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Yan H, Liu G, Liang Y, Wu W, Xia R, Jiao L, Shen H, Jia Z, Wang Q, Wang Z, Kong Y, Ying B, Wang H, Wang C. Up-regulated long noncoding RNA AC007128.1 and its genetic polymorphisms associated with Tuberculosis susceptibility. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1018. [PMID: 34277818 PMCID: PMC8267308 DOI: 10.21037/atm-21-2724] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/17/2021] [Indexed: 02/05/2023]
Abstract
Background Tuberculosis (TB) remains a major public health problem. Long non-coding RNAs (lncRNAs) are important regulators of gene expression. In this study, we explored the association between the expression of lncRNA AC007128.1 and TB susceptibility. Methods Three single-nucleotide polymorphisms (SNPs) (rs12333784, rs6463794, and rs720964) of lncRNA AC007128.1 were selected using the 1000 Genomes Project database and offline software Haploview V4.2, and were genotyped by a customized 2×48-Plex SNPscan™ Kit. Results We identified two differentially expressed lncRNA including AC007128.1 and AP001065.3 in comparisons of expression profiles between ATB vs. LTBI, LTBI vs. HCs, and AC700128.1 expression was specifically and significantly up-regulated in TB patients by verification of external data. Gene Ontology functional enrichment analysis and co-expression network showed up-regulated mRNA was mainly involved in negative regulation of the G protein-coupled receptor (GPCR) signaling pathway, and FPR1 and CYP27B1 were involved in the co-expression of AC007128.1. Using the 1000 Genomes Project, software Haploview V4.2, and SNP genotype, we screened out SNP rs12333784 which locus at 7p21.3 in AC007128.1 associated with TB susceptibility. The G carrier of rs12333784 was then finally verified to be significantly associated with pulmonary TB (PTB) and extrapulmonary tuberculosis (EPTB) susceptibility (pBonferroni =0.03878), and a similar but more significant effect was observed under the dominant model analysis (pBonferroni =0.013, OR =1.349, 95% CI, 1.065–1.709). In addition, the GG + GA genotype of SNP rs12333784 was significantly correlated with higher glucose (GLU) (P=0.03), higher gamma-glutamyl transferase (GGT) (P=0.05), and higher erythrocyte sedimentation rate (ESR) (P=0.05). Conclusions Our findings show lncRNA AC007128.1 can be regarded as biomarkers discriminating between ATB and LTBI and may also be a diagnostic biomarker for LBTI. These findings may aid clinical decision making in the management of TB.
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Affiliation(s)
- Hong Yan
- Department of Clinical Laboratory Medicine, the First Medical Center, Chinese PLA General Hospital, Beijing, China.,Laboratory Medicine Center, the Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Guoye Liu
- Department of Laboratory Medicine, Affiliated Brain Hospital of Nanjing Medical University (Chest Branch), Nanjing, China
| | - Yuan Liang
- The Affiliated Cancer Hospital & Hepatobiliary Center, First Affiliated Hospital, Nanjing Medical University, Nanjing, China.,Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Wei Wu
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Research Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Rui Xia
- Department of Laboratory Medicine, Affiliated Brain Hospital of Nanjing Medical University (Chest Branch), Nanjing, China
| | - Lin Jiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Han Shen
- Department of Clinical Laboratory, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Zhijun Jia
- Department of Nuclear Medicine, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Qian Wang
- Department of Laboratory Medicine, Affiliated Brain Hospital of Nanjing Medical University (Chest Branch), Nanjing, China
| | - Zhiqiang Wang
- Department of Laboratory Medicine, Affiliated Brain Hospital of Nanjing Medical University (Chest Branch), Nanjing, China
| | - Yi Kong
- Department of Clinical Laboratory Medicine, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hualiang Wang
- Department of Molecular Biology, Shanghai Centre for Clinical Laboratory, Shanghai, China
| | - Chengbin Wang
- Department of Clinical Laboratory Medicine, the First Medical Center, Chinese PLA General Hospital, Beijing, China
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Abstract
Objective To determine the contribution of paternal factors to the risk of adverse birth outcomes. Methods This is a retrospective cross-sectional analysis using birth certificate data from 2004 to 2015 retrieved from the Finger Lakes Regional Perinatal Data System. Primiparous women with singleton pregnancies were analyzed in the study. Two multivariate logistic regression models were conducted to assess potential paternal risk factors including age, race/ethnicity, and education on four birth outcomes, including preterm birth (PTB), low birthweight (LBW), high birthweight (HBW), and small for gestational age (SGA). Results A total of 36,731 singleton births were included in the analysis. Less paternal education was significantly related to an elevated risk of PTB, LBW, and SGA, even after adjustment for maternal demographic, medical, and lifestyle factors (P < 0.05). Paternal race/ethnicity was also significantly associated with all four birth outcomes (P < 0.05) while controlling for maternal factors. Older paternal age was associated with increased odds (OR 1.012, 95% CI 1.003-1.022) of LBW. Maternal race/ethnicity partially mediated the association of paternal race/ethnicity with HBW and SGA. Maternal education partially mediated the relationship between paternal education and SGA. Conclusion Paternal factors were important predictors of adverse birth outcomes. Our results support the inclusion of fathers in future studies and clinical programs aimed at reducing adverse birth outcomes.
