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Kalyanakrishnan K, Beaudin A, Jetté A, Ghezelbash S, Hotea DI, Chen J, Lefrançois P, Laurin M. ARHGEF3 Regulates Hair Follicle Morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.13.612256. [PMID: 39314354 PMCID: PMC11419159 DOI: 10.1101/2024.09.13.612256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
During embryogenesis, cells arrange into precise patterns that enable tissues and organs to develop specialized functions. Despite its critical importance, the molecular choreography behind these collective cellular behaviors remains elusive, posing a major challenge in developmental biology and limiting advances in regenerative medicine. By using the mouse hair follicle as a mini-organ system to study the formation of bud-like structures during embryonic development, our work uncovers a crucial role for the Rho GTPase regulator ARHGEF3 in hair follicle morphogenesis. We demonstrate that Arhgef3 expression is upregulated at the onset of hair follicle placode formation. In Arhgef3 knockout animals, we observed defects in placode compaction, leading to impaired hair follicle downgrowth. Through cell culture models, we show that ARHGEF3 promotes F-actin accumulation at the cell cortex and P-cadherin enrichment at cell-cell junctions. Collectively, our study identifies ARHGEF3 as a new regulator of cell shape rearrangements during hair placode morphogenesis, warranting further exploration of its role in other epithelial appendages that arise from similar developmental processes.
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Affiliation(s)
- Krithika Kalyanakrishnan
- Centre de recherche du CHU de Québec - Université Laval, axe Oncologie, Québec, Canada
- Programme de biologie moléculaire et cellulaire, Université Laval
- Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval
- Faculté de médecine, Université Laval
- Centre de recherche sur le cancer de l'Université Laval (CRC)
- Centre de recherche en organogénèse expérimentale (LOEX)
| | - Amy Beaudin
- Centre de recherche du CHU de Québec - Université Laval, axe Oncologie, Québec, Canada
- Programme de biologie moléculaire et cellulaire, Université Laval
- Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval
- Faculté de médecine, Université Laval
- Centre de recherche sur le cancer de l'Université Laval (CRC)
- Centre de recherche en organogénèse expérimentale (LOEX)
| | - Alexandra Jetté
- Centre de recherche du CHU de Québec - Université Laval, axe Oncologie, Québec, Canada
- Centre de recherche sur le cancer de l'Université Laval (CRC)
- Centre de recherche en organogénèse expérimentale (LOEX)
| | - Sarah Ghezelbash
- Cancer Axis, Lady Davis Institute for Medical Research, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Québec, Canada
| | - Diana Ioana Hotea
- Centre de recherche du CHU de Québec - Université Laval, axe Oncologie, Québec, Canada
- Programme de biologie moléculaire et cellulaire, Université Laval
- Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval
- Faculté de médecine, Université Laval
- Centre de recherche sur le cancer de l'Université Laval (CRC)
- Centre de recherche en organogénèse expérimentale (LOEX)
| | - Jie Chen
- Department of Cell & Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61801
| | - Philippe Lefrançois
- Cancer Axis, Lady Davis Institute for Medical Research, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Québec, Canada
- Division of Dermatology, Department of Medicine, McGill University, Montréal, QC, Canada
| | - Mélanie Laurin
- Centre de recherche du CHU de Québec - Université Laval, axe Oncologie, Québec, Canada
- Programme de biologie moléculaire et cellulaire, Université Laval
- Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval
- Faculté de médecine, Université Laval
- Centre de recherche sur le cancer de l'Université Laval (CRC)
- Centre de recherche en organogénèse expérimentale (LOEX)
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Zhu D, Yang J, Zhang M, Han Z, Shao M, Fan Q, Ma Y, Xie D, Xiao W. Identification of neoantigens and immunological subtypes in clear cell renal cell carcinoma for mRNA vaccine development and patient selection. Aging (Albany NY) 2023; 15:204798. [PMID: 37315301 PMCID: PMC10292886 DOI: 10.18632/aging.204798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 05/26/2023] [Indexed: 06/16/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a common urological malignancy with diverse histological types. This study aimed to detect neoantigens in ccRCC to develop mRNA vaccines and distinguish between ccRCC immunological subtypes for construction of an immune landscape to select patients suitable for vaccination. Using The Cancer Genome Atlas SpliceSeq database, The Cancer Genome Atlas, and the International Cancer Genome Consortium cohorts, we comprehensively analysed potential tumour antigens of ccRCC associated with aberrant alternative splicing, somatic mutation, nonsense-mediated mRNA decay factors, antigen-presenting cells, and overall survival. Immune subtypes (C1/C2) and nine immune gene modules of ccRCC were identified by consistency clustering and weighted correlation network analysis. The immune landscape as well as molecular and cellular characteristics of immunotypes were assessed. Rho-guanine nucleotide exchange factor 3 (ARHGEF3) was identified as a new ccRCC antigen for development of an mRNA vaccine. A higher tumour mutation burden, differential expression of immune checkpoints, and immunogenic cell death were observed in cases with the C2 immunotype. Cellular characteristics increased the complexity of the immune environment, and worse outcomes were observed in ccRCC cases with the C2 immunotype. We constructed the immune landscape for selecting patients with the C2 immunotype suitable for vaccination.
