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Garske KM, Kar A, Comenho C, Balliu B, Pan DZ, Bhagat YV, Rosenberg G, Koka A, Das SS, Miao Z, Sinsheimer JS, Kaprio J, Pietiläinen KH, Pajukanta P. Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes. Nat Commun 2023; 14:4214. [PMID: 37452040 PMCID: PMC10349101 DOI: 10.1038/s41467-023-39919-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 07/04/2023] [Indexed: 07/18/2023] Open
Abstract
Obesity-induced adipose tissue dysfunction can cause low-grade inflammation and downstream obesity comorbidities. Although preadipocytes may contribute to this pro-inflammatory environment, the underlying mechanisms are unclear. We used human primary preadipocytes from body mass index (BMI) -discordant monozygotic (MZ) twin pairs to generate epigenetic (ATAC-sequence) and transcriptomic (RNA-sequence) data for testing whether increased BMI alters the subnuclear compartmentalization of open chromatin in the twins' preadipocytes, causing downstream inflammation. Here we show that the co-accessibility of open chromatin, i.e. compartmentalization of chromatin activity, is altered in the higher vs lower BMI MZ siblings for a large subset ( ~ 88.5 Mb) of the active subnuclear compartments. Using the UK Biobank we show that variants within these regions contribute to systemic inflammation through interactions with BMI on C-reactive protein. In summary, open chromatin co-accessibility in human preadipocytes is disrupted among the higher BMI siblings, suggesting a mechanism how obesity may lead to inflammation via gene-environment interactions.
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Affiliation(s)
- Kristina M Garske
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Asha Kar
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Caroline Comenho
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Brunilda Balliu
- Department of Computational Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - David Z Pan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, 90095, USA
| | - Yash V Bhagat
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Gregory Rosenberg
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Amogha Koka
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Sankha Subhra Das
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Zong Miao
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, 90095, USA
| | - Janet S Sinsheimer
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
- Department of Computational Medicine, UCLA, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, 90095, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, 00014, Finland
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland
- Obesity Center, Abdominal Center, Helsinki University Hospital and University of Helsinki, Helsinki, 00014, Finland
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
- Department of Computational Medicine, UCLA, Los Angeles, CA, 90095, USA.
- Institute for Precision Heath, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
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Darci-Maher N, Alvarez M, Arasu UT, Selvarajan I, Lee SHT, Pan DZ, Miao Z, Das SS, Kaminska D, Örd T, Benhammou JN, Wabitsch M, Pisegna JR, Männistö V, Pietiläinen KH, Laakso M, Sinsheimer JS, Kaikkonen MU, Pihlajamäki J, Pajukanta P. Cross-tissue omics analysis discovers ten adipose genes encoding secreted proteins in obesity-related non-alcoholic fatty liver disease. EBioMedicine 2023; 92:104620. [PMID: 37224770 PMCID: PMC10277924 DOI: 10.1016/j.ebiom.2023.104620] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 04/14/2023] [Accepted: 05/03/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is a fast-growing, underdiagnosed, epidemic. We hypothesise that obesity-related inflammation compromises adipose tissue functions, preventing efficient fat storage, and thus driving ectopic fat accumulation into the liver. METHODS To identify adipose-based mechanisms and potential serum biomarker candidates (SBCs) for NAFLD, we utilise dual-tissue RNA-sequencing (RNA-seq) data in adipose tissue and liver, paired with histology-based NAFLD diagnosis, from the same individuals in a cohort of obese individuals. We first scan for genes that are differentially expressed (DE) for NAFLD in obese individuals' subcutaneous adipose tissue but not in their liver; encode proteins secreted to serum; and show preferential adipose expression. Then the identified genes are filtered to key adipose-origin NAFLD genes by best subset analysis, knockdown experiments during human preadipocyte differentiation, recombinant protein treatment experiments in human liver HepG2 cells, and genetic analysis. FINDINGS We discover a set of genes, including 10 SBCs, that may modulate NAFLD pathogenesis by impacting adipose tissue function. Based on best subset analysis, we further follow-up on two SBCs CCDC80 and SOD3 by knockdown in human preadipocytes and subsequent differentiation experiments, which show that they modulate crucial adipogenesis genes, LPL, SREBPF1, and LEP. We also show that treatment of the liver HepG2 cells with the CCDC80 and SOD3 recombinant proteins impacts genes related to steatosis and lipid processing, including PPARA, NFE2L2, and RNF128. Finally, utilizing the adipose NAFLD DE gene cis-regulatory variants associated with serum triglycerides (TGs) in extensive genome-wide association studies (GWASs), we demonstrate a unidirectional effect of serum TGs on NAFLD with Mendelian Randomization (MR) analysis. We also demonstrate that a single SNP regulating one of the SBC genes, rs2845885, produces a significant MR result by itself. This supports the conclusion that genetically regulated adipose expression of the NAFLD DE genes may contribute to NAFLD through changes in serum TG levels. INTERPRETATION Our results from the dual-tissue transcriptomics screening improve the understanding of obesity-related NAFLD by providing a targeted set of 10 adipose tissue-active genes as new serum biomarker candidates for the currently grossly underdiagnosed fatty liver disease. FUNDING The work was supported by NIH grants R01HG010505 and R01DK132775. The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. The KOBS study (J. P.) was supported by the Finnish Diabetes Research Foundation, Kuopio University Hospital Project grant (EVO/VTR grants 2005-2019), and the Academy of Finland grant (Contract no. 138006). This study was funded by the European Research Council under the European Union's Horizon 2020 research and innovation program (Grant No. 802825 to M. U. K.). K. H. P. was funded by the Academy of Finland (grant numbers 272376, 266286, 314383, and 335443), the Finnish Medical Foundation, Gyllenberg Foundation, Novo Nordisk Foundation (grant numbers NNF10OC1013354, NNF17OC0027232, and NNF20OC0060547), Finnish Diabetes Research Foundation, Finnish Foundation for Cardiovascular Research, University of Helsinki, and Helsinki University Hospital and Government Research Funds. I. S. was funded by the Instrumentarium Science Foundation. Personal grants to U. T. A. were received from the Matti and Vappu Maukonen Foundation, Ella och Georg Ehrnrooths Stiftelse and the Finnish Foundation for Cardiovascular Research.
