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Kwon H, Joh JY, Hong KU. Human CKAP2L shows a cell cycle-dependent expression pattern and exhibits microtubule-stabilizing properties. FEBS Open Bio 2024. [PMID: 39073037 DOI: 10.1002/2211-5463.13864] [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: 10/31/2023] [Revised: 04/30/2024] [Accepted: 07/11/2024] [Indexed: 07/30/2024] Open
Abstract
Cytoskeleton-associated protein 2-like (CKAP2L) is a paralogue of cytoskeleton-associated protein 2 (CKAP2). We characterized the expression pattern, subcellular localization, and microtubule-stabilizing properties of human CKAP2L. The levels of both CKAP2L transcript and protein were cell cycle phase-dependent, peaking during the G2/M phase and relatively high in certain human tissues, including testis, intestine, and spleen. CKAP2L protein was detectable in all human cancer cell lines we tested. CKAP2L localized to the mitotic spindle apparatus during mitosis, as reported previously. During interphase, however, CKAP2L localized mainly to the nucleus. Ectopic overexpression of CKAP2L resulted in 'microtubule bundling', and, consequently, an elevated CKAP2L level led to prolonged mitosis. These findings support the mitotic role of CKAP2L during the human cell cycle.
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Affiliation(s)
- Hyerim Kwon
- School of Medicine, Sungkyunkwan University, Suwon, Korea
| | - Jonathan Y Joh
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, KY, USA
| | - Kyung U Hong
- College of Pharmacy and Health Sciences, Western New England University, Springfield, MA, USA
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2
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Qiao X, Ma D, Zhang X. Identification of hub genes and potential molecular mechanisms in MSS/MSI classifier primary colorectal cancer based on multiple datasets. Discov Oncol 2024; 15:290. [PMID: 39023715 PMCID: PMC11258107 DOI: 10.1007/s12672-024-01148-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024] Open
Abstract
OBJECTIVE MSI has a better prognosis than MSS in colorectal cancer patients, and the main objective of this study was to screen for differentially expressed molecules between MSI and MSS primary colorectal cancers using bioinformatics. MATERIAL AND METHODS Two gene expression datasets (GSE13294 and GSE13067) were downloaded from GEO, and differential expressed genes (DEGs) were analyzed using GEO2R. Gene Ontology, Kyoto Encyclopedia of Genomes, and Gene Set Enrichment Analysis were conducted using the DEGs. Furthermore, a Protein-Protein Interaction Networks (PPI) was constructed to screen for significant modules and identify hub genes. The hub genes were analyzed in colorectal cancer using GEPIA. The expression of hub genes in clinical samples was visualized using the online Human Protein Atlas (HPA). RESULTS A total of 265 common DEGs were identified in MSS primary colorectal cancer compared to MSI primary colorectal cancer. Among these, 178 DEGs were upregulated, and 87 DEGs were downregulated. Enrichment analysis showed that these DEGs were associated with the response to mechanical stimulus, regulation of cellular response to stress, G protein-coupled receptor binding, and other processes. A total of 5 hub genes was identified by cytoHubba: HNRNPL, RBM39, HNRNPH1, TRA2A, SRSF6. GEPIA software online analysis, 5 hub gene expression in colorectal cancer survival curve did not have significant differences. The expression of RBM39 was significantly different in different stages of colorectal cancer. The HPA online database results showed that the expression of the five hub proteins varied widely in CRC patients. CONCLUSION The hub genes, such as HNRNPH1and RBM39, and the spliceosome resulting from DEGs, which may provide novel insights and evidence for the future diagnosis and targeted therapy of MSS/MSI PCRC.
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Affiliation(s)
- Xia Qiao
- Institute of Medical Science, General Hospital of Ningxia Medical University, Yinchuan, 750004, China
| | - Duan Ma
- Institute of Medical Science, General Hospital of Ningxia Medical University, Yinchuan, 750004, China.
| | - Xu Zhang
- Institute of Medical Science, General Hospital of Ningxia Medical University, Yinchuan, 750004, China.
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Zeng H, Zhuang Y, Yan X, He X, Qiu Q, Liu W, Zhang Y. Machine learning-based identification of novel hub genes associated with oxidative stress in lupus nephritis: implications for diagnosis and therapeutic targets. Lupus Sci Med 2024; 11:e001126. [PMID: 38637124 PMCID: PMC11029281 DOI: 10.1136/lupus-2023-001126] [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: 12/07/2023] [Accepted: 03/28/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Lupus nephritis (LN) is a complication of SLE characterised by immune dysfunction and oxidative stress (OS). Limited options exist for LN. We aimed to identify LN-related OS, highlighting the need for non-invasive diagnostic and therapeutic approaches. METHODS LN-differentially expressed genes (DEGs) were extracted from Gene Expression Omnibus datasets (GSE32591, GSE112943 and GSE104948) and Molecular Signatures Database for OS-associated DEGs (OSEGs). Functional enrichment analysis was performed for OSEGs related to LN. Weighted gene co-expression network analysis identified hub genes related to OS-LN. These hub OSEGs were refined as biomarker candidates via least absolute shrinkage and selection operator. The predictive value was validated using receiver operating characteristic (ROC) curves and nomogram for LN prognosis. We evaluated LN immune cell infiltration using single-sample gene set enrichment analysis and CIBERSORT. Additionally, gene set enrichment analysis explored the functional enrichment of hub OSEGs in LN. RESULTS The study identified four hub genes, namely STAT1, PRODH, TXN2 and SETX, associated with OS related to LN. These genes were validated for their diagnostic potential, and their involvement in LN pathogenesis was elucidated through ROC and nomogram. Additionally, alterations in immune cell composition in LN correlated with hub OSEG expression were observed. Immunohistochemical analysis reveals that the hub gene is most correlated with activated B cells and CD8 T cells. Finally, we uncovered that the enriched pathways of OSEGs were mainly involved in the PI3K-Akt pathway and the Janus kinase-signal transducer and activator of transcription pathway. CONCLUSION These findings contribute to advancing our understanding of the complex interplay between OS, immune dysregulation and molecular pathways in LN, laying a foundation for the identification of potential diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Huiqiong Zeng