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Affiliation(s)
- Daoqi Zhu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Jiabin Yang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Minyi Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Zhongxiao Han
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Meng Shao
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Qin Fan
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Yun Ma
- Department of pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Dandan Xie
- The Affiliated TCM Hospital of Guangzhou Medical University, Guangzhou 510130, Guangdong, China
| | - Wei Xiao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, Guangdong, China
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ARHGEF3 regulates the stability of ACLY to promote the proliferation of lung cancer. Cell Death Dis 2022; 13:870. [PMID: 36241648 PMCID: PMC9568610 DOI: 10.1038/s41419-022-05297-4] [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: 05/28/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/18/2022]
Abstract
Rho GTPases play an essential role in many cellular processes, including cell cycle progress, cell motility, invasion, migration, and transformation. Several studies indicated that the dysregulation of Rho GTPase signaling is closely related to tumorigenesis. Rho GEFs considered being positive regulators of Rho GTPase, promoting the dissociation of Rho protein from GDP and binding to GTP, thus activating the downstream signaling pathway. Herein, we demonstrated that ARHGEF3, a member of the Rho GEFs family, played an important role in non-small cell lung cancer (NSCLC). We found that ARHGEF3 was highly expressed in non-small cell lung cancer and facilitated cancer cell proliferation of NSCLC cells in vitro and in vivo. Further studies demonstrated that ARHGEF3 enhanced the protein homeostasis of ATP-citrate lyase (ACLY) by reducing its acetylation on Lys17 and Lys86, leading to the dissociation between ACLY and its E3 ligase-NEDD4. Interestingly, this function of ARHGEF3 on the protein homeostasis of ACLY was independent of its GEF activity. Taken together, our findings uncover a novel function of ARHGEF3, suggesting that ARHGEF3 is a promising therapeutic target in non-small cell lung cancer.
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Zhang Z, Xiang S, Cui R, Peng H, Mridul R, Xiang M. ILP-2: A New Bane and Therapeutic Target for Human Cancers. Front Oncol 2022; 12:922596. [PMID: 35814477 PMCID: PMC9260022 DOI: 10.3389/fonc.2022.922596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
Inhibitor of apoptosis protein-related-like protein-2 (ILP-2), also known as BIRC-8, is a member of the inhibitor of apoptosis protein (IAPs) family, which mainly encodes the negative regulator of apoptosis. It is selectively overexpressed in a variety of human tumors and can help tumor cells evade apoptosis, promote tumor cell growth, increase tumor cell aggressiveness, and appears to be involved in tumor cell resistance to chemotherapeutic drugs. Several studies have shown that downregulation of ILP-2 expression increases apoptosis, inhibits metastasis, reduces cell growth potential, and sensitizes tumor cells to chemotherapeutic drugs. In addition, ILP-2 inhibits apoptosis in a unique manner; it does not directly inhibit the activity of caspases but induces apoptosis by cooperating with other apoptosis-related proteins. Here, we review the current understanding of the various roles of ILP-2 in the apoptotic cascade and explore the use of interfering ILP-2, and the combination of related anti-tumor agents, as a novel strategy for cancer therapy.
