Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans

Investigation of the degree of family history of diabetes in different clusters of newly diagnosed type 2 diabetes in Thailand

AIM

Type 2 diabetes is a heterogeneous disease with strong genetic components. We showed earlier that newly diagnosed type 2 diabetes in Thai patients could be categorized into four clusters. This study aimed to determine the evidence of hereditary factors in these type 2 diabetes clusters.

METHODS

A total of 487 subjects who were diagnosed with type 2 diabetes in two years were enrolled in the Siriraj Diabetes Center, Siriraj Hospital Bangkok, Bangkok, Thailand. They were divided into four clusters as previously described. The associations between patients' characteristics, degree of family history of diabetes (FHD), and type 2 diabetes clusters were tested using multinomial logistic regression.

RESULTS

Among four clusters of newly diagnosed type 2 diabetes, there were significant differences in characteristics at baseline, including age at diagnosis, BMI, waist circumference, blood sugar levels, vital signs, triglyceride, HDL, calculated LDL, creatinine and eGFR (all p < .05). A relatively young age at the time of diabetes diagnosis was associated with having second-degree relatives with diabetes (p < .05) in all clusters when using mild age-related diabetes (MARD) cluster with no FHD as a control. Patients in the severe insulin-deficient diabetes (SIDD) cluster had more first-degree relatives with diabetes (odds ratio = 1.85; p = .0354), while patients in the metabolic syndrome diabetes (MSD) cluster (odds ratio = 10.73; p < .001) and the mild obesity-related diabetes (MOD) group (odds ratio = 6.66; p = .002), had more second-degree relatives with diabetes.

CONCLUSIONS

Genetic factors might have various roles in the pathogenesis of type 2 diabetes, at least in newly diagnosed Thai patients. Our findings supported that genetic heterogeneity contributed to clinical heterogeneity or four different clusters. Further studies are needed in a larger sample size of these patients is needed to identify genetic loci associated with each cluster.

Gene-based therapies for steatotic liver disease

Advances in nucleic acid delivery have positioned the liver as a key target for gene therapy, with adeno-associated virus vectors showing long-term effectiveness in treating hemophilia. Steatotic liver disease (SLD), the most common liver condition globally, primarily results from metabolic dysfunction-associated and alcohol-associated liver diseases. In some individuals, SLD progresses from simple steatosis to steatohepatitis, cirrhosis, and eventually hepatocellular carcinoma, driven by a complex interplay of genetic, metabolic, and environmental factors. Genetic variations in various lipid metabolism-related genes, such as patatin-like phospholipase domain-containing protein 3 (PNPLA3), 17β-hydroxysteroid dehydrogenase type 13 (HSD17B13), and mitochondrial amidoxime-reducing component 1 (MTARC1), impact the progression of SLD and offer promising therapeutic targets. This review largely focuses on genes identified through clinical association studies, as they are more likely to be effective and safe for therapeutic intervention. While preclinical research continues to deepen our understanding of genetic factors, early-stage clinical trials involving gene-based SLD therapies, including transient antisense and small-molecule approaches, are helping prioritize therapeutic targets. Meanwhile, hepatocyte gene editing technologies are advancing rapidly, offering alternatives to transient methods. As such, gene-based therapies show significant potential for preventing the progression of SLD and enhancing long-term liver health.

The breadth and impact of the Global Lipids Genetics Consortium

PURPOSE OF REVIEW

This review highlights contributions of the Global Lipids Genetics Consortium (GLGC) in advancing the understanding of the genetic etiology of blood lipid traits, including total cholesterol, LDL cholesterol, HDL cholesterol, triglycerides, and non-HDL cholesterol. We emphasize the consortium's collaborative efforts, discoveries related to lipid and lipoprotein biology, methodological advancements, and utilization in areas extending beyond lipid research.

RECENT FINDINGS

The GLGC has identified over 923 genomic loci associated with lipid traits through genome-wide association studies (GWASs), involving more than 1.65 million individuals from globally diverse populations. Many loci have been functionally validated by individuals inside and outside the GLGC community. Recent GLGC studies show increased population diversity enhances variant discovery, fine-mapping of causal loci, and polygenic score prediction for blood lipid levels. Moreover, publicly available GWAS summary statistics have facilitated the exploration of lipid-related genetic influences on cardiovascular and noncardiovascular diseases, with implications for therapeutic development and drug repurposing.

SUMMARY

The GLGC has significantly advanced the understanding of the genetic basis of lipid levels and serves as the leading resource of GWAS summary statistics for these traits. Continued collaboration will be critical to further understand lipid and lipoprotein biology through large-scale genetic assessments in diverse populations.