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Affiliation(s)
- Nicholas Darci-Maher
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Marcus Alvarez
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Uma Thanigai Arasu
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ilakya Selvarajan
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Seung Hyuk T Lee
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - David Z Pan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Zong Miao
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Sankha Subhra Das
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Dorota Kaminska
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA; Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Tiit Örd
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jihane N Benhammou
- Vatche and Tamar Manoukian Division of Digestive Diseases, and Gastroenterology, Hepatology and Parenteral Nutrition, David Geffen School of Medicine at UCLA and VA Greater Los Angeles HCS, Los Angeles, USA
| | - Martin Wabitsch
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University of Ulm, Ulm, Germany
| | - Joseph R Pisegna
- Department of Medicine and Human Genetics, Division of Gastroenterology, Hepatology and Parenteral Nutrition, David Geffen School of Medicine at UCLA and VA Greater Los Angeles HCS, Los Angeles, USA
| | - Ville Männistö
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Obesity Center, Abdominal Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Kuopio University Hospital, University of Eastern Finland, Kuopio, Finland
| | - Janet S Sinsheimer
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA; Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, USA; Department of Computational Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jussi Pihlajamäki
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, Kuopio, Finland
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA; Bioinformatics Interdepartmental Program, UCLA, Los Angeles, USA; Institute for Precision Health, David Geffen School of Medicine at UCLA, Los Angeles, USA.
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Conway J, Pouryahya M, Gindin Y, Pan DZ, Carrasco-Zevallos OM, Mountain V, Subramanian GM, Montalto MC, Resnick M, Beck AH, Huss RS, Myers RP, Taylor-Weiner A, Wapinski I, Chung C. Integration of deep learning-based histopathology and transcriptomics reveals key genes associated with fibrogenesis in patients with advanced NASH. Cell Rep Med 2023; 4:101016. [PMID: 37075704 PMCID: PMC10140650 DOI: 10.1016/j.xcrm.2023.101016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 12/31/2022] [Accepted: 03/21/2023] [Indexed: 04/21/2023]
Abstract
Nonalcoholic steatohepatitis (NASH) is the most common chronic liver disease globally and a leading cause for liver transplantation in the US. Its pathogenesis remains imprecisely defined. We combined two high-resolution modalities to tissue samples from NASH clinical trials, machine learning (ML)-based quantification of histological features and transcriptomics, to identify genes that are associated with disease progression and clinical events. A histopathology-driven 5-gene expression signature predicted disease progression and clinical events in patients with NASH with F3 (pre-cirrhotic) and F4 (cirrhotic) fibrosis. Notably, the Notch signaling pathway and genes implicated in liver-related diseases were enriched in this expression signature. In a validation cohort where pharmacologic intervention improved disease histology, multiple Notch signaling components were suppressed.
