The hepatic transcriptome of human insulin resistance: Effects of metabolic dysfunction and fatty liver in Finnish individuals with obesity
Sylve, Eija (2024)
Sylve, Eija
2024
Bioteknologian ja biolääketieteen tekniikan maisteriohjelma - Master's Programme in Biotechnology and Biomedical Engineering
Lääketieteen ja terveysteknologian tiedekunta - Faculty of Medicine and Health Technology
This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited.
Hyväksymispäivämäärä
2024-10-09
Julkaisun pysyvä osoite on
https://urn.fi/URN:NBN:fi:tuni-202408268297
https://urn.fi/URN:NBN:fi:tuni-202408268297
Tiivistelmä
Non-alcoholic fatty liver disease (NAFLD) is the most prevalent chronic liver disorder world-wide. The development of NAFLD is influenced by acquired risk factors such as abdominal obesity, which leads to metabolic dysfunction and insulin resistance (IR), and by a strong genetic component. Hepatic IR is a key pathogenic feature of NAFLD and invariably precedes the onset of type 2 diabetes (T2D), which associates with increased severity and progression of liver disease. In addition, common genetic variants predisposing to NAFLD account for more than a fifth of the population-attributable risk for chronic liver disease. A deeper understanding of how IR, T2D, and genetic factors together affect liver function could help identify new biomarkers and therapeutic targets for NAFLD and IR. This can be investigated by measuring changes in hepatic gene expression through transcriptomic analysis of human liver tissue. However, the hepatic transcriptome in insulin-resistant individuals reflects a complex interplay of factors, including alterations due to IR, T2D, and liver fat accumulation, as well as influences of age and sex. Because many of these factors are closely interrelated, identifying transcriptomic changes specifically attributable to the distinct components of NAFLD is methodologically challenging.
The aims of this Master’s thesis study were to 1) discover hepatic transcriptome differences between insulin-sensitive and insulin-resistant obese individuals (body mass index [BMI] > 30 kg/m2); 2) distinguish which of these differences are attributable to hepatic IR and which occur due to the liver fat accumulation per se; and 3) determine changes that are more closely related to T2D, which associates with insulin deficiency and often reflects long-standing hepatic IR.
The material of this thesis consisted of two RNA-seq (ribonucleic acid sequencing) datasets with a total of 238 samples obtained from Finnish obese individuals undergoing a liver biopsy during bariatric surgery. Genotyping of NAFLD-associated risk variants was also available. After exclusions for technical and clinical reasons, 153 samples remained in the integrated dataset. To analyze transcriptomic changes attributable to liver fat accumulation independent of IR, a polygenic risk score (PRS) of liver fat content was calculated for each individual by summing the number of trait-associated alleles weighted by their effect sizes. Differential gene expression (DE) analyses were conducted having as target variables: 1) Homeostatic model assessment of IR (HOMA-IR, an index of hepatic IR); 2) NAFLD PRS; and 3) T2D status, with adjustments for confounding variables. The biological relevance of the DE genes was studied by gene set enrichment analyses (GSEA) and weighted gene co-expression analysis (WGCNA), and validated by the Ingenuity Pathway Analysis (QIAGEN) software.
The NAFLD PRS as the target variable did not result in statistically significant DE genes (padj <0.05), which means that the accumulation of metabolically inert triglycerides per se is likely not a major driver of NAFLD-related transcriptomic alterations. However, 1606 DE genes were associated to IR independent of T2D and 4 DE genes were associated to T2D independent of IR. The hepatic transcriptome of IR was characterized by the response to endoplasmic reticulum stress: attenuation of protein translation, acceleration of transport from ER to Golgi, collapse of ATP production by mitochondrial dysfunction, inflammation, fibrosis, altered lipid metabolism, apoptosis, and increased autophagy.
The aims of this Master’s thesis study were to 1) discover hepatic transcriptome differences between insulin-sensitive and insulin-resistant obese individuals (body mass index [BMI] > 30 kg/m2); 2) distinguish which of these differences are attributable to hepatic IR and which occur due to the liver fat accumulation per se; and 3) determine changes that are more closely related to T2D, which associates with insulin deficiency and often reflects long-standing hepatic IR.
The material of this thesis consisted of two RNA-seq (ribonucleic acid sequencing) datasets with a total of 238 samples obtained from Finnish obese individuals undergoing a liver biopsy during bariatric surgery. Genotyping of NAFLD-associated risk variants was also available. After exclusions for technical and clinical reasons, 153 samples remained in the integrated dataset. To analyze transcriptomic changes attributable to liver fat accumulation independent of IR, a polygenic risk score (PRS) of liver fat content was calculated for each individual by summing the number of trait-associated alleles weighted by their effect sizes. Differential gene expression (DE) analyses were conducted having as target variables: 1) Homeostatic model assessment of IR (HOMA-IR, an index of hepatic IR); 2) NAFLD PRS; and 3) T2D status, with adjustments for confounding variables. The biological relevance of the DE genes was studied by gene set enrichment analyses (GSEA) and weighted gene co-expression analysis (WGCNA), and validated by the Ingenuity Pathway Analysis (QIAGEN) software.
The NAFLD PRS as the target variable did not result in statistically significant DE genes (padj <0.05), which means that the accumulation of metabolically inert triglycerides per se is likely not a major driver of NAFLD-related transcriptomic alterations. However, 1606 DE genes were associated to IR independent of T2D and 4 DE genes were associated to T2D independent of IR. The hepatic transcriptome of IR was characterized by the response to endoplasmic reticulum stress: attenuation of protein translation, acceleration of transport from ER to Golgi, collapse of ATP production by mitochondrial dysfunction, inflammation, fibrosis, altered lipid metabolism, apoptosis, and increased autophagy.