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Affiliation(s)
- Zhiliang Zhang
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Siqi Xiang
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Ruxia Cui
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Hang Peng
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Roy Mridul
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Mingjun Xiang
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
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Liang X, Wang Y, Pei L, Tan X, Dong C. Identification of Prostate Cancer Risk Genetics Biomarkers Based on Intergraded Bioinformatics Analysis. Front Surg 2022; 9:856446. [PMID: 35372462 PMCID: PMC8967941 DOI: 10.3389/fsurg.2022.856446] [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: 01/17/2022] [Accepted: 02/09/2022] [Indexed: 12/04/2022] Open
Abstract
Background Prostate cancer (PCa) is one of the most popular cancer types in men. Nevertheless, the pathogenic mechanisms of PCa are poorly understood. Hence, we aimed to identify the potential genetic biomarker of PCa in the present study. Methods High-throughput data set GSE46602 was obtained from the comprehensive gene expression database (GEO) for screening differentially expressed genes (DEGs). The common DEGs were further screened out using The Cancer Genome Atlas (TCGA) dataset. Functional enrichment analysis includes Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to study related mechanisms. The Cox and Lasso regression analyses were carried out to compress the target genes and construct the high-risk and low-risk gene model. Survival analyses were performed based on the gene risk signature model. The CIBERSORT algorithm was performed to clarify the correlation of the high- and low-risk gene model in risk and infiltration of immune cells in PCa. Results A total of 385 common DEGs were obtained. The results of functional enrichment analysis show that common DEGs play an important role in PCa. A three-gene signature model (KCNK3, AK5, and ARHGEF38) was established, and the model was significantly associated with cancer-related pathways, overall survival (OS), and tumor microenvironment (TME)-related immune cells in PCa. Conclusion This new risk model may contribute to further investigation in the immune-related pathogenesis in progression of PCa.
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Affiliation(s)
| | | | | | | | - Chunhui Dong
- Department of Urology, The Fourth Hospital of Hebei Medical University, Shijiahzuang, China
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Yoon J, Kumar V, Goutam RS, Kim SC, Park S, Lee U, Kim J. Bmp Signal Gradient Modulates Convergent Cell Movement via Xarhgef3.2 during Gastrulation of Xenopus Embryos. Cells 2021; 11:44. [PMID: 35011606 PMCID: PMC8750265 DOI: 10.3390/cells11010044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 01/31/2023] Open
Abstract
Gastrulation is a critical step in the establishment of a basic body plan during development. Convergence and extension (CE) cell movements organize germ layers during gastrulation. Noncanonical Wnt signaling has been known as major signaling that regulates CE cell movement by activating Rho and Rac. In addition, Bmp molecules are expressed in the ventral side of a developing embryo, and the ventral mesoderm region undergoes minimal CE cell movement while the dorsal mesoderm undergoes dynamic cell movements. This suggests that Bmp signal gradient may affect CE cell movement. To investigate whether Bmp signaling negatively regulates CE cell movements, we performed microarray-based screening and found that the transcription of Xenopus Arhgef3.2 (Rho guanine nucleotide exchange factor) was negatively regulated by Bmp signaling. We also showed that overexpression or knockdown of Xarhgef3.2 caused gastrulation defects. Interestingly, Xarhgef3.2 controlled gastrulation cell movements through interacting with Disheveled (Dsh2) and Dsh2-associated activator of morphogenesis 1 (Daam1). Our results suggest that Bmp gradient affects gastrulation cell movement (CE) via negative regulation of Xarhgef3.2 expression.
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Affiliation(s)
- Jaeho Yoon
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 24252, Korea; (J.Y.); (V.K.); (R.S.G.); (S.-C.K.)
- National Cancer Institute, Frederick, MD 21702, USA
| | - Vijay Kumar
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 24252, Korea; (J.Y.); (V.K.); (R.S.G.); (S.-C.K.)
| | - Ravi Shankar Goutam
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 24252, Korea; (J.Y.); (V.K.); (R.S.G.); (S.-C.K.)
| | - Sung-Chan Kim
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 24252, Korea; (J.Y.); (V.K.); (R.S.G.); (S.-C.K.)
| | - Soochul Park
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea;
| | - Unjoo Lee
- Department of Electrical Engineering, Hallym University, Chuncheon 24252, Korea;
| | - Jaebong Kim
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 24252, Korea; (J.Y.); (V.K.); (R.S.G.); (S.-C.K.)