- Traditional Chinese Medicine Department of Immunology, Women & Children Health Institute Futian Shenzhen, Shenzhen, China
| | - Yu Zhuang
- Department of Rheumatology and Immunology, Huizhou Central People's Hospital, Huizhou, China
| | - Xiaodong Yan
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, China
| | - Xiaoyan He
- Department of Fu Xin Community Health Service Center, The Eighth Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Qianwen Qiu
- Traditional Chinese Medicine Department of Immunology, Women & Children Health Institute Futian Shenzhen, Shenzhen, China
| | - Wei Liu
- Department of Rheumatology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Ye Zhang
- Traditional Chinese Medicine Department of Immunology, Women & Children Health Institute Futian Shenzhen, Shenzhen, China
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Wang B, Duan G, Liu L, Long Z, Bai X, Ou M, Wang P, Jiang D, Li D, Sun W. UvHOS3-mediated histone deacetylation is essential for virulence and negatively regulates ustilaginoidin biosynthesis in Ustilaginoidea virens. MOLECULAR PLANT PATHOLOGY 2024; 25:e13429. [PMID: 38353606 PMCID: PMC10866089 DOI: 10.1111/mpp.13429] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024]
Abstract
Ustilaginoidea virens is the causal agent of rice false smut, which has recently become one of the most important rice diseases worldwide. Ustilaginoidins, a major type of mycotoxins produced in false smut balls, greatly deteriorates grain quality. Histone acetylation and deacetylation are involved in regulating secondary metabolism in fungi. However, little is yet known on the functions of histone deacetylases (HDACs) in virulence and mycotoxin biosynthesis in U. virens. Here, we characterized the functions of the HDAC UvHOS3 in U. virens. The ΔUvhos3 deletion mutant exhibited the phenotypes of retarded growth, increased mycelial branches and reduced conidiation and virulence. The ΔUvhos3 mutants were more sensitive to sorbitol, sodium dodecyl sulphate and oxidative stress/H2 O2 . ΔUvhos3 generated significantly more ustilaginoidins. RNA-Seq and metabolomics analyses also revealed that UvHOS3 is a key negative player in regulating secondary metabolism, especially mycotoxin biosynthesis. Notably, UvHOS3 mediates deacetylation of H3 and H4 at H3K9, H3K18, H3K27 and H4K8 residues. Chromatin immunoprecipitation assays indicated that UvHOS3 regulates mycotoxin biosynthesis, particularly for ustilaginoidin and sorbicillinoid production, by modulating the acetylation level of H3K18. Collectively, this study deepens the understanding of molecular mechanisms of the HDAC UvHOS3 in regulating virulence and mycotoxin biosynthesis in phytopathogenic fungi.
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Affiliation(s)
- Bo Wang
- College of Plant Protection and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green ManagementChina Agricultural UniversityBeijingChina
- College of Plant ProtectionJilin Agricultural UniversityChangchunChina
- College of Plant ProtectionSanya Institute of China Agricultural UniversitySanyaChina
| | - Guohua Duan
- College of Plant ProtectionJilin Agricultural UniversityChangchunChina
| | - Ling Liu
- College of Plant ProtectionJilin Agricultural UniversityChangchunChina
| | - Zhaoyi Long
- College of Plant ProtectionJilin Agricultural UniversityChangchunChina
| | - Xiaolong Bai
- College of Plant ProtectionJilin Agricultural UniversityChangchunChina
| | - Mingming Ou
- College of Plant ProtectionJilin Agricultural UniversityChangchunChina
| | - Peiying Wang
- College of Plant ProtectionJilin Agricultural UniversityChangchunChina
| | - Du Jiang
- College of Plant Protection and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green ManagementChina Agricultural UniversityBeijingChina
- College of Plant ProtectionSanya Institute of China Agricultural UniversitySanyaChina
| | - Dayong Li
- College of Plant ProtectionJilin Agricultural UniversityChangchunChina
| | - Wenxian Sun
- College of Plant Protection and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green ManagementChina Agricultural UniversityBeijingChina
- College of Plant ProtectionJilin Agricultural UniversityChangchunChina
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Suwatthanarak T, Tanjak P, Suwatthanarak T, Acharayothin O, Thanormjit K, Chaiboonchoe A, Tawantanakorn T, Phalanusitthepha C, Trakarnsanga A, Methasate A, Pithukpakorn M, Okamoto R, Chinswangwatanakul V. Exploring extracellular matrix and prostaglandin pathway alterations across varying resection margin distances of right-sided colonic adenocarcinoma. BMC Cancer 2023; 23:1202. [PMID: 38062443 PMCID: PMC10702019 DOI: 10.1186/s12885-023-11595-7] [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: 07/06/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Surgical resection followed by indicated adjuvant therapy offers potential curative treatment in colonic adenocarcinoma. Beyond the well-established seed and soil theory of colon cancer progression, the 'normal-appearing' tissues near the tumor are not genuinely normal and remain as remnants in patients following surgery. Our objective was to elucidate the alteration of gene expression and pathways across various distances of resection margins in right-sided colonic adenocarcinoma. METHODS Twenty-seven fresh samples of primary cancer and 56 matched non-tumor tissues adjacent to the tumor (NAT) were collected from patients with resectable right-sided colon cancer. NAT were systematically obtained at varying distances (1, 5, and 10 cm) on both proximal and distal sides. Comprehensive gene expression analysis was performed using 770-gene PanCancer Progression Panel, delineating distinctive pathways and functional predictions for each region. RESULTS Distinctive gene signatures and pathways exhibited by normal-appearing tissues were discovered at varying distances from cancer. Notably, SFRP2, PTGDS, COL1A1, IL1B, THBS2, PTGIS, COL1A2, NPR1, and BGN were upregulated, while ENPEP, MMP1, and NRCAM were downregulated significantly in 1-cm tissue compared to farther distances. Substantial alterations in the extracellular matrix (ECM) and prostaglandin/thromboxane synthesis were significantly evident at the 1-cm distance. Functional analysis indicated enhanced cell viability and survival, alongside reduced cellular death and apoptosis. CONCLUSIONS Different distances exerted a significant impact on gene alteration within the normal-looking mucosa surrounding primary cancer, influenced by various mechanisms. These findings may highlight potential therapeutic targets related to the ECM and prostaglandin/thromboxane pathways for treatment strategies.