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Pan DZ, Odorizzi PM, Schoenichen A, Abdelghany M, Chen S, Osinusi A, Patterson SD, Downie B, Juneja K, Wallin JJ. Remdesivir improves biomarkers associated with disease severity in COVID-19 patients treated in an outpatient setting. Commun Med (Lond) 2023; 3:2. [PMID: 36596885 PMCID: PMC9809529 DOI: 10.1038/s43856-022-00232-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/16/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Remdesivir (RDV) is an intravenous antiviral with activity against SARS-CoV-2 for treatment of hospitalized COVID-19 patients with moderate-to-severe disease. Biomarkers associated with clinical outcomes have been identified for COVID-19, but few evaluated in context of antiviral treatment. Here, we assessed baseline (day 1, prior to first RDV dose) biomarkers and the impact of RDV treatment on longitudinal biomarker readouts. METHODS Recently, RDV was evaluated in high-risk, non-hospitalized patients with confirmed SARS-CoV-2 infection and was highly effective at preventing disease progression. The randomized, double-blind, placebo-controlled Phase 3 study included 562 participants who received at least 1 dose of study drug, of which 312 consented for longitudinal biomarker assessments at baseline, day 3, and day 14. We assessed sixteen baseline biomarkers and the impact of RDV treatment on longitudinal biomarker readouts. RESULTS Six well-known, inflammation-associated biomarkers are elevated at baseline in participants meeting the primary endpoint of hospitalization or death by day 28. Moreover, in comparison to placebo, biomarkers in RDV-treated participants show accelerated improvement, including reduction of soluble angiopoietin-2, D-dimer, and neutrophil-to-lymphocyte ratio, as well as an increase in lymphocyte counts. CONCLUSIONS Overall, the findings in this study suggest that RDV treatment may accelerate the improvement of multiple biomarkers of COVID-19 severity, which are associated with better clinical outcomes during infection. These findings have implications for better understanding the activity of antiviral treatments in COVID-19.
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Affiliation(s)
- David Z. Pan
- grid.418227.a0000 0004 0402 1634Gilead Sciences Inc., Foster City, CA 94404 USA
| | - Pamela M. Odorizzi
- grid.418227.a0000 0004 0402 1634Gilead Sciences Inc., Foster City, CA 94404 USA
| | - Andre Schoenichen
- grid.418227.a0000 0004 0402 1634Gilead Sciences Inc., Foster City, CA 94404 USA
| | - Mazin Abdelghany
- grid.418227.a0000 0004 0402 1634Gilead Sciences Inc., Foster City, CA 94404 USA
| | - Shuguang Chen
- grid.418227.a0000 0004 0402 1634Gilead Sciences Inc., Foster City, CA 94404 USA
| | - Anu Osinusi
- grid.418227.a0000 0004 0402 1634Gilead Sciences Inc., Foster City, CA 94404 USA
| | - Scott D. Patterson
- grid.418227.a0000 0004 0402 1634Gilead Sciences Inc., Foster City, CA 94404 USA
| | - Bryan Downie
- grid.418227.a0000 0004 0402 1634Gilead Sciences Inc., Foster City, CA 94404 USA
| | - Kavita Juneja
- grid.418227.a0000 0004 0402 1634Gilead Sciences Inc., Foster City, CA 94404 USA
| | - Jeffrey J. Wallin
- grid.418227.a0000 0004 0402 1634Gilead Sciences Inc., Foster City, CA 94404 USA
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5
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Garske KM, Comenho C, Pan DZ, Alvarez M, Mohlke K, Laakso M, Pietiläinen KH, Pajukanta P. Long-range chromosomal interactions increase and mark repressed gene expression during adipogenesis. Epigenetics 2022; 17:1849-1862. [PMID: 35746833 PMCID: PMC9665133 DOI: 10.1080/15592294.2022.2088145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Obesity perturbs central functions of human adipose tissue, centred on differentiation of preadipocytes to adipocytes, i.e., adipogenesis. The large environmental component of obesity makes it important to elucidate epigenetic regulatory factors impacting adipogenesis. Promoter Capture Hi-C (pCHi-C) has been used to identify chromosomal interactions between promoters and associated regulatory elements. However, long range interactions (LRIs) greater than 1 Mb are often filtered out of pCHi-C datasets, due to technical challenges and their low prevalence. To elucidate the unknown role of LRIs in adipogenesis, we investigated preadipocyte differentiation to adipocytes using pCHi-C and bulk and single nucleus RNA-seq data. We first show that LRIs are reproducible between biological replicates, and they increase >2-fold in frequency across adipogenesis. We further demonstrate that genomic loci containing LRIs are more epigenetically repressed than regions without LRIs, corresponding to lower gene expression in the LRI regions. Accordingly, as preadipocytes differentiate into adipocytes, LRI regions are more likely to contain repressed preadipocyte marker genes; whereas these same LRI regions are depleted of actively expressed adipocyte marker genes. Finally, we show that LRIs can be used to restrict multiple testing of the long-range cis-eQTL analysis to identify variants that regulate genes via LRIs. We exemplify this by identifying a putative long range cis regulatory mechanism at the LYPLAL1/TGFB2 obesity locus. In summary, we identify LRIs that mark repressed regions of the genome, and these interactions increase across adipogenesis, pinpointing developmental regions that need to be repressed in a cell-type specific way for adipogenesis to proceed.
