1
|
Austermann C, Schierwagen R, Mohr R, Anadol E, Klein S, Pohlmann A, Jansen C, Strassburg CP, Schwarze-Zander C, Boesecke C, Rockstroh JK, Odenthal M, Trebicka J. microRNA-200a: A stage-dependent biomarker and predictor of steatosis and liver cell injury in human immunodeficiency virus patients. Hepatol Commun 2017; 1:36-45. [PMID: 29404431 PMCID: PMC5747028 DOI: 10.1002/hep4.1017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/27/2016] [Accepted: 01/08/2017] [Indexed: 12/17/2022] Open
Abstract
Nonalcoholic fatty liver disease contributes to liver-related mortality and has a high prevalence among patients with human immunodeficiency virus (HIV). The early detection of steatosis could prevent disease progression through life-style changes. However, as the common serum markers are nonspecific and the gold standard for the detection of nonalcoholic fatty liver disease remains the invasive liver biopsy, its verification is limited. Therefore, the search for novel biomarkers is essential. Several studies have emphasized the role of microRNAs (miRNAs) as biomarkers for certain liver diseases. With our study, we aimed to investigate the potential of miR-200a as a biomarker for liver injury, fibrosis, and steatosis in HIV patients. The study cohort consisted of 89 HIV patients. Clinical and laboratory parameters were assessed twice, within a median follow-up period of 12 months. miR-200a serum levels were determined by real-time polymerase chain reaction and normalized to spiked-in RNA (SV40). miR-200a serum levels showed a significant correlation with the patients' controlled attenuation parameter scores and their body weight at baseline and with alanine aminotransferase serum levels at follow-up. At baseline, we observed a stage-dependent increase in miR-200a serum levels according to the degree of steatosis. More importantly, patients with higher baseline levels of miR-200a recorded a progression of steatosis at follow-up. Remarkably, miR-200a not only reveals a prognostic value for steatosis but possibly also for liver damage and metabolic adaptions as patients with an increase in alanine aminotransferase/aspartate aminotransferase serum levels over time also recorded higher baseline miR-200a levels. Conclusion : Our study reveals miR-200a not only to be a stage-dependent biomarker of steatosis but also to be a predictor of steatosis progression and probably liver cell injury in HIV patients. (Hepatology Communications 2017;1:36-45).
Collapse
Affiliation(s)
| | | | - Raphael Mohr
- Department of Internal Medicine I University of Bonn Bonn Germany.,German Center for Infection Research, partner site Bonn-Cologne Bonn Germany
| | - Evrim Anadol
- Department of Internal Medicine I University of Bonn Bonn Germany
| | - Sabine Klein
- Department of Internal Medicine I University of Bonn Bonn Germany
| | | | - Christian Jansen
- Department of Internal Medicine I University of Bonn Bonn Germany
| | | | | | | | - Jürgen K Rockstroh
- Department of Internal Medicine I University of Bonn Bonn Germany.,German Center for Infection Research, partner site Bonn-Cologne Bonn Germany
| | | | - Jonel Trebicka
- Department of Internal Medicine I University of Bonn Bonn Germany.,Faculty of Health Sciences University of Southern Denmark Odense Denmark.,European Foundation for Chronic Liver Failure Barcelona Spain
| |
Collapse
|
2
|
Gokcumen O, Zhu Q, Mulder LCF, Iskow RC, Austermann C, Scharer CD, Raj T, Boss JM, Sunyaev S, Price A, Stranger B, Simon V, Lee C. Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence. PLoS Genet 2013; 9:e1003404. [PMID: 23593015 PMCID: PMC3623772 DOI: 10.1371/journal.pgen.1003404] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 02/07/2013] [Indexed: 11/25/2022] Open
Abstract
Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10−15). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003) and positive Tajima's D (p = 0.00285) statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human–Neandertal divergence and is evolving under balancing selection, especially among European populations. Natural selection shapes the genome in a non-random way, as an allele that contributes more to the reproductive fitness of a species increases in frequency within the population. Under balancing selection, a particular kind of natural selection, more than one allele increases in frequency in the population, likely due to a reproductive advantage of individuals carrying both alleles. Only a handful of loci have been well documented to evolve under balancing selection, with the HBB gene (sickle cell locus) being the best studied. Here, we report a non-coding (but putatively functional) locus that has maintained two divergent alleles in the human population since before the Human–Neandertal divergence and is therefore likely to be under balancing selection. These findings also provide a clear example for ancient African substructure.
Collapse
Affiliation(s)
- Omer Gokcumen
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Qihui Zhu
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lubbertus C. F. Mulder
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Rebecca C. Iskow
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christian Austermann
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Christopher D. Scharer
- Department of Microbiology, Emory University, Atlanta, Georgia, United States of America
| | - Towfique Raj
- Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Jeremy M. Boss
- Department of Microbiology, Emory University, Atlanta, Georgia, United States of America
| | - Shamil Sunyaev
- Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Alkes Price
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Barbara Stranger
- Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Viviana Simon
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, New York, New York, United States of America
- Division of Infectious Diseases, Department of Medicine, New York, New York, United States of America
- * E-mail: (VS); (CL)
| | - Charles Lee
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (VS); (CL)
| |
Collapse
|