1
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Ramalho S, Dopler A, Faller W. Ribosome specialization in cancer: a spotlight on ribosomal proteins. NAR Cancer 2024; 6:zcae029. [PMID: 38989007 PMCID: PMC11231584 DOI: 10.1093/narcan/zcae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 06/11/2024] [Accepted: 06/19/2024] [Indexed: 07/12/2024] Open
Abstract
In the past few decades, our view of ribosomes has changed substantially. Rather than passive machines without significant variability, it is now acknowledged that they are heterogeneous, and have direct regulatory capacity. This 'ribosome heterogeneity' comes in many flavors, including in both the RNA and protein components of ribosomes, so there are many paths through which ribosome specialization could arise. It is easy to imagine that specialized ribosomes could have wide physiological roles, through the translation of specific mRNA populations, and there is now evidence for this in several contexts. Translation is highly dysregulated in cancer, needed to support oncogenic phenotypes and to overcome cellular stress. However, the role of ribosome specialization in this is not clear. In this review we focus on specialized ribosomes in cancer. Specifically, we assess the impact that post-translational modifications and differential ribosome incorporation of ribosomal proteins (RPs) have in this disease. We focus on studies that have shown a ribosome-mediated change in translation of specific mRNA populations, and hypothesize how such a process could be driving other phenotypes. We review the impact of RP-mediated heterogeneity in both intrinsic and extrinsic oncogenic processes, and consider how this knowledge could be leveraged to benefit patients.
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Affiliation(s)
- Sofia Ramalho
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Anna Dopler
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - William James Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, Netherlands
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2
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Yadav C, Yadav R, Nanda S, Ranga S, Ahuja P, Tanwar M. Role of HOX genes in cancer progression and their therapeutical aspects. Gene 2024; 919:148501. [PMID: 38670395 DOI: 10.1016/j.gene.2024.148501] [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: 01/19/2024] [Revised: 03/28/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
HOX genes constitute a family of evolutionarily conserved transcription factors that play pivotal roles in embryonic development, tissue patterning, and cell differentiation. These genes are essential for the precise spatial and temporal control of body axis formation in vertebrates. In addition to their developmental functions, HOX genes have garnered significant attention for their involvement in various diseases, including cancer. Deregulation of HOX gene expression has been observed in numerous malignancies, where they can influence tumorigenesis, progression, and therapeutic responses. This review provides an overview of the diverse roles of HOX genes in development, disease, and potential therapeutic targets, highlighting their significance in understanding biological processes and their potential clinical implications.
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Affiliation(s)
- Chetna Yadav
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Ritu Yadav
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India.
| | - Smiti Nanda
- Retd. Senior Professor and Head, Department of Gynaecology and Obstetrics, Pt. B.D. Sharma University of Health Sciences, Rohtak 124001, India
| | - Shalu Ranga
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Parul Ahuja
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Mukesh Tanwar
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India
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3
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Cheng X, Luo J, Cao J. Identification of HOXC Gene Family as Prognostic and Immune-Related Biomarkers in Breast Cancer Through mRNA Transcriptional Profile and Experimental Validation. Biochem Genet 2024:10.1007/s10528-024-10884-5. [PMID: 38995528 DOI: 10.1007/s10528-024-10884-5] [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: 04/09/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
Breast cancer (BC) is the most common malignancy in women worldwide, and more effective biomarkers are urgently needed for the prevention and treatment of BC. Our study aimed to investigate the role of the HOXC gene family (HOXCs) and its relationship with the immune response in BC. The differential expression of HOXCs and its clinical prognostic significance in BC were explored using bioinformatics analysis, and the cBioPortal database was used to evaluate the genetic mutation profile of the HOXCs in BC. The results indicated that the expression levels of HOXC4, 10, 11, 12, and 13 were significantly increased in BC tissues compared with the normal tissues, and expressions of these genes were closely associated with BC stage, among them, high expression levels of HOXC10 and HOXC13 predicted poor outcome in BC patients. In addition, to elucidate the essential role of HOXCs in the tumor microenvironment and immunotherapeutic response of BC, the impact of HOXCs on the regulation of immune infiltration in BC was comprehensively assessed. The result showed that HOXC10 and HOXC13 expressions were significantly positively linked with the infiltration levels of CD8+T cell and M1 macrophage, while they were negatively related to Mast and Natural killer cells, suggesting the important influence of HOXCs on regulating tumor immunity in BC patients. Lastly, the RT-qPCR assay was employed to validate HOXCs expression in samples of BC patients. In conclusion, HOXCs may be a promising prognostic indicator and could regulate the immune infiltration in BC patients, thus being a promising targeted immunotherapy for BC.
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Affiliation(s)
- Xiongtao Cheng
- Graduate School, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Jie Luo
- Department of Traditional Chinese Medicine, Yunnan University of Traditional Chinese Medicine, Kunming, Yunnan, China
| | - Jianxiong Cao
- Department of Oncology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China.
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4
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Zhu R, Mao Y, Xu X, Li Y, Zheng J. HOXA1 silencing inhibits cisplatin resistance of oral squamous cell carcinoma cells via IκB/NF-κB signaling pathway. Anticancer Drugs 2024; 35:492-500. [PMID: 38477942 DOI: 10.1097/cad.0000000000001592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The resistance of oral squamous cell carcinoma (OSCC) cells to cisplatin remains a tough nut to crack in OSCC therapy. Homeobox A1 (HOXA1) overexpression has been detected in head and neck squamous carcinoma (HNSC). Accordingly, this study aims to explore the potential role and mechanism of HOXA1 on cisplatin resistance in OSCC. The expression of HOXA1 in HNSC and its role in overall survival (OS) rate of OSCC patients were analyzed by bioinformatic analysis. Following transfection as needed, OSCC cells were induced by different concentrations of cisplatin, and the cell viability and apoptosis were evaluated by cell counting kit-8 and flow cytometry assays. The mRNA and protein expression levels of HOXA1 and the phosphorylation of IκBα and p65 were determined by real-time quantitative PCR and western blot. HOXA1 expression level was upregulated in HNSC tissues and OSCC cells. Overexpressed HOXA1 was correlated with a low OS rate of OSCC patients. Cisplatin exerted an anti-cancer effect on OSCC cells. HOXA1 silencing or cisplatin suppressed OSCC cell viability, boosted the apoptosis, and repressed the phosphorylation of IκBα and p65. Intriguingly, the combination of HOXA1 silencing and cisplatin generated a stronger anti-cancer effect on OSCC cells than their single use. HOXA1 silencing attenuates cisplatin resistance of OSCC cells via IκB/NF-κB signaling pathway, hinting that HOXA1 is a biomarker associated with OSCC and HOXA1 silencing can enhance the sensitivity of OSCC cells to cisplatin.
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Affiliation(s)
- Ruifeng Zhu
- School of Stomatology, Xuzhou Medical University
| | - Yiting Mao
- School of Stomatology, Xuzhou Medical University
| | - Xianzhi Xu
- School of Stomatology, Xuzhou Medical University
| | - Yingying Li
- School of Stomatology, Xuzhou Medical University
| | - Jiwei Zheng
- School of Stomatology, Xuzhou Medical University
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
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5
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Morton LM, Lee OW, Karyadi DM, Bogdanova TI, Stewart C, Hartley SW, Breeze CE, Schonfeld SJ, Cahoon EK, Drozdovitch V, Masiuk S, Chepurny M, Zurnadzhy LY, Dai J, Krznaric M, Yeager M, Hutchinson A, Hicks BD, Dagnall CL, Steinberg MK, Jones K, Jain K, Jordan B, Machiela MJ, Dawson ET, Vij V, Gastier-Foster JM, Bowen J, Mabuchi K, Hatch M, Berrington de Gonzalez A, Getz G, Tronko MD, Thomas GA, Chanock SJ. Genomic characterization of cervical lymph node metastases in papillary thyroid carcinoma following the Chornobyl accident. Nat Commun 2024; 15:5053. [PMID: 38871684 PMCID: PMC11176192 DOI: 10.1038/s41467-024-49292-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/23/2024] [Indexed: 06/15/2024] Open
Abstract
Childhood radioactive iodine exposure from the Chornobyl accident increased papillary thyroid carcinoma (PTC) risk. While cervical lymph node metastases (cLNM) are well-recognized in pediatric PTC, the PTC metastatic process and potential radiation association are poorly understood. Here, we analyze cLNM occurrence among 428 PTC with genomic landscape analyses and known drivers (131I-exposed = 349, unexposed = 79; mean age = 27.9 years). We show that cLNM are more frequent in PTC with fusion (55%) versus mutation (30%) drivers, although the proportion varies by specific driver gene (RET-fusion = 71%, BRAF-mutation = 38%, RAS-mutation = 5%). cLNM frequency is not associated with other characteristics, including radiation dose. cLNM molecular profiling (N = 47) demonstrates 100% driver concordance with matched primary PTCs and highly concordant mutational spectra. Transcriptome analysis reveals 17 differentially expressed genes, particularly in the HOXC cluster and BRINP3; the strongest differentially expressed microRNA also is near HOXC10. Our findings underscore the critical role of driver alterations and provide promising candidates for elucidating the biological underpinnings of PTC cLNM.
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Affiliation(s)
- Lindsay M Morton
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Olivia W Lee
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Danielle M Karyadi
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tetiana I Bogdanova
- Laboratory of Morphology of the Endocrine System, V.P. Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen W Hartley
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles E Breeze
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sara J Schonfeld
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth K Cahoon
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vladimir Drozdovitch
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergii Masiuk
- National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Mykola Chepurny
- National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Liudmyla Yu Zurnadzhy
- Laboratory of Morphology of the Endocrine System, V.P. Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Jieqiong Dai
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Marko Krznaric
- Department of Surgery and Cancer, Imperial College London, Charing Cross Hospital, London, United Kingdom
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Casey L Dagnall
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Mia K Steinberg
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Komal Jain
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Ben Jordan
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Mitchell J Machiela
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eric T Dawson
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Nvidia Corporation, Santa Clara, CA, USA
| | - Vibha Vij
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Julie M Gastier-Foster
- Nationwide Children's Hospital, Biospecimen Core Resource, Columbus, OH, USA
- Departments of Pathology and Pediatrics, Ohio State University College of Medicine, Columbus, OH, USA
| | - Jay Bowen
- Nationwide Children's Hospital, Biospecimen Core Resource, Columbus, OH, USA
| | - Kiyohiko Mabuchi
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maureen Hatch
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy Berrington de Gonzalez
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Mykola D Tronko
- Department of Fundamental and Applied Problems of Endocrinology, V.P. Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Gerry A Thomas
- Department of Surgery and Cancer, Imperial College London, Charing Cross Hospital, London, United Kingdom
| | - Stephen J Chanock
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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6
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Han J, Ji R, Zheng S, Xia X, Du W, He H, Han C, Zhao W, Li X, Wang Y, Zhang L. HOXB9 promotes osteosarcoma cell survival and malignancy under glucose starvation via upregulating SPP1 expression. Biochem Pharmacol 2024; 224:116208. [PMID: 38621423 DOI: 10.1016/j.bcp.2024.116208] [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: 12/20/2023] [Revised: 03/29/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
Homeobox B9 (HOXB9) has been shown to play a critical role in several tumors. However, the precise biological mechanisms and functions of HOXB9 in osteosarcoma remain largely unknown. In this study, we found that HOXB9 was increased upon glucose starvation. Elevated HOXB9 suppressed osteosarcoma cell death and supported cell growth and migration under glucose starvation. Further mechanistic studies demonstrated that HOXB9 directly bound to the promoter of secreted phosphoprotein 1 (SPP1) and transcriptionally upregulated SPP1 expression which then led cell death decrease and cell growth increase under glucose deprivation environment. Clinically, HOXB9 was significantly upregulated in osteosarcoma compared with normal tissues and increase of HOXB9 expression was positively associated with the elevation of SPP1 in osteosarcoma. Overall, our study illustrates that HOXB9 contributes to malignancy in osteosarcoma and inhibits cell death through transcriptional upregulating SPP1 under glucose starvation.
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Affiliation(s)
- Jian Han
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, PR China; Dalian NO.3 People's Hospital, Department of Orthopedics, Dalian, Liaoning, 116044, PR China
| | - Renchen Ji
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, PR China; College of Stomatology Dalian Medical University, Dalian, Liaoning, 116044, PR China
| | - Shuo Zheng
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, PR China
| | - Xin Xia
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, PR China
| | - Wenxiao Du
- School of Life Sciences, Yantai University, Yantai, Shandong, 264005, PR China
| | - Hongtao He
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, PR China
| | - Chuanchun Han
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, 116044, PR China
| | - Wenzhi Zhao
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, PR China.
| | - Xiaojie Li
- College of Stomatology Dalian Medical University, Dalian, Liaoning, 116044, PR China.
| | - Yuan Wang
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, PR China.
| | - Lu Zhang
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, PR China.
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7
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Rath MF. Homeobox gene-encoded transcription factors in development and mature circadian function of the rodent pineal gland. J Pineal Res 2024; 76:e12950. [PMID: 38558122 DOI: 10.1111/jpi.12950] [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: 10/03/2023] [Revised: 02/15/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024]
Abstract
Homeobox genes encode transcription factors that are widely known to control developmental processes. This is also the case in the pineal gland, a neuroendocrine brain structure devoted to nighttime synthesis of the hormone melatonin. Thus, in accordance with high prenatal gene expression, knockout studies have identified a specific set of homeobox genes that are essential for development of the pineal gland. However, as a special feature of the pineal gland, homeobox gene expression persists into adulthood, and gene product abundance exhibits 24 h circadian rhythms. Recent lines of evidence show that some homeobox genes even control expression of enzymes catalyzing melatonin synthesis. We here review current knowledge of homeobox genes in the rodent pineal gland and suggest a model for dual functions of homeobox gene-encoded transcription factors in developmental and circadian mature neuroendocrine function.
