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Gangwar PK, Sankhwar SN, Pant S, Singh BP, Mahdi AA, Singh R. Male infertility is not liked with HSF1, HSF2 and UBE2I gene polymorphisms among Indian subjects. Bioinformation 2021; 17:715-720. [PMID: 35540693 PMCID: PMC9049099 DOI: 10.6026/97320630017715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 11/23/2022] Open
Abstract
We analysed the polymorphisms at rs78202224 (C/A) for HSF1 gene, rs139496713 (C/T) and rs45504694 (C/A) for HSF2 gene and rs116868327 (G/A) for UBE2I gene in 547 infertile cases (non-obstructive azoospermia = 464, asthenozoospermia = 83) and 419 proven fertile controls of similar age group and ethnicity. SNP genotyping was done using AgenaMassARRY platform (Agena Bioscience, CA). Common, heterozygous, rare genotypes and allelic frequencies were analysed using dominant, recessive and co-dominant models. Data shows no significant association between HSF1, HSF2 polymorphisms and male infertility. However, under dominant (GG vs GA+AA) and co-dominanat (GG vs GA) model, polymorphism at the rs116868327 (G/A) locus in UBE2I gene was found to be linked with asthenozoospermia in males with a significant odd-ratio of 6.91 (confidence interval at 95% was 1.52-31.46; p=0.017). Moreover, frequency of rare allele was higher (2.4%) compared to controls (0.4%). Thus, this data showed a significant risk of developing asthenozoospermic condition in males (Odds ratio= 6.75; Confidence interval at 95%= 1.50-30.49; P= 0.018]. Hence, more number of genotyping studies along with the functional assay in multiple cohorts is needed to validate potential variants associated with male infertility.
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Affiliation(s)
- Pravin Kumar Gangwar
- Department of Urology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | | | - Shriya Pant
- Department of Urology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Bhupendra Pal Singh
- Department of Urology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Abbas Ali Mahdi
- Department of Biochemistry, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Rajender Singh
- Division of Endocrinology, Central Drug Research Institute, Lucknow, Uttar Pradesh, India
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Li Y, Liu D, Li T, Zhu Y. Bayesian differential analysis of gene regulatory networks exploiting genetic perturbations. BMC Bioinformatics 2020; 21:12. [PMID: 31918656 PMCID: PMC6953167 DOI: 10.1186/s12859-019-3314-3] [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: 05/07/2019] [Accepted: 12/12/2019] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Gene regulatory networks (GRNs) can be inferred from both gene expression data and genetic perturbations. Under different conditions, the gene data of the same gene set may be different from each other, which results in different GRNs. Detecting structural difference between GRNs under different conditions is of great significance for understanding gene functions and biological mechanisms.
Results
In this paper, we propose a Bayesian Fused algorithm to jointly infer differential structures of GRNs under two different conditions. The algorithm is developed for GRNs modeled with structural equation models (SEMs), which makes it possible to incorporate genetic perturbations into models to improve the inference accuracy, so we name it BFDSEM. Different from the naive approaches that separately infer pair-wise GRNs and identify the difference from the inferred GRNs, we first re-parameterize the two SEMs to form an integrated model that takes full advantage of the two groups of gene data, and then solve the re-parameterized model by developing a novel Bayesian fused prior following the criterion that separate GRNs and differential GRN are both sparse.
Conclusions
Computer simulations are run on synthetic data to compare BFDSEM to two state-of-the-art joint inference algorithms: FSSEM and ReDNet. The results demonstrate that the performance of BFDSEM is comparable to FSSEM, and is generally better than ReDNet. The BFDSEM algorithm is also applied to a real data set of lung cancer and adjacent normal tissues, the yielded normal GRN and differential GRN are consistent with the reported results in previous literatures. An open-source program implementing BFDSEM is freely available in Additional file 1.
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Prince TL, Lang BJ, Guerrero-Gimenez ME, Fernandez-Muñoz JM, Ackerman A, Calderwood SK. HSF1: Primary Factor in Molecular Chaperone Expression and a Major Contributor to Cancer Morbidity. Cells 2020; 9:E1046. [PMID: 32331382 PMCID: PMC7226471 DOI: 10.3390/cells9041046] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 02/07/2023] Open
Abstract
Heat shock factor 1 (HSF1) is the primary component for initiation of the powerful heat shock response (HSR) in eukaryotes. The HSR is an evolutionarily conserved mechanism for responding to proteotoxic stress and involves the rapid expression of heat shock protein (HSP) molecular chaperones that promote cell viability by facilitating proteostasis. HSF1 activity is amplified in many tumor contexts in a manner that resembles a chronic state of stress, characterized by high levels of HSP gene expression as well as HSF1-mediated non-HSP gene regulation. HSF1 and its gene targets are essential for tumorigenesis across several experimental tumor models, and facilitate metastatic and resistant properties within cancer cells. Recent studies have suggested the significant potential of HSF1 as a therapeutic target and have motivated research efforts to understand the mechanisms of HSF1 regulation and develop methods for pharmacological intervention. We review what is currently known regarding the contribution of HSF1 activity to cancer pathology, its regulation and expression across human cancers, and strategies to target HSF1 for cancer therapy.
