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Zaidi SAA, Chughtai N, Abbassi ZA, Alam J, Malick TS, Salim A, Saleem S. TUSC3, p53 and p21 genetic association with development of oral submucous fibrosis and oral squamous cell carcinoma among addictive tobacco chewers of Pakistan. BMC Oral Health 2024; 24:780. [PMID: 38992585 PMCID: PMC11241966 DOI: 10.1186/s12903-024-04501-5] [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: 03/07/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND This study delves into the intricate landscape of oral cancer, a global concern with a high incidence in Asian countries. We focus on oral squamous cell carcinoma (OSCC), primarily driven by the consumption of betel nut and its derivatives. OSCC often arises from premalignant lesions like oral submucous fibrosis (OSF). In Pakistan, OSCC is prevalent among men due to various addictive substances, including smokeless tobacco and chewing materials. Mutations in tumor suppressor genes, such as TP53 and p21, play crucial roles in this malignancy's development. We also explore the involvement of TUSC3 gene deletion in OSCC and OSF. METHODS In this study we investigated demographics, TUSC3 gene expression, deletion analysis, and TP53 and p21 genetic alterations in OSCC and OSF patients (blood and tissue of 50 samples in each condition) who had tobacco derivates usage history. The association analysis was carried out mainly through PCR based genotyping. RESULTS The study's patient cohort (OSCC and OSF) displayed a wide age range from 13 to 65 years (Mean = 32.96 years). Both conditions were more prevalent in males, with a male-female ratio of approximately 2.5:1. Chewing habits analysis revealed high frequencies of gutka use in both OSF and OSCC patients. TUSC3 expression analysis in OSCC cell lines indicated significant downregulation. Genotyping showed no TUSC3 deletion in OSF cases, but a deletion rate of over 22% in OSCC tissue samples. Analysis supported a significant association of TUSC3 deletion with OSCC development but not with OSF. Polymorphism in p53 exon 4 and p21 (rs1801270) were significantly associated with both OSCC and OSF, adding to their pathogenesis. Our findings further revealed a strong correlation between TUSC3 deletion and the excessive use of tobacco and related products, shedding light on the genetic underpinnings of OSCC development. CONCLUSIONS Notably, our study provides a crucial insight into genetic aspects underlying OSCC and OSF in response of addictive consumption of areca nut, betel quid, and tobacco derivatives. A significant association between TUSC3 deletion and OSCC development, along with polymorphisms in TP53 and p21, underscores the importance of further research into the molecular mechanisms driving oral cancer progression for improved diagnosis and treatment outcomes.
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Affiliation(s)
- Syed Aqib Ali Zaidi
- The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Karachi, Pakistan
- Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, China
| | | | - Zubair Ahmed Abbassi
- Department of Dentistry, Jinnah Sindh Medical University (JSMU), Karachi, Pakistan
| | - Jehan Alam
- Department of Dentistry, Jinnah Postgraduate Medical Centre (JPMC), Karachi, 75510, Pakistan
| | - Tuba Shakil Malick
- Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Asmat Salim
- Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Saima Saleem
- The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Karachi, Pakistan.
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Stocker N, Radzikowska U, Wawrzyniak P, Tan G, Huang M, Ding M, Akdis CA, Sokolowska M. Regulation of angiotensin-converting enzyme 2 isoforms by type 2 inflammation and viral infection in human airway epithelium. Mucosal Immunol 2023; 16:5-16. [PMID: 36642382 PMCID: PMC9836991 DOI: 10.1016/j.mucimm.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 12/06/2022] [Indexed: 01/15/2023]
Abstract
SARS-CoV-2 enters human cells through its main receptor, angiotensin-converting enzyme 2 (ACE2), which constitutes a limiting factor of infection. Recent findings demonstrating novel ACE2 isoforms implicate that this receptor is regulated in a more complex way than previously anticipated. However, it remains unknown how various inflammatory conditions influence the abundance of these ACE2 variants. Hence, we studied expression of ACE2 messenger RNA (mRNA) and protein isoforms, together with its glycosylation and spatial localization in primary human airway epithelium upon allergic inflammation and viral infection. We found that interleukin-13, the main type 2 cytokine, decreased expression of long ACE2 mRNA and reduced glycosylation of full-length ACE2 protein via alteration of N-linked glycosylation process, limiting its availability on the apical side of ciliated cells. House dust mite allergen did not affect the expression of ACE2. Rhinovirus infection increased short ACE2 mRNA, but it did not influence its protein expression. In addition, by screening other SARS-CoV-2 related host molecules, we found that interleukin-13 and rhinovirus significantly regulated mRNA, but not protein of transmembrane serine protease 2 and neuropilin 1. Regulation of ACE2 and other host proteins was comparable in healthy and asthmatic epithelium, underlining the lack of intrinsic differences but dependence on the inflammatory milieu in the airways.
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Affiliation(s)
- Nino Stocker
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Urszula Radzikowska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland; Christine Kühne - Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Paulina Wawrzyniak
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland; Department of Gastroenterology and Hepatology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
| | - Ge Tan
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Mengting Huang
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Mei Ding
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland; Christine Kühne - Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland; Christine Kühne - Center for Allergy Research and Education (CK-CARE), Davos, Switzerland.