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Affiliation(s)
- Martin F Rath
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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8
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Liu Y, Wang Y, Liu B, Liu W, Ma Y, Cao Y, Yan S, Zhang P, Zhou L, Zhan Q, Wu N. Targeting lncRNA16 by GalNAc-siRNA conjugates facilitates chemotherapeutic sensibilization via the HBB/NDUFAF5/ROS pathway. SCIENCE CHINA. LIFE SCIENCES 2024; 67:663-679. [PMID: 38155279 DOI: 10.1007/s11427-023-2434-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 12/30/2023]
Abstract
Chemoresistance is a significant barrier to effective cancer treatment. Potential mechanisms for chemoresistance include reactive oxygen species (ROS) accumulation and expression of chemoresistance-promoting genes. Here, we report a novel function of lncRNA16 in the inhibition of ROS generation and the progression of chemoresistance. By analyzing the serum levels of lncRNA16 in a cohort of 35 patients with non-small cell lung cancer (NSCLC) and paired serum samples pre- and post-treatment from 10 NSCLC patients receiving neoadjuvant platinum-based chemotherapy, performing immunohistochemistry (IHC) assays on 188 NSCLC tumor samples, using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) assays, as well as RNA immunoprecipitation (RIP) and RNA pull-down analyses, we discovered that patients with increased serum levels of lncRNA16 exhibited a poor response to platinum-based chemotherapy. The expression of hemoglobin subunit beta (HBB) and NDUFAF5 significantly increases with the development of chemoresistance. LncRNA16 binds to HBB and promotes HBB accumulation by inhibiting autophagy. LncRNA16 can also inhibit ROS generation via the HBB/NDUFAF5 axis and function as a scaffold to facilitate the colocalization of HBB and NDUFAF5 in the mitochondria. Importantly, preclinical studies in mouse models of chemo-resistant NSCLC have suggested that lncRNA16 targeting by trivalent N-acetylgalactosamine (GalNAc)-conjugated siRNA restores chemosensitivity and results in tumor growth inhibition with no detectable toxicity in vivo. Overall, lncRNA16 is a promising therapeutic target for overcoming chemoresistance, and the combination of first-line platinum-based chemotherapy with lncRNA16 intervention can substantially enhance anti-tumor efficacy.
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Affiliation(s)
- Yanfang Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Bing Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Wenzhong Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yuanyuan Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yiren Cao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Shi Yan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Panpan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Oncology II, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Lixin Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Qimin Zhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
- Peking University International Cancer Institute, Beijing, 100191, China.
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
| | - Nan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
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9
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Malik A, Jayarathna DK, Fisher M, Barbhuiya TK, Gandhi NS, Batra J. Dynamics and recognition of homeodomain containing protein-DNA complex of IRX4. Proteins 2024; 92:282-301. [PMID: 37861198 DOI: 10.1002/prot.26604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
Iroquois Homeobox 4 (IRX4) belongs to a family of homeobox TFs having roles in embryogenesis, cell specification, and organ development. Recently, large scale genome-wide association studies and epigenetic studies have highlighted the role of IRX4 and its associated variants in prostate cancer. No studies have investigated and characterized the structural aspect of the IRX4 homeodomain and its potential to bind to DNA. The current study uses sequence analysis, homology modeling, and molecular dynamics simulations to explore IRX4 homeodomain-DNA recognition mechanisms and the role of somatic mutations affecting these interactions. Using publicly available databases, gene expression of IRX4 was found in different tissues, including prostate, heart, skin, vagina, and the protein expression was found in cancer cell lines (HCT166, HEK293), B cells, ascitic fluid, and brain. Sequence conservation of the homeodomain shed light on the importance of N- and C-terminal residues involved in DNA binding. The specificity of IRX4 homodimer bound to consensus human DNA sequence was confirmed by molecular dynamics simulations, representing the role of conserved amino acids including R145, A194, N195, S190, R198, and R199 in binding to DNA. Additional N-terminal residues like T144 and G143 were also found to have specific interactions highlighting the importance of N-terminus of the homeodomain in DNA recognition. Additionally, the effects of somatic mutations, including the conserved Arginine (R145, R198, and R199) residues on DNA binding elucidated the importance of these residues in stabilizing the protein-DNA complex. Secondary structure and hydrogen bonding analysis showed the roles of specific residues (R145, T191, A194, N195, R198, and R199) in maintaining the homogeneity of the structure and its interaction with DNA. The differences in relative binding free energies of all the mutants shed light on the structural modularity of this protein and the dynamics behind protein-DNA interaction. We also have predicted that the C-terminal sequence of the IRX4 homeodomain could act as a potential cell-penetrating peptide, emphasizing the role these small peptides could play in targeting homeobox TFs.
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Affiliation(s)
- Adil Malik
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Dulari K Jayarathna
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
- School of Chemistry and Physics, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Mark Fisher
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Tabassum Khair Barbhuiya
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
- School of Chemistry and Physics, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Neha S Gandhi
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
- School of Chemistry and Physics, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Udupi, Karnataka, India
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Queensland, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
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10
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Zhou Y, Wu Q, Guo Y. Deciphering the emerging landscape of HOX genes in cardiovascular biology, atherosclerosis and beyond (Review). Int J Mol Med 2024; 53:17. [PMID: 38131178 PMCID: PMC10781420 DOI: 10.3892/ijmm.2023.5341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Atherosclerosis, a dominant driving force underlying multiple cardiovascular events, is an intertwined and chronic inflammatory disease characterized by lipid deposition in the arterial wall, which leads to diverse cardiovascular problems. Despite unprecedented advances in understanding the pathogenesis of atherosclerosis and the substantial decline in cardiovascular mortality, atherosclerotic cardiovascular disease remains a global public health issue. Understanding the molecular landscape of atherosclerosis is imperative in the field of molecular cardiology. Recently, compelling evidence has shown that an important family of homeobox (HOX) genes endows causality in orchestrating the interplay between various cardiovascular biological processes and atherosclerosis. Despite seemingly scratching the surface, such insight into the realization of biology promises to yield extraordinary breakthroughs in ameliorating atherosclerosis. Primarily recapitulated herein are the contributions of HOX in atherosclerosis, including diverse cardiovascular biology, knowledge gaps, remaining challenges and future directions. A snapshot of other cardiovascular biological processes was also provided, including cardiac/vascular development, cardiomyocyte pyroptosis/apoptosis, cardiac fibroblast proliferation and cardiac hypertrophy, which are responsible for cardiovascular disorders. Further in‑depth investigation of HOX promises to provide a potential yet challenging landscape, albeit largely undetermined to date, for partially pinpointing the molecular mechanisms of atherosclerosis. A plethora of new targeted therapies may ultimately emerge against atherosclerosis, which is rapidly underway. However, translational undertakings are crucially important but increasingly challenging and remain an ongoing and monumental conundrum in the field.
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Affiliation(s)
- Yu Zhou
- Medical College, Guizhou University, Guiyang, Guizhou 550025, P.R. China
- Department of Cardiology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Qiang Wu
- Department of Cardiology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Yingchu Guo
- Department of Clinical Laboratory, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
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11
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Weng M, Lai Y, Ge X, Gu W, Zhang X, Li L, Sun M. HOXC6: A promising biomarker linked to an immunoevasive microenvironment in colorectal cancer based on TCGA analysis and cohort validation. Heliyon 2024; 10:e23500. [PMID: 38192826 PMCID: PMC10772581 DOI: 10.1016/j.heliyon.2023.e23500] [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: 04/26/2023] [Revised: 10/22/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024] Open
Abstract
HOXC6 plays an essential part of the carcinogenesis of solid tumors, but its functional relevance within the immune contexture in patients with colorectal cancer (CRC) is still uncertain. We intended to investigate the predictive value of HOXC6 expression for survival outcomes and its correlation with immune contexture in CRC patients by utilizing the Cancer Genome Atlas database (n = 619). Validation was performed in cohorts from Zhongshan Hospital (n = 200) and Shanghai Cancer Center (n = 300). Immunohistochemical (IHC) staining was utilized to compare the levels of immunocytes infiltrating the tumor between the groups with high and low expression of HOXC6. Elevated levels of HOXC6 expression in CRC tissues were linked to malignant progression and poor prognosis. HOXC6 as a risk factor for survival of CRC patients was confirmed. Receiver operating characteristic analysis confirmed its diagnostic value, and a reliable prognostic nomogram was constructed. KEGG analysis and GSEA showed that HOXC6 participated in immune regulation, and its expression was tightly linked to the abundance of infiltrating immunocytes. HOXC6 was upregulated in patients diagnosed with CRC within the two cohorts, and high HOXC6 levels were correlated with a worse prognosis. The high-HOXC6 expression group showed increased infiltration of Treg cells, CD68+ macrophages, CD66b+ neutrophils, and CD8+ T-cells and elevated levels of PD-L1 and PD-1, but decreased levels of granzyme B and perforin. These findings suggest that HOXC6 abundance in patients with CRC determines a poor prognosis, promotes an immunoevasive environment, and directs CD8+ T-cell dysfunction. HOXC6 is expected to become a prospective biomarker for the outcome of CRC.
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Affiliation(s)
- Meilin Weng
- Department of Anesthesiology, Zhongshan hospital, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Zhongshan hospital, Fudan University, Shanghai, 200032, China
| | - Yuling Lai
- Department of Anesthesiology, Zhongshan hospital, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Zhongshan hospital, Fudan University, Shanghai, 200032, China
| | - Xiaodong Ge
- Department of Anesthesiology, Zhongshan hospital, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Zhongshan hospital, Fudan University, Shanghai, 200032, China
| | - Wenchao Gu
- Department of Diagnostic and Interventional Radiology, University of Tsukuba, Faculty of medicine, Ibaraki, Tsukuba, Japan
| | - Xixue Zhang
- Department of Anesthesiology, Huadong Hospital Affiliated to Fudan University, No 221, West Yan'an Road, Shanghai 200040, China
| | - Lihong Li
- Department of Anesthesiology, Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
| | - Minli Sun
- Department of Anesthesiology, Zhongshan hospital, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Zhongshan hospital, Fudan University, Shanghai, 200032, China
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12
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Zhu M, Xu T, Ji L, Jiang B, Wu K. MIR143HG promotes methylation of transcription factor HOXB7 promoter by recruiting methyltransferase DNMT1 to prevent the progression of colon cancer. FASEB J 2024; 38:e23378. [PMID: 38127104 DOI: 10.1096/fj.202301060rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 11/22/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
In recent years, accumulating evidence has demonstrated the role of long noncoding RNAs (lncRNAs) in colon cancer. We aim to investigate the role of MIR143HG, also known as CARMN (Cardiac mesoderm enhancer-associated noncoding RNA) in colon cancer and explore the related mechanisms. An RNAseq data analysis was performed to screen differentially expressed lncRNAs associated with colon cancer. Next, MIR143HG expression was quantified in colon cancer cells. Moreover, the contributory roles of MIR143HG in the progression of colon cancer with the involvement of DNMT1 and HOXB7 (Homeobox B7) were evaluated after restored MIR143HG or depleted HOXB7. Finally, the effects of MIR143HG were investigated in vivo by measuring tumor formation in nude mice. High-throughput transcriptome sequencing was employed to validate the specific mechanisms by which MIR143HG and HOXB7 affect tumor growth in vivo. MIR143HG was found to be poorly expressed, while HOXB7 was highly expressed in colon cancer. MIR143HG could promote HOXB7 methylation by recruiting DNMT1 to reduce HOXB7 expression. Upregulation of MIR143HG or downregulation of HOXB7 inhibited cell proliferation, invasion and migration and facilitated apoptosis in colon cancer cells so as to delay the progression of colon cancer. The same trend was identified in vivo. Our study provides evidence that restoration of MIR143HG suppressed the progression of colon cancer via downregulation of HOXB7 through DNMT1-mediated HOXB7 promoter methylation. Thus, MIR143HG may be a potential candidate for the treatment of colon cancer.
