnostic targets for early CRC detection.
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Affiliation(s)
- Saeedeh Hajebi Khaniki
- Department of Biostatistics, School of Health, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Mathematical Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Farhad Shokoohi
- Department of Mathematical Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Habibollah Esmaily
- Department of Biostatistics, School of Health, Mashhad University of Medical Sciences, Mashhad, Iran
- Social Determinants of Health Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Short Linear Motifs in Colorectal Cancer Interactome and Tumorigenesis. Cells 2022; 11:cells11233739. [PMID: 36496998 PMCID: PMC9737320 DOI: 10.3390/cells11233739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Colorectal tumorigenesis is driven by alterations in genes and proteins responsible for cancer initiation, progression, and invasion. This multistage process is based on a dense network of protein-protein interactions (PPIs) that become dysregulated as a result of changes in various cell signaling effectors. PPIs in signaling and regulatory networks are known to be mediated by short linear motifs (SLiMs), which are conserved contiguous regions of 3-10 amino acids within interacting protein domains. SLiMs are the minimum sequences required for modulating cellular PPI networks. Thus, several in silico approaches have been developed to predict and analyze SLiM-mediated PPIs. In this review, we focus on emerging evidence supporting a crucial role for SLiMs in driver pathways that are disrupted in colorectal cancer (CRC) tumorigenesis and related PPI network alterations. As a result, SLiMs, along with short peptides, are attracting the interest of researchers to devise small molecules amenable to be used as novel anti-CRC targeted therapies. Overall, the characterization of SLiMs mediating crucial PPIs in CRC may foster the development of more specific combined pharmacological approaches.
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Wang S, Cheng L, Jing F, Li G. Screening and identification of immune-related genes for immunotherapy and prognostic assessment in colorectal cancer patients. BMC Med Genomics 2022; 15:177. [PMID: 35941638 PMCID: PMC9358808 DOI: 10.1186/s12920-022-01329-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022] Open
Abstract
Background Increasing evidence indicates that the immune microenvironment plays a key role in the genesis and progression of colorectal cancer (CRC). This study aimed to establish an immune-related gene (IRG) signature and determine its clinical prognostic value in patients with CRC. Methods The RNA sequencing and associated clinical data of CRC were downloaded from The Cancer Genome Atlas (TCGA) database. We then screened for differentially expressed IRGs by intersecting with IRGs obtained from the Immunology Database and Analysis Portal. Functional enrichment analyses were carried out to determine the potential biological functions and pathways of the IRGs. We also explored the specific molecular mechanisms of the IRGs by constructing regulatory networks. Prognostic IRGs were obtained by LASSO regression analysis, and subsequently, gene models were constructed in the TCGA dataset to confirm the predictive capacity of these IRGs. Finally, we used the TIMER tool to assess the immune properties of prognostic IRGs and correlate them with immune cells. Results We identified 409 differentially expressed IRGs in patients with CRC. Kyoto Encyclopaedia of Genes and Genomes and Gene Ontology enrichment analyses suggested that these differentially expressed IRGs were significantly related to 102 cancer signalling pathways and various biological functions. Based on the prediction and interaction results, we obtained 59 TF–IRG, 48 miRNA–IRG, and 214 drug–IRG interaction networks for CRC. Four prognostic genes (POMC, TNFRSF19, FGF2, and SCG2) were developed by integrating 47 survival-related IRGs and 42 characteristic CRC genes. The results of gene model showed that patients in the low risk group had better survival outcomes compared to those in the high risk group. The expression of POMC, TNFRSF19, FGF2, and SCG2 was significantly correlated with immune cells. Conclusion This study identified some valid IRGs, and these findings can provide strong evidence for precision immunotherapy in patients with CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01329-2.
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Affiliation(s)
- Shuwei Wang
- Department of General Surgery, Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, 214000, China.
| | - Liang Cheng
- Department of General Surgery, Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, 214000, China
| | - Fa Jing
- Department of General Surgery, Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, 214000, China
| | - Gan Li
- Department of General Surgery, Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, 214000, China.