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Alldredge J, Kumar V, Nguyen J, Sanders BE, Gomez K, Jayachandran K, Zhang J, Schwarz J, Rahmatpanah F. Endogenous Retrovirus RNA Expression Differences between Race, Stage and HPV Status Offer Improved Prognostication among Women with Cervical Cancer. Int J Mol Sci 2023; 24:1492. [PMID: 36675007 PMCID: PMC9864224 DOI: 10.3390/ijms24021492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/29/2022] [Accepted: 12/31/2022] [Indexed: 01/15/2023] Open
Abstract
Endogenous human retroviruses (ERVs) are remnants of exogenous retroviruses that have integrated into the human genome. Using publicly available RNA-seq data from 63 cervical cancer patients, we investigated the expression of ERVs in cervical cancers. Four aspects of cervical cancer were investigated: patient ancestral background, tumor HPV type, tumor stage and patient survival. Between the racial subgroups, 74 ERVs were significantly differentially expressed, with Black Americans having 30 upregulated and 44 downregulated (including MER21C, HERV9-int, and HERVH-int) ERVs when compared to White Americans. We found that 3313 ERVs were differentially expressed between HPV subgroups, including MER41A, HERVH-int and HERVK9. There were 28 downregulated (including MLT1D and HERVH-int) and 61 upregulated (including MER41A) ERVs in locally advanced-stage compared to early-stage samples. Tissue microarrays of cervical cancer patients were used to investigate the protein expression of ERVs with protein coding potential (i.e., HERVK and ERV3). Significant differences in protein expression of ERV3 (p = 0.000905) were observed between early-stage and locally advanced-stage tumors. No significant differential expression at the protein level was found for HERVK7 (p = 0.243). We also investigated a prognostic model, supplementing a baseline prediction model using FIGO stage, age and HPV positivity with ERVs data. The expression levels of all ERVs in the HERVd were input into a Lasso-Cox proportional hazards model, developing a predictive 67-ERV panel. When ERVs expression levels were supplemented with the clinical data, a significant increase in prognostic power (p = 9.433 × 10-15) relative to that obtained with the clinical parameters alone (p = 0.06027) was observed. In summary, ERV RNA expression in cervical cancer tumors is significantly different among racial cohorts, HPV subgroups and disease stages. The combination of the expression of certain ERVs in cervical cancers with clinical factors significantly improved prognostication compared to clinical factors alone; therefore, ERVs may serve as future prognostic biomarkers and therapeutic targets. Novelty and Impact: When endogenous retroviral (ERV) expression signatures were combined with currently employed clinical prognosticators of relapse of cervical cancer, the combination outperformed prediction models based on clinical prognosticators alone. ERV expression signatures in tumor biopsies may therefore be useful to help identify patients at greater risk of recurrence. The novel ERV expression signatures or adjacent genes possibly impacted by ERV expression described here may also be targets for the development of future therapeutic interventions.
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Affiliation(s)
- Jill Alldredge
- Department of Obstetrics and Gynecology, University of Colorado, Aurora, CO 80045, USA
| | - Vinay Kumar
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - James Nguyen
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Brooke E. Sanders
- Department of Obstetrics and Gynecology, University of Colorado, Aurora, CO 80045, USA
| | - Karina Gomez
- Department of Obstetrics and Gynecology, University of Colorado, Aurora, CO 80045, USA
| | - Kay Jayachandran
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jin Zhang
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63108, USA
- Institute for Informatics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Julie Schwarz
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA
- Institute for Informatics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Farah Rahmatpanah
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
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Vadgama N, Ameen M, Sundaram L, Gaddam S, Gifford C, Nasir J, Karakikes I. De novo and inherited variants in coding and regulatory regions in genetic cardiomyopathies. Hum Genomics 2022; 16:55. [PMID: 36357925 PMCID: PMC9647983 DOI: 10.1186/s40246-022-00420-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/24/2022] [Indexed: 11/11/2022] Open
Abstract
Abstract
Background
Cardiomyopathies are a leading cause of progressive heart failure and sudden cardiac death; however, their genetic aetiology remains poorly understood. We hypothesised that variants in noncoding regulatory regions and oligogenic inheritance mechanisms may help close the diagnostic gap.
Methods
We first analysed whole-genome sequencing data of 143 parent–offspring trios from Genomics England 100,000 Genomes Project. We used gene panel testing and a phenotype-based, variant prioritisation framework called Exomiser to identify candidate genes in trios. To assess the contribution of noncoding DNVs to cardiomyopathies, we intersected DNVs with open chromatin sequences from single-cell ATAC-seq data of cardiomyocytes. We also performed a case–control analysis in an exome-negative cohort, including 843 probands and 19,467 controls, to assess the association between noncoding variants in known cardiomyopathy genes and disease.