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Affiliation(s)
- Mo Zhu
- Department of Gastrointestinal Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, P.R. China
| | - Ting Xu
- Hematology Research Laboratory, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, P.R. China
| | - Lindong Ji
- Department of Gastrointestinal Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, P.R. China
| | - Baofei Jiang
- Department of Gastrointestinal Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, P.R. China
- Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, Shanghai, P.R. China
| | - Kun Wu
- Department of Gastrointestinal Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, P.R. China
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13
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Patel RA, Sayar E, Coleman I, Roudier MP, Hanratty B, Low JY, Jaiswal N, Ajkunic A, Dumpit R, Ercan C, Salama N, O’Brien VP, Isaacs WB, Epstein JI, De Marzo AM, Trock BJ, Luo J, Brennen WN, Tretiakova M, Vakar-Lopez F, True LD, Goodrich DW, Corey E, Morrissey C, Nelson PS, Hurley PJ, Gulati R, Haffner MC. Characterization of HOXB13 expression patterns in localized and metastatic castration-resistant prostate cancer. J Pathol 2024; 262:105-120. [PMID: 37850574 PMCID: PMC10871027 DOI: 10.1002/path.6216] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/16/2023] [Accepted: 09/08/2023] [Indexed: 10/19/2023]
Abstract
HOXB13 is a key lineage homeobox transcription factor that plays a critical role in the differentiation of the prostate gland. Several studies have suggested that HOXB13 alterations may be involved in prostate cancer development and progression. Despite its potential biological relevance, little is known about the expression of HOXB13 across the disease spectrum of prostate cancer. To this end, we validated a HOXB13 antibody using genetic controls and investigated HOXB13 protein expression in murine and human developing prostates, localized prostate cancers, and metastatic castration-resistant prostate cancers. We observed that HOXB13 expression increases during later stages of murine prostate development. All localized prostate cancers showed HOXB13 protein expression. Interestingly, lower HOXB13 expression levels were observed in higher-grade tumors, although no significant association between HOXB13 expression and recurrence or disease-specific survival was found. In advanced metastatic prostate cancers, HOXB13 expression was retained in the majority of tumors. While we observed lower levels of HOXB13 protein and mRNA levels in tumors with evidence of lineage plasticity, 84% of androgen receptor-negative castration-resistant prostate cancers and neuroendocrine prostate cancers (NEPCs) retained detectable levels of HOXB13. Notably, the reduced expression observed in NEPCs was associated with a gain of HOXB13 gene body CpG methylation. In comparison to the commonly used prostate lineage marker NKX3.1, HOXB13 showed greater sensitivity in detecting advanced metastatic prostate cancers. Additionally, in a cohort of 837 patients, 383 with prostatic and 454 with non-prostatic tumors, we found that HOXB13 immunohistochemistry had a 97% sensitivity and 99% specificity for prostatic origin. Taken together, our studies provide valuable insight into the expression pattern of HOXB13 during prostate development and cancer progression. Furthermore, our findings support the utility of HOXB13 as a diagnostic biomarker for prostate cancer, particularly to confirm the prostatic origin of advanced metastatic castration-resistant tumors. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Radhika A. Patel
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Erolcan Sayar
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ilsa Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jin-Yih Low
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Neha Jaiswal
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Azra Ajkunic
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ruth Dumpit
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Caner Ercan
- Institute of Pathology and Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Nina Salama
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Valerie P. O’Brien
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - William B. Isaacs
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Jonathan I. Epstein
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Department of Pathology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Angelo M. De Marzo
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Department of Pathology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Bruce J. Trock
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Jun Luo
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - W Nathaniel Brennen
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Maria Tretiakova
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Funda Vakar-Lopez
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - David W. Goodrich
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Paula J. Hurley
- Departments of Medicine and Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Roman Gulati
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
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14
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Liu L, Xue W. Thalidomide suppresses migration and invasion of colorectal cancer cells by inhibiting HOXB7-mediated activation of the Wnt/β-catenin signaling pathway. Chem Biol Drug Des 2024; 103:e14434. [PMID: 38230780 DOI: 10.1111/cbdd.14434] [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: 09/07/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024]
Abstract
Heaps of studies have verified the effects of thalidomide (THA) on colorectal cancer (CRC). Howbeit, the corresponding mechanism awaits illustration, which is the foothold of this study. Following the treatment of 0, 1.94, 7.75, or 19.36 μM THA, CRC cell viability, apoptosis, migration, and invasion were evaluated by methyl tetrazolium, flow cytometry, wound-healing, and transwell assays. Homeobox B7 (HOXB7) expression in CRC was analyzed and detected by bioinformatics analysis, quantitative real-time PCR or western blot. After the corresponding transfection or treatment with inhibitor of catenin-responsive transcription-3 (iCRT-3), abovementioned CRC cell biological behaviors as well as expression levels of HOXB7 and β-catenin were evaluated. 7.75 and 19.36 μM THA dwindled CRC cell viability, migration, and invasion, and facilitated apoptosis. HOXB7 upregulation was detected in CRC cells, which promoted the viability, migration, invasion, and β-catenin expression, and weakened the apoptosis of CRC cells. Also, HOXB7 upregulation counteracted the effects of THA on CRC cells. iCRT-3 restrained β-catenin expression, viability, migration, and invasion, whereas promoting the apoptosis of CRC cells. In addition, iCRT-3 antagonized the effects of overexpressed HOXB7 on CRC cells. THA inhibits the migration and invasion of CRC cells, which is achieved by suppressing HOXB7-mediated activation of Wnt/β-catenin signaling pathway.
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Affiliation(s)
- Liyang Liu
- Department of Anoretal, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Wusong Xue
- Department of Anoretal, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
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15
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Gilyazova I, Gimalova G, Nizamova A, Galimova E, Ishbulatova E, Pavlov V, Khusnutdinova E. Non-Coding RNAs as Key Regulators in Lung Cancer. Int J Mol Sci 2023; 25:560. [PMID: 38203731 PMCID: PMC10778604 DOI: 10.3390/ijms25010560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
For several decades, most lung cancer investigations have focused on the search for mutations in candidate genes; however, in the last decade, due to the fact that most of the human genome is occupied by sequences that do not code for proteins, much attention has been paid to non-coding RNAs (ncRNAs) that perform regulatory functions. In this review, we principally focused on recent studies of the function, regulatory mechanisms, and therapeutic potential of ncRNAs including microRNA (miRNA), long ncRNA (lncRNA), and circular RNA (circRNA) in different types of lung cancer.
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Affiliation(s)
- Irina Gilyazova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, 450054 Ufa, Russia
- Institute of Urology and Clinical Oncology, Department of Medical Genetics and Fundamental Medicine, Bashkir State Medical University, 450008 Ufa, Russia
| | - Galiya Gimalova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, 450054 Ufa, Russia
- Institute of Urology and Clinical Oncology, Department of Medical Genetics and Fundamental Medicine, Bashkir State Medical University, 450008 Ufa, Russia
| | - Aigul Nizamova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, 450054 Ufa, Russia
| | - Elmira Galimova
- Department of Pathological Physiology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Ekaterina Ishbulatova
- Institute of Urology and Clinical Oncology, Department of Medical Genetics and Fundamental Medicine, Bashkir State Medical University, 450008 Ufa, Russia
| | - Valentin Pavlov
- Institute of Urology and Clinical Oncology, Department of Urology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, 450054 Ufa, Russia
- Institute of Urology and Clinical Oncology, Department of Medical Genetics and Fundamental Medicine, Bashkir State Medical University, 450008 Ufa, Russia
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16
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Tan X, Li Z, Xie H, Chen J, Xiao J, Zhi Y, Mo H, Huang Y, Liu A. Pan-cancer analysis of homeodomain-containing gene C10 and its carcinogenesis in lung adenocarcinoma. Aging (Albany NY) 2023; 15:15243-15266. [PMID: 38154103 PMCID: PMC10781453 DOI: 10.18632/aging.205348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/07/2023] [Indexed: 12/30/2023]
Abstract
We found elevated homeodomain-containing gene C10 (HOXC10) showed dual roles in cancers' prognosis. Some signal pathways associated with tumor were totally positively enriched in HOXC10 for whole cancers. On the contrary, Notch signaling, Wnt-beta catenin signaling, myogenesis, and Hedgehog signaling were almost negatively enriched in HOXC10. Some pathways showed dual roles such as Kras signaling, interferon gram and alpha response, IL6/JAK/STAT3, IL2/STAT5 signaling. HOXC10 was associated with tumor mutation burden and microsatellite instability. HOXC10 also was associated with tumor microenvironment and immune status. HOXC10 was negatively associated with immune score in most cancers except colon adenocarcinoma. The correlations of HOXC10 with immune-related genes presented dual roles in different cancers. Results from our clinical samples indicated that HOXC10 was an independent predictor for distant metastasis-free survival in lung adenocarcinoma (LUAD). Notably, the high levels of HOXC10 were positively correlated with the expression of angiogenic markers, vascular endothelial growth factor and microvessel density, and the number of CTC clusters. Our results demonstrated that aberrant expression happened in most cancers, which also affected the clinical prognosis and involved in progression via multiple signal pathways cancers. HOXC10 overexpression plays an important role in the aggression and metastasis in LUAD, which indicated a potential therapeutic target and an independent factor for the prognosis for LUAD patients.
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Affiliation(s)
- Xiangyuan Tan
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Zhanzhan Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Huayan Xie
- Department of Anesthesiology, The First Affiliated Hospital of Jinan University, Guangzhou 510000, Heyuan, China
| | - Jiarong Chen
- Department of Oncology, Jiangmen Central Hospital, Jiangmen 529030, Guangdong, China
| | - Jian Xiao
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yaofeng Zhi
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen 529030, Guangdong, China
| | - Haixin Mo
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen 529030, Guangdong, China
| | - Yanming Huang
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen 529030, Guangdong, China
| | - Aibin Liu
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
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17
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Hu X, Wang Y, Zhang X, Li C, Zhang X, Yang D, Liu Y, Li L. DNA methylation of HOX genes and its clinical implications in cancer. Exp Mol Pathol 2023; 134:104871. [PMID: 37696326 DOI: 10.1016/j.yexmp.2023.104871] [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: 03/29/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Homeobox (HOX) genes encode highly conserved transcription factors that play vital roles in embryonic development. DNA methylation is a pivotal regulatory epigenetic signaling mark responsible for regulating gene expression. Abnormal DNA methylation is largely associated with the aberrant expression of HOX genes, which is implicated in a broad range of human diseases, including cancer. Numerous studies have clarified the mechanisms of DNA methylation in both physiological and pathological processes. In this review, we focus on how DNA methylation regulates HOX genes and briefly discuss drug development approaches targeting these mechanisms.
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Affiliation(s)
- Xin Hu
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Yong Wang
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China; Laboratory of Precision Medicine, Zhangqiu District People's Hospital of Jinan, Jinan 250200, Shandong, China
| | - Xiaoyu Zhang
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Chensheng Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
| | - Xikun Zhang
- Department of Minimally Invasive Interventional, The Third Affiliated Hospital of Shandong First Medical University, Jinan 250031, Shandong, China
| | - Dongxia Yang
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China
| | - Yuanyuan Liu
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China
| | - Lianlian Li
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China; Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China.
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18
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Zhang C, Xie L, Lin Z. Homeobox-D 1 and FTO form a transcriptional-epigenetic feedback loop to promote head and neck cancer proliferation. Cell Biol Int 2023; 47:1987-1998. [PMID: 37655555 DOI: 10.1002/cbin.12087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/29/2023] [Accepted: 08/20/2023] [Indexed: 09/02/2023]
Abstract
Transcription factors (TFs) and N6-methyladenosine (m6A) modifiers are involved in tumor progression through transcriptional regulation and posttranscriptional regulation of genes, respectively. However, the crosstalk and role of these two types of gene expression regulators in head and neck squamous cell carcinoma (HNSC) remains poorly understood. In this study, we demonstrate that the TF homeobox-D1 (HOXD1) and the m6A demethylase fat mass and obesity-associated protein (FTO) form a positive feedback loop to promote cell proliferation and survival in HNSC. Clinically, HOXD1 expression is dysregulated in multiple cancer types and is associated with worse prognosis in patients with HNSC, stomach adenocarcinoma, uterine corpus endometrial carcinoma, and pheochromocytoma and paraganglioma. Mechanistically, FTO is overexpressed in HNSC tumor samples and positively regulates HOXD1 expression in an m6A-dependent manner. Functionally, deficiency of HOXD1 relieved the resistance of HNSC cells to apoptosis and arrested tumor cells at the G0/G1 phase, thereby inhibiting cell growth, whereas overexpression of HOXD1 caused the opposite effect. Furthermore, HOXD1 activates the transcription of the oncogenic factor FTO by directly targeting its promoter. Downregulation of FTO mimicked the biological effect of HOXD1 knockdown on HNSC. Importantly, overexpression of HOXD1 significantly rescued the proliferation inhibition and apoptosis promotion of HNSC cells induced by deficiency of FTO. Together, our findings reveal HOXD1 as a novel prognostic predictor and a potential target for HNSC, providing mechanistic insights into the role of the HOXD1-FTO circuit in this cancer.
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Affiliation(s)
- Chunyan Zhang
- Department of Clinical Laboratory, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Linsen Xie
- Department of Clinical Laboratory, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Zhen Lin
- Department of Clinical Laboratory, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
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19
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Malvi P, Chava S, Cai G, Hu K, Zhu LJ, Edwards YJK, Green MR, Gupta R, Wajapeyee N. HOXC6 drives a therapeutically targetable pancreatic cancer growth and metastasis pathway by regulating MSK1 and PPP2R2B. Cell Rep Med 2023; 4:101285. [PMID: 37951219 PMCID: PMC10694669 DOI: 10.1016/j.xcrm.2023.101285] [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: 02/09/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/13/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers, which lacks effective therapies. Here, we demonstrate that the transcription factor, homeobox C6 (HOXC6), is overexpressed in most PDACs, and its inhibition blocks PDAC tumor growth and metastasis. HOXC6 transcriptionally activates tumor-promoting kinase MSK1 and suppresses tumor-inhibitory protein PPP2R2B in PDAC. HOXC6-induced PPP2R2B suppression causes mammalian target of rapamycin (mTOR) pathway activation, which facilitates PDAC growth. Also, MSK1 upregulation by HOXC6 is necessary for PDAC growth because of its ability to suppress apoptosis via its substrate DDX17. Combinatorial pharmacological inhibition of MSK1 and mTOR potently suppressed PDAC tumor growth and metastasis in PDAC mouse models. PDAC cells with acquired resistance to MSK1/mTOR-inhibitors displayed activated insulin-like growth factor 1 receptor (IGF1R) signaling and were successfully eradicated by IGF1R inhibitor. Furthermore, MEK inhibitor trametinib enhanced the efficacy of dual MSK1 and mTOR inhibition. Collectively, these results identify therapeutic vulnerabilities of PDAC and an approach to overcome acquired drug resistance to prolong therapeutic benefit.