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Ieranò C, Righelli D, D'Alterio C, Napolitano M, Portella L, Rea G, Auletta F, Santagata S, Trotta AM, Guardascione G, Liotti F, Prevete N, Maiolino P, Luciano A, Barbieri A, Di Mauro A, Roma C, Esposito Abate R, Tatangelo F, Pacelli R, Normanno N, Melillo RM, Scala S. In PD-1+ human colon cancer cells NIVOLUMAB promotes survival and could protect tumor cells from conventional therapies. J Immunother Cancer 2022; 10:jitc-2021-004032. [PMID: 35246475 PMCID: PMC8900051 DOI: 10.1136/jitc-2021-004032] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most prevalent and deadly tumors worldwide. The majority of CRC is resistant to anti-programmed cell death-1 (PD-1)-based cancer immunotherapy, with approximately 15% with high-microsatellite instability, high tumor mutation burden, and intratumoral lymphocytic infiltration. Programmed death-ligand 1 (PD-L1)/PD-1 signaling was described in solid tumor cells. In melanoma, liver, and thyroid cancer cells, intrinsic PD-1 signaling activates oncogenic functions, while in lung cancer cells, it has a tumor suppressor effect. Our work aimed to evaluate the effects of the anti-PD-1 nivolumab (NIVO) on CRC cells. METHODS In vitro NIVO-treated human colon cancer cells (HT29, HCT116, and LoVo) were evaluated for cell growth, chemo/radiotherapeutic sensitivity, apoptosis, and spheroid growth. Total RNA-seq was assessed in 6-24 hours NIVO-treated human colon cancer cells HT29 and HCT116 as compared with NIVO-treated PES43 human melanoma cells. In vivo mice carrying HT29 xenograft were intraperitoneally treated with NIVO, OXA (oxaliplatin), and NIVO+OXA, and the tumors were characterized for growth, apoptosis, and pERK1/2/pP38. Forty-eight human primary colon cancers were evaluated for PD-1 expression through immunohistochemistry. RESULTS In PD-1+ human colon cancer cells, intrinsic PD-1 signaling significantly decreased proliferation and promoted apoptosis. On the contrary, NIVO promoted proliferation, reduced apoptosis, and protected PD-1+ cells from chemo/radiotherapy. Transcriptional profile of NIVO-treated HT29 and HCT116 human colon cancer cells revealed downregulation of BATF2, DRAM1, FXYD3, IFIT3, MT-TN, and TNFRSF11A, and upregulation of CLK1, DCAF13, DNAJC2, MTHFD1L, PRPF3, PSMD7, and SCFD1; the opposite regulation was described in NIVO-treated human melanoma PES43 cells. Differentially expressed genes (DEGs) were significantly enriched for interferon pathway, innate immune, cytokine-mediated signaling pathways. In vivo, NIVO promoted HT29 tumor growth, thus reducing OXA efficacy as revealed through significant Ki-67 increase, pERK1/2 and pP38 increase, and apoptotic cell reduction. Eleven out of 48 primary human colon cancer biopsies expressed PD-1 (22.9%). PD-1 expression is significantly associated with lower pT stage. CONCLUSIONS In PD-1+ human colon cancer cells, NIVO activates tumor survival pathways and could protect tumor cells from conventional therapies.
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Affiliation(s)
- Caterina Ieranò
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | | | - Crescenzo D'Alterio
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Maria Napolitano
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Luigi Portella
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Giuseppina Rea
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Federica Auletta
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Sara Santagata
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Anna Maria Trotta
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Giuseppe Guardascione
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Federica Liotti
- Institute of Endocrinology and Experimental Oncology (IEOS), CNR-NA1, Napoli, Italy
| | - Nella Prevete
- Institute of Endocrinology and Experimental Oncology (IEOS), CNR-NA1, Napoli, Italy.,Traslational Medical Sciences, University of Naples Federico II, Napoli, Italy
| | - Piera Maiolino
- Pharmacy, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Antonio Luciano
- Animal Facility, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Antonio Barbieri
- Animal Facility, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Annabella Di Mauro
- Pathology, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Cristin Roma
- Cell Biology and Biotherapy, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Fabiana Tatangelo
- Pathology, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Roberto Pacelli
- Advanced Biomedical Sciences, University of Naples Federico II, Napoli, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Rosa Marina Melillo
- Institute of Endocrinology and Experimental Oncology (IEOS), CNR-NA1, Napoli, Italy.,Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | - Stefania Scala
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
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