Associations of Blood Lipid-Related Polygenic Scores, Lifestyle Factors and Their Combined Effects with Risk of Coronary Artery Disease in the UK Biobank Cohort

Circulating lipids play a crucial role in the development of coronary artery disease (CAD). However, it is unclear whether the genetic susceptibility to hyperlipidemia may interact with lifestyle factors in CAD risk. Using UK Biobank data from 328,606 participants, we evaluated combined effects of genetic susceptibility to hyperlipidemia and lifestyle factors with risk of CAD. We found that both blood lipid-related polygenic score (PGS) and healthy lifestyle score (HLS) are independently associated with CAD risk, and individuals with the highest-risk lipid-related PGS and the least healthy HLS had the highest CAD risk. This association was stronger in younger (< 60 years, hazard ratio: 4.46, 95% confidence interval: 3.44-5.78) than older adults (2.54, 2.13-3.03). Our study suggests that individuals, particularly younger adults, with higher-risk PGSs of blood lipid traits would benefit more substantially by adherence to a healthy lifestyle than those with lower PGSs.

Systematic interrogation of functional genes underlying cholesterol and lipid homeostasis

BACKGROUND

Dyslipidemia or hypercholesterolemia are among the main risk factors for cardiovascular diseases. Unraveling the molecular basis of lipid or cholesterol homeostasis would help to identify novel drug targets and develop effective therapeutics.

RESULTS

Here, we adopt a systematic approach to catalog the genes underlying lipid and cholesterol homeostasis by combinatorial use of high-throughput CRISPR screening, RNA sequencing, human genetic variant association analysis, and proteomic and metabolomic profiling. Such integrative multi-omics efforts identify gamma-glutamyltransferase GGT7 as an intriguing potential cholesterol and lipid regulator. As a SREBP2-dependent target, GGT7 positively regulates cellular cholesterol levels and affects the expression of several cholesterol metabolism genes. Furthermore, GGT7 interacts with actin-dependent motor protein MYH10 to control low-density lipoprotein cholesterol (LDL-C) uptake into the cells. Genetic ablation of Ggt7 in mice leads to reduced serum cholesterol levels, supporting an in vivo role of Ggt7 during cholesterol homeostasis.

CONCLUSIONS

Our study not only provides a repertoire of lipid or cholesterol regulatory genes from multiple angles but also reveals a causal link between a gamma-glutamyltransferase and cholesterol metabolism.

Genetic mapping of serum metabolome to chronic diseases among Han Chinese

Serum metabolites are potential regulators for chronic diseases. To explore the genetic regulation of metabolites and their roles in chronic diseases, we quantified 2,759 serum metabolites and performed genome-wide association studies (GWASs) among Han Chinese individuals. We identified 184 study-wide significant (p < 1.81 × 10-11) metabolite quantitative trait loci (metaboQTLs), 88.59% (163) of which were novel. Notably, we identified Asian-ancestry-specific metaboQTLs, including the SNP rs2296651 for taurocholic acid and taurochenodesoxycholic acid. Leveraging the GWAS for 37 clinical traits from East Asians, Mendelian randomization analyses identified 906 potential causal relationships between metabolites and clinical traits, including 27 for type 2 diabetes and 38 for coronary artery disease. Integrating genetic regulation of the transcriptome and proteome revealed putative regulators of several metabolites. In summary, we depict a landscape of the genetic architecture of the serum metabolome among Han Chinese and provide insights into the role of serum metabolites in chronic diseases.

PCSK9-antibodies fail to block PCSK9-induced inflammation in macrophages and cannot recapitulate protective effects of PCSK9-deficiency in experimental myocardial infarction

Background and aims

Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a crucial role in cholesterol homeostasis by regulating low-density lipoprotein (LDL) receptor levels. Despite its known effects on cholesterol metabolism, the role of PCSK9 in cardiac function, especially post-myocardial infarction (MI), remains unclear. This study investigates the impact of PCSK9 on heart function post-MI and evaluates the effects of PCSK9 inhibition via Alirocumab.

Methods

We used PCSK9 knockout (KO) mice and wildtype (WT) mice and in vivo treatment with Alirocumab to analyze cardiac function and survival post-MI induced by permanent ligation of the left anterior descending artery. PCSK9 and LDL receptor levels were measured using ELISA and qRT-PCR. Cardiac function was assessed via echocardiography and isolated working heart model experiments. Gene expression changes were evaluated using RNA sequencing, and inflammatory responses in bone marrow-derived macrophages (BMDMs) were analyzed in vitro.

Results

PCSK9 was expressed in murine heart tissue at levels comparable to the liver, despite minimal heart RNA expression. PCSK9 KO mice had lower plasma cholesterol levels and showed reduced cardiac functions in the working heart model compared to WT mice. Post-MI, PCSK9 KO mice demonstrated significantly improved survival and reduced ventricular rupture compared to WT mice. Alirocumab treatment, while effective in lowering plasma cholesterol, did not replicate the survival benefits seen in PCSK9 KO mice and even worsened cardiac function post-MI. In vitro, PCSK9 induced significant inflammatory responses in macrophages, which were not mitigated by Alirocumab.