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Grants
- R016241047 Foundation for Cancer Care, Siriraj Hospital, Thailand
- R016241047 Foundation for Cancer Care, Siriraj Hospital, Thailand
- R016241047 Foundation for Cancer Care, Siriraj Hospital, Thailand
- R016241047 Foundation for Cancer Care, Siriraj Hospital, Thailand
- R016241047 Foundation for Cancer Care, Siriraj Hospital, Thailand
- 63-117 Health Systems Research Institute (HSRI) of Thailand
- 63-117 Health Systems Research Institute (HSRI) of Thailand
- 63-117 Health Systems Research Institute (HSRI) of Thailand
- 63-117 Health Systems Research Institute (HSRI) of Thailand
- 63-117 Health Systems Research Institute (HSRI) of Thailand
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Affiliation(s)
- Tharathorn Suwatthanarak
- Graduate School of Medical and Dental Sciences, Joint Degree Doctoral Program in Medical Sciences between Tokyo Medical and Dental University, Tokyo, Japan
- Mahidol University, Bangkok, Thailand
- Division of General Surgery, Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, 12th Floor, Syamindra Building, 2, Prannok Road, Bangkok Noi, Bangkok, 10700, Thailand
| | - Pariyada Tanjak
- Division of General Surgery, Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, 12th Floor, Syamindra Building, 2, Prannok Road, Bangkok Noi, Bangkok, 10700, Thailand
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thanawat Suwatthanarak
- Division of General Surgery, Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, 12th Floor, Syamindra Building, 2, Prannok Road, Bangkok Noi, Bangkok, 10700, Thailand
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Onchira Acharayothin
- Division of General Surgery, Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, 12th Floor, Syamindra Building, 2, Prannok Road, Bangkok Noi, Bangkok, 10700, Thailand
| | - Kullanist Thanormjit
- Division of General Surgery, Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, 12th Floor, Syamindra Building, 2, Prannok Road, Bangkok Noi, Bangkok, 10700, Thailand
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Amphun Chaiboonchoe
- Siriraj Center of Research Excellence for Systems Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thikhamporn Tawantanakorn
- Division of General Surgery, Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, 12th Floor, Syamindra Building, 2, Prannok Road, Bangkok Noi, Bangkok, 10700, Thailand
| | - Chainarong Phalanusitthepha
- Division of General Surgery, Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, 12th Floor, Syamindra Building, 2, Prannok Road, Bangkok Noi, Bangkok, 10700, Thailand
| | - Atthaphorn Trakarnsanga
- Division of General Surgery, Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, 12th Floor, Syamindra Building, 2, Prannok Road, Bangkok Noi, Bangkok, 10700, Thailand
| | - Asada Methasate
- Division of General Surgery, Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, 12th Floor, Syamindra Building, 2, Prannok Road, Bangkok Noi, Bangkok, 10700, Thailand
| | - Manop Pithukpakorn
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ryuichi Okamoto
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Vitoon Chinswangwatanakul
- Division of General Surgery, Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, 12th Floor, Syamindra Building, 2, Prannok Road, Bangkok Noi, Bangkok, 10700, Thailand.
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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Woischke C, Michl M, Neumann J. [Molecular pathology of colorectal cancer]. PATHOLOGIE (HEIDELBERG, GERMANY) 2023; 44:279-286. [PMID: 37277480 DOI: 10.1007/s00292-023-01201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/20/2023] [Indexed: 06/07/2023]
Abstract
In recent years, the treatment of colorectal carcinoma has experienced increasing individualization. In addition to RAS and BRAF mutational status that is firmly established in routine diagnostics, new therapeutic options evolved based on MSI and HER2 status as well as primary tumour localization. Offering the best targeted options in therapy requires new evidence-based decision-making algorithms regarding timing and scope of molecular pathological diagnostics in order for patients to receive an optimized therapy according to current treatment guidelines. New targeted therapies, some of which are about to be approved and for which pathology has to provide new molecular pathological biomarkers, will also play an increasingly important role in the future.
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Affiliation(s)
- Christine Woischke
- Pathologisches Institut, Medizinische Fakultät, Ludwig-Maximilians-Universität München, Thalkirchner Str. 36, 80337, München, Deutschland
| | - Marlies Michl
- Medizinische Klinik und Poliklinik III, Klinikum der Universität München, Ludwig-Maximilians-Universität München, München, Deutschland
- Facharztpraxis für Innere Medizin, Hämatologie und Onkologie mit Tagesklinik, Praxis Dr. Michl, München, Deutschland
| | - Jens Neumann
- Pathologisches Institut, Medizinische Fakultät, Ludwig-Maximilians-Universität München, Thalkirchner Str. 36, 80337, München, Deutschland.
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Fang D, He Y, Yi Y, Mei J, Liu C. Hub gene associated with prognosis in bladder cancer is a novel therapeutic target. PeerJ 2023; 11:e15670. [PMID: 37601252 PMCID: PMC10439716 DOI: 10.7717/peerj.15670] [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: 03/27/2023] [Accepted: 06/09/2023] [Indexed: 08/22/2023] Open
Abstract
Objective Bladder cancer is a clinical and social conundrum due to its high incidence and recurrence rate. It is urgent to find new targets for the diagnosis and treatment of bladder cancer and improve the prognosis and survival rate of bladder cancer patients. We sought a prognosis-related gene, built related models of evaluated bladder cancer and identified the function of the hub gene in bladder cancer. Methods We downloaded the data of bladder cancer patients from the TCGA database, and used differentially expressed genes (DEGs), copy number variation (CNV) and survival analysis to scan the hub genes associated with prognosis in bladder cancer. Then, multi-factor cox regression was used to obtain the bladder cancer prognosis correlation model. Then, we analyzed the relationship between the expression of hub gene and immune microenvironment of bladder cancer. The relationship between the expression of hub gene and prognosis in bladder cancer patients was verified by immunohistochemistry. Cell proliferation assay and drug sensitivity test in vivo were used to verify the inhibition of bladder cancer by targeted inhibitors. Results In bladder cancer, we screened seven hub genes (ACLY, CNP, NKIRAS2, P3H4, PDIA6, VPS25 and XPO1) associated with survival. Moreover, the multifactor regression model constructed with hub gene can well distinguish the prognosis of bladder cancer. Hub gene is mostly associated with immune microenvironment. Immunohistochemical results basically confirmed the importance of XPO1 in bladder cancer. Selinexor (an inhibitor of XPO1) could effectively inhibit the proliferation of bladder cancer in the cell proliferation experiments by CCK-8 assays and it could suppress the growth of bladder cancer in mouse bladder cancer model. Conclusions In this study, a prognostic model with seven hub genes has provided great help for the prognosis prediction of bladder cancer patients. And XPO1 is an important target affecting the prognosis of bladder cancer, and inhibition of XPO1 can effectively inhibit bladder cancer proliferation and growth.