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ARHGEF3 Associated with Invasion, Metastasis, and Proliferation in Human Osteosarcoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:3381957. [PMID: 34350290 PMCID: PMC8328732 DOI: 10.1155/2021/3381957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/08/2021] [Indexed: 11/23/2022]
Abstract
Background Osteosarcoma is a malignant bone tumor composed of mesenchymal cells producing osteoid and immature bone. This study is aimed at developing novel potential prognostic biomarkers and constructing a miRNA-mRNA network for progression in osteosarcoma. Method GSE70367 and GSE70414 were obtained in the Gene Expression Omnibus (GEO) database. GEO software and the GEO2R calculation method were used to analyze two gene profiles. The coexpression of differentially expressed miRNAs (DEMs) and genes (DEGs) was identified and searched for in the FunRich database for pathway and ontology analysis. Cytoscape was utilized to construct the mRNA-miRNA network. Survival analysis of identified miRNAs and mRNAs was performed by utilizing the Kaplan-Meier Plotter. Besides, expression levels of DEMs and target mRNAs were verified by performing quantitative real-time PCR (qRT-PCR) and Western blot (WB). Results Six differentially expressed microRNAs (DEMs) were identified, and 8 target genes were selected after screening. By using the KM Plotter software, miRNA-124 and ARHGEF3 were obviously associated with the overall survival of patients with osteosarcoma. Furthermore, ARHGEF3 was found downregulated in osteosarcoma cells by performing qRT-PCR and WB experiments. Results also showed that downregulated ARHGEF3 may associate with invasion, metastasis, and proliferation. Conclusions By using microarray and bioinformatics analysis, DEMs were selected, and a complete miRNA-mRNA network was constructed. ARHGEF3 may act as a therapeutic and prognostic target of osteosarcoma.
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Loss of the MAF Transcription Factor in Laryngeal Squamous Cell Carcinoma. Biomolecules 2021; 11:biom11071035. [PMID: 34356658 PMCID: PMC8301809 DOI: 10.3390/biom11071035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 12/24/2022] Open
Abstract
MAF is a transcription factor that may act either as a tumor suppressor or as an oncogene, depending on cell type. We have shown previously that the overexpressed miR-1290 influences MAF protein levels in LSCC (laryngeal squamous cell carcinoma) cell lines. In this study, we shed further light on the interaction between miR-1290 and MAF, as well as on cellular MAF protein localization in LSCC. We confirmed the direct interaction between miR-1290 and MAF 3′UTR by a dual-luciferase reporter assay. In addition, we used immunohistochemistry staining to analyze MAF protein distribution and observed loss of MAF nuclear expression in 58% LSCC samples, of which 10% showed complete absence of MAF, compared to nuclear and cytoplasmatic expression in 100% normal mucosa. Using TCGA data, bisulfite pyrosequencing and CNV analysis, we excluded the possibility that loss-of-function mutations, promoter region DNA methylation or CNV are responsible for MAF loss in LSCC. Finally, we identified genes involved in the regulation of apoptosis harboring the MAF binding motif in their promoter region by applied FIMO and DAVID GO analysis. Our results highlight the role of miR-1290 in suppressing MAF expression in LSCC. Furthermore, MAF loss or mislocalization in FFPE LSCC tumor samples might suggest that MAF acts as a LSCC tumor suppressor by regulating apoptosis.
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Genetic risk factors for colorectal cancer in multiethnic Indonesians. Sci Rep 2021; 11:9988. [PMID: 33976257 PMCID: PMC8113452 DOI: 10.1038/s41598-021-88805-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/14/2021] [Indexed: 11/09/2022] Open
Abstract
Colorectal cancer is a common cancer in Indonesia, yet it has been understudied in this resource-constrained setting. We conducted a genome-wide association study focused on evaluation and preliminary discovery of colorectal cancer risk factors in Indonesians. We administered detailed questionnaires and collecting blood samples from 162 colorectal cancer cases throughout Makassar, Indonesia. We also established a control set of 193 healthy individuals frequency matched by age, sex, and ethnicity. A genome-wide association analysis was performed on 84 cases and 89 controls passing quality control. We evaluated known colorectal cancer genetic variants using logistic regression and established a genome-wide polygenic risk model using a Bayesian variable selection technique. We replicate associations for rs9497673, rs6936461 and rs7758229 on chromosome 6; rs11255841 on chromosome 10; and rs4779584, rs11632715, and rs73376930 on chromosome 15. Polygenic modeling identified 10 SNP associated with colorectal cancer risk. This work helps characterize the relationship between variants in the SCL22A3, SCG5, GREM1, and STXBP5-AS1 genes and colorectal cancer in a diverse Indonesian population. With further biobanking and international research collaborations, variants specific to colorectal cancer risk in Indonesians will be identified.