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Affiliation(s)
- Parmanand Malvi
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Suresh Chava
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Guoping Cai
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kai Hu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Yvonne J K Edwards
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Michael R Green
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Romi Gupta
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA; O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Narendra Wajapeyee
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA; O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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20
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Mamatjan Y, Voisin MR, Nassiri F, Moraes FY, Bunda S, So J, Salih M, Shirahata M, Ono T, Shimizu H, Schrimpf D, von Deimling A, Aldape KD, Zadeh G. Integrated molecular analysis reveals hypermethylation and overexpression of HOX genes to be poor prognosticators in isocitrate dehydrogenase mutant glioma. Neuro Oncol 2023; 25:2028-2041. [PMID: 37474126 PMCID: PMC10628942 DOI: 10.1093/neuonc/noad126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Diffuse gliomas represent over 80% of malignant brain tumors ranging from low-grade to aggressive high-grade lesions. Within isocitrate dehydrogenase (IDH)-mutant gliomas, there is a high variability in survival and a need to more accurately predict outcome. METHODS To identify and characterize a predictive signature of outcome in gliomas, we utilized an integrative molecular analysis (using methylation, mRNA, copy number variation (CNV), and mutation data), analyzing a total of 729 IDH-mutant samples including a test set of 99 from University Health Network (UHN) and 2 validation cohorts including the German Cancer Research Center (DKFZ) and The Cancer Genome Atlas (TCGA). RESULTS Cox regression analysis of methylation data from the UHN cohort identified CpG-based signatures that split the glioma cohort into 2 prognostic groups strongly predicting survival that were validated using 2 independent cohorts from TCGA and DKFZ (all P-values < .0001). The methylation signatures that predicted poor outcomes also exhibited high CNV instability and hypermethylation of HOX gene probes. Integrated multi-platform analyses using mRNA and methylation (iRM) showed that parallel HOX gene overexpression and simultaneous hypermethylation were significantly associated with increased mutational load, high aneuploidy, and worse survival (P-value < .0001). A 7-HOX gene signature was developed and validated using the most significantly associated HOX genes with patient outcome in both 1p/19q codeleted and non-codeleted IDHmut gliomas. CONCLUSIONS HOX gene methylation and expression provide important prognostic information in IDH-mutant gliomas that are not captured by current molecular diagnostics. A 7-HOX gene signature of outcome shows significant survival differences in both 1p/19q codeleted and non-codeleted IDH-mutant gliomas.
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Affiliation(s)
- Yasin Mamatjan
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
- Faculty of Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Mathew R Voisin
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Farshad Nassiri
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Fabio Y Moraes
- Department of Oncology, Queens University, Kingston, Ontario, Canada
| | - Severa Bunda
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Jonathan So
- Department of Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mira Salih
- Mount Sinai Hospital, New York, New York, USA
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Mitsuaki Shirahata
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Takahiro Ono
- Department of Neurosurgery, Akita University Graduate School of Medicine, Akita, Japan
| | - Hiroaki Shimizu
- Department of Neurosurgery, Akita University Graduate School of Medicine, Akita, Japan
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Gelareh Zadeh
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
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21
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Zhang Z, Ren P, Cao Y, Wang T, Huang G, Li Y, Zhou S, Yang W, Yang L, Liu G, Xiang Y, Pei Y, Chen Q, Chen J, Lv S. HOXD-AS2-STAT3 feedback loop attenuates sensitivity to temozolomide in glioblastoma. CNS Neurosci Ther 2023; 29:3430-3445. [PMID: 37308741 PMCID: PMC10580348 DOI: 10.1111/cns.14277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 06/14/2023] Open
Abstract
AIMS Glioblastoma multiforme (GBM) is the deadliest glioma and its resistance to temozolomide (TMZ) remains intractable. Long non-coding RNAs (lncRNAs) play crucial roles in that and this study aimed to investigate underlying mechanism of HOXD-AS2-affected temozolomide sensitivity in glioblastoma. METHODS We analyzed and validated the aberrant HOXD-AS2 expression in glioma specimens. Then we explored the function of HOXD-AS2 in vivo and in vitro and a clinical case was also reviewed to examine our findings. We further performed mechanistic experiments to investigate the mechanism of HOXD-AS2 in regulating TMZ sensitivity. RESULTS Elevated HOXD-AS2 expression promoted progression and negatively correlated with prognosis of glioma; HOXD-AS2 attenuated temozolomide sensitivity in vitro and in vivo; The clinical case also showed that lower HOXD-AS2 sensitized glioblastoma to temozolomide; STAT3-induced HOXD-AS2 could interact with IGF2BP2 protein to form a complex and sequentially upregulate STAT3 signaling, thus forming a positive feedback loop regulating TMZ sensitivity in glioblastoma. CONCLUSION Our study elucidated the crucial role of the HOXD-AS2-STAT3 positive feedback loop in regulating TMZ sensitivity, suggesting that this could be provided as a potential therapeutic candidate of glioblastoma.
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Affiliation(s)
- Zuo‐Xin Zhang
- Department of Neurosurgery, Xinqiao HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Peng Ren
- Department of Neurosurgery, Xinqiao HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Yong‐Yong Cao
- School of MedicineChongqing UniversityChongqingChina
| | - Ting‐Ting Wang
- Department of Neurosurgery, Xinqiao HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Guo‐Hao Huang
- Department of Neurosurgery, Xinqiao HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Yao Li
- Department of Neurosurgery, Xinqiao HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Shuo Zhou
- School of MedicineChongqing UniversityChongqingChina
| | - Wei Yang
- Department of Neurosurgery, Xinqiao HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Lin Yang
- Department of Neurosurgery, Xinqiao HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Guo‐Long Liu
- Department of Neurosurgery, Xinqiao HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Yan Xiang
- Department of Neurosurgery, Xinqiao HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Yu‐Chun Pei
- Department of Neurosurgery, Xinqiao HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Qiu‐Zi Chen
- Department of Neurosurgery, Xinqiao HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Ju‐Xiang Chen
- Department of NeurosurgeryChanghai Hospital, Second Military Medical UniversityShanghaiChina
| | - Sheng‐Qing Lv
- Department of Neurosurgery, Xinqiao HospitalThird Military Medical University (Army Medical University)ChongqingChina
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22
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Wu S, Zhu D, Feng H, Li Y, Zhou J, Li Y, Hou T. Comprehensive analysis of HOXC8 associated with tumor microenvironment characteristics in colorectal cancer. Heliyon 2023; 9:e21346. [PMID: 37885723 PMCID: PMC10598528 DOI: 10.1016/j.heliyon.2023.e21346] [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: 12/31/2022] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023] Open
Abstract
Background Accumulating evidence have highlighted the essential roles of HOX genes in embryonic development and carcinogenesis. As a member of the HOX gene family, the abnormal expression of HOXC8 gene is associated with the progression and metastasis of various tumors. However, potential roles of HOXC8 in colorectal cancer (CRC) prognosis and tumor microenvironment (TME) remodeling remain unclear. Methods We conducted an integrated analysis of clinical and molecular characteristics, relevant oncogenic and immune regulation roles and drug sensitivity features of HOXC8 in CRC. Results HOXC8 expression was markedly high expressed in CRC samples compared to normal samples, and the upregulated expression of HOXC8 was associated with poor prognosis. High HOXC8 expression was significantly associated with invasion-related pathways especially epithelial-mesenchymal transition (EMT). In vitro experiments showed significantly up-regulated HOXC8 expression in some CRC cell lines and its promoting effect on EMT and cell proliferation. TME categorization through transcriptomic analysis of CRC patients with high HOXC8 expression identified two different TME subtypes known as immune-enriched with fibrotic subtype and immune-depleted subtype. Patients with immune-enriched, fibrotic subtype exhibited significantly longer progression-free survival (PFS), upregulated PD-L1 and CTLA4 expression and higher TMB than those with the immune-depleted subtype. Conclusions HOXC8 overexpression was associated with poor prognosis and specific TME subtypes in CRC. This study provided valuable resource for further exploring the potential mechanisms and therapeutic targets of HOX genes in CRC.
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Affiliation(s)
- Sifan Wu
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China
- Guangdong Center for Clinical Laboratory, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Dandan Zhu
- Guangdong Center for Clinical Laboratory, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Huolun Feng
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Yafang Li
- The First Affiliated Hospital of Xiamen University (Tongan Branch), The Third Hospital of Xiamen, Xiamen, Fujian, 316000, China
| | - Jianlong Zhou
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Yong Li
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
- Department of Gastrointestinal Surgery, Ganzhou Municipal Hospital, Ganzhou, China
| | - Tieying Hou
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China
- Guangdong Center for Clinical Laboratory, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
- Hospital Office, Huazhong University of Science and Technology Union Shenzhen Hospital/Shenzhen Nanshan People's Hospital, Shenzhen, Guangdong, 518052, China
- Shenzhen University Medical School, Shenzhen, Guangdong, 518073, China
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23
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Ye J, Liu W, Yu X, Wu L, Chen Z, Yu Y, Wang J, Bai S, Zhang M. TRAF7-targeted HOXA5 acts as a tumor suppressor in prostate cancer progression and stemness via transcriptionally activating SPRY2 and regulating MEK/ERK signaling. Cell Death Discov 2023; 9:378. [PMID: 37845209 PMCID: PMC10579307 DOI: 10.1038/s41420-023-01675-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/23/2023] [Accepted: 10/03/2023] [Indexed: 10/18/2023] Open
Abstract
Homeobox A5 (HOXA5), a homeodomain transcription factor, is considered a tumor suppressor in cancer progression; however, its function in prostate cancer (PCa) remains unclear. This study focused on the relevance of HOXA5 in PCa progression. We identified the downregulation of HOXA5 in PCa tissues based on the TCGA database and further verified in 30-paired PCa and adjacent normal tissues. Functional studies revealed that HOXA5 upregulation impaired the stem-like characteristics and malignant behaviors of PCa cells in vitro and in vivo. Mechanistically, HOXA5 was found to be regulated by tumor necrosis factor receptor-associated factor 7 (TRAF7), a putative E3-ubiquitin ligase. We observed that TRAF7 was overexpressed in PCa and subsequently enhanced the degradation of HOXA5 protein via its ubiquitin ligase activity, contributing to the acquisition of an aggressive PCa phenotype. For its downstream mechanism, we demonstrated that sprouty RTK signaling antagonist 2 (SPRY2) served as a downstream target of HOXA5. HOXA5 could directly bind to the SPRY2 promoter, thereby regulating the SPRY2-mediated MEK/ERK signaling pathway. Silencing SPRY2 largely compromised the tumor-suppressive effect of HOXA5 in PCa progression and cancer stemness. Our findings highlight the previously-underappreciated signaling axis of TRAF7-HOXA5-SPRY2, which provides a novel prognostic and therapeutic target for PCa treatment.
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Affiliation(s)
- Jianfeng Ye
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wangmin Liu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xueyang Yu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Lina Wu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhengjie Chen
- Department of Urology, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yufei Yu
- Department of Urology, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jianfeng Wang
- Department of Urology, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Song Bai
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Mo Zhang
- Department of Urology, the First Hospital of China Medical University, Shenyang, Liaoning, China.
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24
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Amin MR, Hasan M, Arnab SP, DeGiorgio M. Tensor Decomposition-based Feature Extraction and Classification to Detect Natural Selection from Genomic Data. Mol Biol Evol 2023; 40:msad216. [PMID: 37772983 PMCID: PMC10581699 DOI: 10.1093/molbev/msad216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/10/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023] Open
Abstract
Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involved development of summary statistic and likelihood methods. However, such techniques are grounded in simple patterns or theoretical models that limit the complexity of settings they can explore. Due to the renaissance in artificial intelligence, machine learning methods have taken center stage in recent efforts to detect natural selection, with strategies such as convolutional neural networks applied to images of haplotypes. Yet, limitations of such techniques include estimation of large numbers of model parameters under nonconvex settings and feature identification without regard to location within an image. An alternative approach is to use tensor decomposition to extract features from multidimensional data although preserving the latent structure of the data, and to feed these features to machine learning models. Here, we adopt this framework and present a novel approach termed T-REx, which extracts features from images of haplotypes across sampled individuals using tensor decomposition, and then makes predictions from these features using classical machine learning methods. As a proof of concept, we explore the performance of T-REx on simulated neutral and selective sweep scenarios and find that it has high power and accuracy to discriminate sweeps from neutrality, robustness to common technical hurdles, and easy visualization of feature importance. Therefore, T-REx is a powerful addition to the toolkit for detecting adaptive processes from genomic data.