Conclusion

PCSK9 accumulation in the heart post-MI contributes to adverse cardiac remodeling and inflammation. Genetic deletion of PCSK9 confers protection against post-infarct mortality, whereas pharmacological inhibition with Alirocumab fails to reproduce these benefits and may exacerbate cardiac dysfunction. These findings highlight the complex role of PCSK9 in cardiac pathology and caution against the assumption that PCSK9 inhibitors will necessarily yield cardiovascular benefits similar to genetic PCSK9 deficiency.

Low LDL cholesterol and risk of bacterial and viral infections: observational and Mendelian randomization studies

Aims

Low levels of LDL cholesterol may be associated with risk of infectious disease. We tested the hypothesis that low LDL cholesterol due to genetic variation in the LDLR, PCSK9, and HMGCR genes and a polygenic LDL cholesterol score is associated with risk of infectious diseases in the general population.

Methods and results

Using observational and Mendelian randomization designs, we examined associations of low plasma LDL cholesterol with risk of bacterial and viral infections in 119 805 individuals from the Copenhagen General Population Study/Copenhagen City Heart Study, 468 701 from the UK Biobank, and up to 376 773 from the FinnGen Research Project. Observationally, low LDL cholesterol concentrations were associated with risk of hospitalization for both bacterial and viral infections. In genetic analyses, a 1 mmol/L lower LDL cholesterol was associated with lower plasma PCSK9 {-0.55 nmol/L [95% confidence interval (CI): -1.06 to -0.05]; P = 0.03}, leucocyte count [-0.42 × 109/L (-0.61 to -0.24); P < 0.001], and high-sensitivity C-reactive protein [-0.44 mg/L (-0.79 to -0.09); P = 0.014]. Using an LDLR, HMGCR, and PCSK9 score, a 1 mmol/L lower LDL cholesterol was associated with risk ratios of 0.91 (95% CI: 0.86-0.97; P = 0.002) for unspecified bacterial infection, of 0.92 (0.87-0.97; P = 0.004) for diarrhoeal disease, and of 1.15 (1.03-1.29; P = 0.012) for unspecified viral infections and 1.64 (1.13-2.39; P = 0.009) for HIV/AIDS. Using a polygenic LDL cholesterol score largely showed similar results and in addition a lower risk of 0.85 (0.76-0.96; P = 0.006) for bacterial pneumonia and 0.91 (0.82-0.99; P = 0.035) for sepsis.

Conclusion

Genetically low LDL cholesterol concentrations were associated with lower concentration of markers of inflammation; lower risk of hospitalization for unspecified bacterial infections, infectious diarrhoeal diseases, bacterial pneumonia, and sepsis; and higher risk of viral infections and HIV/AIDS.

Prioritizing protein targets for dyslipidaemia and cardiovascular diseases using Mendelian randomization in South Asians

South Asians are at higher risk of dyslipidaemia-a modifiable risk factor for cardiovascular diseases (CVDs). We aimed to identify protein targets for dyslipidaemia and CVDs in this population. We used a two-sample Mendelian randomization (MR) approach, supplemented with MR-Egger, weighted median, colocalization, and generalized MR (GMR), to evaluate the effect of 2,800 plasma proteins on high/low/non-high-density lipoprotein cholesterol (HDL-C/LDL-C/nonHDL-C), total cholesterol, and triglycerides. Observational analyses were conducted on MR findings with strong colocalization (posterior probability≥ 80%) and GMR findings. Univariate MR assessed lipid-associated proteins' effect on CVDs. Finally, we compared the potential causal effects of plasma proteins on lipids in South Asians with those in Europeans to study heterogeneity in the MR effects. We identified 29 genetically proxied proteins potentially causal to at least one lipid measure, 12 of which showed strong colocalization and GMR evidence, including ANGPTL3 and PCSK9. Notably, PCSK9 demonstrated a stronger association with LDL-C in European compared to South Asian (βEuropean= 0.37; 95% Confidence Interval (CI)= (0.36, 0.38), βSouth Asian= 0.16; 95% CI= (0.11, 0.21)). Observational analysis suggested significant interaction between PCSK9 levels with LDL-C levels in South Asians with South Asians having a significantly lower effect compared to other ethnicities (PCSK9*South Asian; β= -0.14; 95% CI= (-0.174, -0.107)). Additionally, we showed that CELSR2 is also linked with CAD in South Asians. Our study highlighted potential causal links between plasma proteins, dyslipidaemia, and CVD in South Asians, with significant heterogeneity across genetic ancestry groups. Larger studies in South Asians are needed to validate these findings.