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Wang Y, Jiang Q, Cai H, Xu Z, Wu W, Gu B, Li L, Cai W. Genetic variants in RET, ARHGEF3 and CTNNAL1, and relevant interaction networks, contribute to the risk of Hirschsprung disease. Aging (Albany NY) 2020; 12:4379-4393. [PMID: 32139661 PMCID: PMC7093166 DOI: 10.18632/aging.102891] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 02/25/2020] [Indexed: 12/18/2022]
Abstract
Hirschsprung disease (HSCR), the most common enteric neuropathy, stands as a model for complex genetic disorders. It has recently been demonstrated that both ARHGEF3 and CTNNAL1 map to the RET-dependent HSCR susceptibility loci. We therefore sought to explore whether genetic variants within RET, ARHGEF3 and CTNNAL1, and their genetic interaction networks are associated with HSCR. Taking advantage of a strategy that combined the MassArray system and gene-gene interaction analysis with case-control study, we interrogated 38 polymorphisms within RET, ARHGEF3 and CTNNAL1 in 1015 subjects (502 HSCR cases and 513 controls) of Han Chinese origin. There were statistically significant associations between 20 genetic variants in these three genes and HSCR. Haplotype analysis also revealed some significant global P values, i.e. RET_ rs2435357-rs752978-rs74400468-rs2435353-rs2075913-rs17028-rs2435355 (P = 3.79×10-58). Using the MDR and GeneMANIA platforms, we found strong genetic interactions among RET, ARHGEF3, and CTNNAL1 and our previously studied GAL, GAP43, NRSN1, PTCH1, GABRG2 and RELN genes. These results offer the first indication that genetic markers of RET, ARHGEF3 and CTNNAL1 and relevant genetic interaction networks confer the altered risk to HSCR in the Han Chinese population.
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Affiliation(s)
- Yang Wang
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Qian Jiang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, China
| | - Hao Cai
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Ze Xu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wenjie Wu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Beilin Gu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Long Li
- Department of General Surgery, Capital Institute of Pediatrics Affiliated Children's Hospital, Beijing, China
| | - Wei Cai
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
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Yang Z, Deng J, Li D, Sun T, Xia L, Xu W, Zeng L, Jiang H, Yang X. Analysis of Population Structure and Differentially Selected Regions in Guangxi Native Breeds by Restriction Site Associated with DNA Sequencing. G3 (BETHESDA, MD.) 2020; 10:379-386. [PMID: 31744899 PMCID: PMC6945025 DOI: 10.1534/g3.119.400827] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023]
Abstract
Guangxi indigenous chicken breeds play a very important role in promoting the high-quality development of the broiler industry in China. However, studies on genomic information of Guangxi indigenous chicken to date remain poorly explored. To decipher the population genetic structure and differentially selected regions (DSRs) in Guangxi indigenous chickens, we dug into numerous SNPs from seven Guangxi native chickens (GX) by employing the restriction site associated with DNA sequencing (RAD-seq) technology. Another three breeds, Cobb, White Leghorn, and Chahua (CH) chicken, were used as a control. After quality control, a total of 185,117 autosomal SNPs were kept for further analysis. The results showed a significant difference in population structure, and the control breeds were distinctly separate from the Guangxi native breeds, which was also strongly supported by the phylogenetic tree. Distribution of FST indicated that there were three SNPs with big genetic differentiation (FST value all reach to 0. 9427) in GX vs. CH group, which were located on chr1-96,859,720,chr4-86,139,601, and chr12-8,128,322, respectively. Besides, we identified 717 DSRs associated with 882 genes in GX vs. Cobb group, 769 DSRs with 476 genes in GX vs. Leghorn group, and 556 DSRs with 779 genes in GX vs. CH group. GO enrichment showed that there were two significant terms, namely GPI-linked ephrin receptor activity and BMP receptor binding, which were enriched in GX vs. Leghorn group. In conclusion, this study suggests that Guangxi native chickens have a great differentiation with Cobb and Leghorn. Our findings would be beneficial to fully evaluate the genomic information on Guangxi native chicken and facilitate the application of these resources in chicken breeding.