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Affiliation(s)
- Kristina M. Garske
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Caroline Comenho
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - David Z. Pan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA,Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
| | - Marcus Alvarez
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Karen Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Markku Laakso
- Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Kirsi H. Pietiläinen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland,Obesity Center, Abdominal Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA,Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA,Institute for Precision Heath, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA,CONTACT Päivi Pajukanta Department of Human Genetics David Geffen School of Medicine at UCLA
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6
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Hsu YC, Suri V, Nguyen MH, Huang YT, Chen CY, Chang IW, Tseng CH, Wu CY, Lin JT, Pan DZ, Gaggar A, Podlaha O. Inhibition of Viral Replication Reduces Transcriptionally Active Distinct Hepatitis B Virus Integrations With Implications on Host Gene Dysregulation. Gastroenterology 2022; 162:1160-1170.e1. [PMID: 34995536 DOI: 10.1053/j.gastro.2021.12.286] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 12/02/2021] [Accepted: 12/29/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Hepatocellular carcinogenesis of hepatitis B virus (HBV) infection may arise from integration of viral DNA into the host genome. We aimed to gauge the effect of viral inhibition on transcriptionally active HBV-host integration events and explore the correlation of viral integrations with host gene dysregulation. METHODS We leveraged data and biospecimens from an interventional trial, in which patients with HBV viremia above 2000 IU/mL and minimally raised serum liver enzyme were randomized to receive tenofovir disoproxil fumarate (TDF) or placebo for 3 years. Total RNA-sequencing was performed on paired liver biopsies taken before and after the 3-year intervention in 119 patients. Virus-host chimeric reads were captured to quantify the number of distinct viral integrations. Dysregulation of a host gene disrupted by viral integration was defined by aberrant expression >2 standard deviations away from samples without viral integration. RESULTS The TDF (n = 64) and placebo groups (n = 55) were comparable at baseline. Expressed viral integrations were detected in all pre- and posttreatment samples. The number of distinct viral integrations significantly correlated with circulatory biomarkers indicative of viral activities including HBV DNA, RNA, and viral antigens (P < .0003 for all correlations). Moreover, TDF vs placebo achieved a significantly greater reduction in distinct viral integrations, with 3.28-fold and 1.81-fold decreases in the expressed integrations per million reads, respectively (analysis of covariance, P = .037). Besides, viral integrations significantly correlated with host gene dysregulation. CONCLUSION Inhibition of viral replication reduces the number of transcriptionally active distinct HBV-host DNA integrations in patients with substantial viremia. Given the mutagenic potentials of viral integrations, such treatment effects should be considered in patient management.
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Affiliation(s)
- Yao-Chun Hsu
- Division of Gastroenterology and Hepatology, E-Da Hospital, Kaohsiung, Taiwan; School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan; Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan; Division of Gastroenterology and Hepatology, Fu-Jen Catholic University Hospital, New Taipei, Taiwan
| | - Vithika Suri
- Gilead Sciences Inc., Foster City, California, USA
| | - Mindie H Nguyen
- Division of Gastroenterology and Hepatology, Stanford University Medical Center, Palo Alto, California, USA; Department of Epidemiology and Population Health, Stanford University Medical Center, Palo Alto, California, USA
| | - Yen-Tsung Huang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Chi-Yi Chen
- Division of Gastroenterology and Hepatology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - I-Wei Chang
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Department of Clinical Pathology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Cheng-Hao Tseng
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan; Division of Gastroenterology and Hepatology, E-Da Cancer Hospital, Kaohsiung, Taiwan
| | - Chun-Ying Wu
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan; Division of Translational Research, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jaw-Town Lin
- Division of Gastroenterology and Hepatology, E-Da Hospital, Kaohsiung, Taiwan
| | - David Z Pan
- Gilead Sciences Inc., Foster City, California, USA
| | - Anuj Gaggar
- Gilead Sciences Inc., Foster City, California, USA
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7
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Miao Z, Garske KM, Pan DZ, Koka A, Kaminska D, Männistö V, Sinsheimer JS, Pihlajamäki J, Pajukanta P. Identification of 90 NAFLD GWAS loci and establishment of NAFLD PRS and causal role of NAFLD in coronary artery disease. HGG Adv 2022; 3:100056. [PMID: 35047847 PMCID: PMC8756520 DOI: 10.1016/j.xhgg.2021.100056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/19/2021] [Indexed: 12/20/2022] Open
Abstract
The prevalence of non-alcoholic fatty liver disease (NAFLD), now also known as metabolic dysfunction-associated fatty liver disease (MAFLD), is rapidly increasing worldwide due to the ongoing obesity epidemic. However, currently the NALFD diagnosis requires non-readily available imaging technologies or liver biopsy, which has drastically limited the sample sizes of NAFLD studies and hampered the discovery of its genetic component. Here we utilized the large UK Biobank (UKB) to accurately estimate the NAFLD status in UKB based on common serum traits and anthropometric measures. Scoring all individuals in UKB for NAFLD risk resulted in 28,396 NAFLD cases and 108,652 healthy individuals at a >90% confidence level. Using this imputed NAFLD status to perform the largest NAFLD genome-wide association study (GWAS) to date, we identified 94 independent (R2 < 0.2) NAFLD GWAS loci, of which 90 have not been identified before; built a polygenic risk score (PRS) model to predict the genetic risk of NAFLD; and used the GWAS variants of imputed NAFLD for a tissue-aware Mendelian randomization analysis that discovered a significant causal effect of NAFLD on coronary artery disease (CAD). In summary, we accurately estimated the NAFLD status in UKB using common serum traits and anthropometric measures, which empowered us to identify 90 GWAS NAFLD loci, build NAFLD PRS, and discover a significant causal effect of NAFLD on CAD.