Barriers in Translating Existing Nutrigenetics Insights to Precision Nutrition for Cardiometabolic Health in Ethnically Diverse Populations

BACKGROUND

Cardiometabolic diseases pose a significant threat to global public health, with a substantial majority of cardiovascular disease mortality (more than three-quarters) occurring in low- and middle-income countries. There have been remarkable advances in recent years in identifying genetic variants that alter disease susceptibility by interacting with dietary factors. Despite the remarkable progress, several factors need to be considered before the translation of nutrigenetics insights to personalised and precision nutrition in ethnically diverse populations. Some of these factors include variations in genetic predispositions, cultural and lifestyle factors as well as socio-economic factors.

SUMMARY

This review aimed to explore the factors that need to be considered in bridging the gap between existing nutrigenetics insights and the implementation of personalised and precision nutrition across diverse ethnicities. Several factors might influence variations among individuals with regard to dietary exposures and metabolic responses, and these include genetic diversity, cultural and lifestyle factors as well as socio-economic factors. A multi-omics approach involving disciplines such as metabolomics, epigenetics, and the gut microbiome might contribute to improved understanding of the underlying mechanisms of gene-diet interactions and the implementation of precision nutrition although more research is needed to confirm the practicality and effectiveness of this approach. Conducting gene-diet interaction studies in diverse populations is essential and studies utilising large sample sizes are required as this improves the power to detect interactions with minimal effect sizes. Future studies should focus on replicating initial findings to enhance reliability and promote comparison across studies. Once findings have been replicated in independent samples, dietary intervention studies will be required to further strengthen the evidence and facilitate their application in clinical practice.

KEY MESSAGES

Nutrigenetics has a potential role to play in the prevention and management of cardiometabolic diseases. Conducting gene-diet interaction studies in diverse populations is essential giving the genetic diversity and variations in dietary patterns. Integrating data from disciplines such as metabolomics, epigenetics, and the gut microbiome could help in early identification of individuals at risk of cardiometabolic diseases as well as the implementation of precise dietary interventions for preventing and managing cardiometabolic diseases.

Influence of Common Gene Variants on Lipid Levels and Risk of Coronary Heart Disease in Afro-Caribbeans

A lower mortality rate from coronary artery disease (CAD) and a more favourable lipid profile have been reported in Afro-Caribbeans compared with people of European ancestry. The aim of this study was to determine whether common lipid variants identified in other populations are associated with lipid levels and CAD in Afro-Caribbeans. We studied 705 Afro-Caribbeans (192 with CAD) who were genotyped for 13 lipid-associated variants. We calculated three polygenic risk scores (PRSs) for elevated LDL (LDL-PRS), decreased HDL (HDL-PRS), and elevated triglycerides (TG-PRS). LDL-PRS, HDL-PRS, and TG-PRS were associated with LDL, HDL, and TG levels, respectively. The LDL-PRS was positively associated with LDL > 2.6 mmol/L and with LDL > 3.0 mmol/L with ORs (odds ratios) of 1.33 (95% confidence interval (CI) = 1.14-1.56) and 1.40 (CI = 1.21-1.62), respectively. The HDL-PRS was associated with a low HDL category (HDL < 1.03 mmol/L) with an OR of 1.3 (CI = 1.04-1.63) and inversely associated with a high HDL category (HDL > 1.55 mmol/L) with an OR of 0.79 (CI = 0.65-0.96). The LDL-PRS was positively associated with CAD after adjustment for age, gender, hypertension, diabetes, and smoking with an OR of 1.27 (CI = 1.06-1.51) but not the HDL-PRS nor the TG-PRS. Results of the present study indicate that common lipid variants are associated with lipid levels and prevalent CAD in Afro-Caribbeans.

Interaction between genetic risk score and dietary fat intake on lipid-related traits in Brazilian young adults

The occurrence of dyslipidaemia, which is an established risk factor for cardiovascular diseases, has been attributed to multiple factors including genetic and environmental factors. We used a genetic risk score (GRS) to assess the interactions between genetic variants and dietary factors on lipid-related traits in a cross-sectional study of 190 Brazilians (mean age: 21 ± 2 years). Dietary intake was assessed by a trained nutritionist using three 24-h dietary recalls. The high GRS was significantly associated with increased concentration of TAG (beta = 0·10 mg/dl, 95 % CI 0·05-0·16; P < 0·001), LDL-cholesterol (beta = 0·07 mg/dl, 95 % CI 0·04, 0·11; P < 0·0001), total cholesterol (beta = 0·05 mg/dl, 95 % CI: 0·03, 0·07; P < 0·0001) and the ratio of TAG to HDL-cholesterol (beta = 0·09 mg/dl, 95 % CI: 0·03, 0·15; P = 0·002). Significant interactions were found between the high GRS and total fat intake on TAG:HDL-cholesterol ratio (Pinteraction = 0·03) and between the high GRS and SFA intake on TAG:HDL-cholesterol ratio (Pinteraction = 0·03). A high intake of total fat (>31·5 % of energy) and SFA (>8·6 % of energy) was associated with higher TAG:HDL-cholesterol ratio in individuals with the high GRS (beta = 0·14, 95 % CI: 0·06, 0·23; P < 0·001 for total fat intake; beta = 0·13, 95 % CI: 0·05, 0·22; P = 0·003 for SFA intake). Our study provides evidence that the genetic risk of high TAG:HDL-cholesterol ratio might be modulated by dietary fat intake in Brazilians, and these individuals might benefit from limiting their intake of total fat and SFA.