Results
In the trio analysis, a definite or probable genetic diagnosis was identified in 21 probands according to the American College of Medical Genetics guidelines. We identified novel DNVs in diagnostic-grade genes (RYR2, TNNT2, PTPN11, MYH7, LZR1, NKX2-5), and five cases harbouring a combination of prioritised variants, suggesting that oligogenic inheritance and genetic modifiers contribute to cardiomyopathies. Phenotype-based ranking of candidate genes identified in noncoding DNV analysis revealed JPH2 as the top candidate. Moreover, a case–control analysis revealed an enrichment of rare noncoding variants in regulatory elements of cardiomyopathy genes (p = .035, OR = 1.43, 95% Cl = 1.095–1.767) versus controls. Of the 25 variants associated with disease (p< 0.5), 23 are novel and nine are predicted to disrupt transcription factor binding motifs.
Conclusion
Our results highlight complex genetic mechanisms in cardiomyopathies and reveal novel genes for future investigations.
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Deng R, Lu X, Hong C, Cai R, Wang P, Xiong L, Wang X, Chen Q, Lin J. Downregulation of TUSC3 promotes EMT and hepatocellular carcinoma progression through LIPC/AKT axis. Lab Invest 2022; 20:485. [PMID: 36274132 PMCID: PMC9590144 DOI: 10.1186/s12967-022-03690-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/06/2022] [Indexed: 11/26/2022]
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most common and malignant tumors in the digestive tract. Tumor Suppressor Candidate 3 (TUSC3) is one subunit of the endoplasmic reticulum Oligosaccharyl transferase (OST) complex, which plays an important role in N-glycosylation during the protein folding process. However, the role of TUSC3 in the initiation and progression of HCC has not been mentioned yet. In the present study, we aim to investigate the effects of TUSC3 on the initiation and progression of HCC. Methods Immunohistochemical assay and qRT-PCR were used to detect the expression of TUSC3 and lipase C hepatic type (LIPC) in HCC tissue and cells. Loss-of-function and gain-of-function were applied to detect the function of TUSC3 and LIPC in vivo and in vitro. Immunofluorescence assay and co-immunoprecipitation were used to detect the relationship between TUSC3 and LPC. Western blot was applied to detect the expression of epithelial–mesenchymal transition (EMT) markers and the Akt signaling pathway. Results TUSC3 was aberrantly decreased in hepatocellular carcinoma tissues compared to the matched adjacent normal tissues, which resulted in bigger size of tumor (P = 0.001, Table 2), worse differentiation (P = 0.006, Table 2) and an advanced BCLC stage. Down-regulation of TUSC3 led to the enhanced proliferation and migration of hepatocellular carcinoma cells in vivo and vitro, whereas the opposite effect could be observed in the TUSC3-overexpression group. The analysis of TUSC3 microarray showed that LIPC, a glycoprotein primarily synthesized and secreted by hepatocytes, was a downstream target of TUSC3, and it negatively modulated the development of HCC. The morphological changes in HCC cells indicated that TUSC3 regulated the epithelial-mesenchymal transition (EMT). Mechanistically, TUSC3 inhibited EMT progression through the LIPC/AKT axis. Conclusion Down-regulation of TUSC3 promotes EMT progression by activating AKT signaling via targeting LIPC in HCC, which is probably the possible mechanism driving TUSC3-deficient hepatocellular carcinoma cells toward a malignant phenotype.
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Yeh SJ, Chen BS. Systems Medicine Design based on Systems Biology Approaches and Deep Neural Network for Gastric Cancer. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3019-3031. [PMID: 34232888 DOI: 10.1109/tcbb.2021.3095369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Gastric cancer (GC) is the third leading cause of cancer death in the world. It is associated with the stimulation of microenvironment, aberrant epigenetic modification, and chronic inflammation. However, few researches discuss the GC molecular progression mechanisms from the perspective of the system level. In this study, we proposed a systems medicine design procedure to identify essential biomarkers and find corresponding drugs for GC. At first, we did big database mining to construct candidate protein-protein interaction network (PPIN) and candidate gene regulation network (GRN). Second, by leveraging the next-generation sequencing (NGS) data, we performed system modeling and applied system identification and model selection to obtain real genome-wide genetic and epigenetic networks (GWGENs). To make the real GWGENs easy to analyze, the principal network projection method was used to extract the core signaling pathways denoted by KEGG pathways. Subsequently, based on the identified biomarkers, we trained a deep neural network of drug-target interaction (DeepDTI) with supervised learning and filtered our candidate drugs considering drug regulation ability and drug sensitivity. With the proposed systematic strategy, we not only shed the light on the progression of GC but also suggested potential multiple-molecule drugs efficiently.