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Affiliation(s)
- Zong Miao
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
| | - Kristina M. Garske
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - David Z. Pan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
| | - Amogha Koka
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Dorota Kaminska
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Institute of Public Health and Clinical Nutrition UEF, Kuopio, Finland
- Turku PET Centre, Turku University Hospital, Turku, Finland
| | - Ville Männistö
- Department of Medicine, UEF and Kuopio University Hospital, Kuopio, Finland
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC at University of Amsterdam, Amsterdam, the Netherlands
| | - Janet S. Sinsheimer
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, UCLA, Los Angeles, CA, USA
| | - Jussi Pihlajamäki
- Institute of Public Health and Clinical Nutrition UEF, Kuopio, Finland
- Department of Medicine, Endocrinology, and Clinical Nutrition, Kuopio University Hospital, Kuopio, Finland
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
- Institute for Precision Health, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Corresponding author
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8
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Pan DZ, Miao Z, Comenho C, Rajkumar S, Koka A, Lee SHT, Alvarez M, Kaminska D, Ko A, Sinsheimer JS, Mohlke KL, Mancuso N, Muñoz-Hernandez LL, Herrera-Hernandez M, Tusié-Luna MT, Aguilar-Salinas C, Pietiläinen KH, Pihlajamäki J, Laakso M, Garske KM, Pajukanta P. Correction to: Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes. Genome Med 2021; 13:139. [PMID: 34461981 PMCID: PMC8406603 DOI: 10.1186/s13073-021-00954-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- David Z Pan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA.,Bioinformatics Interdepartmental Program, UCLA, Los Angeles, USA
| | - Zong Miao
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA.,Bioinformatics Interdepartmental Program, UCLA, Los Angeles, USA
| | - Caroline Comenho
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Sandhya Rajkumar
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA.,Computational and Systems Biology Interdepartmental Program, UCLA, Los Angeles, USA
| | - Amogha Koka
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Seung Hyuk T Lee
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Marcus Alvarez
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Dorota Kaminska
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA.,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Arthur Ko
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Janet S Sinsheimer
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA.,Department of Computational Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Linda Liliana Muñoz-Hernandez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ave. Morones Prieto 3000, Monterrey, N.L., México, 64710.,Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.,Departamento de Endocrinología y Metabolismo del Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Miguel Herrera-Hernandez
- Departamento de Cirugía, Instituto Nacional de Ciencias Médicas y Nutrición, Mexico City, Mexico
| | - Maria Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas UNAM/ Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Carlos Aguilar-Salinas
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.,Departamento de Endocrinología y Metabolismo del Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Obesity Center, Endocrinology, Abdominal Center, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Jussi Pihlajamäki
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.,Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Kristina M Garske
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA. .,Bioinformatics Interdepartmental Program, UCLA, Los Angeles, USA. .,Institute for Precision Health at UCLA, Los Angeles, USA.
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9
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Pan DZ, Miao Z, Comenho C, Rajkumar S, Koka A, Lee SHT, Alvarez M, Kaminska D, Ko A, Sinsheimer JS, Mohlke KL, Mancuso N, Muñoz-Hernandez LL, Herrera-Hernandez M, Tusié-Luna MT, Aguilar-Salinas C, Pietiläinen KH, Pihlajamäki J, Laakso M, Garske KM, Pajukanta P. Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes. Genome Med 2021; 13:123. [PMID: 34340684 PMCID: PMC8327600 DOI: 10.1186/s13073-021-00939-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 07/14/2021] [Indexed: 12/14/2022] Open
Abstract
Background Obesity predisposes individuals to multiple cardiometabolic disorders, including type 2 diabetes (T2D). As body mass index (BMI) cannot reliably differentiate fat from lean mass, the metabolically detrimental abdominal obesity has been estimated using waist-hip ratio (WHR). Waist-hip ratio adjusted for body mass index (WHRadjBMI) in turn is a well-established sex-specific marker for abdominal fat and adiposity, and a predictor of adverse metabolic outcomes, such as T2D. However, the underlying genes and regulatory mechanisms orchestrating the sex differences in obesity and body fat distribution in humans are not well understood. Methods We searched for genetic master regulators of WHRadjBMI by employing integrative genomics approaches on human subcutaneous adipose RNA sequencing (RNA-seq) data (n ~ 1400) and WHRadjBMI GWAS data (n ~ 700,000) from the WHRadjBMI GWAS cohorts and the UK Biobank (UKB), using co-expression network, transcriptome-wide association study (TWAS), and polygenic risk score (PRS) approaches. Finally, we functionally verified our genomic results using gene knockdown experiments in a human primary cell type that is critical for adipose tissue function. Results Here, we identified an adipose gene co-expression network that contains 35 obesity GWAS genes and explains a significant amount of polygenic risk for abdominal obesity and T2D in the UKB (n = 392,551) in a sex-dependent way. We showed that this network is preserved in the adipose tissue data from the Finnish Kuopio Obesity Study and Mexican Obesity Study. The network is controlled by a novel adipose master transcription factor (TF), TBX15, a WHRadjBMI GWAS gene that regulates the network in trans. Knockdown of TBX15 in human primary preadipocytes resulted in changes in expression of 130 network genes, including the key adipose TFs, PPARG and KLF15, which were significantly impacted (FDR < 0.05), thus functionally verifying the trans regulatory effect of TBX15 on the WHRadjBMI co-expression network. Conclusions Our study discovers a novel key function for the TBX15 TF in trans regulating an adipose co-expression network of 347 adipose, mitochondrial, and metabolically important genes, including PPARG, KLF15, PPARA, ADIPOQ, and 35 obesity GWAS genes. Thus, based on our converging genomic, transcriptional, and functional evidence, we interpret the role of TBX15 to be a main transcriptional regulator in the adipose tissue and discover its importance in human abdominal obesity. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00939-2.
