introduction
Cirrhosis is a chronic liver disease characterized by widespread necrosis and fibrosis of liver cells, resulting in severe destruction of liver structure and function. In recent years, with the development of genetics and genomics, people have a deeper understanding of the genetic basis of liver cirrhosis. The pathogenesis of cirrhosis is complex and involves the interaction of multiple genes and environmental factors. Genome-wide Association Studies (GWAS) is an effective way to study the correlation between genetic variants and diseases, which analyzes the genomic data of large numbers of individuals to find genetic markers associated with specific diseases. Study "Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis" published April 17 in Nature Genetics , by integrating the analysis of common and rare variants, explored the genetic architecture of cirrhosis, with the aim of revealing the main genetic factors influencing the development of cirrhosis. The study first undertook a phase of GWAS meta-analysis in the European population, involving nine studies involving 15,225 cases of cirrhosis and 1,564,786 control individuals. This meta-analysis showed the effect of genetic diversity, with 12 genome-wide significant variants identified and 5 reported for the first time in cirrhosis GWAS. The study also explored the effects of these variants in different ethnic groups, and found that some variants had heterogeneous effects in European and East Asian populations. The second phase of the study was a meta-analysis of cross-ethnic GWAS that explored genetic differences between different races. In addition, the study also estimated heritability, which is the proportion of disease variants that are explained by genetic factors. The estimation of heritability helps to understand the importance of genetic factors in the development of a disease. The study found that single nucleotide polymorphisms (SNPs) in Europeans and East Asians were consistent based on heritability estimates, despite limited statistical power. In addition, studies created polygenic risk scores (PRS) based on specific SNPs and compared the effectiveness of these scores in predicting the risk of cirrhosis. Through these sophisticated analyses, the study not only advances our understanding of the genetics of cirrhosis, but also provides potential genetic markers that may be used in the future to predict disease risk and develop personalized treatment strategies.
Highlights
Large-scale multi-ethnic genomic association study: The study covered 18,265 cases of cirrhosis and 1,782,047 control individuals, and was a large-scale sample study across ethnicities, including Europeans, East Asians, African Americans, and Hispanics, which helped to identify genetic factors associated with cirrhosis more broadly. Discovery of new risk loci: The study identified 14 new genetic loci associated with cirrhosis risk, many of which are located near genes involved in hepatic lipid metabolism in the liver. Genomic discovery with multiple phenotype-driven information: studies have enhanced the ability to identify genetic risk factors for cirrhosis by using the results of genome-association studies related to liver enzyme levels as a priori information. Focus on rare coding variants: Among the genes prioritized in general variant analysis, rare coding variants are found in the GPAM gene and are associated with lower alanine aminotransferase (ALT) levels, supporting GPAM as a potential therapeutic target. Polygenic risk score (PRS): a multivariate genetic risk score has been developed that correlates with the risk of progression from cirrhosis to hepatocellular carcinoma (HCC).
Overall design and main results of the studya. The first phase was a meta-analysis of the genomic broad association study (GWAS) for the European population, and the second phase was a cross-ethnic GWAS meta-analysis. This design can reveal the impact of genetic differences between different ethnic groups on the risk of cirrhosis. b. Miami plot of cirrhosis GWAS. The transverse axis shows the chromosomal position of single nucleotide polymorphisms (SNPs), and the vertical axis shows the association strength (denoted by -log10(P)). （Credit: Nature Genetics）
Strategies
In this study, multi-omics data were integrated to analyze the effects of genome-wide association studies (GWAS) on cirrhosis and its associated endophenotypes, such as alanine aminotransferase (ALT) and γ γ-glutamyl transferase, GGT). Meta-analysis of 18,265 cases of cirrhosis and 1,782,047 controls from 12 cohorts was performed with the aim of identifying new risk loci associated with cirrhosis. First, the researchers conducted a GWAS meta-analysis of the European population, analyzing data from 15,225 cases of cirrhosis and 1,564,786 controls. The analytical tools used included genomic inflation factor (λGC) and linkage disequilibrium score regression (LDSC) to assess genetic heterogeneity and polygenicity. At this stage, the researchers identified 12 genome-wide salient variants. In the second phase, the researchers conducted a cross-ancestry fixed-effects meta-analysis, including 18,265 cases and 1,782,047 controls from different ancestry. At this stage, they identified 15 variant loci, 8 of which had not been previously reported. In addition, by associating the liver enzyme GWAS as a priori information, the researchers enhanced the capabilities of genomic discovery, analyzing data from up to 1 million individuals of European ancestry to identify independent genomic signals associated with ALT and GGT. Finally, the study also used multivariable Mendelian randomization (MVMR) techniques to evaluate the potential mediating role of non-alcoholic fatty liver disease (NAFLD) in the relationship between obesity and alcohol intake and the risk of cirrhosis.