Multipartite network analysis to identify environmental and genetic associations of metabolic syndrome in the Korean population

Network analysis has become a crucial tool in genetic research, enabling the exploration of associations between genes and diseases. Its utility extends beyond genetics to include the assessment of environmental factors. Unipartite network analysis is commonly used in genomics to visualize initial insights and relationships among variables. Syndromic diseases, such as metabolic syndrome, are characterized by the simultaneous occurrence of various signs, symptoms, and clinicopathological features. Metabolic syndrome encompasses hypertension, diabetes, obesity, and dyslipidemia, and both genetic and environmental factors contribute to its development. Given that relevant data often consist of distinct sets of variables, a more intuitive visualization method is needed. This study applied multipartite network analysis as an effective method to understand the associations among genetic, environmental, and disease components in syndromic diseases. We considered three distinct variable sets: genetic factors, environmental factors, and disease components. The process involved projecting a tripartite network onto a two-mode bipartite network and then simplifying it into a one-mode network. This approach facilitated the visualization of relationships among factors across different sets and within individual sets. To transition from multipartite to unipartite networks, we suggest both sequential and concurrent projection methods. Data from the Korean Association Resource (KARE) project were utilized, including 352,228 SNPs from 8840 individuals, alongside information on environmental factors such as lifestyle, dietary, and socioeconomic factors. The single-SNP analysis step filtered SNPs, supplemented by reference SNPs reported in a genome-wide association study catalog. The resulting network patterns differed significantly by sex: demographic factors and fat intake were crucial for women, while alcohol consumption was central for men. Indirect relationships were identified through projected bipartite networks, revealing that SNPs such as rs4244457, rs2156552, and rs10899345 had lifestyle interactions on metabolic components. Our approach offers several advantages: it simplifies the visualization of complex relationships among different datasets, identifies environmental interactions, and provides insights into SNP clusters sharing common environmental factors and metabolic components. This framework provides a comprehensive approach to elucidate the mechanisms underlying complex diseases like metabolic syndrome.

Impact of rs599839 Polymorphism on Coronary Artery Disease Risk in Saudi Diabetic Patients

Background

Coronary artery diseases may be affected by several genetic and nongenetic factors. Single-nucleotide polymorphism (SNP) rs599839 and type 2 diabetes mellitus (T2DM) can affect the occurrence and severity of coronary artery disease (CAD).

Methods

Our aim was to investigate how T2DM and the rs599839 variant affected serum lipid levels and the degree of CAD patients' coronary artery stenosis. rs599839 polymorphism genotyping was done on Saudi patients with coronary angiography performed previously. Patients enrolled were divided into group A (360 DM patients), group B (225 DM patients with CAD), and group C (190 healthy volunteers as control).

Results

Individuals with diabetes and CAD who possessed the GG genotype in rs599839 exhibited markedly reduced means of total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG; 224.5, 116.2, and 221.4 versus 251.6, 131.3, and 261.7 mg/dl, p=0.003, 0.007, and 0.025, respectively) than AA genotype. The odds ratio and the confidence interval of 95% for G allele carriers of rs599839 were OR = 0.62, 95% CI: 0.41-0.82, and p=0.003, among diabetic patients with CAD.

Conclusions

In patients with diabetic CAD, the locus 1p13.3 polymorphism rs599839 was found to be substantially correlated with serum lipid levels. Furthermore, among Saudi patients with diabetes, the G allele of rs599839 variant lowers the CAD risk.

Multifaceted roles of APOE in Alzheimer disease

For the past three decades, apolipoprotein E (APOE) has been known as the single greatest genetic modulator of sporadic Alzheimer disease (AD) risk, influencing both the average age of onset and the lifetime risk of developing AD. The APOEε4 allele significantly increases AD risk, whereas the ε2 allele is protective relative to the most common ε3 allele. However, large differences in effect size exist across ethnoracial groups that are likely to depend on both global genetic ancestry and local genetic ancestry, as well as gene-environment interactions. Although early studies linked APOE to amyloid-β - one of the two culprit aggregation-prone proteins that define AD - in the past decade, mounting work has associated APOE with other neurodegenerative proteinopathies and broader ageing-related brain changes, such as neuroinflammation, energy metabolism failure, loss of myelin integrity and increased blood-brain barrier permeability, with potential implications for longevity and resilience to pathological protein aggregates. Novel mouse models and other technological advances have also enabled a number of therapeutic approaches aimed at either attenuating the APOEε4-linked increased AD risk or enhancing the APOEε2-linked AD protection. This Review summarizes this progress and highlights areas for future research towards the development of APOE-directed therapeutics.