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Affiliation(s)
- Zhuliang Yang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China,
| | - Jixian Deng
- Guangxi Institute of Animal Science, Nanning, 530001, China, and
| | - Dongfeng Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tiantian Sun
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Li Xia
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Wenwen Xu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Linghu Zeng
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Hesheng Jiang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Xiurong Yang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China,
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Joyner C, McMahan C, Baurley J, Pardamean B. A two-phase Bayesian methodology for the analysis of binary phenotypes in genome-wide association studies. Biom J 2019; 62:191-201. [PMID: 31482590 DOI: 10.1002/bimj.201900050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 06/10/2019] [Accepted: 07/11/2019] [Indexed: 11/06/2022]
Abstract
Recent advances in sequencing and genotyping technologies are contributing to a data revolution in genome-wide association studies that is characterized by the challenging large p small n problem in statistics. That is, given these advances, many such studies now consider evaluating an extremely large number of genetic markers (p) genotyped on a small number of subjects (n). Given the dimension of the data, a joint analysis of the markers is often fraught with many challenges, while a marginal analysis is not sufficient. To overcome these obstacles, herein, we propose a Bayesian two-phase methodology that can be used to jointly relate genetic markers to binary traits while controlling for confounding. The first phase of our approach makes use of a marginal scan to identify a reduced set of candidate markers that are then evaluated jointly via a hierarchical model in the second phase. Final marker selection is accomplished through identifying a sparse estimator via a novel and computationally efficient maximum a posteriori estimation technique. We evaluate the performance of the proposed approach through extensive numerical studies, and consider a genome-wide application involving colorectal cancer.
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Affiliation(s)
- Chase Joyner
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC, USA
| | - Christopher McMahan
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC, USA.,Bioinformatics and Data Science Research Center, Bina Nusantara University, Kebon Jeruk, Indonesia
| | - James Baurley
- BioRealm LLC, Walnut, CA, USA.,Bioinformatics and Data Science Research Center, Bina Nusantara University, Kebon Jeruk, Indonesia
| | - Bens Pardamean
- Bioinformatics and Data Science Research Center, Bina Nusantara University, Kebon Jeruk, Indonesia
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Farhat F, Daulay ER, Chrestella J, Asnir RA, Yudhistira A, Susilo RR. Correlation of P38 Mitogen-Activated Protein Kinase Expression to Clinical Stage in Nasopharyngeal Carcinoma. Open Access Maced J Med Sci 2018; 6:1982-1985. [PMID: 30559847 PMCID: PMC6290411 DOI: 10.3889/oamjms.2018.355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/04/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is uncommon and usually diagnosed at the advanced stage. A subfamily of mitogen-activated protein kinase which is called p38 mitogen-activated protein kinase (MAPK) involved in response to stress, and plays an important role in cell regulation. There is a suggestion that p38 mitogen-activated protein kinase could be a potential biomarker to determine the clinical stage of nasopharyngeal carcinoma. AIM The aim of this study is for observing and analysing the correlation of p38 mitogen-activated protein kinase expression in regards to nasopharyngeal carcinoma patient's clinical stage. METHODS This study involved 126 nasopharyngeal carcinoma patients admitted to Haji Adam Malik General Hospital. RESULTS The result of this study indicates that nasopharyngeal carcinoma mostly found in the age group 41-60 years, male, non-keratinizing squamous cell carcinoma, and stage IV group. In immunohistochemistry evaluation, most of p38 mitogen-activated protein kinase overexpressed in non-keratinizing squamous cell carcinoma, T3-T4, N2-N3 and clinical stage III-IV. Spearman's test for categorical correlation yield p-value of < 0.001. CONCLUSION In conclusion, there is a significant correlation between p38 mitogen-activated protein kinase expression and the clinical stage of nasopharyngeal carcinoma.