Behind the Scenes
Cirrhosis is a chronic liver disease characterized by permanent changes in the structure of the liver, including extensive fibrosis of normal liver tissue and the formation of abnormal nodules. These changes lead to a loss of liver function, which in turn affects the health of the entire body. According to the Global Burden of Disease Study, cirrhosis is one of the leading causes of high mortality worldwide. Data from 2019 show that cirrhosis and its complications cause about 1.2 million deaths worldwide each year. The incidence and mortality of cirrhosis vary from region to region of the world, especially in developing countries.
Pathophysiology Basis The development of cirrhosis is usually divided into several stages, ranging from minor damage to hepatocytes to complete structural remodeling. Here are a few key steps in the development of cirrhosis: Hepatocyte damage and inflammation: Long-term liver damage, such as long-term alcohol consumption, nonalcoholic fatty liver disease (NAFLD) or viral hepatitis, can lead to liver cell death. Dead liver cells trigger an inflammatory response that attracts immune cells to the site of injury and promotes the release of inflammatory cytokines. Fibrosis: Chronic inflammation promotes the activation of hepatic stellate cells, which are transformed into myofibroblasts that produce large amounts of collagen and other extracellular matrix proteins, leading to cirrhosis of the liver tissue and the formation of fibrous bands. Hemodynamic changes: As the structure of liver tissue changes, the blood vessels of the liver are also affected. Increased intrahepatic vascular resistance leads to portal hypertension, one of the most serious complications of cirrhosis. Portal hypertension can lead to serious problems such as splenomegaly, ascites, and esophageal varices. Liver failure: As cirrhosis progresses, the liver's detoxification, metabolism, and synthesis functions gradually decline. This can lead to a variety of metabolic abnormalities, including decreased protein synthesis, coagulopathy, and bilirubin metabolism. Increased risk of liver cancer: chronic hepatitis and ongoing hepatocellular regeneration processes increase the risk of hepatocellular carcinoma (HCC). This cancer usually occurs in people who already have an underlying cirrhosis.
The Genetic Susceptibility and Cirrhosis Study found that in European populations, heritability estimates based on SNPs (single nucleotide polymorphisms) showed that genetic variation explained 5.1% (confidence interval: 3.5%-6.8%) of phenotypic variation in cirrhosis. In East Asian populations, the figure is 2.7% (CI: -2.7%-8.1%). This suggests that there are differences in the influence of genetic factors on cirrhosis among different ethnic groups.
Major genetic variants specific to liver enzyme levels, such as PNPLA3 rs738409 and TM6SF2 rs58542926, were significantly associated with high liver enzyme levels (ALT) and risk of cirrhosis. For example, each additional allele for the TM6SF2 rs58542926 variant was associated with a 0.10 standard deviation increase in ALT levels (CI: 0.07–0.13) and a significant association with the risk of cirrhosis (RR: 1.09, CI: 1.06–1.12).
Polygenic Risk Scores (PRS) and Liver Disease OutcomesBy constructing multiple genetic risk scores (PRS), the study assessed the association of these PRSs with liver disease outcomes such as liver cancer (HCC) and cirrhosis. PRS15-SNP significantly improves the risk prediction ability of HCC. In the UK Biobank (UKB), patients with cirrhosis who had a high PRS15-SNP score (top 20% of the PRS distribution) had a 10-year HCC risk of 15.0% (CI: 9.7%–22.0%), significantly higher than those in the bottom 80% of the PRS distribution (5.8%, CI: 4.3%–7.6%).
Liver disease mechanisms and genetic variants were analyzed by PheWAS, which further explored the phenotypic broad impact of specific genetic variants such as PNPLA3 p.Ile148Met (rs738409). This variant shows a proportional effect with cirrhosis, non-alcoholic fatty liver disease (NAFLD), and alcoholic liver disease (ALD). In addition, this variant interacted significantly with environmental factors such as high alcohol intake, body mass index (BMI) > 30 kg/m^2, and type 2 diabetes (T2D), increasing the risk of hepatocellular carcinoma and all causes of liver disease.
Effect of Rare Coding Variants on Cirrhosis Rare coding variants generally refer to those genetic variants that occur less frequently in the population, and these variants usually involve mutations in the coding region of the gene that may lead to changes in the structure or function of the protein.
Disease association analysis of rare variantsIn analyzing the genetic basis of cirrhosis, the research team paid particular attention to rare variants that may increase the risk of cirrhosis by altering key physiological processes such as liver metabolism or immune response. For example, the p.Ile148Met (rs738409) variant in the PNPLA3 gene is a rare coding variant known to be strongly associated with hepatic fatty deposition and liver disease progression. In addition, rare variants in the TM6SF2 gene were found to be associated with elevated liver enzyme levels (ALT) and an increased risk of cirrhosis (OR: 1.09, 95% CI: 1.06–1.12).
Functional and phenotypic breadth was explored by locating molecular QTLs that affect gene expression, such as expression level mapping (eQTL) and protein-level mapping (pQTL), to further explore the link between rare variants and disease characteristics. For example, by comparing the association data of expression QTL analysis with cirrhosis, researchers can infer which genes may play a key role in the development of cirrhosis. In addition, using colocalization analysis, researchers were able to assess causal associations between cirrhosis risk loci and specific gene expression.