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Chang Wu Z, Wang Y, Huang X, Wu S, Bao W. A genome-wide association study of important reproduction traits in large white pigs. Gene 2022; 838:146702. [PMID: 35772658 DOI: 10.1016/j.gene.2022.146702] [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: 01/25/2022] [Revised: 06/13/2022] [Accepted: 06/24/2022] [Indexed: 11/04/2022]
Abstract
Augmenting the reproductive efficiency of sows remains the predominant challenge in the swine industry. This work was aimed at scrutinizing vital genetic markers for reproductive traits in this animal. This entailed probing of the records of vital attributes of Large White pigs (n = 695) inclusive of the total number of born (TNB), number of born alive (NBA), number of weaned pigs (NWP), number of healthy births (NHS), total litter weight of piglets born alive (BALWT), weaning litter weight (WNWT), and corrected litter weight at 21 days (W21). A genome-wide association study (GWAS) for the four litter traits and three traits of litter weight in the Denmark Large White population then ensued. We discovered seven significantly related SNPs and eleven potential candidate genes (e.g., TUSC3, THRB for TNB; STT3B for NBA). The subsequent functional enrichment analysis of these genes showed that the significant gene were associated with steroid hormone receptor activity. Our findings indicated that the genes TUSC3, THRB and STT3B probably contribute to litter traits in this population. This work reveals genetic mechanisms of reproduction traits and also supports ensuing genetic improvement employing marker-assisted selection in Large White pigs.
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Affiliation(s)
- Zheng Chang Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China; College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, P. R. China.
| | - Yifu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China.
| | - Xiaoguo Huang
- Jiangsu Engineering Research Centre for Molecular Breeding of Pig, Changzhou 215000, Jiangsu Province, China.
| | - Shenglong Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China.
| | - Wenbin Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China.
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Powell DR, Revelli JP, Doree DD, DaCosta CM, Desai U, Shadoan MK, Rodriguez L, Mullens M, Yang QM, Ding ZM, Kirkpatrick LL, Vogel P, Zambrowicz B, Sands AT, Platt KA, Hansen GM, Brommage R. High-Throughput Screening of Mouse Gene Knockouts Identifies Established and Novel High Body Fat Phenotypes. Diabetes Metab Syndr Obes 2021; 14:3753-3785. [PMID: 34483672 PMCID: PMC8409770 DOI: 10.2147/dmso.s322083] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/04/2021] [Indexed: 01/05/2023] Open
Abstract
PURPOSE Obesity is a major public health problem. Understanding which genes contribute to obesity may better predict individual risk and allow development of new therapies. Because obesity of a mouse gene knockout (KO) line predicts an association of the orthologous human gene with obesity, we reviewed data from the Lexicon Genome5000TM high throughput phenotypic screen (HTS) of mouse gene KOs to identify KO lines with high body fat. MATERIALS AND METHODS KO lines were generated using homologous recombination or gene trapping technologies. HTS body composition analyses were performed on adult wild-type and homozygous KO littermate mice from 3758 druggable mouse genes having a human ortholog. Body composition was measured by either DXA or QMR on chow-fed cohorts from all 3758 KO lines and was measured by QMR on independent high fat diet-fed cohorts from 2488 of these KO lines. Where possible, comparisons were made to HTS data from the International Mouse Phenotyping Consortium (IMPC). RESULTS Body fat data are presented for 75 KO lines. Of 46 KO lines where independent external published and/or IMPC KO lines are reported as obese, 43 had increased body fat. For the remaining 29 novel high body fat KO lines, Ksr2 and G2e3 are supported by data from additional independent KO cohorts, 6 (Asnsd1, Srpk2, Dpp8, Cxxc4, Tenm3 and Kiss1) are supported by data from additional internal cohorts, and the remaining 21 including Tle4, Ak5, Ntm, Tusc3, Ankk1, Mfap3l, Prok2 and Prokr2 were studied with HTS cohorts only. CONCLUSION These data support the finding of high body fat in 43 independent external published and/or IMPC KO lines. A novel obese phenotype was identified in 29 additional KO lines, with 27 still lacking the external confirmation now provided for Ksr2 and G2e3 KO mice. Undoubtedly, many mammalian obesity genes remain to be identified and characterized.
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Affiliation(s)
- David R Powell
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Jean-Pierre Revelli
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Deon D Doree
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Christopher M DaCosta
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Urvi Desai
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Melanie K Shadoan
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Lawrence Rodriguez
- Department of Information Technology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Michael Mullens
- Department of Information Technology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Qi M Yang
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Zhi-Ming Ding
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Laura L Kirkpatrick
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Peter Vogel
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Brian Zambrowicz
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
- Department of Information Technology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Arthur T Sands
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
- Department of Information Technology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Kenneth A Platt
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Gwenn M Hansen
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Robert Brommage
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
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Zhang L, Zhang W, Li H, Tang X, Xu S, Wu M, Wan L, Su F, Zhang Y. Five Circular RNAs in Metabolism Pathways Related to Prostate Cancer. Front Genet 2021; 12:636419. [PMID: 33574834 PMCID: PMC7870709 DOI: 10.3389/fgene.2021.636419] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
Prostate cancer (PCa) is the most common malignant tumor in men, and its incidence increases with age. Serum prostate-specific antigen and tissue biopsy remain the standard for diagnosis of suspected PCa. However, these clinical indicators may lead to aggressive overtreatment in patients who have been treated sufficiently with active surveillance. Circular RNAs (circRNAs) have been recently recognized as a new type of regulatory RNA that is not easily degraded by RNases and other exonucleases because of their covalent closed cyclic structure. Thus, we utilized high-throughput sequencing data and bioinformatics analysis to identify specifically expressed circRNAs in PCa and filtered out five specific circRNAs for further analysis—hsa_circ_0006410, hsa_circ_0003970, hsa_circ_0006754, hsa_circ_0005848, and a novel circRNA, hsa_circ_AKAP7. We constructed a circRNA-miRNA regulatory network and used miRNA and differentially expressed mRNA interactions to predict the function of the selected circRNAs. Furthermore, survival analysis of their cognate genes and PCR verification of these five circRNAs revealed that they are closely related to well-known PCa pathways such as the MAPK signaling pathway, P53 pathway, androgen receptor signaling pathway, cell cycle, hormone-mediated signaling pathway, and cellular lipid metabolic process. By understanding the related metabolism of circRNAs, these circRNAs could act as metabolic biomarkers, and monitoring their levels could help diagnose PCa. Meanwhile, the exact regulatory mechanism for AR-related regulation in PCa is still unclear. The circRNAs we found can provide new solutions for research in this field.