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Affiliation(s)
- Ying Meng
- Clinical and Translational Science Institute, University of Rochester, 601 Elmwood Avenue, Rochester, NY, 14642, USA.
- School of Nursing, University of Rochester, 601 Elmwood Avenue, Rochester, NY, 14642, USA.
| | - Susan W Groth
- School of Nursing, University of Rochester, 601 Elmwood Avenue, Rochester, NY, 14642, USA
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3
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Strauss JF, Romero R, Gomez-Lopez N, Haymond-Thornburg H, Modi BP, Teves ME, Pearson LN, York TP, Schenkein HA. Spontaneous preterm birth: advances toward the discovery of genetic predisposition. Am J Obstet Gynecol 2018; 218:294-314.e2. [PMID: 29248470 PMCID: PMC5834399 DOI: 10.1016/j.ajog.2017.12.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 02/08/2023]
Abstract
Evidence from family and twin-based studies provide strong support for a significant contribution of maternal and fetal genetics to the timing of parturition and spontaneous preterm birth. However, there has been only modest success in the discovery of genes predisposing to preterm birth, despite increasing sophistication of genetic and genomic technology. In contrast, DNA variants associated with other traits/diseases have been identified. For example, there is overwhelming evidence that suggests that the nature and intensity of an inflammatory response in adults and children are under genetic control. Because inflammation is often invoked as an etiologic factor in spontaneous preterm birth, the question of whether spontaneous preterm birth has a genetic predisposition in the case of pathologic inflammation has been of long-standing interest to investigators. Here, we review various genetic approaches used for the discovery of preterm birth genetic variants in the context of inflammation-associated spontaneous preterm birth. Candidate gene studies have sought genetic variants that regulate inflammation in the mother and fetus; however, the promising findings have often not been replicated. Genome-wide association studies, an approach to the identification of chromosomal loci responsible for complex traits, have also not yielded compelling evidence for DNA variants predisposing to preterm birth. A recent genome-wide association study that included a large number of White women (>40,000) revealed that maternal loci contribute to preterm birth. Although none of these loci harbored genes directly related to innate immunity, the results were replicated. Another approach to identify DNA variants predisposing to preterm birth is whole exome sequencing, which examines the DNA sequence of protein-coding regions of the genome. A recent whole exome sequencing study identified rare mutations in genes encoding for proteins involved in the negative regulation (dampening) of the innate immune response (eg, CARD6, CARD8, NLRP10, NLRP12, NOD2, TLR10) and antimicrobial peptide/proteins (eg, DEFB1, MBL2). These findings support the concept that preterm labor, at least in part, has an inflammatory etiology, which can be induced by pathogens (ie, intraamniotic infection) or "danger signals" (alarmins) released during cellular stress or necrosis (ie, sterile intraamniotic inflammation). These findings support the notion that preterm birth has a polygenic basis that involves rare mutations or damaging variants in multiple genes involved in innate immunity and host defense mechanisms against microbes and their noxious products. An overlap among the whole exome sequencing-identified genes and other inflammatory conditions associated with preterm birth, such as periodontal disease and inflammatory bowel disease, was observed, which suggests a shared genetic substrate for these conditions. We propose that whole exome sequencing, as well as whole genome sequencing, is the most promising approach for the identification of functionally significant genetic variants responsible for spontaneous preterm birth, at least in the context of pathologic inflammation. The identification of genes that contribute to preterm birth by whole exome sequencing, or whole genome sequencing, promises to yield valuable population-specific biomarkers to identify the risk for spontaneous preterm birth and potential strategies to mitigate such a risk.