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Affiliation(s)
- Dengpan Fang
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- Department of Urology, The Sixth Hospital of Wuhan, Affiliated Hospital of Jianghan University, Wuhan, China
| | - Yuanqiao He
- Center of Laboratory Animal Science, Nanchang University,, Nanchang, China
- Jiangxi Province Key Laboratory of Laboratory Animal, Nanchang, China
- Nanchang Royo Biotechnology, Nanchang, China
| | - Yun Yi
- The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jiaqi Mei
- The First Clinical Medical College, Nanchang University, Nanchang, China
| | - Cundong Liu
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
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Wang C, He Y, He Y, Liang W, Zhou C, Wu M, Meng Z, Li W, Cao J. Prognostic and biological function value of OSBPL3 in colorectal cancer analyzed by multi-omic data analysis. BMC Gastroenterol 2023; 23:270. [PMID: 37550605 PMCID: PMC10408063 DOI: 10.1186/s12876-023-02824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/17/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common malignancies in the world. This study proposes to reveal prognostic biomarkers for the prognosis and treatment of CRC patients. METHODS Differential analysis of OSBPL3 was performed in pan-cancer, and the correlation between clinical stage and OSBPL3 was analyzed. Multiple omics analysis was used to compare the relationship between survival of patients and copy number variation, single nucleotide variant, and methylation status. Survival differences between high and low OSBPL3 expression groups were analyzed. Differentially expressed genes (DEGs) between high and low OSBPL3 expression groups were obtained, and functional enrichment analysis was implemented. Correlations between immune cells and OSBPL3 was analyzed. Drug sensitivity between the two OSBPL3 expression groups was compared. Moreover, the expression of OSBPL3 was verified by immunohistochemistry and real-time quantitative PCR. RESULTS OSBPL3 was differentially expressed in 13 tumors and had some correlations with T and N stages. OSBPL3 expression was regulated by methylation and higher OSBPL3 expression was associated with poorer prognosis in CRC. 128 DEGs were obtained and they were mainly involved in signaling receptor activator activity, aspartate and glutamate metabolism. T cell gamma delta and T cell follicular helper were significantly different in the high and low OSBPL3 expression groups. Moreover, OSBPL3 showed negative correlations with multiple drugs. OSBPL3 was significantly upregulated in CRC samples compared to normal samples. CONCLUSIONS A comprehensive analysis demonstrated that OSBPL3 had potential prognostic value, and guiding significance for CRC chemotherapeutic.
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Affiliation(s)
- Chengxing Wang
- The First Affiliated Hospital, Jinan University, Guangzhou, 529000, Guangdong, China
- Department of Gastrointestinal Surgery, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Yaoming He
- Department of Gastrointestinal Surgery, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Yu He
- National Drug Clinical Trial Institution, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Weijun Liang
- Department of Gastrointestinal Surgery, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Chaorong Zhou
- Department of Gastrointestinal Surgery, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Meimei Wu
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Zijie Meng
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Wanglin Li
- The First Affiliated Hospital, Jinan University, Guangzhou, 529000, Guangdong, China.
| | - Jie Cao
- The First Affiliated Hospital, Jinan University, Guangzhou, 529000, Guangdong, China.
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Ke H, Li Z, Li P, Ye S, Huang J, Hu T, Zhang C, Yuan M, Chen Y, Wu X, Lan P. Dynamic heterogeneity of colorectal cancer during progression revealed clinical risk-associated cell types and regulations in single-cell resolution and spatial context. Gastroenterol Rep (Oxf) 2023; 11:goad034. [PMID: 37360193 PMCID: PMC10290555 DOI: 10.1093/gastro/goad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 06/28/2023] Open
Abstract
Background Tumor heterogeneity is contributed by tumor cells and the microenvironment. Dynamics of tumor heterogeneity during colorectal cancer (CRC) progression have not been elucidated. Methods Eight single-cell RNA sequencing (scRNA-seq) data sets of CRC were included. Milo was utilized to reveal the differential abundance of cell clusters during progression. The differentiation trajectory was imputed by using the Palantir algorithm and metabolic states were assessed by using scMetabolism. Three spatial transcription sequencing (ST-seq) data sets of CRC were used to validate cell-type abundances and colocalization. Cancer-associated regulatory hubs were defined as communication networks affecting tumor biological behaviors. Finally, quantitative reverse transcription polymerase chain reaction and immunohistochemistry staining were performed for validation. Results TM4SF1+, SOX4+, and MKI67+ tumor cells; CXCL12+ cancer-associated fibroblasts; CD4+ resident memory T cells; Treg; IgA+ plasma cells; and several myeloid subsets were enriched in stage IV CRC, most of which were associated with overall survival of patients. Trajectory analysis indicated that tumor cells from patients with advanced-stage CRC were less differentiated, when metabolic heterogeneity showed a highest metabolic signature in terminal states of stromal cells, T cells, and myeloid cells. Moreover, ST-seq validated cell-type abundance in a spatial context and also revealed the correlation of immune infiltration between tertiary lymphoid structures and tumors followed by validation in our cohort. Importantly, analysis of cancer-associated regulatory hubs revealed a cascade of activated pathways including leukocyte apoptotic process, MAPK pathway, myeloid leukocyte differentiation, and angiogenesis during CRC progression. Conclusions Tumor heterogeneity was dynamic during progression, with the enrichment of immunosuppressive Treg, myeloid cells, and fibrotic cells. The differential state of tumor cells was associated with cancer staging. Assessment of cancer-associated regulatory hubs suggested impaired antitumor immunity and increased metastatic ability during CRC progression.