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Affiliation(s)
- Farhat Farhat
- Universitas Sumatera Utara Fakultas Kedokteran, Otorhynolaryngology Head and Neck Surgery Jl. Dr. T. Mansyur No. 9, Medan, North Sumatera 20155, Indonesia
| | - Elvita Rahmi Daulay
- Universitas Sumatera Utara Fakultas Kedokteran, Radiology Medan, North Sumatera, Indonesia
| | - Jessy Chrestella
- Universitas Sumatera Utara Fakultas Kedokteran, Pathology Medan, Sumatera Utara, Indonesia
| | - Rizalina Arwinati Asnir
- Universitas Sumatera Utara Fakultas Kedokteran, Otorhynolaryngology Head and Neck Surgery Jl. Dr. T. Mansyur No. 9, Medan, North Sumatera 20155, Indonesia
| | - Ashri Yudhistira
- Universitas Sumatera Utara Fakultas Kedokteran, Otorhynolaryngology Head and Neck Surgery Jl. Dr. T. Mansyur No. 9, Medan, North Sumatera 20155, Indonesia
| | - Riko Radityatama Susilo
- Universitas Sumatera Utara Fakultas Kedokteran, Otorhynolaryngology Head and Neck Surgery Jl. Dr. T. Mansyur No. 9, Medan, North Sumatera 20155, Indonesia
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Isolation of cancer cells with augmented spheroid-forming capability using a novel tool equipped with removable filter. Oncotarget 2018; 9:33931-33946. [PMID: 30338036 PMCID: PMC6188051 DOI: 10.18632/oncotarget.26092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 08/27/2018] [Indexed: 12/12/2022] Open
Abstract
Three-dimensional (3D) cell culture systems have been used to obtain multicellular spheroidal cell aggregates, or spheroids, from cancer cells. However, it is difficult to efficiently prepare large tumor-derived spheroids from cancer cells. To circumvent this problem, we here used a tool equipped with removal membrane, called Spheroid Catch, for the selection and enrichment of large-sized and/or size-matched spheroids from human squamous cell carcinoma (SAS cells) without loss of recovery. After a five-round process of selection and enrichment, we successfully isolated a subpopulation of SAS cells with augmented spheroid-forming capability, named eSAS: the efficiency of spheroid formation is 28.5% (eSAS) vs 16.8% (parental SAS). Notably, we found that some of eSAS cells survived after exposure of high doses of cisplatin in 3D culture. Moreover, orthotopic implantation by injecting eSAS cells into the tongues of nude mice showed reduced survival rate and increased tumor growth compared with those of nude mice injected with SAS cells. These results suggest that spheroids exhibiting properties of higher spheroid forming capacity can be efficiently collected by using Spheroid Catch. Indeed, genome-wide cDNA microarray and western blot analyses demonstrated higher mRNA and protein levels of hedgehog acyltransferase (HHAT), which is associated with stem maintenance in cell carcinoma by catalysing the N-palmitoylation of Hedgehog proteins, in eSAS cells than in SAS cells. We propose that Spheroid Catch could be useful for the study of spheroids, and potentially organoids, in the basic and clinical sciences, as an alternative method to other type of cell strainers.
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Wen X, Tang X, Li Y, Ren X, He Q, Yang X, Zhang J, Wang Y, Ma J, Liu N. Microarray Expression Profiling of Long Non-Coding RNAs Involved in Nasopharyngeal Carcinoma Metastasis. Int J Mol Sci 2016; 17:ijms17111956. [PMID: 27886062 PMCID: PMC5133950 DOI: 10.3390/ijms17111956] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/15/2016] [Accepted: 11/15/2016] [Indexed: 11/24/2022] Open
Abstract
Increasing evidence has demonstrated a significant role for long non-coding RNAs (lncRNAs) in tumorigenesis. However, their functions in nasopharyngeal carcinoma (NPC) metastasis remain largely unknown. In this study, a model comparing high and low metastatic NPC cell lines (5-8F vs. 6-10B and S18 vs. S26) was constructed to determine the expression profile of lncRNAs using the microarray analysis, and we found 167 lncRNAs and 209 mRNAs were differentially expressed. Bioinformatic analysis indicated that the dysregulated mRNAs participated in important biological regulatory functions in NPC. Validation of 26 significantly dysregulated lncRNAs by qRT-PCR showed the expression patterns of 22 lncRNAs were in accordance with the microarray data. Furthermore, the expression level of ENST00000470135, which was the most upregulated lncRNA in high metastatic cell lines, was significantly higher in NPC cell lines and tissues with lymph node metastasis (LNM) and knocking down ENST00000470135 suppressed the migration, invasion and proliferation of NPC cells in vitro. In conclusion, our study revealed expression patterns of lncRNAs in NPC metastasis. The dysregulated lncRNAs may act as novel biomarkers and therapeutic targets for NPC.
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Affiliation(s)
- Xin Wen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, China.
| | - Xinran Tang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, China.
| | - Yingqin Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, China.
| | - Xianyue Ren
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, China.
| | - Qingmei He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, China.
| | - Xiaojing Yang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, China.
| | - Jian Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, China.
| | - Yaqin Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, China.
| | - Jun Ma
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, China.
| | - Na Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, China.
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