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Affiliation(s)
- David Z Pan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA.,Bioinformatics Interdepartmental Program, UCLA, Los Angeles, USA
| | - Zong Miao
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA.,Bioinformatics Interdepartmental Program, UCLA, Los Angeles, USA
| | - Caroline Comenho
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Sandhya Rajkumar
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA.,Computational and Systems Biology Interdepartmental Program, UCLA, Los Angeles, USA
| | - Amogha Koka
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Seung Hyuk T Lee
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Marcus Alvarez
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Dorota Kaminska
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA.,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Arthur Ko
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Janet S Sinsheimer
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA.,Department of Computational Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Linda Liliana Muñoz-Hernandez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ave. Morones Prieto 3000, Monterrey, N.L., México, 64710.,Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.,Departamento de Endocrinología y Metabolismo del Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Miguel Herrera-Hernandez
- Departamento de Cirugía, Instituto Nacional de Ciencias Médicas y Nutrición, Mexico City, Mexico
| | - Maria Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas UNAM/ Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Carlos Aguilar-Salinas
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.,Departamento de Endocrinología y Metabolismo del Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Obesity Center, Endocrinology, Abdominal Center, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Jussi Pihlajamäki
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.,Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Kristina M Garske
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA. .,Bioinformatics Interdepartmental Program, UCLA, Los Angeles, USA. .,Institute for Precision Health at UCLA, Los Angeles, USA.
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10
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Ying Z, Feng C, Zhao Z, Dhar S, Dalir H, Gu J, Cheng Y, Soref R, Pan DZ, Chen RT. Electronic-photonic arithmetic logic unit for high-speed computing. Nat Commun 2020; 11:2154. [PMID: 32358492 PMCID: PMC7195421 DOI: 10.1038/s41467-020-16057-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 04/06/2020] [Indexed: 11/09/2022] Open
Abstract
The past two decades have witnessed the stagnation of the clock speed of microprocessors followed by the recent faltering of Moore's law as nanofabrication technology approaches its unavoidable physical limit. Vigorous efforts from various research areas have been made to develop power-efficient and ultrafast computing machines in this post-Moore's law era. With its unique capacity to integrate complex electro-optic circuits on a single chip, integrated photonics has revolutionized the interconnects and has shown its striking potential in optical computing. Here, we propose an electronic-photonic computing architecture for a wavelength division multiplexing-based electronic-photonic arithmetic logic unit, which disentangles the exponential relationship between power and clock rate, leading to an enhancement in computation speed and power efficiency as compared to the state-of-the-art transistors-based circuits. We experimentally demonstrate its practicality by implementing a 4-bit arithmetic logic unit consisting of 8 high-speed microdisk modulators and operating at 20 GHz. This approach paves the way to future power-saving and high-speed electronic-photonic computing circuits.
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Affiliation(s)
- Zhoufeng Ying
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA
| | - Chenghao Feng
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA
| | - Zheng Zhao
- Computer Engineering Research Center, The University of Texas at Austin, Austin, TX, 78705, USA
| | - Shounak Dhar
- Computer Engineering Research Center, The University of Texas at Austin, Austin, TX, 78705, USA
| | - Hamed Dalir
- Omega Optics, Inc., 8500 Shoal Creek Boulevard, Building 4, Suite 200, Austin, TX, 78757, USA
| | - Jiaqi Gu
- Computer Engineering Research Center, The University of Texas at Austin, Austin, TX, 78705, USA
| | - Yue Cheng
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA
| | - Richard Soref
- Department of Engineering, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - David Z Pan
- Computer Engineering Research Center, The University of Texas at Austin, Austin, TX, 78705, USA
| | - Ray T Chen
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA. .,Omega Optics, Inc., 8500 Shoal Creek Boulevard, Building 4, Suite 200, Austin, TX, 78757, USA.