GALNT2 expression is associated with glucose control and serum metabolites in patients with type 2 diabetes

AIMS

Aim of this study was to investigate in type 2 diabetes whether expression level of GALNT2, a positive modulator of insulin sensitivity, is associated with a metabolic signature.

METHODS

Five different metabolite families, including acylcarnitines, aminoacids, biogenic amines, phospholipids and sphingolipids were investigated in fasting serum of 70 patients with type 2 diabetes, by targeted metabolomics. GALNT2 expression levels were measured in peripheral white blood cells by RT-PCR. The association between GALNT2 expression and serum metabolites was assessed using false discovery rate followed by stepwise selection and, finally, multivariate model including several clinical parameters as confounders. The association between GALNT2 expression and the same clinical parameters was also investigated.

RESULTS

GALNT2 expression was independently correlated with HbA1c levels (P value = 0.0052), a finding that is the likely consequence of the role of GALNT2 on insulin sensitivity. GALNT2 expression was also independently associated with serum levels of the aminoacid glycine (P value = 0.014) and two biogenic amines phenylethylamine (P value = 0.0065) and taurine (P value = 0.0011). The association of GALNT2 expression with HbA1c was not mediated by these three metabolites.

CONCLUSIONS

Our data indicate that in type 2 diabetes the expression of GALNT2 is associated with several serum metabolites. This association needs to be further investigated to understand in depth its role in mediating the effect of GALNT2 on insulin sensitivity, glucose control and other clinical features in people with diabetes.

An overview of detecting gene-trait associations by integrating GWAS summary statistics and eQTLs

Detecting genes that affect specific traits (such as human diseases and crop yields) is important for treating complex diseases and improving crop quality. A genome-wide association study (GWAS) provides new insights and directions for understanding complex traits by identifying important single nucleotide polymorphisms. Many GWAS summary statistics data related to various complex traits have been gathered recently. Studies have shown that GWAS risk loci and expression quantitative trait loci (eQTLs) often have a lot of overlaps, which makes gene expression gradually become an important intermediary to reveal the regulatory role of GWAS. In this review, we review three types of gene-trait association detection methods of integrating GWAS summary statistics and eQTLs data, namely colocalization methods, transcriptome-wide association study-oriented approaches, and Mendelian randomization-related methods. At the theoretical level, we discussed the differences, relationships, advantages, and disadvantages of various algorithms in the three kinds of gene-trait association detection methods. To further discuss the performance of various methods, we summarize the significant gene sets that influence high-density lipoprotein, low-density lipoprotein, total cholesterol, and triglyceride reported in 16 studies. We discuss the performance of various algorithms using the datasets of the four lipid traits. The advantages and limitations of various algorithms are analyzed based on experimental results, and we suggest directions for follow-up studies on detecting gene-trait associations.

Diagnostic potential of SORT1 gene in coronary artery disease

BACKGROUND

Genome-wide association studies identify SORT1 gene associated with risk of coronary artery disease (CAD). Sortilin protein enhances LDL absorption, form cell development, and atherosclerosis in macrophages.

AIM

We therefore explored SORT1 expression in CAD patients and its gene expression's predictive usefulness for the severity of the disease.

METHODOLOGY

This is a case control study and Quantitative real-time PCR; Sandwich ELISA and western blotting were used to determine the expression of SORT1 gene at the mRNA and protein level in two hundred healthy controls and two hundred patients with various CAD syndromes.

RESULTS

CAD patients exhibit higher SORT1 gene expression in CAD patients, a higher concentration of sortilin in their plasma, and distinct expression patterns in various CAD syndromes. The study reveals a positive correlation between gene expression and the severity of coronary artery stenosis, the number of diseased vessels, and the presence of diabetes. ROC curve analysis of SORT1 gene expression both at mRNA and protein level showed strong discrimination between significant CAD and control subjects.

CONCLUSION

Therefore, elevated SORT1 gene expression in various CAD syndromes may be a potential biomarker for the disease.