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Affiliation(s)
- Jerome F Strauss
- Department of Obstetrics and Gynecology, Virginia Commonwealth University School of Medicine, Richmond, VA; Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA.
| | - Roberto Romero
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD and Detroit, MI; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI; Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI.
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD and Detroit, MI; Department of Obstetrics and Gynecology and the Department of Immunology, Microbiology and Biochemistry, Wayne State University School of Medicine, Detroit, MI
| | - Hannah Haymond-Thornburg
- Department of Obstetrics and Gynecology, Virginia Commonwealth University School of Medicine, Richmond, VA
| | - Bhavi P Modi
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Maria E Teves
- Department of Obstetrics and Gynecology, Virginia Commonwealth University School of Medicine, Richmond, VA
| | - Laurel N Pearson
- Department of Anthropology, Pennsylvania State University, University Park, PA
| | - Timothy P York
- Department of Obstetrics and Gynecology, Virginia Commonwealth University School of Medicine, Richmond, VA; Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA
| | - Harvey A Schenkein
- Department of Periodontics, Virginia Commonwealth University School of Dentistry, Richmond, VA
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Sheikh IA, Ahmad E, Jamal MS, Rehan M, Assidi M, Tayubi IA, AlBasri SF, Bajouh OS, Turki RF, Abuzenadah AM, Damanhouri GA, Beg MA, Al-Qahtani M. Spontaneous preterm birth and single nucleotide gene polymorphisms: a recent update. BMC Genomics 2016; 17:759. [PMID: 27766960 PMCID: PMC5073925 DOI: 10.1186/s12864-016-3089-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Background Preterm birth (PTB), birth at <37 weeks of gestation, is a significant global public health problem. World-wide, about 15 million babies are born preterm each year resulting in more than a million deaths of children. Preterm neonates are more prone to problems and need intensive care hospitalization. Health issues may persist through early adulthood and even be carried on to the next generation. Majority (70 %) of PTBs are spontaneous with about a half without any apparent cause and the other half associated with a number of risk factors. Genetic factors are one of the significant risks for PTB. The focus of this review is on single nucleotide gene polymorphisms (SNPs) that are reported to be associated with PTB. Results A comprehensive evaluation of studies on SNPs known to confer potential risk of PTB was done by performing a targeted PubMed search for the years 2007–2015 and systematically reviewing all relevant studies. Evaluation of 92 studies identified 119 candidate genes with SNPs that had potential association with PTB. The genes were associated with functions of a wide spectrum of tissue and cell types such as endocrine, tissue remodeling, vascular, metabolic, and immune and inflammatory systems. Conclusions A number of potential functional candidate gene variants have been reported that predispose women for PTB. Understanding the complex genomic landscape of PTB needs high-throughput genome sequencing methods such as whole-exome sequencing and whole-genome sequencing approaches that will significantly enhance the understanding of PTB. Identification of high risk women, avoidance of possible risk factors, and provision of personalized health care are important to manage PTB. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3089-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ishfaq A Sheikh
- King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, Jeddah, 21589, Saudi Arabia
| | - Ejaz Ahmad
- King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, Jeddah, 21589, Saudi Arabia
| | - Mohammad S Jamal
- King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, Jeddah, 21589, Saudi Arabia
| | - Mohd Rehan
- King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, Jeddah, 21589, Saudi Arabia
| | - Mourad Assidi
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Iftikhar A Tayubi
- Faculty of Computing and Information Technology, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Samera F AlBasri
- Department of Obstetrics and Gynecology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Osama S Bajouh
- Department of Obstetrics and Gynecology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rola F Turki
- Department of Obstetrics and Gynecology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.,KACST Innovation Center in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Adel M Abuzenadah
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.,KACST Innovation Center in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ghazi A Damanhouri
- King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, Jeddah, 21589, Saudi Arabia
| | - Mohd A Beg
- King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, Jeddah, 21589, Saudi Arabia.