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Affiliation(s)
| | | | | | - Shubiao Ye
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology ,The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Junfeng Huang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology ,The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Tuo Hu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology ,The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Chi Zhang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology ,The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Ming Yuan
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology ,The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Yuan Chen
- School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, P. R. China
| | - Xianrui Wu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology ,The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Ping Lan
- Corresponding author. Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, No. 26 Yuancun Erheng Road, Guangzhou, Guangdong 510655, China. Tel: +86-20-38254009;
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Wang R, Wang Y, Yao W, Ge W, Jiang T, Zhou B. Transcriptome Sequencing and WGCNA Reveal Key Genes in Response to Leaf Blight in Poplar. Int J Mol Sci 2023; 24:10047. [PMID: 37373194 DOI: 10.3390/ijms241210047] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Leaf blight is a fungal disease that mainly affects the growth and development of leaves in plants. To investigate the molecular mechanisms of leaf blight defense in poplar, we performed RNA-Seq and enzyme activity assays on the Populus simonii × Populus nigra leaves inoculated with Alternaria alternate fungus. Through weighted gene co-expression network analysis (WGCNA), we obtained co-expression gene modules significantly associated with SOD and POD activities, containing 183 and 275 genes, respectively. We then constructed a co-expression network of poplar genes related to leaf blight resistance based on weight values. Additionally, we identified hub transcription factors (TFs) and structural genes in the network. The network was dominated by 15 TFs, and four out of them, including ATWRKY75, ANAC062, ATMYB23 and ATEBP, had high connectivity in the network, which might play important functions in leaf blight defense. In addition, GO enrichment analysis revealed a total of 44 structural genes involved in biotic stress, resistance, cell wall and immune-related biological processes in the network. Among them, there were 16 highly linked structural genes in the central part, which may be directly involved in poplar resistance to leaf blight. The study explores key genes associated with leaf blight defense in poplar, which further gains an understanding of the molecular mechanisms of biotic stress response in plants.
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Affiliation(s)
- Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yuting Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Wenjing Yao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Wengong Ge
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Boru Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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11
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Li XX, Li H, Jin LQ, Tan YB. Exploration and Validation of Pancreatic Cancer Hub Genes Based on Weighted Gene Co-Expression Network Analysis and Immune Infiltration Score Analysis. Pharmgenomics Pers Med 2023; 16:467-480. [PMID: 37252337 PMCID: PMC10216855 DOI: 10.2147/pgpm.s403116] [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: 01/12/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023] Open
Abstract
Objective To find pancreatic cancer (PC)-related hub genes based on weighted gene co-expression network analysis (WGCNA) construction and immune infiltration score analysis and validate them immunohistochemically by clinical cases, to generate new concepts or therapeutic targets for the early diagnosis and treatment of PC. Material and Methods In this study, WGCNA and immune infiltration score were utilized to identify the relevant core modules of PC and the hub genes within these core modules. Results Using WGCNA analysis, data from PC and normal pancreas integrated with TCGA and GTEX were analyzed and brown modules were chosen from the six modules. Five hub genes, including DPYD, FXYD6, MAP6, FAM110B, and ANK2, were discovered to have differential survival significance via validation tests utilizing survival analysis curves and the GEPIA database. The DPYD gene was the only gene associated with PC survival side effects. Validation of the Human Protein Atlas (HPA) database and immunohistochemical testing of clinical samples showed positive results for DPYD expression in PC. Conclusion In this study, we identified DPYD, FXYD6, MAP6, FAM110B, and ANK2, as immune-related candidate markers for PC. Only the DPYD gene had a negative impact on the survival of PC patients. Through validation of the HPA database and immunohistochemical testing of clinical cases, we believe that the DPYD gene brings novel ideas and therapeutic targets in the diagnosis and treatment of PC.
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Affiliation(s)
- Xiao-Xi Li
- Dali University of Clinical Medicine School, Dali, Yunnan, 671000, People’s Republic of China
| | - Hong Li
- Department of Radiology, Affiliated Renhe Hospital of China Three Gorges University, Hubei, 443001, People’s Republic of China
| | - Li-Quan Jin
- Department of General Surgery, The First of Affiliated Hospital of Dali University, Dali, Yunnan, 671000, People’s Republic of China
| | - Yun-Bo Tan
- Dali University of Clinical Medicine School, Dali, Yunnan, 671000, People’s Republic of China
- Department of General Surgery, The First of Affiliated Hospital of Dali University, Dali, Yunnan, 671000, People’s Republic of China
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12
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Deng S, Shen S, Liu K, El-Ashram S, Alouffi A, Cenci-Goga BT, Ye G, Cao C, Luo T, Zhang H, Li W, Li S, Zhang W, Wu J, Chen C. Integrated bioinformatic analyses investigate macrophage-M1-related biomarkers and tuberculosis therapeutic drugs. Front Genet 2023; 14:1041892. [PMID: 36845395 PMCID: PMC9945105 DOI: 10.3389/fgene.2023.1041892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/16/2023] [Indexed: 02/10/2023] Open
Abstract
Tuberculosis (TB) is a common infectious disease linked to host genetics and the innate immune response. It is vital to investigate new molecular mechanisms and efficient biomarkers for Tuberculosis because the pathophysiology of the disease is still unclear, and there aren't any precise diagnostic tools. This study downloaded three blood datasets from the GEO database, two of which (GSE19435 and 83456) were used to build a weighted gene co-expression network for searching hub genes associated with macrophage M1 by the CIBERSORT and WGCNA algorithms. Furthermore, 994 differentially expressed genes (DEGs) were extracted from healthy and TB samples, four of which were associated with macrophage M1, naming RTP4, CXCL10, CD38, and IFI44. They were confirmed as upregulation in TB samples by external dataset validation (GSE34608) and quantitative real-time PCR analysis (qRT-PCR). CMap was used to predict potential therapeutic compounds for tuberculosis using 300 differentially expressed genes (150 downregulated and 150 upregulated genes), and six small molecules (RWJ-21757, phenamil, benzanthrone, TG-101348, metyrapone, and WT-161) with a higher confidence value were extracted. We used in-depth bioinformatics analysis to investigate significant macrophage M1-related genes and promising anti-Tuberculosis therapeutic compounds. However, more clinical trials were necessary to determine their effect on Tuberculosis.