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Affiliation(s)
- Md Ruhul Amin
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Mahmudul Hasan
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Sandipan Paul Arnab
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
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25
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Song C, Kim KB, Lee GS, Shin S, Kim B. Is HOXA5 a Novel Prognostic Biomarker for Uterine Corpus Endometrioid Adenocarcinoma? Int J Mol Sci 2023; 24:14758. [PMID: 37834206 PMCID: PMC10573156 DOI: 10.3390/ijms241914758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Endometrial cancer (EC) is one of the most pervasive malignancies in females worldwide. HOXA5 is a member of the homeobox (HOX) family and encodes the HOXA5 protein. HOXA5 is associated with various cancers; however, its association with EC remains unclear. This study aimed to determine the association between HOXA5 gene expression and the prognosis of endometrioid adenocarcinoma, a subtype of EC (EAEC). Microarray data of HOXA5 were collected from the Gene Expression Omnibus datasets, consisting of 79 samples from GSE17025 and 20 samples from GSE29981. RNA-sequencing, clinical, and survival data on EC were obtained from The Cancer Genome Atlas cohort. Survival analysis revealed that HOXA5 overexpression was associated with poor overall survival in patients with EAEC (p = 0.044, HR = 1.832, 95% CI = 1.006-3.334). Cox regression analysis revealed that HOXA5 was an independent risk factor for poor prognosis in EAEC. The overexpression of HOXA5 was associated with a higher histological grade of EAEC, and it was also associated with TP53 mutation or the high copy number of EC. Our findings suggest the potential of HOXA5 as a novel biomarker for predicting poor survival outcomes in patients with EAEC.
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Affiliation(s)
- Changho Song
- Department of Obstetrics and Gynecology, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan 44033, Republic of Korea;
| | - Kyoung Bo Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu 42601, Republic of Korea;
| | - Gi Su Lee
- Department of Obstetrics and Gynecology, Keimyung University School of Medicine, Daegu 42601, Republic of Korea;
| | - Soyoung Shin
- Department of Pediatrics, Keimyung University School of Medicine, Daegu 42601, Republic of Korea;
| | - Byoungje Kim
- Department of Radiology, Keimyung University School of Medicine, Daegu 42601, Republic of Korea
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26
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Li J, Ran H, Zeng X, Yang D, Zeng X, Zhang P. Identification of HOXB9 based on comprehensive bioinformatics analysis for predicting prognosis of head and neck squamous cell carcinoma. Medicine (Baltimore) 2023; 102:e35035. [PMID: 37657018 PMCID: PMC10476753 DOI: 10.1097/md.0000000000035035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/10/2023] [Indexed: 09/03/2023] Open
Abstract
To evaluate the correlation between HOXB9 expression, and the prognosis and immune infiltration in head and neck squamous cell carcinoma (HNSCC). Pan-cancer HOXB9 expression was analyzed through TIMER2.0. The HOXB9 expression data of HNSCC and normal tissues were compared using the gene expression profiling interactive analysis (GEPIA) and the cancer genome atlas (TCGA) databases. The University of Alabama at Birmingham (UALCAN) database was used to analyze the relative expression of HOXB9 in HNSCC subgroups based on clinicopathological features, including cancer stage, tumor grade and lymph node stage. Survival analysis was performed using GEPIA, TCGA-Portal, Kaplan-Meier Plotter, and UALCAN databases. The genes co-expressed with HOXB9 were identified using TCGA data, and functionally annotated by GO and KEGG analyses. Protein-protein interaction network was constructed using the STRING database and Cytoscape 3.7.1. Single-sample gene set enrichment analysis was performed to assess the correlation between HOXB9 and immune infiltration based on TCGA data. TIMER 2.0 database was used to explore the correlation between HOXB9 expression and immune infiltration multiple cancers. HOXB9 mRNA is elevated in multiple cancers, and was upregulated in HNSCC tissues compared to non-paired (P < .05 in GEPIA; P < .0001 in TCGA) as well as paired (P < .0001 in TCGA) normal tissues. In addition, HOXB9 expression was positively correlated with tumor malignancy in the GEPIA and UALCAN databases (P < .05), and negatively with patient prognosis in both databases (P < .05). High HOXB9 expression was associated with increased infiltration of aDCs, NK CD56bright cells, NK cells, and Th2 cells (P < .05), while low HOXB9 expression was associated with an increase in the proportion of DCs, iDCs, mast cells, neutrophils, and Th17 cells (P < .05). HOXB9 likely functions as an oncogene in HNSCC by disrupting the immune landscape, and is a promising prognostic biomarker and therapeutic target.
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Affiliation(s)
- Juanjuan Li
- Department of Otorhinolaryngology, Longgang Otorhinolaryngology Hospital & Shenzhen Key Laboratory of Otorhinolaryngology, Shenzhen Institute of Otorhinolaryngology, Shenzhen, Guangdong, China
| | - Hong Ran
- Department of Otorhinolaryngology, Longgang Otorhinolaryngology Hospital & Shenzhen Key Laboratory of Otorhinolaryngology, Shenzhen Institute of Otorhinolaryngology, Shenzhen, Guangdong, China
- Department of Graduate and Scientific Research, Zunyi Medical University Zhuhai Campus, Zhuhai, Guangdong, China
| | - Xiaoxia Zeng
- Department of Otorhinolaryngology, Longgang Otorhinolaryngology Hospital & Shenzhen Key Laboratory of Otorhinolaryngology, Shenzhen Institute of Otorhinolaryngology, Shenzhen, Guangdong, China
| | - Dunhui Yang
- Department of Otorhinolaryngology, Longgang Otorhinolaryngology Hospital & Shenzhen Key Laboratory of Otorhinolaryngology, Shenzhen Institute of Otorhinolaryngology, Shenzhen, Guangdong, China
- Department of Graduate and Scientific Research, Zunyi Medical University Zhuhai Campus, Zhuhai, Guangdong, China
| | - Xianhai Zeng
- Department of Otorhinolaryngology, Longgang Otorhinolaryngology Hospital & Shenzhen Key Laboratory of Otorhinolaryngology, Shenzhen Institute of Otorhinolaryngology, Shenzhen, Guangdong, China
| | - Peng Zhang
- Department of Otorhinolaryngology, Longgang Otorhinolaryngology Hospital & Shenzhen Key Laboratory of Otorhinolaryngology, Shenzhen Institute of Otorhinolaryngology, Shenzhen, Guangdong, China
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27
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Mierzejewski B, Grabowska I, Michalska Z, Zdunczyk K, Zareba F, Irhashava A, Chrzaszcz M, Patrycy M, Streminska W, Janczyk-Ilach K, Koblowska M, Iwanicka-Nowicka R, Gromadka A, Kowalski K, Ciemerych MA, Brzoska E. SDF-1 and NOTCH signaling in myogenic cell differentiation: the role of miRNA10a, 425, and 5100. Stem Cell Res Ther 2023; 14:204. [PMID: 37582765 PMCID: PMC10426160 DOI: 10.1186/s13287-023-03429-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 07/25/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND Skeletal muscle regeneration is a complex process regulated by many cytokines and growth factors. Among the important signaling pathways regulating the myogenic cell identity are these involving SDF-1 and NOTCH. SDF-1 participates in cell mobilization and acts as an important chemoattractant. NOTCH, on the other hand, controls cell activation and myogenic determination of satellite cells. Knowledge about the interaction between SDF-1 and NOTCH signaling is limited. METHODS We analyzed two populations of myogenic cells isolated from mouse skeletal muscle, that is, myoblasts derived from satellite cells (SCs) and muscle interstitial progenitor cells (MIPCs). First, microRNA level changes in response to SDF-1 treatment were analyzed with next-generation sequencing (NGS). Second, myogenic cells, i.e., SC-derived myoblasts and MIPCs were transfected with miRNA mimics, selected on the basis of NGS results, or their inhibitors. Transcriptional changes, as well as proliferation, migration, and differentiation abilities of SC-derived myoblasts and MIPCs, were analyzed in vitro. Naive myogenic potential was assessed in vivo, using subcutaneous engrafts and analysis of cell contribution to regeneration of the skeletal muscles. RESULTS SDF-1 treatment led to down-regulation of miR10a, miR151, miR425, and miR5100 in myoblasts. Interestingly, miR10a, miR425, and miR5100 regulated the expression of factors involved in the NOTCH signaling pathway, including Dll1, Jag2, and NICD. Furthermore, miR10a, miR425, and miR5100 down-regulated the expression of factors involved in cell migration: Acta1, MMP12, and FAK, myogenic differentiation: Pax7, Myf5, Myod, Mef2c, Myog, Musk, and Myh3. However, these changes did not significantly affect myogenic cell migration or fusion either in vitro or in vivo, except when miR425 was overexpressed, or miR5100 inhibitor was used. These two molecules increased the fusion of MIPCs and myoblasts, respectively. Furthermore, miR425-transfected MIPC transplantation into injured skeletal muscle resulted in more efficient regeneration, compared to control cell transplantation. However, skeletal muscles that were injected with miR10a transfected myoblasts regenerated less efficiently. CONCLUSIONS SDF-1 down-regulates miR10a, miR425, and miR5100, what could affect NOTCH signaling, differentiation of myogenic cells, and their participation in skeletal muscle regeneration.
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Affiliation(s)
- Bartosz Mierzejewski
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Iwona Grabowska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Zuzanna Michalska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Kamila Zdunczyk
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Franciszek Zareba
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Aliksandra Irhashava
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Marta Chrzaszcz
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Magdalena Patrycy
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Wladyslawa Streminska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Katarzyna Janczyk-Ilach
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Marta Koblowska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-096, Warsaw, Poland
- Laboratory of Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Roksana Iwanicka-Nowicka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-096, Warsaw, Poland
- Laboratory of Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Agnieszka Gromadka
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Kamil Kowalski
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Maria Anna Ciemerych
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Edyta Brzoska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland.
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Liu J, Feng H, Wang D, Wang Y, Luo J, Xu S, Zhao F, Qin G. HOXA13 promotes the proliferation, migration, and invasion of nasopharyngeal carcinoma HNE1 cells by upregulating the expression of Snail and MMP-2. Sci Rep 2023; 13:12978. [PMID: 37563232 PMCID: PMC10415404 DOI: 10.1038/s41598-023-40041-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 08/03/2023] [Indexed: 08/12/2023] Open
Abstract
Homeobox A13 (HOXA13) has been verified as an oncogen in some malignancies. However, its role in nasopharyngeal carcinoma (NPC) is still unclear. This study aims to explore the role of HOXA13 in NPC and its underlying mechanism. The mRNA expression of HOXA13 in NPC was obtained from the GSE53819 and GSE64634 datasets in the Gene Expression Omnibus (GEO) database. MTT, colony formation and transwell assays and xenograft tumour models were used to investigate the effects of HOXA13 on NPC HNE1 cells in vitro and in vivo. The expression of HOXA13, epithelial-mesenchymal transition-transcription factor (EMT-TF) Snail and matrix metalloproteinase 2 (MMP-2) was detected by immunohistochemistry, quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting. The results showed that HOXA13 was upregulated in NPC. Silencing HOXA13 suppressed the proliferation, migration, and invasion of HNE1 cells, which inhibited tumour growth, while overexpression of HOXA13 induced the opposite effects. In addition, the expression of Snail and MMP-2 at the transcriptional and protein levels was associated with the expression of HOXA13. In summary, our results suggest that HOXA13 plays a role as a cancer-promoting gene in NPC. The underlying mechanism may be related to the upregulation of Snail and MMP-2.
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Affiliation(s)
- Jinping Liu
- Department of Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Southwest Medical University, NO: 25, Taiping Street, Jiangyang District, Luzhou, 646000, China
| | - Huajun Feng
- Department of Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Southwest Medical University, NO: 25, Taiping Street, Jiangyang District, Luzhou, 646000, China
| | - Dingting Wang
- Department of Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Southwest Medical University, NO: 25, Taiping Street, Jiangyang District, Luzhou, 646000, China
| | - Yuanyuan Wang
- Department of Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Southwest Medical University, NO: 25, Taiping Street, Jiangyang District, Luzhou, 646000, China
| | - Jian Luo
- Department of Otolaryngology Head and Neck Surgery, The First People's Hospital of Yibin, Yibin, 644000, China
| | - Shengen Xu
- Department of Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Southwest Medical University, NO: 25, Taiping Street, Jiangyang District, Luzhou, 646000, China
| | - Feipeng Zhao
- Department of Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Southwest Medical University, NO: 25, Taiping Street, Jiangyang District, Luzhou, 646000, China
| | - Gang Qin
- Department of Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Southwest Medical University, NO: 25, Taiping Street, Jiangyang District, Luzhou, 646000, China.
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Chin FW, Chan SC, Veerakumarasivam A. Homeobox Gene Expression Dysregulation as Potential Diagnostic and Prognostic Biomarkers in Bladder Cancer. Diagnostics (Basel) 2023; 13:2641. [PMID: 37627900 PMCID: PMC10453580 DOI: 10.3390/diagnostics13162641] [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: 05/30/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 08/27/2023] Open
Abstract
Homeobox genes serve as master regulatory transcription factors that regulate gene expression during embryogenesis. A homeobox gene may have either tumor-promoting or tumor-suppressive properties depending on the specific organ or cell lineage where it is expressed. The dysregulation of homeobox genes has been reported in various human cancers, including bladder cancer. The dysregulated expression of homeobox genes has been associated with bladder cancer clinical outcomes. Although bladder cancer has high risk of tumor recurrence and progression, it is highly challenging for clinicians to accurately predict the risk of tumor recurrence and progression at the initial point of diagnosis. Cystoscopy is the routine surveillance method used to detect tumor recurrence. However, the procedure causes significant discomfort and pain that results in poor surveillance follow-up amongst patients. Therefore, the development of reliable non-invasive biomarkers for the early detection and monitoring of bladder cancer is crucial. This review provides a comprehensive overview of the diagnostic and prognostic potential of homeobox gene expression dysregulation in bladder cancer.