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Affiliation(s)
- Lili Zhang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Zhang
- Department of Pathology, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hexin Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaokun Tang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Siyuan Xu
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Meng Wu
- Department of Urology, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Li Wan
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Su
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yaqun Zhang
- Department of Urology, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
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Hui AS, Chau MHK, Chan YM, Cao Y, Kwan AH, Zhu X, Kwok YK, Chen Z, Lao TT, Choy KW, Leung TY. The role of chromosomal microarray analysis among fetuses with normal karyotype and single system anomaly or nonspecific sonographic findings. Acta Obstet Gynecol Scand 2020; 100:235-243. [PMID: 32981064 DOI: 10.1111/aogs.14003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/19/2020] [Accepted: 09/17/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Chromosomal microarray analysis is recommended as the first-tier test for the evaluation of fetuses with structural anomalies. This study aims to investigate the incremental diagnostic yield of chromosomal microarray over conventional karyotyping analysis in fetuses with anomalies restricted to one anatomic system and those with nonspecific anomalies detected by sonography. MATERIAL AND METHODS This is a retrospective cohort analysis of 749 fetuses undergoing prenatal diagnosis for abnormal ultrasound findings isolated to one anatomic system and normal karyotype, utilizing chromosomal microarray. Overall, 495 (66%) fetuses had anomalies confined to one anatomic system and 254 (34%) had other nonspecific anomalies including increased nuchal translucency (≥3.5 mm), cystic hygroma, intrauterine growth restriction and hydrops fetalis. RESULTS Fetuses with ultrasound anomalies restricted to one anatomic system had a 3.0% risk of carrying a pathogenic copy number variant; the risk varied dependent on the anatomic system affected. Fetuses with confined anomalies of the cardiac system had the highest diagnostic yield at 4.6%, but there were none in the urogenital system. Fetuses with nonspecific ultrasound anomalies had the highest diagnostic yield in fetuses with an intrauterine growth restriction at 5.9%. Overall, fetuses with a nonspecific ultrasound anomaly were affected with pathogenic copy number variants in 1.6% in the cases. CONCLUSIONS The diagnostic yield of chromosomal microarray in fetuses with normal karyotype and ultrasound abnormality confined to a single anatomic system was highest if it involved cardiac defects or intrauterine growth restriction. This diagnostic yield ranges from 0% to 4.6% depending on the anatomic system involved. Chromosomal microarray has considerable diagnostic value in these pregnancies.
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Affiliation(s)
- Annie Sy Hui
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yiu Man Chan
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Adept Medical Center, Hong Kong SAR, China
| | - Ye Cao
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Angel Hw Kwan
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiaofan Zhu
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yvonne K Kwok
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zihan Chen
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Terence T Lao
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kwong Wai Choy
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, China, Hong Kong SAR, China
| | - Tak Yeung Leung
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, China, Hong Kong SAR, China
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Kong L, Sun Y, Chen M, Dai Y, Liu Z. Downregulation of microRNA-320a inhibits proliferation and induces apoptosis of retinoblastoma cells via targeting TUSC3. Exp Ther Med 2020; 20:9. [PMID: 32934674 PMCID: PMC7471862 DOI: 10.3892/etm.2020.9137] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 05/20/2020] [Indexed: 02/07/2023] Open
Abstract
MicroRNA (miR)-320a is specific to vertebrates and has been indicated to serve a role in a number of cancer types, such as gastric, colorectal, pancreatic and ovarian cancer. miR-320a has been reported to be expressed at high levels in retinoblastoma tissues; however its role and mechanism of function in retinoblastoma remain to be elucidated. The aim of the present study was to investigate the role of miR-320a in retinoblastoma cells and the underlying mechanisms. The expression of miR-320a in retinoblastoma cell lines Y79 and WERI-Rb-1, and normal human retinal pigment epithelial cell line ARPE-19 was examined via reverse transcription-quantitative PCR (RT-qPCR). TargetScan bioinformatics analysis and dual-luciferase reporter assay were used to predict and reveal the target gene of miR-320a. Target gene expression was detected via RT-qPCR in retinoblastoma cell lines and ARPE-19 cells. Subsequently, gain- or loss-of-function experiments for miR-320a and tumor suppressor candidate 3 (TUSC3) were performed to study the role of miR-320a/TUSC3 in retinoblastoma cells. Cell viability and apoptosis were assessed via MTT and flow cytometry analysis, respectively. Compared with ARPE-19 cells, miR-320a was prominently expressed in retinoblastoma cell lines. TUSC3 was predicted to be a target gene of miR-320a. Compared with ARPE-19 cells, the expression of TUSC3 in retinoblastoma cell lines was reduced. The results of MTT and flow cytometry analysis revealed that overexpression of TUSC3 reduced the viability of retinoblastoma cells and induced apoptosis. Additional analysis indicated that miR-320a inhibitor enhanced the expression of the target gene TUSC3, thereby inhibiting retinoblastoma cell viability and inducing apoptosis. The effects of miR-320a inhibitor on retinoblastoma cells were inhibited by TUSC3-short hairpin RNA. miR-320a regulated the viability and apoptosis of retinoblastoma cells via targeting TUSC3. Therefore, the present study provided a reference for investigating a potential target for the clinical treatment of retinoblastoma.