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Affiliation(s)
- Siqi Deng
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Shijie Shen
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Keyu Liu
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Saeed El-Ashram
- Faculty of Science, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Abdulaziz Alouffi
- King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | | | - Guomin Ye
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Chengzhang Cao
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Tingting Luo
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Hui Zhang
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Weimin Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Siyuan Li
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Wanjiang Zhang
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Jiangdong Wu
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China,*Correspondence: Jiangdong Wu, ; Chuangfu Chen,
| | - Chuangfu Chen
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China,*Correspondence: Jiangdong Wu, ; Chuangfu Chen,
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13
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Liu Z, Zhang J, Shen D, Hu X, Ke Z, Ehrich Lister IN, Sihombing B. Prognostic significance of CKAP2L expression in patients with clear cell renal cell carcinoma. Front Genet 2023; 13:873884. [PMID: 36699449 PMCID: PMC9870291 DOI: 10.3389/fgene.2022.873884] [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: 02/11/2022] [Accepted: 12/09/2022] [Indexed: 01/11/2023] Open
Abstract
Background: Cytoskeleton-associated protein 2-like protein (CKAP2L) is thought to promote the progression of glioma, breast cancer, and ovarian cancer. However, the role of cytoskeleton-associated protein 2-like protein in clear cell renal cell carcinoma (ccRCC) is still unclear. The study aimed to investigate the roles and mechanisms of cytoskeleton-associated protein 2-like protein in clear cell renal cell carcinoma. Methods: The level of cytoskeleton-associated protein 2-like protein in tumors was explored by using UALCAN and Oncomine databases. Gene expression datasets of clear cell renal cell carcinoma from The Cancer Genome Atlas and Gene Expression Omnibus (GEO) were also used to validate the cytoskeleton-associated protein 2-like protein level in clear cell renal cell carcinoma. Survival analysis was performed to investigate the relationship between cytoskeleton-associated protein 2-like protein level and prognosis of clear cell renal cell carcinoma patients. Cox regression analysis was used for identifying the independent prognostic factors. Gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), protein-protein interaction analysis, co-expression analysis, and immune infiltration analysis were used to explore the potential mechanisms of cytoskeleton-associated protein 2-like protein in clear cell renal cell carcinoma. Moreover, the levels of cytoskeleton-associated protein 2-like protein in clinical clear cell renal cell carcinoma tissues were also measured using RT-PCR, immunohistochemical analysis, and Western blotting. M1 macrophages and CD4+ T cells were also detected by immunohistochemistry between tumor and normal tissues. Results: The level of cytoskeleton-associated protein 2-like protein was upregulated in clear cell renal cell carcinoma according to multiple databases and experimental verification. Upregulated cytoskeleton-associated protein 2-like protein is an independent prognostic factor, which might activate the JAK-STAT signaling pathway, the P53 signaling pathway, the TGF-β signaling pathway, the WNT signaling pathway, etc., in clear cell renal cell carcinoma. Protein-protein interaction analysis and co-expression analysis suggest that cytoskeleton-associated protein 2-like protein might interact with some proliferation proteins. Immune infiltration analysis indicates that cytoskeleton-associated protein 2-like protein may affect the level of activated CD4+ memory T cells, M1 macrophages, CD8+ T cells, and neutrophils in clear cell renal cell carcinoma. More M1 macrophage infiltrations in tumor tissues with higher cytoskeleton-associated protein 2-like protein were validated by clear cell renal cell carcinoma tumor tissues. Conclusion: Cytoskeleton-associated protein 2-like protein is upregulated in clear cell renal cell carcinoma tissues, which may promote progression of the disease. Cytoskeleton-associated protein 2-like protein is a potential target for prognostic markers and a potential treatment target in clear cell renal cell carcinoma.
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Affiliation(s)
- Zhi Liu
- Department of Urology Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jun Zhang
- Department of Urinary Surgery, The 901st Hospital of the Joint Logistics Support Force of PLA, Hefei, Anhui, China
| | - Deyun Shen
- Department of Urology Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Xuechun Hu
- Department of Urology Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Zongpan Ke
- Department of Urology Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - I Nyoman Ehrich Lister
- Universitas Prima Indonesia (UNPRI), Medan, North Sumatra, Indonesia,*Correspondence: Bungaran Sihombing, ; I Nyoman Ehrich Lister,
| | - Bungaran Sihombing
- Universitas Prima Indonesia (UNPRI), Medan, North Sumatra, Indonesia,*Correspondence: Bungaran Sihombing, ; I Nyoman Ehrich Lister,
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Qu J, Shao C, Ying Y, Wu Y, Liu W, Tian Y, Yin Z, Li X, Yu Z, Shuai J. The spring-like effect of microRNA-31 in balancing inflammatory and regenerative responses in colitis. Front Microbiol 2022; 13:1089729. [PMID: 36590397 PMCID: PMC9800619 DOI: 10.3389/fmicb.2022.1089729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders caused by the disruption of immune tolerance to the gut microbiota. MicroRNA-31 (MIR31) has been proven to be up-regulated in intestinal tissues from patients with IBDs and colitis-associated neoplasias. While the functional role of MIR31 in colitis and related diseases remain elusive. Combining mathematical modeling and experimental analysis, we systematically explored the regulatory mechanism of MIR31 in inflammatory and epithelial regeneration responses in colitis. Level of MIR31 presents an "adaptation" behavior in dextran sulfate sodium (DSS)-induced colitis, and the similar behavior is also observed for the key cytokines of p65 and STAT3. Simulation analysis predicts MIR31 suppresses the activation of p65 and STAT3 but accelerates the recovery of epithelia in colitis, which are validated by our experimental observations. Further analysis reveals that the number of proliferative epithelial cells, which characterizes the inflammatory process and the recovery of epithelia in colitis, is mainly determined by the inhibition of MIR31 on IL17RA. MIR31 promotes epithelial regeneration in low levels of DSS-induced colitis but inhibits inflammation with high DSS levels, which is dominated by the competition for MIR31 to either inhibit inflammation or promote epithelial regeneration by binding to different targets. The binding probability determines the functional transformation of MIR31, but the functional strength is determined by MIR31 levels. Thus, the role of MIR31 in the inflammatory response can be described as the "spring-like effect," where DSS, MIR31 action strength, and proliferative epithelial cell number are regarded as external force, intrinsic spring force, and spring length, respectively. Overall, our study uncovers the vital roles of MIR31 in balancing inflammation and the recovery of epithelia in colitis, providing potential clues for the development of therapeutic targets in drug design.