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Affiliation(s)
- Fee-Wai Chin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
| | - Soon-Choy Chan
- School of Liberal Arts, Science and Technology, Perdana University, Kuala Lumpur 50490, Malaysia
| | - Abhi Veerakumarasivam
- School of Medical and Life Sciences, Sunway University, Bandar Sunway 47500, Selangor, Malaysia
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Ohnmacht AJ, Rajamani A, Avar G, Kutkaite G, Gonçalves E, Saur D, Menden MP. The pharmacoepigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity. Commun Biol 2023; 6:825. [PMID: 37558831 PMCID: PMC10412573 DOI: 10.1038/s42003-023-05198-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023] Open
Abstract
Aberrant DNA methylation accompanies genetic alterations during oncogenesis and tumour homeostasis and contributes to the transcriptional deregulation of key signalling pathways in cancer. Despite increasing efforts in DNA methylation profiling of cancer patients, there is still a lack of epigenetic biomarkers to predict treatment efficacy. To address this, we analyse 721 cancer cell lines across 22 cancer types treated with 453 anti-cancer compounds. We systematically detect the predictive component of DNA methylation in the context of transcriptional and mutational patterns, i.e., in total 19 DNA methylation biomarkers across 17 drugs and five cancer types. DNA methylation constitutes drug sensitivity biomarkers by mediating the expression of proximal genes, thereby enhancing biological signals across multi-omics data modalities. Our method reproduces anticipated associations, and in addition, we find that the NEK9 promoter hypermethylation may confer sensitivity to the NEDD8-activating enzyme (NAE) inhibitor pevonedistat in melanoma through downregulation of NEK9. In summary, we envision that epigenomics will refine existing patient stratification, thus empowering the next generation of precision oncology.
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Affiliation(s)
- Alexander Joschua Ohnmacht
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Anantharamanan Rajamani
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Ismaninger Str. 22, 81675, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Göksu Avar
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Ginte Kutkaite
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Emanuel Gonçalves
- Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001, Lisbon, Portugal
- INESC-ID, 1000-029, Lisbon, Portugal
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Ismaninger Str. 22, 81675, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Michael Patrick Menden
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany.
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany.
- Department of Biochemistry and Pharmacology, University of Melbourne, Victoria, VIC, 3010, Australia.
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31
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Surendran H, Palaniyandi T, Natarajan S, Hari R, Viwanathan S, Baskar G, Abdul Wahab MR, Ravi M, Rajendran BK. Role of homeobox d10 gene targeted signaling pathways in cancers. Pathol Res Pract 2023; 248:154643. [PMID: 37406379 DOI: 10.1016/j.prp.2023.154643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/07/2023]
Abstract
Homeobox D10 (HOXD10) is a transcription factor from the homeobox gene family that controls cell differentiation and morphogenesis throughout development.Due to their functional interaction, changes in HOXD10 gene expression might induce tumors. This narrative review focuses on how and why the dysregulation in the signaling pathways linked with HOXD10 contributes to the metastatic development of cancer. Organ development and tissue homeostasis need highly conserved homeotic transcription factors from homeobox (HOX) genes. Their dysregulation disrupts regulatory molecule action, causing tumors. The HOXD10 gene is upregulated in breast, gastric, hepatocellular, colorectal, bladder, cholangiocellular carcinoma and prostate cancer. Tumor signaling pathways are affected by HOXD10 gene expression changes. This study examines HOXD10-associated signaling pathway dysregulation, which may alter metastatic cancer signaling. In addition, the theoretical foundations that alter HOXD10-mediated therapeutic resistance in malignancies has been presented. New cancer therapy methods will be simpler to develop with the newly discovered knowledge. This review showed that HOXD10 may be a tumor suppressor gene and a new cancer treatment target signaling pathway.
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Affiliation(s)
- Hemapreethi Surendran
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Deemed to be University, Chennai 600095 Tamil Nadu, India
| | - Thirunavukkarasu Palaniyandi
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Deemed to be University, Chennai 600095 Tamil Nadu, India; Department of Anatomy, Biomedical Research Unit and Laboratory Animal Centre, Saveetha Dental College and Hospital, SIMATS, Saveetha University, Chennai, Tamilnadu, India.
| | - Sudhakar Natarajan
- Department of Virology and Biotechnology, ICMR - National institute for Research in Tuberculosis (NIRT), Chetpet, Chennai 600031 Tamil Nadu, India
| | - Rajeswary Hari
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Deemed to be University, Chennai 600095 Tamil Nadu, India
| | - Sandhiya Viwanathan
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Deemed to be University, Chennai 600095 Tamil Nadu, India
| | - Gomathy Baskar
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Deemed to be University, Chennai 600095 Tamil Nadu, India
| | - Mugip Rahaman Abdul Wahab
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Deemed to be University, Chennai 600095 Tamil Nadu, India
| | - Maddaly Ravi
- Department of Human Genetics, Sri Ramachandra Institute of Higher Education and Research, Chennai 600116 Tamil Nadu, India
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Yi C, Wei W, Wan M, Chen Y, Zhang B, Wu W. Expression Patterns of HOX Gene Family Defines Tumor Microenvironment and Immunotherapy in Hepatocellular Carcinoma. Appl Biochem Biotechnol 2023; 195:5072-5093. [PMID: 36976502 DOI: 10.1007/s12010-023-04443-8] [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] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
Hepatocellular carcinoma (HCC) pathophysiology is prevalently related with HOX genes. However, the study on associations of extensive HOX genes with tumor microenvironment and drug sensitivity of HCC remains scarce. The data sets of HCC were downloaded from TCGA, ICGC, and GEO by bioinformatics method and analyzed. Based on a computational frame, HCC samples were divided into a high and a low HOXscore group, and significantly shorter survival time in the high HOXscore was observed relative to low HOXscore group using survival analysis. Gene set enrichment analysis (GSEA) revealed that the high HOXscore group was more likely to be enriched in cancer-specific pathways. Furthermore, the high HOXscore group was involved in the infiltration of inhibitory immune cells. In response to anti-cancer drugs, the high HOXscore group was more sensitive to mitomycin and cisplatin. Importantly, the HOXscore was associated with the therapeutic efficacy of PD-L1 blockade, suggesting that the development of potential drugs targeting these HOX genes to aid the clinical benefits of immunotherapy is needed. In addition, RT-qPCR and immunohistochemistry showed 10 HOX genes mRNA expression was higher in HCC compared to the normal tissues. This study provides a comprehensive analysis of HOX genes family in HCC and revealed the potential function of these HOX genes family in tumor microenvironment (TME) and identified their therapeutic liability in targeted therapy and immunotherapy. Eventually, this work highlights the cross-talk and potential clinical utility of HOX genes family in HCC therapy.
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Affiliation(s)
- Changhong Yi
- Department of Interventional Radiology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Wei Wei
- Department of Interventional, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
| | - Maolin Wan
- Department of Interventional, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
| | - Ya Chen
- Department of Interventional, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
| | - Bo Zhang
- Department of Interventional, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
| | - Wenze Wu
- Department of Interventional, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China.
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Zhang S, Zhang X, Zhang C, Xu S, Wang D, Guo C. Developmental Genetic Basis of Hoxd9 Homeobox Domain Deletion in Pampus argenteus Pelvic Fin Deficiency. Int J Mol Sci 2023; 24:11769. [PMID: 37511526 PMCID: PMC10380636 DOI: 10.3390/ijms241411769] [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: 05/31/2023] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Pampus argenteus is important for commercial fishery catch species and is an emerging target for aquaculture production. Notably, P. argenteus has a bizarre morphology and lacks pelvic fins. However, the reason for the lack of pelvic fins remains unclear, ultimately leading to frequent upside-down floating of P. argenteus during breeding and marked consumption of physical energy. Some lineages, including whales, fugu, snakes, and seahorse, independently lost the pelvic appendages over evolutionary time. Do different taxa employ the same molecular genetic pathways when they independently evolve similar developmental morphologies? Through analysis of the gene responsible for appendage localization, Hoxd9, it was discovered that the Hox domain was absent in the Hoxd9 gene of P. argenteus, and the Hoxd9b gene lacked the Hox9 activation region, a feature not observed in the Hoxd9 gene of other fish species. Interestingly, those distinctive characteristics are not observed in the Hoxd9 gene of other fish species. To determine the association between the Hoxd9 gene characteristics and the pelvic fin deletion in P. argenteus, the full-length cDNA of the Hoxd9a gene was cloned, and morphological observations of the species' juveniles were performed using stereomicroscopy and scanning electron microscopy. Thereafter, the tissue localization of Hoxd9a in the species was analyzed at the gene and protein levels. Based on the results, deletion of the Hoxd9a structural domain possibly leads to disruptions in the protein translation and the pelvic fin localization in P. argenteus during its early ontogenetic developmental stage, resulting in the absence of pelvic fins.
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Affiliation(s)
- Shun Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo 315211, China
| | - Xiaodong Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo 315211, China
| | - Cheng Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo 315211, China
| | - Shanliang Xu
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, Ningbo 315211, China
| | - Danli Wang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Green Mariculture (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, Ningbo 315211, China
| | - Chunyang Guo
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Green Mariculture (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, Ningbo 315211, China
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Zhao J, Jia X, Li Q, Zhang H, Wang J, Huang S, Hu Z, Li C. Genomic and transcriptional characterization of early esophageal squamous cell carcinoma. BMC Med Genomics 2023; 16:153. [PMID: 37393256 PMCID: PMC10315050 DOI: 10.1186/s12920-023-01588-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/20/2023] [Indexed: 07/03/2023] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is a highly heterogeneous cancer that lacks comprehensive understanding and effective treatment. Although multi-omics study has revealed features and underlying drivers of advanced ESCC, research on molecular characteristics of the early stage ESCC is quite limited. MATERIALS AND METHODS We presented characteristics of genomics and transcriptomics in 10 matched pairs of tumor and normal tissues of early ESCC patients in the China region. RESULTS We identified the specific patterns of cancer gene mutations and copy number variations. We also found a dramatic change in the transcriptome, with more than 4,000 genes upregulated in cancer. Among them, more than one-third of HOX family genes were specifically and highly expressed in early ESCC samples of China and validated by RT-qPCR. Gene regulation network analysis indicated that alteration of Hox family genes promoted the proliferation and metabolism remodeling of early ESCC. CONCLUSIONS We characterized the genomic and transcriptomic landscape of 10 paired normal adjacent and early ESCC tissues in the China region, and provided a new perspective to understand the development of ESCC and insight into potential prevention and diagnostic targets for the management of early ESCC in China.
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Affiliation(s)
- Jingjing Zhao
- Department of Gastroenterology, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiya Jia
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qiaojuan Li
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hena Zhang
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jianjun Wang
- Department of Pediatric Medicine, Gansu Provincial People's Hospital, Lanzhou City, , Gansu Province, China
| | - Shenglin Huang
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhixiang Hu
- Department of Gastroenterology, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Caiping Li
- Department of Gastroenterology, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.
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Amin MR, Hasan M, Arnab SP, DeGiorgio M. Tensor decomposition based feature extraction and classification to detect natural selection from genomic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.527731. [PMID: 37034767 PMCID: PMC10081272 DOI: 10.1101/2023.03.27.527731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involved development of summary statistic and likelihood methods. However, such techniques are grounded in simple patterns or theoretical models that limit the complexity of settings they can explore. Due to the renaissance in artificial intelligence, machine learning methods have taken center stage in recent efforts to detect natural selection, with strategies such as convolutional neural networks applied to images of haplotypes. Yet, limitations of such techniques include estimation of large numbers of model parameters under non-convex settings and feature identification without regard to location within an image. An alternative approach is to use tensor decomposition to extract features from multidimensional data while preserving the latent structure of the data, and to feed these features to machine learning models. Here, we adopt this framework and present a novel approach termed T-REx , which extracts features from images of haplotypes across sampled individuals using tensor decomposition, and then makes predictions from these features using classical machine learning methods. As a proof of concept, we explore the performance of T-REx on simulated neutral and selective sweep scenarios and find that it has high power and accuracy to discriminate sweeps from neutrality, robustness to common technical hurdles, and easy visualization of feature importance. Therefore, T-REx is a powerful addition to the toolkit for detecting adaptive processes from genomic data.
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Lee SY, Miller KM, Kim JJ. Clinical and Mechanistic Implications of R-Loops in Human Leukemias. Int J Mol Sci 2023; 24:ijms24065966. [PMID: 36983041 PMCID: PMC10052022 DOI: 10.3390/ijms24065966] [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: 03/04/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Genetic mutations or environmental agents are major contributors to leukemia and are associated with genomic instability. R-loops are three-stranded nucleic acid structures consisting of an RNA-DNA hybrid and a non-template single-stranded DNA. These structures regulate various cellular processes, including transcription, replication, and DSB repair. However, unregulated R-loop formation can cause DNA damage and genomic instability, which are potential drivers of cancer including leukemia. In this review, we discuss the current understanding of aberrant R-loop formation and how it influences genomic instability and leukemia development. We also consider the possibility of R-loops as therapeutic targets for cancer treatment.