Potential LimitationsImbalanced Sample Distribution In the study, the sample of European descent was the highest, while the sample of African Americans and Hispanics was relatively small, making it impossible to effectively estimate the genetic susceptibility of these groups. The uneven distribution of the sample may affect the generalizability of the findings and limit the possibility of discovering genetic variants that are specific to other races.
Genetic Heterogeneity Studies have found that certain genetic variants manifest differently in different ethnic groups, such as ALDH2 and SERPINA1 gene variants that are more common in East Asian populations and less common in other ethnic groups. This genetic heterogeneity can lead to increased complexity in cross-ethnic studies, making it more difficult to predict disease risk and develop treatment strategies for specific genetic variants.
Study Design and Execution Limitations Despite the use of multiple cohorts and large samples to improve the statistical power of the study, the study faced some design and execution limitations. For example, incomplete information on genetic variants in some datasets (eg, the absence of ALDH2 rs671 variants in non-East Asian populations) has affected a comprehensive assessment of the relationship between these variants and the risk of cirrhosis.
Statistical Power Limitations The small sample size of non-European descendants may limit the statistical power of genetic susceptibility studies conducted in these populations, resulting in an inaccurate estimation of the impact of genetic variation on the risk of cirrhosis. In addition, the results of the Multivariable Mendelian Randomization analysis may be affected by insufficient sample size, and the possibility that genetic variation affects the risk of cirrhosis through indirect pathways cannot be completely ruled out.
Reproducibility and Verifiability Although the association of some of the genetic variants in the study with cirrhosis was validated in the replication cohort, there were some variants whose effects were not statistically significant in the replication analysis. This may indicate that some of the findings are contingent and require further validation in larger, more diverse populations.
Complexity of Phenotypic Definitions As a complex disease, the pathogenesis of cirrhosis involves a variety of factors. Although the study attempts to explore the association of genetic variation with other health conditions through PheWAS, there may be differences in the definition and measurement of phenotypes, affecting the overall understanding of the mechanism of action of genetic variation.
Potential Research Directions: Analysis of Gene-Environment InteractionsAs the interaction between genetic risk factors and environmental factors such as alcohol intake, obesity, and type 2 diabetes mellitus has become increasingly evident in the risk of liver cirrhosis, future studies can explore these interactions in more depth. With a wider population and more detailed environmental data, studies can more accurately reveal how these factors work together to contribute to the development and progression of cirrhosis.
Multi-omics and Phenome-Wide Association StudiesThe integration of multi-omics data and phenome-wide association studies (PheWAS) can provide new perspectives for the genetic study of liver cirrhosis. By combining genomic, proteomic, and metabolomic data, researchers can gain a more comprehensive understanding of the biological mechanisms of cirrhosis and potentially discover new biomarkers and therapeutic targets.
Replication and Discovery of Therapeutic TargetsAlthough multiple genetic variants associated with cirrhosis have been identified, these findings need to be validated in larger, diverse samples. In addition, based on the genetic variants of these associations, future research should focus on the development of new therapeutics, especially those targeted drugs that can block the disease process at an early stage.
Integrated Predictive Models of Genotype and Environmental FactorsThe construction of a comprehensive prediction model that includes genetic and environmental factors can more accurately predict the risk of developing liver cirrhosis in individuals. This model will help to enable individualized prevention strategies and early intervention, especially in high-risk populations.
Extensive Research on Genetic DiversityCurrent research is mainly focused on people of European descent, and needs to be extended to populations of other ethnic and geographic regions to ensure universal applicability and validity of the findings. Exploring the genetic differences in different populations will contribute to a comprehensive understanding of the genetic structure of cirrhosis and may reveal unique risk factors in specific populations.
Link to original article
Ghouse J, Sveinbjörnsson G, Vujkovic M, Seidelin AS, Gellert-Kristensen H, Ahlberg G, Tragante V, Rand SA, Brancale J, Vilarinho S, Lundegaard PR, Sørensen E, Erikstrup C, Bruun MT, Jensen BA, Brunak S, Banasik K, Ullum H; DBDS Genomic Consortium; Verweij N, Lotta L, Baras A; Regeneron Genetics Center; Mirshahi T, Carey DJ; Geisinger-Regeneron DiscovEHR Collaboration; VA Million Veteran Program; Kaplan DE, Lynch J, Morgan T, Schwantes-An TH, Dochtermann DR, Pyarajan S, Tsao PS; Estonian Biobank Research Team; Laisk T, Mägi R, Kozlitina J, Tybjærg-Hansen A, Jones D, Knowlton KU, Nadauld L, Ferkingstad E, Björnsson ES, Ulfarsson MO, Sturluson Á, Sulem P, Pedersen OB, Ostrowski SR, Gudbjartsson DF, Stefansson K, Olesen MS, Chang KM, Holm H, Bundgaard H, Stender S. Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis. Nat Genet. 2024 Apr 17. doi: 10.1038/s41588-024-01720-y. Epub ahead of print. PMID: 38632349.
https://www.nature.com/articles/s41588-024-01720-y
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