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Affiliation(s)
- Jing Qu
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Chunlei Shao
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yongfa Ying
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Yuning Wu
- Department of Mathematics and Physics, Fujian Jiangxia University, Fuzhou, China
| | - Wen Liu
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Yuhua Tian
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhiyong Yin
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Xiang Li
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zhengquan Yu
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jianwei Shuai
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), University of Chinese Academy of Sciences, Wenzhou, China
- Wenzhou Institute, Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, China
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Zhang M, Meng L, Zhang Z, Wu J, Chen X, Wang Y, He J. The relationships of OSBPL3 expression with KI-67 expression and KRAS mutations in CRC: implications for diagnosis and prognosis. BMC Med Genomics 2022; 15:259. [PMID: 36517805 PMCID: PMC9753258 DOI: 10.1186/s12920-022-01402-w] [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: 12/19/2021] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND OSBPL3 is overexpressed in a variety of malignancies and is closely associated with tumor growth and metastasis. However, its expression and function in colorectal cancer (CRC) are unclear. We aimed to investigate its prognostic and therapeutic value in this disease by detecting its expression in CRC and its correlation with the clinicopathological characteristics and prognosis of patients. METHODS A total of 92 CRC samples were included in this study. According to the 2020 WHO diagnostic criteria, the criteria of the American Joint Committee on Cancer (AJCC) 8th edition staging system were used. OSBPL3 and Ki-67 expression in these samples was detected by immunohistochemistry. OSBPL3 mRNA expression was detected by qRT-PCR. KRAS/NRAS mutations were detected by an amplification refractory mutation system (ARMS). Data analysis was performed using the statistical analysis software Prism 8. RESULTS OSBPL3 was found to be significantly overexpressed in CRC tumor tissues and was associated with worse progression-free survival and overall survival in patients. Additionally, OSBPL3 expression was negatively correlated with the degree of tumor differentiation. KRAS mutations were detected in approximately 32.6% of patients and were significantly associated with high OSBPL3 expression. In addition, OSBPL3 and Ki-67 expression was significantly correlated. CONCLUSIONS OSBPL3 is highly expressed in CRC samples and predicts a worse prognosis. OSBPL3 may become a new potential therapeutic target for CRC.
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Affiliation(s)
- Min Zhang
- grid.59053.3a0000000121679639Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001 Anhui China
| | - Lei Meng
- grid.59053.3a0000000121679639Department of Gastrointestinal Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001 Anhui China
| | - Zhaoxuan Zhang
- grid.59053.3a0000000121679639Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001 Anhui China
| | - Jing Wu
- grid.59053.3a0000000121679639Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001 Anhui China
| | - Xi Chen
- grid.59053.3a0000000121679639Department of Gastrointestinal Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001 Anhui China
| | - Yuejing Wang
- grid.186775.a0000 0000 9490 772XAnhui Medical University, Hefei, Anhui China
| | - Jie He
- grid.59053.3a0000000121679639Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001 Anhui China
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Luo Y, Liu H, Fu H, Ding GS, Teng F. A cellular senescence-related classifier based on a tumorigenesis- and immune infiltration-guided strategy can predict prognosis, immunotherapy response, and candidate drugs in hepatocellular carcinoma. Front Immunol 2022; 13:974377. [PMID: 36458010 PMCID: PMC9705748 DOI: 10.3389/fimmu.2022.974377] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/25/2022] [Indexed: 09/05/2023] Open
Abstract
BACKGROUND Cellular senescence plays an irreplaceable role in tumorigenesis, progression, and tumor microenvironment (TME) remodeling. However, to date, there is limited research delineating the landscape of cellular senescence in hepatocellular carcinoma (HCC), and an improved understanding on the interaction of tumor-associated cellular senescence with HCC prognosis, TME, and response to immunotherapy is warrant. METHODS Tumorigenic and immune infiltration-associated senescence genes were determined by weighted gene co-expression network analysis (WGCNA) and the Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) algorithm, and subsequently, a prognostic scoring model (named TIS) was constructed using multiple survival analysis algorithms to classify the senescence-related subtypes of HCC. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were conducted to identify the distinct hallmark pathways between high- and low-risk subtypes. Additionally, we carried out correlation analyses for TIS and clinical traits, senescence-associated secretory phenotype (SASP), immune infiltration and evasion, immune checkpoint factors, drug response, and immunotherapeutic efficacy. External experimental validation was conducted to delineate the association of CPEP3 (a TIS gene) with HCC phenotypes through assays of proliferation, colony formation, and invasion. RESULTS A five-gene TIS, composed of NET1, ATP6V0B, MMP1, GTDC1, and CPEB3, was constructed and validated using TCGA and ICGC datasets, respectively, and showed a highly robust and plausible signature for overall survival (OS) prediction of HCC in both training and validation cohorts. Patients in the TIS-high group were accompanied by worse OS, activation of carcinogenetic pathways, infiltration of immunosuppressive cells, exclusion of effector killing cells, overexpression of immunomodulatory genes and SASP, and unsatisfied response to immunotherapy. In response to anticancer drugs, patients in the TIS-high group exhibited enhanced susceptibility to several conventional chemotherapeutic agents (5-fluorouracil, docetaxel, doxorubicin, gemcitabine, and etoposide), as well as several inhibitors of pathways involved in cellular senescence (cell-cycle inhibitors, bromodomain and extraterminal domain family (BET) inhibitors, PI3K-AKT pathway inhibitors, and multikinase inhibitors). Additionally, four putative drugs (palbociclib, JAK3 inhibitor VI, floxuridine, and lestaurtinib) were identified as potential compounds for patients in the TIS-high group. Notably, in vitro functional validation showed that CPEB3 knockdown boosted the phenotypes of proliferation, clonogenicity, and invasion in HCC cells, whereas CPEB3 overexpression attenuated these phenotypes. CONCLUSIONS Our study provides comprehensive clues demonstrating the role of novel TIS in predicting HCC prognosis, immunotherapeutic response, and candidate drugs. This work highlights the significance of tumorigenesis- and immune infiltration-related cellular senescence in cancer therapy.
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Affiliation(s)
- Yi Luo
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Hao Liu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Hong Fu
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Guo-Shan Ding
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Fei Teng
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai, China
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Lin L, Zeng X, Liang S, Wang Y, Dai X, Sun Y, Wu Z. Construction of a co-expression network and prediction of metastasis markers in colorectal cancer patients with liver metastasis. J Gastrointest Oncol 2022; 13:2426-2438. [PMID: 36388701 PMCID: PMC9660078 DOI: 10.21037/jgo-22-965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a common global malignancy associated with high invasiveness, high metastasis, and poor prognosis. CRC commonly metastasizes to the liver, where the treatment of metastasis is both difficult and an important topic in current CRC management. METHODS Microarrays data of human CRC with liver metastasis (CRCLM) were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database to identify potential key genes. Differentially expressed (DE) genes (DEGs) and DEmiRNAs of primary CRC tumor tissues and metastatic liver tissues were identified. Microenvironment Cell Populations (MCP)-counter was used to estimate the abundance of immune cells in the tumor micro-environment (TME), and weighted gene correlation network analysis (WGCNA) was used to construct the co-expression network analysis. Gene Ontology and Kyoto Encyclopaedia of Gene and Genome (KEGG) pathway enrichment analyses were conducted, and the protein-protein interaction (PPI) network for the DEGs were constructed and gene modules were screened. RESULTS Thirty-five pairs of matched colorectal primary cancer and liver metastatic gene expression profiles were screened, and 610 DEGs (265 up-regulated and 345 down-regulated) and 284 DEmiRNAs were identified. The DEGs were mainly enriched in the complement and coagulation cascade pathways and renin secretion. Immune infiltrating cells including neutrophils, monocytic lineage, and cancer-associated fibroblasts (CAFs) differed significantly between primary tumor tissues and metastatic liver tissues. WGCN analysis obtained 12 modules and identified 62 genes with significant interactions which were mainly related to complement and coagulation cascade and the focal adhesion pathway. The best subset regression analysis and backward stepwise regression analysis were performed, and eight genes were determined, including F10, FGG, KNG1, MBL2, PROC, SERPINA1, CAV1, and SPP1. Further analysis showed four genes, including FGG, KNG1, CAV1, and SPP1 were significantly associated with CRCLM. CONCLUSIONS Our study implies complement and coagulation cascade and the focal adhesion pathway play a significant role in the development and progression of CRCLM, and FGG, KNG1, CAV1, and SPP1 may be metastatic markers for its early diagnosis.