| | - Mohammed Al-Qahtani
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
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5
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Smits A, van den Anker JN, Allegaert K. Clinical pharmacology of analgosedatives in neonates: ways to improve their safe and effective use. ACTA ACUST UNITED AC 2016; 69:350-360. [PMID: 27364566 DOI: 10.1111/jphp.12599] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 06/11/2016] [Indexed: 12/19/2022]
Abstract
OBJECTIVES To propose approaches tailored to the specific needs of neonates, such as structured product development programmes, with the ultimate goal to improve the safe and effective use of analgosedatives in these fragile patients. KEY FINDINGS The feasibility and relevance of a structured product development programme in neonates (optimal study design based on preliminary data; model development; internal, external and prospective evaluation; an individualized dosing regimen; long-term safety; pharmacogenetics) are illustrated for the use of morphine. Based on changes in clinical practices, similar development plans are in progress for short-acting analgosedatives such as propofol, but are in need of tailored pharmacodynamic tools to assess and quantify effects. Furthermore, for drugs like paracetamol where there is already sufficient clinical pharmacology knowledge, attention needs to be given to long-term safety aspects. Finally, new covariates such as pharmacogenetics might further improve neonatal pain management, but clearly need to be integrated with other well-established covariates like age or weight. SUMMARY Product development programmes for analgosedatives in neonates are needed. These programmes should be tailored to their specific needs (short-acting sedation, pain relief), should include long-term safety and should incorporate the exploration of newer covariates like pharmacogenetics.
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Affiliation(s)
- Anne Smits
- Neonatal Intensive Care Unit, VU Medical Center, Amsterdam, The Netherlands.,Neonatal Intensive Care Unit, University Hospitals Leuven, Leuven, Belgium
| | - John N van den Anker
- Intensive Care and Department of Surgery, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands.,Division of Paediatric Pharmacology and Pharmacometrics, University Children's Hospital Basel, Basel, Switzerland.,Division of Pediatric Clinical Pharmacology, Children's National Medical Center, Washington, DC, USA.,Departments of Pediatrics, Integrative Systems Biology, Pharmacology & Physiology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Karel Allegaert
- Intensive Care and Department of Surgery, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
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Feng Y, Zhao X, Zhou C, Yang L, Liu Y, Bian C, Gou J, Lin X, Wang Z, Zhao X. The associations between the Val158Met in the catechol-O-methyltransferase (COMT) gene and the risk of uterine leiomyoma (ULM). Gene 2013; 529:296-9. [PMID: 23939469 DOI: 10.1016/j.gene.2013.07.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 06/14/2013] [Accepted: 07/02/2013] [Indexed: 10/26/2022]
Abstract
The Val158Met polymorphism of the COMT gene has been implicated in susceptibility to uterine leiomyoma (ULM), but the reported results were inconclusive. The aim of the study was to evaluate the Val158Met polymorphism of the COMT gene and the risk of ULM by meta-analysis. A comprehensive electronic search for relevant articles was conducted in Pubmed, Embase, CNKI, Wanfang, and Weipu databases. Statistical analysis was performed by using the Revman4.2 software and Stata10.0 software. A total of 7 articles including 12 case-control studies were identified in this meta-analysis. The results showed that the polymorphism was associated with decreased risk of ULM (Met/Met+Val/Met vs. Met/Met: OR=0.84, 95% CI=0.70-0.99, Z=2.07, p=0.04). In the subgroup analyses by ethnicity, significant decreased risk was found among the black populations (OR=0.68, 95% CI=0.48-0.97, Z=2.15, p=0.03). The current meta-analysis suggested that the Val158Met polymorphism in the COMT gene was associated with decreased risk of ULM, especially in the black population. Future studies are needed to validate our conclusions.
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Affiliation(s)
- Yi Feng
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second Hospital, Chengdu 610041, Sichuan, PR China
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