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Affiliation(s)
- Li Kong
- Department of Ophthalmology, Chongqing Aier Eye Hospital, Chongqing 400020, P.R. China
| | - Yang Sun
- Department of Ophthalmology, Chongqing Aier Eye Hospital, Chongqing 400020, P.R. China
| | - Maosheng Chen
- Department of Ophthalmology, Chongqing Aier Eye Hospital, Chongqing 400020, P.R. China
| | - Yan Dai
- Department of Ophthalmology, Mianyang Central Hospital, Mianyang, Sichuan 621000, P.R. China
| | - Zhen Liu
- Department of Ophthalmology, Chongqing Aier Eye Hospital, Chongqing 400020, P.R. China
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Sabo A, Murdock D, Dugan S, Meng Q, Gingras MC, Hu J, Muzny D, Gibbs R. Community-based recruitment and exome sequencing indicates high diagnostic yield in adults with intellectual disability. Mol Genet Genomic Med 2020; 8:e1439. [PMID: 32767738 PMCID: PMC7549560 DOI: 10.1002/mgg3.1439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/12/2020] [Accepted: 07/01/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Establishing a genetic diagnosis for individuals with intellectual disability (ID) benefits patients and their families as it may inform the prognosis, lead to appropriate therapy, and facilitate access to medical and supportive services. Exome sequencing has been successfully applied in a diagnostic setting, but most clinical exome referrals are pediatric patients, with many adults with ID lacking a comprehensive genetic evaluation. METHODS Our unique recruitment strategy involved partnering with service and education providers for individuals with ID. We performed exome sequencing and analysis, and clinical variant interpretation for each recruited family. RESULTS All five families enrolled in the study opted-in for the return of genetic results. In three out of five families exome sequencing analysis identified pathogenic or likely pathogenic variants in KANSL1, TUSC3, and MED13L genes. Families discussed the results and any potential medical follow-up in an appointment with a board certified clinical geneticist. CONCLUSION Our study suggests high yield of exome sequencing as a diagnostic tool in adult patients with ID who have not undergone comprehensive sequencing-based genetic testing. Research studies including an option of return of results through a genetic clinic could help minimize the disparity in exome diagnostic testing between pediatric and adult patients with ID.
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Affiliation(s)
- Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - David Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
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Platelets and Defective N-Glycosylation. Int J Mol Sci 2020; 21:ijms21165630. [PMID: 32781578 PMCID: PMC7460655 DOI: 10.3390/ijms21165630] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022] Open
Abstract
N-glycans are covalently linked to an asparagine residue in a simple acceptor sequence of proteins, called a sequon. This modification is important for protein folding, enhancing thermodynamic stability, and decreasing abnormal protein aggregation within the endoplasmic reticulum (ER), for the lifetime and for the subcellular localization of proteins besides other functions. Hypoglycosylation is the hallmark of a group of rare genetic diseases called congenital disorders of glycosylation (CDG). These diseases are due to defects in glycan synthesis, processing, and attachment to proteins and lipids, thereby modifying signaling functions and metabolic pathways. Defects in N-glycosylation and O-glycosylation constitute the largest CDG groups. Clotting and anticlotting factor defects as well as a tendency to thrombosis or bleeding have been described in CDG patients. However, N-glycosylation of platelet proteins has been poorly investigated in CDG. In this review, we highlight normal and deficient N-glycosylation of platelet-derived molecules and discuss the involvement of platelets in the congenital disorders of N-glycosylation.