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11
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Garske KM, Pan DZ, Miao Z, Bhagat YV, Comenho C, Robles CR, Benhammou JN, Alvarez M, Ko A, Ye CJ, Pisegna JR, Mohlke KL, Sinsheimer JS, Laakso M, Pajukanta P. Reverse gene-environment interaction approach to identify variants influencing body-mass index in humans. Nat Metab 2019; 1:630-642. [PMID: 31538139 PMCID: PMC6752726 DOI: 10.1038/s42255-019-0071-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Identifying gene-environment interactions (GxEs) contributing to human cardiometabolic disorders is challenging. Here we apply a reverse GxE candidate search by deriving candidate variants from promoter-enhancer interactions that respond to dietary fatty acid challenge through altered chromatin accessibility in human primary adipocytes. We then test all variants residing in the lipid-responsive open chromatin sites within adipocyte promoter-enhancer contacts for interaction effects between the genotype and dietary saturated fat intake on body mass index (BMI) in the UK Biobank. We discover 14 novel GxE variants in 12 lipid-responsive promoters, including well-known lipid genes (LIPE, CARM1, and PLIN2) and novel genes, such as LDB3, for which we provide further functional and integrative genomics evidence. We further identify 24 GxE variants in enhancers, totaling 38 new GxE variants for BMI in the UK Biobank, demonstrating that molecular genomics data produced in physiologically relevant contexts can discover new functional GxE mechanisms in humans.
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Affiliation(s)
- Kristina M Garske
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA, 90095
| | - David Z Pan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA, 90095
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA, 90095
| | - Zong Miao
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA, 90095
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA, 90095
| | - Yash V Bhagat
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA, 90095
| | - Caroline Comenho
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA, 90095
| | | | - Jihane N Benhammou
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA, 90095
- Vache and Tamar Manoukian Division of Digestive Diseases, UCLA, Los Angeles, CA, USA, 90095
| | - Marcus Alvarez
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA, 90095
| | - Arthur Ko
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA, 90095
| | - Chun Jimmie Ye
- Institute for Human Genetics, Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA, 94143
| | - Joseph R Pisegna
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA, 90095
- Vache and Tamar Manoukian Division of Digestive Diseases, UCLA, Los Angeles, CA, USA, 90095
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA, 27599
| | - Janet S Sinsheimer
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA, 90095
- Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA, 90095
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland, FI-70210
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA, 90095
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA, 90095
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland, FI-70210
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12
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Ying Z, Zhao Z, Feng C, Mital R, Dhar S, Pan DZ, Soref R, Chen RT. Automated logic synthesis for electro-optic logic-based integrated optical computing. Opt Express 2018; 26:28002-28012. [PMID: 30469856 DOI: 10.1364/oe.26.028002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/20/2018] [Indexed: 06/09/2023]
Abstract
Integrated optical computing attracts increasing interest recently as Moore's law approaches the physical limitation. Among all the approaches of integrated optical computing, directed logic that takes the full advantage of integrated photonics and electronics has received lots of investigation since its first introduction in 2007. Meanwhile, as integrated photonics matures, it has become critical to develop automated methods for synthesizing optical devices for large-scale optical designs. In this paper, we propose a general electro-optic (EO) logic in a higher level to explore its potential in integrated computing. Compared to the directed logic, the EO logic leads to a briefer design with shorter optical paths and fewer components. Then a comprehensive gate library based on EO logic is summarized. At last, an And-Inverter Graphs (AIGs) based automated logic synthesis algorithm is described as an example to implement the EO logic, which offers an instruction for the design automation of high-speed integrated optical computing circuits.
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13
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Pan DZ, Garske KM, Alvarez M, Bhagat YV, Boocock J, Nikkola E, Miao Z, Raulerson CK, Cantor RM, Civelek M, Glastonbury CA, Small KS, Boehnke M, Lusis AJ, Sinsheimer JS, Mohlke KL, Laakso M, Pajukanta P, Ko A. Author Correction: Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS. Nat Commun 2018; 9:3472. [PMID: 30135520 PMCID: PMC6105720 DOI: 10.1038/s41467-018-05849-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In the original version of this Article, Supplementary Table 10 contained incorrect primer sequences for the mobility shift assay for SNP rs4776984. These errors have now been fixed and the corrected version of the Supplementary Information PDF is available to download from the HTML version of the Article.