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Affiliation(s)
- Lihong Lin
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Xiuxiu Zeng
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Shanyan Liang
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Yunzhi Wang
- School of Health Sciences, University of Sydney, Lidcombe, NSW, Australia
| | - Xiaoyu Dai
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Yuechao Sun
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China;,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Zhou Wu
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
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18
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Genomic analysis of an aggressive case with metastatic intrahepatic mucinous cholangiocarcinoma. Clin J Gastroenterol 2022; 15:809-817. [PMID: 35699889 DOI: 10.1007/s12328-022-01649-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/22/2022] [Indexed: 12/09/2022]
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19
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Identification of co-expression hub genes for ferroptosis in kidney renal clear cell carcinoma based on weighted gene co-expression network analysis and The Cancer Genome Atlas clinical data. Sci Rep 2022; 12:4821. [PMID: 35314744 PMCID: PMC8938444 DOI: 10.1038/s41598-022-08950-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/15/2022] [Indexed: 12/14/2022] Open
Abstract
Renal clear cell carcinoma (KIRC) is one of the most common tumors worldwide and has a high mortality rate. Ferroptosis is a major mechanism of tumor occurrence and development, as well as important for prognosis and treatment of KIRC. Here, we conducted bioinformatics analysis to identify KIRC hub genes that target ferroptosis. By Weighted gene co-expression network analysis (WGCNA), 11 co-expression-related genes were screened out. According to Kaplan Meier's survival analysis of the data from the gene expression profile interactive analysis database, it was identified that the expression levels of two genes, PROM2 and PLIN2, are respectively related to prognosis. In conclusion, our findings indicate that PROM2 and PLIN2 may be effective new targets for the treatment and prognosis of KIRC.
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Liu T, Chen L, Gao G, Liang X, Peng J, Zheng M, Li J, Ye Y, Shao C. Development of a Gene Risk Signature for Patients of Pancreatic Cancer. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:4136825. [PMID: 35035831 PMCID: PMC8759853 DOI: 10.1155/2022/4136825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/25/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Pancreatic cancer is a highly malignant solid tumor with a high lethality rate, but there is a lack of clinical biomarkers that can assess patient prognosis to optimize treatment. METHODS Gene-expression datasets of pancreatic cancer tissues and normal pancreatic tissues were obtained from the GEO database, and differentially expressed genes analysis and WGCNA analysis were performed after merging and normalizing the datasets. Univariate Cox regression analysis and Lasso Cox regression analysis were used to screen the prognosis-related genes in the modules with the strongest association with pancreatic cancer and construct risk signatures. The performance of the risk signature was subsequently validated by Kaplan-Meier curves, receiver operating characteristic (ROC), and univariate and multivariate Cox analyses. RESULT A three-gene risk signature containing CDKN2A, BRCA1, and UBL3 was established. Based on KM curves, ROC curves, and univariate and multivariate Cox regression analyses in the TRAIN cohort and TEST cohort, it was suggested that the three-gene risk signature had better performance in predicting overall survival. CONCLUSION This study identifies a three-gene risk signature, constructs a nomogram that can be used to predict pancreatic cancer prognosis, and identifies pathways that may be associated with pancreatic cancer prognosis.
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Affiliation(s)
- Tao Liu
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
- Department of Hepatobiliary Surgery, Heze Municipal Hospital, No. 2888, Caozhou Road, Mudan District, Heze 274000, Shandong, China
| | - Long Chen
- Department of Gastrointestinal Surgery, Heze Municipal Hospital, No. 2888, Caozhou Road, Mudan District, Heze 274000, Shandong, China
| | - Guili Gao
- Department of Cardiology, Heze Municipal Hospital, No. 2888, Caozhou Road, Mudan District, Heze 274000, Shandong, China
| | - Xing Liang
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Junfeng Peng
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Minghui Zheng
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Judong Li
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Yongqiang Ye
- Department of Hepatobiliary Surgery, Heze Municipal Hospital, No. 2888, Caozhou Road, Mudan District, Heze 274000, Shandong, China
| | - Chenghao Shao
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
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Chi F, Chen L, Jin X, He G, Liu Z, Han S. CKAP2L, transcriptionally inhibited by FOXP3, promotes breast carcinogenesis through the AKT/mTOR pathway. Exp Cell Res 2022; 412:113035. [DOI: 10.1016/j.yexcr.2022.113035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 12/26/2022]
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Abstract
Almost 25 years have passed since a mutation of a formin gene, DIAPH1, was identified as being responsible for a human inherited disorder: a form of sensorineural hearing loss. Since then, our knowledge of the links between formins and disease has deepened considerably. Mutations of DIAPH1 and six other formin genes (DAAM2, DIAPH2, DIAPH3, FMN2, INF2 and FHOD3) have been identified as the genetic cause of a variety of inherited human disorders, including intellectual disability, renal disease, peripheral neuropathy, thrombocytopenia, primary ovarian insufficiency, hearing loss and cardiomyopathy. In addition, alterations in formin genes have been associated with a variety of pathological conditions, including developmental defects affecting the heart, nervous system and kidney, aging-related diseases, and cancer. This review summarizes the most recent discoveries about the involvement of formin alterations in monogenic disorders and other human pathological conditions, especially cancer, with which they have been associated. In vitro results and experiments in modified animal models are discussed. Finally, we outline the directions for future research in this field.
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Affiliation(s)
| | - Miguel A. Alonso
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain;
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