跨组织组学分析发现十个脂肪组织基因编码与肥胖相关的非酒精性脂肪性肝病相关的分泌蛋白。
Cross-tissue omics analysis discovers ten adipose genes encoding secreted proteins in obesity-related non-alcoholic fatty liver disease.
机构信息
Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA.
A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
出版信息
EBioMedicine. 2023 Jun;92:104620. doi: 10.1016/j.ebiom.2023.104620. Epub 2023 May 22.
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.
背景
非酒精性脂肪性肝病（NAFLD）是一种快速增长、未被充分诊断的流行疾病。我们假设肥胖相关的炎症会损害脂肪组织的功能，阻止有效的脂肪储存，从而导致异位脂肪在肝脏中的积累。
方法
为了确定与肥胖相关的炎症有关的脂肪组织功能障碍的机制和潜在的血清生物标志物候选物（SBCs），我们利用肥胖个体的脂肪组织和肝脏的双组织 RNA 测序（RNA-seq）数据，结合组织学 NAFLD 诊断，从同一个队列中进行分析。我们首先扫描在肥胖个体的皮下脂肪组织中与 NAFLD 差异表达（DE）的基因，但不在肝脏中表达；编码分泌到血清中的蛋白质；并显示出脂肪组织的优先表达。然后，通过最佳子集分析、人类前脂肪细胞分化过程中的基因敲低实验、人肝 HepG2 细胞中重组蛋白处理实验以及遗传分析，对鉴定出的基因进行筛选，以确定关键的脂肪组织起源的 NAFLD 基因。
结果
我们发现了一组基因，包括 10 个 SBCs，它们可能通过影响脂肪组织功能来调节 NAFLD 的发病机制。基于最佳子集分析，我们进一步关注了两个 SBCs CCDC80 和 SOD3，通过在人类前脂肪细胞中的基因敲低以及随后的分化实验，我们发现它们可以调节关键的脂肪生成基因，如 LPL、SREBPF1 和 LEP。我们还表明，用 CCDC80 和 SOD3 的重组蛋白处理肝 HepG2 细胞会影响与脂肪变性和脂质处理相关的基因，包括 PPARA、NFE2L2 和 RNF128。最后，利用与广泛的全基因组关联研究（GWAS）中血清甘油三酯（TGs）相关的脂肪性 NAFLD DE 基因的顺式调控变异，我们通过孟德尔随机化（MR）分析证明了血清 TGs 对 NAFLD 的单向影响。我们还证明了一个调节一个 SBC 基因 rs2845885 的单核苷酸多态性（SNP）本身就能产生显著的 MR 结果。这支持了这样的结论，即与肥胖相关的 NAFLD 的脂肪组织 DE 基因的遗传调节可能通过改变血清 TG 水平来导致 NAFLD。
解释
我们从双组织转录组学筛选中得到的结果通过提供一组有针对性的 10 个脂肪组织活性基因作为目前严重未被诊断的脂肪肝疾病的新的血清生物标志物候选物，提高了对肥胖相关的 NAFLD 的理解。
资金
这项工作得到了美国国立卫生研究院 R01HG010505 和 R01DK132775 资助。组织表达（GTEx）项目得到了美国国立卫生研究院主任办公室共同基金的支持，以及 NCI、NHGRI、NHLBI、NIDA、NIMH 和 NINDS 的支持。KOBS 研究（J.P.）得到了芬兰糖尿病研究基金会、Kuopio 大学医院项目赠款（EVO/VTR 赠款 2005-2019）和芬兰科学院的资助。这项研究由欧洲研究理事会在欧盟 2020 年研究和创新计划下资助（授予 M.U.K. 的 802825 号拨款）。K.H.P. 得到了芬兰科学院（拨款号 272376、266286、314383 和 335443）、芬兰医学基金会、Gyllenberg 基金会、诺和诺德基金会（拨款号 NNF10OC1013354、NNF17OC0027232 和 NNF20OC0060547）、芬兰糖尿病研究基金会、芬兰心血管研究基金会、赫尔辛基大学和赫尔辛基大学医院以及政府研究基金的资助。I.S. 得到了仪器科学基金会的个人资助。U.T.A. 获得了 Matti 和 Vappu Maukonen 基金会、Ella och Georg Ehrnrooths 基金会以及芬兰心血管研究基金会的个人拨款。
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