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Whole-Organ Genomic Characterization of Mucosal Field Effects Initiating Bladder Carcinogenesis. Cell Rep 2020; 26:2241-2256.e4. [PMID: 30784602 DOI: 10.1016/j.celrep.2019.01.095] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 12/12/2018] [Accepted: 01/25/2019] [Indexed: 12/13/2022] Open
Abstract
We used whole-organ mapping to study the locoregional molecular changes in a human bladder containing multifocal cancer. Widespread DNA methylation changes were identified in the entire mucosa, representing the initial field effect. The field effect was associated with subclonal low-allele frequency mutations and a small number of DNA copy alterations. A founder mutation in the RNA splicing gene, ACIN1, was identified in normal mucosa and expanded clonally with an additional 21 mutations in progression to carcinoma. The patterns of mutations and copy number changes in carcinoma in situ and foci of carcinoma were almost identical, confirming their clonal origins. The pathways affected by the DNA copy alterations and mutations, including the Kras pathway, were preceded by the field changes in DNA methylation, suggesting that they reinforced mechanisms that had already been initiated by methylation. The results demonstrate that DNA methylation can serve as the initiator of bladder carcinogenesis.
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15
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Mazzarino RC, Baresova V, Zikánová M, Duval N, Wilkinson TG, Patterson D, Vacano GN. The CRISPR-Cas9 crADSL HeLa transcriptome: A first step in establishing a model for ADSL deficiency and SAICAR accumulation. Mol Genet Metab Rep 2019; 21:100512. [PMID: 31516833 PMCID: PMC6731210 DOI: 10.1016/j.ymgmr.2019.100512] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/23/2019] [Accepted: 08/24/2019] [Indexed: 01/26/2023] Open
Abstract
Adenylosuccinate lyase (ADSL) catalyzes two steps in de novo purine synthesis (DNPS). Mutations in ADSL can result in inborn errors of metabolism characterized by developmental delay and disorder phenotypes, with no effective treatment options. Recently, SAICAR, a metabolic substrate of ADSL, has been found to have alternative roles in the cell, complicating the role of ADSL. crADSL, a CRISPR KO of ADSL in HeLa cells, was constructed to investigate DNPS and ADSL in a human cell line. Here we employ this cell line in an RNA-seq analysis to initially investigate the effect of DNPS and ADSL deficiency on the transcriptome as a first step in establishing a cellular model of ADSL deficiency. We report transcriptome changes in genes relevant to development, vascular development, muscle, and cancer biology, which provide interesting avenues for future research.
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Key Words
- Adenylosuccinate lyase
- Purine synthesis
- RNA-seq
- Transcriptome
- adenosine monophosphate, (AMP)
- adenylosuccinate lyase, (ADSL)
- aminoimidazole carboxamide ribonucleotide, (AICAR)
- de novo purine synthesis, (DNPS)
- differentially expressed gene, (DEG)
- false discovery rate, (FDR)
- fetal calf macroserum, (FCM)
- fragments per kilobase of exon per million reads mapped, (FPKM)
- gene ontology, (GO)
- guanosine monophosphate, (GMP)
- minus adenine crADSL to minus adenine WT comparison, (MM)
- phosphoribosyl pyrophosphate, (PRPP)
- phosphoribosylaminoimidazolesuccinocarboxamide, (SAICAR)
- plus adenine crADSL to plus adenine WT comparison, (PP)
- succinyladenosine monophosphate, (SAMP)
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Affiliation(s)
- Randall C. Mazzarino
- Knoebel Institute for Healthy Aging, University of Denver, 2155 E. Wesley Avenue, Denver, CO 80210, USA
- Eleanor Roosevelt Institute, University of Denver, Denver, CO 80210, USA
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
- Molecular and Cellular Biophysics Program, University of Denver, Denver, CO 80210, USA
| | - Veronika Baresova
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Marie Zikánová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Nathan Duval
- Knoebel Institute for Healthy Aging, University of Denver, 2155 E. Wesley Avenue, Denver, CO 80210, USA
- Eleanor Roosevelt Institute, University of Denver, Denver, CO 80210, USA
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
| | - Terry G. Wilkinson
- Knoebel Institute for Healthy Aging, University of Denver, 2155 E. Wesley Avenue, Denver, CO 80210, USA
- Eleanor Roosevelt Institute, University of Denver, Denver, CO 80210, USA
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
| | - David Patterson
- Knoebel Institute for Healthy Aging, University of Denver, 2155 E. Wesley Avenue, Denver, CO 80210, USA
- Eleanor Roosevelt Institute, University of Denver, Denver, CO 80210, USA
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
- Molecular and Cellular Biophysics Program, University of Denver, Denver, CO 80210, USA
| | - Guido N. Vacano
- Knoebel Institute for Healthy Aging, University of Denver, 2155 E. Wesley Avenue, Denver, CO 80210, USA
- Eleanor Roosevelt Institute, University of Denver, Denver, CO 80210, USA
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
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Gumus E. A Homozygous 1.16 Megabases Microdeletion at 8p22 Including The Whole TUSC3 in A Three Years Old Girl with Intellectual Disability and Speech Delay. CELL JOURNAL 2019; 22:128-132. [PMID: 31606977 PMCID: PMC6791072 DOI: 10.22074/cellj.2020.6606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/23/2019] [Indexed: 12/17/2022]
Abstract
Intellectual disability (ID) is defined as an intelligence quotient (IQ) level below than 70. In the present paper, a 1.16
megabases (Mb) homozygous deletion in the 8p22 region was identified in a three years old girl with ID, speech and
developmental delays. This is the first report from Turkey with this form of ID. The present paper demonstrates that
application of microarray technique to help clinicians, especially when clinical diagnosis includes a complex group of
disorders (such as ID) and differential diagnostic list is broad.