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Affiliation(s)
- Thomas L. Prince
- Department of Molecular Functional Genomics, Geisinger Clinic, Danville, PA 17821, USA
| | - Benjamin J. Lang
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Martin E. Guerrero-Gimenez
- Laboratory of Oncology, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Buenos Aires B1657, Argentina
| | - Juan Manuel Fernandez-Muñoz
- Laboratory of Oncology, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Buenos Aires B1657, Argentina
| | - Andrew Ackerman
- Department of Molecular Functional Genomics, Geisinger Clinic, Danville, PA 17821, USA
| | - Stuart K. Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
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Yang W, Feng B, Meng Y, Wang J, Geng B, Cui Q, Zhang H, Yang Y, Yang J. FAM3C-YY1 axis is essential for TGFβ-promoted proliferation and migration of human breast cancer MDA-MB-231 cells via the activation of HSF1. J Cell Mol Med 2019; 23:3464-3475. [PMID: 30887707 PMCID: PMC6484506 DOI: 10.1111/jcmm.14243] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/22/2018] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
Family with sequence similarity three member C (FAM3C) (interleukin‐like EMT inducer [ILEI]), heat shock factor 1 (HSF1) and Ying‐Yang 1 (YY1) have been independently reported to be involved in the pathogenesis of various cancers. However, whether they are coordinated to trigger the development of cancer remains unknown. This study determined the role and mechanism of YY1 and HSF1 in FAM3C‐induced proliferation and migration of breast cancer cells. In human MDA‐MB‐231 breast cancer cell line, transforming growth factor‐β (TGFβ) up‐regulated FAM3C, HSF1 and YY1 expressions. FAM3C overexpression promoted the proliferation and migration of MDA‐MB‐231 cells with YY1 and HSF1 up‐regulation, whereas FAM3C silencing exerted the opposite effects. FAM3C inhibition repressed TGFβ‐induced HSF1 activation, and proliferation and migration of breast cancer cells. YY1 was shown to directly activate HSF1 transcription to promote the proliferation and migration of breast cancer cells. YY1 silencing blunted FAM3C‐ and TGFβ‐triggered activation of HSF1‐Akt‐Cyclin D1 pathway, and proliferation and migration of breast cancer cells. Inhibition of HSF1 blocked TGFβ‐, FAM3C‐ and YY1‐induced proliferation and migration of breast cancer cells. YY1 and HSF1 had little effect on FAM3C expression. Similarly, inhibition of HSF1 also blunted FAM3C‐ and TGFβ‐promoted proliferation and migration of human breast cancer BT‐549 cells. In human breast cancer tissues, FAM3C, YY1 and HSF1 protein expressions were increased. In conclusion, FAM3C activated YY1‐HSF1 signalling axis to promote the proliferation and migration of breast cancer cells. Furthermore, novel FAM3C‐YY1‐HSF1 pathway plays an important role in TGFβ‐triggered proliferation and migration of human breast cancer MDA‐MB‐231 cells.
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Affiliation(s)
- Weili Yang
- Key Laboratory of Molecular Cardiovascular Sciences of the Ministry of Education, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Non-coding RNA Medicine, Peking University Health Science Center, Beijing, China.,Key Laboratory of Molecular Cardiovascular Sciences of the Ministry of Education, Department of Biomedical Informatics, School of Basic Medical Sciences, Center for Non-coding RNA Medicine, Peking University Health Science Center, Beijing, China
| | - Biaoqi Feng
- Key Laboratory of Molecular Cardiovascular Sciences of the Ministry of Education, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Non-coding RNA Medicine, Peking University Health Science Center, Beijing, China
| | - Yuhong Meng
- Key Laboratory of Molecular Cardiovascular Sciences of the Ministry of Education, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Non-coding RNA Medicine, Peking University Health Science Center, Beijing, China
| | - Junpei Wang
- Key Laboratory of Molecular Cardiovascular Sciences of the Ministry of Education, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Non-coding RNA Medicine, Peking University Health Science Center, Beijing, China.,Key Laboratory of Molecular Cardiovascular Sciences of the Ministry of Education, Department of Biomedical Informatics, School of Basic Medical Sciences, Center for Non-coding RNA Medicine, Peking University Health Science Center, Beijing, China
| | - Bin Geng
- State Key Laboratory of Cardiovascular Disease, Hypertension Center, Fuwai Hospital, Peking University Health Science Center, CAMS & PUMC, Beijing, China
| | - Qinghua Cui
- Key Laboratory of Molecular Cardiovascular Sciences of the Ministry of Education, Department of Biomedical Informatics, School of Basic Medical Sciences, Center for Non-coding RNA Medicine, Peking University Health Science Center, Beijing, China
| | - Hongquan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Yang Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jichun Yang
- Key Laboratory of Molecular Cardiovascular Sciences of the Ministry of Education, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Center for Non-coding RNA Medicine, Peking University Health Science Center, Beijing, China
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