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Affiliation(s)
- Seo-Yun Lee
- Department of Life Science and Multidisciplinary, Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jae-Jin Kim
- Department of Life Science and Multidisciplinary, Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
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Mechanisms of Long Non-Coding RNA in Breast Cancer. Int J Mol Sci 2023; 24:ijms24054538. [PMID: 36901971 PMCID: PMC10002950 DOI: 10.3390/ijms24054538] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
The landscape of pervasive transcription in eukaryotic genomes has made space for the identification of thousands of transcripts that are difficult to frame in a specific functional category. A new class has been broadly named as long non-coding RNAs (lncRNAs) and shortly defined as transcripts that are longer than 200 nucleotides with no or limited coding potential. So far, about 19,000 lncRNAs genes have been annotated in the human genome (Gencode 41), nearly matching the number of protein-coding genes. A key scientific priority is the functional characterization of lncRNAs, a major challenge in molecular biology that has encouraged many high-throughput efforts. LncRNA studies have been stimulated by the enormous clinical potential that these molecules promise and have been based on the characterization of their expression and functional mechanisms. In this review, we illustrate some of these mechanisms as they have been pictured in the context of breast cancer.
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Xu Y, Zhang M, Shi Q, Cheng X, Du R, Li C, Zhang Y. Identification of HOXB9 to predict prognosis of endometrial cancer based on comprehensive bioinformatics analysis. Eur J Med Res 2023; 28:79. [PMID: 36803556 PMCID: PMC9936693 DOI: 10.1186/s40001-022-00979-3] [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: 07/20/2022] [Accepted: 12/30/2022] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND The HOXB9 gene, which plays a key role in embryonic development, is also involved in the regulation of various human cancers. However, the potential relationship between HOXB9 and endometrial cancer (EC) has not yet been comprehensively analyzed and fully understood. METHODS We used multiple bioinformatics tools to explore the role of HOXB9 in EC. RESULTS The expression of HOXB9 was significantly upregulated in pan-cancer, including EC (P < 0.05). Quantitative real time polymerase chain reaction (qRT-PCR) experiment confirmed the high expression of HOXB9 in EC from clinical samples (P < 0.001). Double validated by Enrichr and Metascape, HOXB9 showed a strong correlation with HOX family, suggesting that HOX family may also involve in the development of EC (P < 0.05). Enrichment analysis revealed HOXB9 is mainly associated with cellular process, developmental process, P53 signaling pathway, etc. At the single-cell level, the clusters of cells ranked were glandular and luminal cells c-24, glandular and luminal cells c-9, endothelial cells c-15, compared with the other cells. At the genetic level, promoter methylation levels of HOXB9 were significantly higher in tumors than in normal tissues. Furthermore, variations of HOXB9 were closely associated with overall survival (OS) and recurrence free survival (RFS) in EC patients (P < 0.05). The agreement between univariate and multivariate Cox regression indicated that the results were more reliable. Stages III and IV, G2 and G3, tumor invasion ≥ 50%, mixed or serous histological type, age > 60 years, and high expression of HOXB9 were risk factors strongly associated with OS in EC patients (P < 0.05). Therefore, six factors were incorporated to construct a nomogram for survival prediction. Finally, we used the Kaplan-Meier (KM) curve, receiver operating characteristic (ROC) curve, and time-dependent ROC to assess predictive power of HOXB9. KM curve showed EC patients overexpressing HOXB9 had a worse OS. AUC of diagnostic ROC was 0.880. AUCs of time-dependent ROC were 0.602, 0.591, and 0.706 for 1-year, 5-year, and 10-year survival probabilities (P < 0.001). CONCLUSIONS Our study provids new insights into the diagnosis and prognosis of HOXB9 in EC and constructs a model that can accurately predict the prognosis of EC.
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Affiliation(s)
- Yanhua Xu
- grid.440642.00000 0004 0644 5481Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Medical School of Nantong University, No.20 Xi-Si Road, Nantong, 226001 Jiangsu China
| | - Mu Zhang
- grid.440642.00000 0004 0644 5481Department of Ophthalmology, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu China
| | - Qin Shi
- grid.440642.00000 0004 0644 5481Center For Reproductive Medicine, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu China
| | - Xi Cheng
- grid.440642.00000 0004 0644 5481Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Medical School of Nantong University, No.20 Xi-Si Road, Nantong, 226001 Jiangsu China
| | - Rong Du
- grid.440642.00000 0004 0644 5481Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Medical School of Nantong University, No.20 Xi-Si Road, Nantong, 226001 Jiangsu China
| | - Chenglu Li
- grid.440642.00000 0004 0644 5481Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Medical School of Nantong University, No.20 Xi-Si Road, Nantong, 226001 Jiangsu China
| | - Yuquan Zhang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Medical School of Nantong University, No.20 Xi-Si Road, Nantong, 226001, Jiangsu, China.
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Juárez-Rendón KJ, Castro-García MA, Prada-Ortega DG, Rivera G, Ruíz-Godoy LM, Enríquez-Cárcamo VI, Reyes-Lopez MA. Variants Identified in the HOXC13 and HOXD13 Genes Suggest Association with Cervical Cancer in a Cohort of Mexican Women. Genes (Basel) 2023; 14:genes14020358. [PMID: 36833285 PMCID: PMC9957514 DOI: 10.3390/genes14020358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/11/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
HOX genes have been associated with carcinogenesis. However, the molecular mechanism by which tumors are generated remains unclear. The HOXC13 and HOXD13 genes are of interest for their involvement in the development of genitourinary structures. The aim of this first study in the Mexican population was to search for and analyze variants in the coding region of the HOXC13 and HOXD13 genes in women with cervical cancer. Samples from Mexican women with cervical cancer and healthy women were sequenced (50/50). Allelic and genotypic frequencies were compared between groups. The functional impact of the proteins was determined with two bioinformatics servers (SIFT and PolyPhen-2), and the oncogenic potential of the identified nonsynonymous variants was determined using the CGI server. We identified five unreported gene variants: c.895C>A p.(Leu299Ile) and c.777C>T p.(Arg259Arg) in the HOXC13 gene and c.128T>A p.(Phe43Tyr), c.204G>A p.(Ala68Ala), and c.267G>A p.(Ser89Ser) in the HOXD13 gene. In this study, we suggest that the non-synonymous variants c.895C>A p.(Leu299Ile) and c.128T>A p.(Phe43Tyr) could represent a risk factor for the development of the disease, although additional studies in larger patient populations and in different ethnic groups are needed in order to support the results observed.
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Affiliation(s)
- Karina Janett Juárez-Rendón
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Blvd. del Maestro s/n. Esq. Elías Piña. Col. Narciso Mendoza, Reynosa 88710, Mexico
| | - Manuel Alejandro Castro-García
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Blvd. del Maestro s/n. Esq. Elías Piña. Col. Narciso Mendoza, Reynosa 88710, Mexico
| | - Diddier Giovanni Prada-Ortega
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10027, USA
- Unit for Biomedical Research in Cancer, Instituto Nacional de Cancerología, México City 14080, Mexico
- Department of Biomedical Informatics, Faculty of Medicine, Universidad Nacional Autónoma de México, México City 04510, Mexico
| | - Gildardo Rivera
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Blvd. del Maestro s/n. Esq. Elías Piña. Col. Narciso Mendoza, Reynosa 88710, Mexico
| | | | | | - Miguel Angel Reyes-Lopez
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Blvd. del Maestro s/n. Esq. Elías Piña. Col. Narciso Mendoza, Reynosa 88710, Mexico
- Correspondence: ; Tel.: +52-5557296000 (ext. 87751)
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Feng HM, Zhao Y, Yan WJ, Li B. Genomic and immunogenomic analysis of three prognostic signature genes in LUAD. BMC Bioinformatics 2023; 24:19. [PMID: 36650426 PMCID: PMC9843910 DOI: 10.1186/s12859-023-05137-y] [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: 07/29/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Searching for immunotherapy-related markers is an important research content to screen for target populations suitable for immunotherapy. Prognosis-related genes in early stage lung cancer may also affect the tumor immune microenvironment, which in turn affects immunotherapy. RESULTS We analyzed the differential genes affecting lung cancer patients receiving immunotherapy through the Cancer Treatment Response gene signature DataBase (CTR-DB), and set a threshold to obtain a total of 176 differential genes between response and non-response to immunotherapy. Functional enrichment analysis found that these differential genes were mainly involved in immune regulation-related pathways. The early-stage lung adenocarcinoma (LUAD) prognostic model was constructed through the cancer genome atlas (TCGA) database, and three target genes (MMP12, NFE2, HOXC8) were screened to calculate the risk score of early-stage LUAD. The receiver operating characteristic (ROC) curve indicated that the model had good prognostic value, and the validation set (GSE50081, GSE11969 and GSE42127) from the gene expression omnibus (GEO) analysis indicated that the model had good stability, and the risk score was correlated with immune infiltrations to varying degrees. Multi-type survival analysis and immune infiltration analysis revealed that the transcriptome, methylation and the copy number variation (CNV) levels of the three genes were correlated with patient prognosis and some tumor microenvironment (TME) components. Drug sensitivity analysis found that the three genes may affect some anti-tumor drugs. The mRNA expression of immune checkpoint-related genes showed significant differences between the high and low group of the three genes, and there may be a mutual regulatory network between immune checkpoint-related genes and target genes. Tumor immune dysfunction and exclusion (TIDE) analysis found that three genes were associated with immunotherapy response and maybe the potential predictors to immunotherapy, consistent with the CTR-DB database analysis. CONCLUSIONS From the perspective of data mining, this study suggests that MMP12, NFE2, and HOXC8 may be involved in tumor immune regulation and affect immunotherapy. They are expected to become markers of immunotherapy and are worthy of further experimental research.
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Affiliation(s)
- Hai-Ming Feng
- grid.411294.b0000 0004 1798 9345Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, 82 Cuiyingmen, Chengguan District, Lanzhou, 730030 Gansu People’s Republic of China
| | - Ye Zhao
- grid.411634.50000 0004 0632 4559Department of Radiotherapy, Gansu Provincial People’s Hospital, Lanzhou City, 730030 China
| | - Wei-Jian Yan
- grid.411294.b0000 0004 1798 9345Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, 82 Cuiyingmen, Chengguan District, Lanzhou, 730030 Gansu People’s Republic of China
| | - Bin Li
- grid.411294.b0000 0004 1798 9345Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, 82 Cuiyingmen, Chengguan District, Lanzhou, 730030 Gansu People’s Republic of China
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Oliva M, Demanelis K, Lu Y, Chernoff M, Jasmine F, Ahsan H, Kibriya MG, Chen LS, Pierce BL. DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits. Nat Genet 2023; 55:112-122. [PMID: 36510025 PMCID: PMC10249665 DOI: 10.1038/s41588-022-01248-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/26/2022] [Indexed: 12/14/2022]
Abstract
Studies of DNA methylation (DNAm) in solid human tissues are relatively scarce; tissue-specific characterization of DNAm is needed to understand its role in gene regulation and its relevance to complex traits. We generated array-based DNAm profiles for 987 human samples from the Genotype-Tissue Expression (GTEx) project, representing 9 tissue types and 424 subjects. We characterized methylome and transcriptome correlations (eQTMs), genetic regulation in cis (mQTLs and eQTLs) across tissues and e/mQTLs links to complex traits. We identified mQTLs for 286,152 CpG sites, many of which (>5%) show tissue specificity, and mQTL colocalizations with 2,254 distinct GWAS hits across 83 traits. For 91% of these loci, a candidate gene link was identified by integration of functional maps, including eQTMs, and/or eQTL colocalization, but only 33% of loci involved an eQTL and mQTL present in the same tissue type. With this DNAm-focused integrative analysis, we contribute to the understanding of molecular regulatory mechanisms in human tissues and their impact on complex traits.
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Affiliation(s)
- Meritxell Oliva
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
| | - Kathryn Demanelis
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yihao Lu
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Meytal Chernoff
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Institute for Population and Precision Health, University of Chicago, Chicago, IL, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
- Institute for Population and Precision Health, University of Chicago, Chicago, IL, USA
| | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
| | - Brandon L Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA.
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Segal D, Coulombe S, Sim J, Dostie J. A conserved HOTAIRM1-HOXA1 regulatory axis contributes early to neuronal differentiation. RNA Biol 2023; 20:1523-1539. [PMID: 37743644 PMCID: PMC10619521 DOI: 10.1080/15476286.2023.2258028] [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] [Accepted: 04/03/2023] [Indexed: 09/26/2023] Open
Abstract
HOTAIRM1 is unlike most long non-coding RNAs in that its sequence is highly conserved across mammals. Such evolutionary conservation points to it having a role in key cellular processes. We previously reported that HOTAIRM1 is required to curb premature activation of downstream HOXA genes in a cell model recapitulating their sequential induction during development. We found that it regulates 3' HOXA gene expression by a mechanism involving epigenetic and three-dimensional chromatin changes. Here we show that HOTAIRM1 participates in proper progression through the early stages of neuronal differentiation. We found that it can associate with the HOXA1 transcription factor and contributes to its downstream transcriptional program. Particularly, HOTAIRM1 affects the NANOG/POU5F1/SOX2 core pluripotency network maintaining an undifferentiated cell state. HOXA1 depletion similarly perturbed expression of these pluripotent factors, suggesting that HOTAIRM1 is a modulator of this transcription factor pathway. Also, given that binding of HOTAIRM1 to HOXA1 was observed in different cell types and species, our results point to this ribonucleoprotein complex as an integral part of a conserved HOTAIRM1-HOXA1 regulatory axis modulating the transition from a pluripotent to a differentiated neuronal state.