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Affiliation(s)
- Evren Gumus
- Department of Medical Genetics, Faculty of Medicine, University of Harran, Sanliurfa, Turkey. Electronic Address:.,Department of Medical Genetics, Faculty of Medicine, University of Mugla Sitki Kocman, Mugla, Turkey
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18
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Luo J, Zhu H, Jiang H, Cui Y, Wang M, Ni X, Ma C. The effects of aberrant expression of LncRNA DGCR5/miR-873-5p/TUSC3 in lung cancer cell progression. Cancer Med 2018; 7:3331-3341. [PMID: 29790668 PMCID: PMC6051201 DOI: 10.1002/cam4.1566] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/23/2018] [Accepted: 04/29/2018] [Indexed: 01/17/2023] Open
Abstract
Lung cancer is the most common cause of cancer‐related mortality worldwide, and nonsmall cell lung cancer (NSCLC) accounts for 80% of all pulmonary carcinomas. Recently, long noncoding RNAs (lncRNAs) have been paid attention for exploring treatment of various diseases. Upregulation of DiGeorge syndrome critical region gene 5 (DGCR5) predicts better lung squamous cell carcinoma prognosis; therefore, we explore the role of DGCR5 in lung cancer in our present study. Consecutive patients with LC were treated in our hospital between January 2015 and January 2016. qRT‐PCR demonstrated that DGCR5 was significantly lower in neoplastic tissues than in non‐neoplastic tissues. For in vitro experiments, cell growth, migration, and invasion were significantly lower in A549 cells transfected with pcDNA3.1‐DGCR5 than pcDNA3.1, which were verified by 5‐diphenyltetrazolium bromide (MTT) assay, scratch test, and transwell assay, respectively, with no significant induction on cell apoptosis that was demonstrated by flow cytometry (FCM) assay. Bioinformatics analysis predicted that 3’ untranslated region (UTR) of tumor suppressor candidate 3 (TUSC3, 49‐55 bp) and DGCR5 (801‐807 bp) shared a common hsa‐miR‐873‐5p binding site, and the direct interaction between DGCR5 and hsa‐miR‐873‐5p or hsa‐miR‐873‐5p and TUSC3 was verified by dual‐luciferase reporter assay. qRT‐PCR demonstrated that hsa‐miR‐873‐5p was dramatically higher and TUSC3 was significantly lower in neoplastic tissues than in non‐neoplastic tissues. DGCR5 decreased the protein level of TUSC3 by miR‐873‐5p which was demonstrated by Western blot and immunofluorescence. The role of DGCR5 in tumorigenesis in vivo was consistent with in vitro assays, Ki‐67‐positive cell number (exhibited by immunohistochemical staining), tumor size, and tumor weight of A549‐DGCR5 group were significantly lower in comparison with A549‐control group.
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Affiliation(s)
- Judong Luo
- Department of Oncology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China.,Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, China
| | - Hong Zhu
- Department of Radiation Oncology, Minhang Branch of Cancer Hospital of Fudan University, Shanghai, China
| | - Hua Jiang
- Department of Oncology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Yayun Cui
- Department of Radiation Oncology, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, China
| | - Mengjie Wang
- Department of Oncology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Xinye Ni
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Changsheng Ma
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, China
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Tumor suppressor candidate 3: A novel grading tool and predictor of clinical malignancy in human gliomas. Oncol Lett 2018; 15:5655-5661. [PMID: 29556302 PMCID: PMC5844021 DOI: 10.3892/ol.2018.8082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/21/2017] [Indexed: 01/29/2023] Open
Abstract
For several years, the cause of autosomal recessive mental retardation has been attributed to the deletion or mutation of a gene named tumor suppressor candidate 3 (TUSC3). Previous research has identified that TUSC3 is a potential tumor suppressor gene in oral epidermoid carcinoma, lung cancer and esophageal cancer. However, to the best of our knowledge, no previously published data has existed on the expression of TUSC3 in gliomas. The present study focused on the expression of TUSC3 in brain gliomas. Additionally, the present study sought to identify he association between TUSC3 expression and the typical clinical and pathological disease manifestations of gliomas. TUSC3 levels were evaluated using a western blot assay and immunohistochemistry on tissue microarray slides. Results indicated a significant decrease in TUSC3 expression in glioma tissues compared with the normal adjacent tissues. Furthermore, TUSC3 expression and World Health Organization grade demonstrated an inverse association in patients with glioma. This revealed that lower levels of TUSC3 in gliomas may be associated with a poorly-differentiated (high grade) tumor and thus a higher malignancy. Through the combination of the results of the present study and future research projects, TUSC3 may be a novel grading tool that assists with evaluating tumor malignancy and consequently a more active therapeutic regimen may be used in patients with glioma.
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