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Affiliation(s)
- David Z Pan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, 90095, USA
| | - Kristina M Garske
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Marcus Alvarez
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Yash V Bhagat
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - James Boocock
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Elina Nikkola
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Zong Miao
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, 90095, USA
| | - Chelsea K Raulerson
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Rita M Cantor
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Mete Civelek
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22904, USA
| | | | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College, London, UK
| | - Michael Boehnke
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Aldons J Lusis
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Janet S Sinsheimer
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
- Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, FI-70210, Finland
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute at UCLA, Los Angeles, CA, 90095, USA
| | - Arthur Ko
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute at UCLA, Los Angeles, CA, 90095, USA.
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14
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Ying Z, Wang Z, Zhao Z, Dhar S, Pan DZ, Soref R, Chen RT. Silicon microdisk-based full adders for optical computing. Opt Lett 2018; 43:983-986. [PMID: 29489761 DOI: 10.1364/ol.43.000983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/18/2018] [Indexed: 06/08/2023]
Abstract
Due to the projected saturation of Moore's law, as well as the drastically increasing trend of bandwidth with lower power consumption, silicon photonics has emerged as one of the most promising alternatives that has attracted a lasting interest due to the accessibility and maturity of ultra-compact passive and active integrated photonic components. In this Letter, we demonstrate a ripple-carry electro-optic 2-bit full adder using microdisks, which replaces the core part of an electrical full adder by optical counterparts and uses light to carry signals from one bit to the next with high bandwidth and low power consumption per bit. All control signals of the operands are applied simultaneously within each clock cycle. Thus, the severe latency issue that accumulates as the size of the full adder increases can be circumvented, allowing for an improvement in computing speed and a reduction in power consumption. This approach paves the way for future high-speed optical computing systems in the post-Moore's law era.
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15
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Lucas K, Cork C, Yu B, Luk-Pat G, Painter B, Pan DZ. Implications of triple patterning for 14nm node design and patterning. ACTA ACUST UNITED AC 2012. [DOI: 10.1117/12.920028] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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16
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Integlia RA, Yin L, Ding D, Pan DZ, Gill DM, Jiang W. Parallel-coupled dual racetrack silicon micro-resonators for quadrature amplitude modulation. Opt Express 2011; 19:14892-14902. [PMID: 21934850 DOI: 10.1364/oe.19.014892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A parallel-coupled dual racetrack silicon micro-resonator structure is proposed and analyzed for M-ary quadrature amplitude modulation. The over-coupled, critically coupled, and under-coupled scenarios are systematically studied. Simulations indicate that only the over-coupled structures can generate arbitrary M-ary quadrature signals. Analytic study shows that the large dynamic range of amplitude and phase of a modulated over-coupled structure stems from the strong cross-coupling between two resonators, which can be understood through a delicate balance between the direct sum and the "interaction" terms. Potential asymmetries in the coupling constants and quality factors of the resonators are systematically studied. Compensations for these asymmetries by phase adjustment are shown feasible.
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Affiliation(s)
- Ryan A Integlia
- Department of Electrical and Computer Engineering, Rutgers University, Piscataway, NJ 08854, USA
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17
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Xinyuan D, Wang X, Lin X, Ding D, Pan DZ, Chen RT. Highly flexible polymeric optical waveguide for out-of-plane optical interconnects. Opt Express 2010; 18:16227-16233. [PMID: 20721008 DOI: 10.1364/oe.18.016227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this paper, we reported high speed optical test on polymeric optical waveguide array with embedded 45 masculine micro-mirrors on flexible substrate for out-of-plane optical interconnects. The waveguide array was bent with curvature ranging from 61 mm to 5mm. As the bending radius decreases, the average insertion loss increases from 3.4 dB to 7.7 dB for single-mode fiber (SMF) coupling and from 5.5 dB to 7.9 dB for multi-mode fiber (MMF) coupling, respectively. Eye-diagrams under such bending conditions show that the Q factor decreases from 8.0 to 6.1 and the calculated bit error rate (BER) increases from 10(-16) to 10(-10) at 10 Gbps.
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Affiliation(s)
- Dou Xinyuan
- Department of Electrical and Computer Engineering, University of Texas at Austin, Austin, TX 78758, USA
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18
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Dou X, Wang X, Huang H, Lin X, Ding D, Pan DZ, Chen RT. Polymeric waveguides with embedded micro-mirrors formed by Metallic Hard Mold. Opt Express 2010; 18:378-385. [PMID: 20173857 DOI: 10.1364/oe.18.000378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In this paper, we presented fabrication of nickel based metal mold with 45 degrees tilted surfaces on both ends of the channel waveguide through electroplating process. To obtain a precise 45 degrees tilted angle, a 50microm thick SU-8 layer was UV exposed under de-ionized water, with repeatable error control of 0.5 degrees . The polymeric waveguide array with 45 degrees micro-mirrors, which is formed by a UV imprinting method with the fabricated metallic mold, shows total insertion losses around 4dB, propagation loss around 0.18dB/cm and 75% coupling efficiency.
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Affiliation(s)
- Xinyuan Dou
- Department of Electrical and Computer Engineering, University of Texas at Austin, Austin, TX, 78758, USA
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