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Affiliation(s)
- Dana Segal
- Department of Biochemistry, and Rosalind & Morris Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
| | - Samy Coulombe
- Department of Biochemistry, and Rosalind & Morris Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
- School of Computer Science, and McGill Center for Bioinformatics, McGill University, Montréal, Québec, Canada
| | - Jasper Sim
- Department of Biochemistry, and Rosalind & Morris Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
| | - Josée Dostie
- Department of Biochemistry, and Rosalind & Morris Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
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Gattupalli M, Dey P, Poovizhi S, Patel RB, Mishra D, Banerjee S. The Prospects of RNAs and Common Significant Pathways in Cancer Therapy and Regenerative Medicine. Regen Med 2023. [DOI: 10.1007/978-981-19-6008-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Liu S, Zhang R, Yang Z, Wang Y, Guo X, Zhao Y, Lin H, Xiang Y, Ding C, Dong Z, Xu C. HOXA13 serves as a biomarker to predict neoadjuvant therapy efficacy in advanced colorectal cancer patients. Acta Biochim Biophys Sin (Shanghai) 2022; 55:304-313. [PMID: 36514224 PMCID: PMC10157630 DOI: 10.3724/abbs.2022182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Neoadjuvant therapy (NAT) for advanced colorectal cancer (ACRC) is a kind of well-evidenced therapy, yet a portion of ACRC patients have poor therapeutic response. To date, no suitable biomarker used for assessing NAT efficacy has been reported. Here, we collect 72 colonoscopy biopsy tissue specimens from ACRC patients before undergoing NAT and investigate the relationship between HOXA13 expression and NAT efficacy. The results show that HOXA13 expression in pretreated tumor specimens is negatively associated with tumor regression ( P<0.001) and progression-free survival ( P<0.05) in ACRC patients who underwent NAT. Silencing of HOXA13 or its regulator HOTTIP significantly enhances the chemosensitivity of colorectal cancer (CRC) cells, leading to an increase in cell apoptosis and the DNA damage response (DDR) to chemotherapeutic drug treatment. In contrast, HOXA13 overexpression causes a significant increase in chemoresistance in CRC cells. In summary, we find that the HOTTIP/HOXA13 axis is involved in regulating chemotherapeutic sensitivity in CRC cells by modulating the DDR and that HOXA13 serves as a promising marker for NAT efficacy prediction in ACRC patients.
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Affiliation(s)
- Shuanghui Liu
- Department of Colorectal Surgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China.,Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, China
| | - Rui Zhang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, China
| | - Zhengquan Yang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, China
| | - Yajiao Wang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, China
| | - Xingxiu Guo
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, China
| | - Youjuan Zhao
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, China
| | - Huangjue Lin
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, China
| | - Youqun Xiang
- Department of Colorectal Surgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Chunming Ding
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, China
| | - Zhixiong Dong
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, China
| | - Chang Xu
- Department of Colorectal Surgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
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Shaping Hox gene activity to generate morphological diversity across vertebrate phylogeny. Essays Biochem 2022; 66:717-726. [PMID: 35924372 DOI: 10.1042/ebc20220050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 02/07/2023]
Abstract
The importance of Hox genes for the development and evolution of the vertebrate axial skeleton and paired appendages has been recognized for already several decades. The steady growth of genomic sequence data from an increasing number of vertebrate species, together with the improvement of methods to analyze genomic structure and interactions, as well as to control gene activity in various species has refined our understanding of Hox gene activity in development and evolution. Here, I will review recent data addressing the influence of Hox regulatory processes in the evolution of the fins and the emergence of the tetrapod limb. In addition, I will discuss the involvement of posterior Hox genes in the control of vertebrate axial extension, focusing on an apparently divergent activity that Hox13 paralog group genes have on the regulation of tail bud development in mouse and zebrafish embryos.
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Ervin EH, French R, Chang CH, Pauklin S. Inside the stemness engine: Mechanistic links between deregulated transcription factors and stemness in cancer. Semin Cancer Biol 2022; 87:48-83. [PMID: 36347438 DOI: 10.1016/j.semcancer.2022.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/22/2022] [Accepted: 11/03/2022] [Indexed: 11/07/2022]
Abstract
Cell identity is largely determined by its transcriptional profile. In tumour, deregulation of transcription factor expression and/or activity enables cancer cell to acquire a stem-like state characterised by capacity to self-renew, differentiate and form tumours in vivo. These stem-like cancer cells are highly metastatic and therapy resistant, thus warranting a more complete understanding of the molecular mechanisms downstream of the transcription factors that mediate the establishment of stemness state. Here, we review recent research findings that provide a mechanistic link between the commonly deregulated transcription factors and stemness in cancer. In particular, we describe the role of master transcription factors (SOX, OCT4, NANOG, KLF, BRACHYURY, SALL, HOX, FOX and RUNX), signalling-regulated transcription factors (SMAD, β-catenin, YAP, TAZ, AP-1, NOTCH, STAT, GLI, ETS and NF-κB) and unclassified transcription factors (c-MYC, HIF, EMT transcription factors and P53) across diverse tumour types, thereby yielding a comprehensive overview identifying shared downstream targets, highlighting unique mechanisms and discussing complexities.
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Affiliation(s)
- Egle-Helene Ervin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Rhiannon French
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Chao-Hui Chang
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
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Phillips RV, Wei L, Cardenas A, Hubbard AE, McHale CM, Vermeulen R, Wei H, Smith MT, Zhang L, Lan Q, Rothman N. Epigenome-wide association studies of occupational exposure to benzene and formaldehyde. Epigenetics 2022; 17:2259-2277. [PMID: 36017556 PMCID: PMC9665125 DOI: 10.1080/15592294.2022.2115604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/04/2022] [Accepted: 08/17/2022] [Indexed: 11/03/2022] Open
Abstract
Sufficient evidence supports a relationship between certain myeloid neoplasms and exposure to benzene or formaldehyde. DNA methylation could underlie benzene- and formaldehyde-induced health outcomes, but data in exposed human populations are limited. We conducted two cross-sectional epigenome-wide association studies (EWAS), one in workers exposed to benzene and another in workers exposed to formaldehyde. Using HumanMethylation450 BeadChips, we investigated differences in blood cell DNA methylation among 50 benzene-exposed subjects and 48 controls, and among 31 formaldehyde-exposed subjects and 40 controls. We performed CpG-level and regional-level analyses. In the benzene EWAS, we found genome-wide significant alterations, i.e., FWER-controlled P-values <0.05, in the mean and variance of methylation at 22 and 318 CpG sites, respectively, and in mean methylation of a large genomic region. Pathway analysis of genes corresponding to benzene-associated differential methylation sites revealed an impact on the AMPK signalling pathway. In formaldehyde-exposed subjects compared to controls, 9 CpGs in the DUSP22 gene promoter had genome-wide significant decreased methylation variability and a large region of the HOXA5 promoter with 44 CpGs was hypomethylated. Our findings suggest that DNA methylation may contribute to the pathogenesis of diseases related to benzene and formaldehyde exposure. Aberrant expression and methylation of HOXA5 previously has been shown to be clinically significant in myeloid leukaemias. The tumour suppressor gene DUSP22 is a potential biomarker of exposure to formaldehyde, and irregularities have been associated with multiple exposures and diseases.
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Affiliation(s)
- Rachael V. Phillips
- School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Linqing Wei
- School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Andres Cardenas
- School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Alan E. Hubbard
- School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Cliona M. McHale
- School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Roel Vermeulen
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Universiteit Utrecht (UU), Utrecht, The Netherlands
| | - Hu Wei
- Division of Cancer Epidemiology and Genetics, Occupational and Environmental Epidemiology Branch, NCI, NIH, DHHS, Bethesda, MD, USA
| | - Martyn T. Smith
- School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Luoping Zhang
- School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, Occupational and Environmental Epidemiology Branch, NCI, NIH, DHHS, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, Occupational and Environmental Epidemiology Branch, NCI, NIH, DHHS, Bethesda, MD, USA
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48
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K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas. Nat Genet 2022; 54:1865-1880. [PMID: 36471070 PMCID: PMC9742294 DOI: 10.1038/s41588-022-01205-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/16/2022] [Indexed: 12/12/2022]
Abstract
Canonical (H3.1/H3.2) and noncanonical (H3.3) histone 3 K27M-mutant gliomas have unique spatiotemporal distributions, partner alterations and molecular profiles. The contribution of the cell of origin to these differences has been challenging to uncouple from the oncogenic reprogramming induced by the mutation. Here, we perform an integrated analysis of 116 tumors, including single-cell transcriptome and chromatin accessibility, 3D chromatin architecture and epigenomic profiles, and show that K27M-mutant gliomas faithfully maintain chromatin configuration at developmental genes consistent with anatomically distinct oligodendrocyte precursor cells (OPCs). H3.3K27M thalamic gliomas map to prosomere 2-derived lineages. In turn, H3.1K27M ACVR1-mutant pontine gliomas uniformly mirror early ventral NKX6-1+/SHH-dependent brainstem OPCs, whereas H3.3K27M gliomas frequently resemble dorsal PAX3+/BMP-dependent progenitors. Our data suggest a context-specific vulnerability in H3.1K27M-mutant SHH-dependent ventral OPCs, which rely on acquisition of ACVR1 mutations to drive aberrant BMP signaling required for oncogenesis. The unifying action of K27M mutations is to restrict H3K27me3 at PRC2 landing sites, whereas other epigenetic changes are mainly contingent on the cell of origin chromatin state and cycling rate.
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49
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Mohammadi E, Aliarab A, Babaei G, Habibi NK, Jafari SM, Mir SM, Memar MY. MicroRNAs in esophageal squamous cell carcinoma: Application in prognosis, diagnosis, and drug delivery. Pathol Res Pract 2022; 240:154196. [PMID: 36356334 DOI: 10.1016/j.prp.2022.154196] [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: 09/02/2022] [Revised: 10/26/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022]
Abstract
MicroRNAs (miRNAs) play a vital role in various cell biology processes, including cancer formation. These small non-coding RNAs could function as diagnostic and prognostic markers. They may involve esophageal squamous cell carcinoma (ESCC) and distinctive miRNA expression profiles; they are also known as therapeutic targets in human diseases. Therefore, in this study, the function of miRNAs was reviewed regarding the prognosis and diagnosis of ESCC. The changes in miRNAs before and after cancer therapy and the effects of miRNAs on chemo-susceptibility patterns were also investigated. MiRNA delivery systems in ESCC were also highlighted, providing a perspective on how these systems can improve miRNA efficiency.
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Affiliation(s)
- Elahe Mohammadi
- Department of Nutrition, Khalkhal University of Medical Sciences, Khalkhal, Iran
| | - Azadeh Aliarab
- Department of Clinical Biochemistry, School of Medicine, Tarbiat Modares University, Tehran, Iran
| | - Ghader Babaei
- Department of Clinical Biochemistry, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Nasim Kouhi Habibi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Seyyed Mehdi Jafari
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
| | - Seyed Mostafa Mir
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
| | - Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran.
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50
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Park HW, Kim YR, Lee JY, Ko EJ, Kwon MJ, Kim JH, Kim NK. Association of Polymorphisms in the Long Non-Coding RNA HOTAIR with Recurrent Pregnancy Loss in a Korean Population. Genes (Basel) 2022; 13:2138. [PMID: 36421813 PMCID: PMC9690393 DOI: 10.3390/genes13112138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/05/2022] [Accepted: 11/11/2022] [Indexed: 01/21/2024] Open
Abstract
Recurrent pregnancy loss (RPL) affects 1% to 5% of women, with devastating effects on both reproductive health and psychological well-being. Homeobox (HOX) transcript antisense RNA (HOTAIR) is a long non-coding RNA (lncRNA) produced by HOXC; it plays a major role in invasion and development of ovarian and other cancers. The aim of the present study was to analyze effects of HOTAIR polymorphisms (rs4759314 A>G, rs920778 T>C, rs1899663 G>T, and rs7958904 G>C) on RPL in Korean women. A total of 403 women with RPL and 383 healthy women were selected for this study. Genotyping analysis was performed with the polymerase chain reaction, restriction fragment length polymorphism, and the TaqMan genotyping assay. Clinical characteristics were compared using Student's unpaired t-test and the chi-square test for categorical variables. Logistic regression was performed to evaluate associations between single nucleotide polymorphisms and RPL incidence. In all assays, p < 0.05 was considered significant. HOTAIR polymorphisms rs4759314A>G and rs920778T>C were highly associated with increased risk of RPL, specifically the haplotypes rs4759314A>G/rs1899663G>T (G-T) and rs4759314A>G/rs920778 T>C (G-C). These associations were maintained in haplotypes that contained three polymorphisms (rs4759314 A>G, rs920778 T>C, and rs1899663 G>T) A-C-G, G-T-G, and G-T-T, further indicating that the HOTAIR rs4759314 and rs920778 polymorphisms play significant roles in idiopathic RPL in Korean women.
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Affiliation(s)
- Hyeon Woo Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Young Ran Kim
- CHA Bundang Medical Center, Department of Obstetrics and Gynecology, School of Medicine, CHA University, Seongnam 13496, Republic of Korea
| | - Jeong Yong Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Eun Ju Ko
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Min Jung Kwon
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Ji Hyang Kim
- CHA Bundang Medical Center, Department of Obstetrics and Gynecology, School of Medicine, CHA University, Seongnam 13496, Republic of Korea
| | - Nam Keun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
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