Lipid nanoparticles as the drug carrier for targeted therapy of hepatic disorders

The liver, a complex and vital organ in the human body, is susceptible to various diseases, including metabolic disorders, acute hepatitis, cirrhosis, and hepatocellular carcinoma. In recent decades, these diseases have significantly contributed to global morbidity and mortality. Currently, liver transplantation remains the most effective treatment for hepatic disorders. Nucleic acid therapeutics offer a selective approach to disease treatment through diverse mechanisms, enabling the regulation of relevant genes and providing a novel therapeutic avenue for hepatic disorders. It is expected that nucleic acid drugs will emerge as the third generation of pharmaceuticals, succeeding small molecule drugs and antibody drugs. Lipid nanoparticles (LNPs) represent a crucial technology in the field of drug delivery and constitute a significant advancement in gene therapies. Nucleic acids encapsulated in LNPs are shielded from the degradation of enzymes and effectively delivered to cells, where they are released and regulate specific genes. This paper provides a comprehensive review of the structure, composition, and applications of LNPs in the treatment of hepatic disorders and offers insights into prospects and challenges in the future development of LNPs.

"Oh, Dear We Are in Tribble": An Overview of the Oncogenic Functions of Tribbles 1

Pseudokinases are catalytically inactive proteins in the human genome that lack the ability to transfer phosphate from ATP to their substrates. The Tribbles family of pseudokinases contains three members: Tribbles 1, 2, and 3. Tribbles 1 has recently gained importance because of its involvement in various diseases, including cancer. It acts as a scaffolding protein that brings about the degradation of its substrate proteins, such as C/EBPα/β, MLXIPL, and RAR/RXRα, among others, via the ubiquitin proteasome system. It also serves as an adapter protein, which sequesters different protein molecules and activates their downstream signaling, leading to processes, such as cell survival, cell proliferation, and lipid metabolism. It has been implicated in cancers such as AML, prostate cancer, breast cancer, CRC, HCC, and glioma, where it activates oncogenic signaling pathways such as PI3K-AKT and MAPK and inhibits the anti-tumor function of p53. TRIB1 also causes treatment resistance in cancers such as NSCLC, breast cancer, glioma, and promyelocytic leukemia. All these effects make TRIB1 a potential drug target. However, the lack of a catalytic domain renders TRIB1 "undruggable", but knowledge about its structure, conformational changes during substrate binding, and substrate binding sites provides an opportunity to design small-molecule inhibitors against specific TRIB1 interactions.

ANGPTL3 Downregulation Increases Intracellular Lipids by Reducing Energy Utilization

BACKGROUND

ANGPTL3 (angiopoietin-like protein 3) is a circulating protein with a key role in maintaining lipoprotein homeostasis. A monoclonal antibody against ANGPTL3 is an approved and well-tolerated treatment to reduce lipoproteins in familial hypercholesterolemia homozygotes. However, the reduction of hepatic ANGPTL3 synthesis using an antisense oligonucleotide unexpectedly resulted in a dose-dependent increase in liver lipid content and circulating transaminases, resulting in the termination of the clinical trial. Meanwhile, the use of silencing RNAs remains an area of active investigation. Our study sought to investigate whether intracellular downregulation of ANGPTL3 may lead to a primary increase in neutral lipids within the hepatocyte.

METHODS

We downregulated ANGPTL3 by silencing RNA in primary human hepatocytes 3-dimensional spheroids, HepG2/LX-2 3-dimensional spheroids, and in HepG2, Hep3B2, and Huh7 cultured in 2 dimensions.

RESULTS

ANGPTL3 downregulation increased neutral lipids in all models investigated. Interestingly, ANGPTL3 induced lower intracellular deiodinase type 1 protein levels resulting in a reduction in beta-oxidation and causing an increase in triglycerides stored in lipid droplets.

CONCLUSIONS

In conclusion, intracellular ANGPTL3 downregulation by silencing RNA led to an increase in triglycerides content due to a reduction in energy substrate utilization resembling a primary intracellular hepatocyte hypothyroidism.

ANGPTL3 inhibition, dyslipidemia, and cardiovascular diseases

Optimal management of low-density lipoprotein cholesterol (LDL-C) is a central tenet in the primary and secondary prevention of atherosclerotic cardiovascular disease (ASCVD). However, significant residual cardiovascular risk remains despite achieving guideline-directed LDL-C levels, in part due to mixed hyperlipidemia with elevated fasting and non-fasting triglyceride-rich lipoprotein levels. Advances in human genetics have identified angiopoietin-like 3 (ANGPTL3) as a promising therapeutic target to lower cardiovascular risk. Evidence accrued from genetic epidemiological studies demonstrate that ANGPTL3 loss of function is strongly associated with lowering of circulating LDL-C, triglyceride-rich lipoproteins and concurrent risk reduction in development of coronary artery disease. Pharmacological inhibition of ANGPTL3 with monoclonal antibodies, antisense oligonucleotides and gene editing are in development with early studies showing their safety and efficacy in lowering in both, LDL-C and TGs, circumventing a key limitation of previous therapies. Monoclonal antibodies targeting ANGPTL3 are approved for clinical use in homozygous familial hypercholesteremia in USA and Europe. Although promising, future studies focusing on long-term beneficial effect in reducing cardiovascular events with inhibition of ANGPTL3 are warranted.

DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues

Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with the largest number of disease-associated mutations in the Human Gene Mutation Database (HGMD). Despite numerous structural studies and large-scale analyses of HD DNA binding specificity, HD-DNA recognition is still not fully understood. Here, we analyze 92 human HD mutants, including disease-associated variants and variants of uncertain significance (VUS), for their effects on DNA binding activity. Many of the variants alter DNA binding affinity and/or specificity. Detailed biochemical analysis and structural modeling identifies 14 previously unknown specificity-determining positions, 5 of which do not contact DNA. The same missense substitution at analogous positions within different HDs often exhibits different effects on DNA binding activity. Variant effect prediction tools perform moderately well in distinguishing variants with altered DNA binding affinity, but poorly in identifying those with altered binding specificity. Our results highlight the need for biochemical assays of TF coding variants and prioritize dozens of variants for further investigations into their pathogenicity and the development of clinical diagnostics and precision therapies.

Emerging Roles of UDP-GalNAc Polypeptide N-Acetylgalactosaminyltransferases in Cardiovascular Disease

UDP-GalNAc polypeptide N-acetylgalactosaminyltransferases (GalNAc-Ts) catalyze mucin-type O-glycosylation by transferring α-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to Ser or Thr residues of target proteins. This post-translational modification is common in eukaryotes, yet its biological functions remain unclear. Recent studies have identified specific receptors in the heart and vascular wall cells that can be mucin-type O-glycosylated, and there is now substantial evidence confirming that patients with various cardiovascular diseases (CVDs), such as heart failure, coronary artery disease, myocardial hypertrophy, and vascular calcification, exhibit abnormal changes in GalNAc-Ts. This review aims to highlight recent advances in GalNAc-Ts and their roles in the cardiovascular system, intending to provide evidence for clinical treatment and prevention of CVDs.

Genetic influences on circulating retinol and its relationship to human health

Retinol is a fat-soluble vitamin that plays an essential role in many biological processes throughout the human lifespan. Here, we perform the largest genome-wide association study (GWAS) of retinol to date in up to 22,274 participants. We identify eight common variant loci associated with retinol, as well as a rare-variant signal. An integrative gene prioritisation pipeline supports novel retinol-associated genes outside of the main retinol transport complex (RBP4:TTR) related to lipid biology, energy homoeostasis, and endocrine signalling. Genetic proxies of circulating retinol were then used to estimate causal relationships with almost 20,000 clinical phenotypes via a phenome-wide Mendelian randomisation study (MR-pheWAS). The MR-pheWAS suggests that retinol may exert causal effects on inflammation, adiposity, ocular measures, the microbiome, and MRI-derived brain phenotypes, amongst several others. Conversely, circulating retinol may be causally influenced by factors including lipids and serum creatinine. Finally, we demonstrate how a retinol polygenic score could identify individuals more likely to fall outside of the normative range of circulating retinol for a given age. In summary, this study provides a comprehensive evaluation of the genetics of circulating retinol, as well as revealing traits which should be prioritised for further investigation with respect to retinol related therapies or nutritional intervention.

Leveraging the transcriptome to further our understanding of GWAS findings: eQTLs associated with genes related to LDL and LDL subclasses, in a cohort of African Americans

Background: GWAS discoveries often pose a significant challenge in terms of understanding their underlying mechanisms. Further research, such as an integration with expression quantitative trait locus (eQTL) analyses, are required to decipher the mechanisms connecting GWAS variants to phenotypes. An eQTL analysis was conducted on genes associated with low-density lipoprotein (LDL) cholesterol and its subclasses, with the aim of pinpointing genetic variants previously implicated in GWAS studies focused on lipid-related traits. Notably, the study cohort consisted of African Americans, a population characterized by a heightened prevalence of hypercholesterolemia. Methods: A comprehensive differential expression (DE) analysis was undertaken, with a dataset of 17,948 protein-coding mRNA transcripts extracted from the whole-blood transcriptomes of 416 samples to identify mRNA transcripts associated with LDL, with further granularity delineated between small LDL and large LDL subclasses. Subsequently, eQTL analysis was conducted with a subset of 242 samples for which whole-genome sequencing data were available to identify single-nucleotide polymorphisms (SNPs) associated with the LDL-related mRNA transcripts. Lastly, plausible functional connections were established between the identified eQTLs and genetic variants reported in the GWAS catalogue. Results: DE analysis revealed 1,048, 284, and 94 mRNA transcripts that exhibited differential expression in response to LDL, small LDL, and large LDL, respectively. The eQTL analysis identified a total of 9,950 significant SNP-mRNA associations involving 6,955 SNPs including a subset 101 SNPs previously documented in GWAS of LDL and LDL-related traits. Conclusion: Through comprehensive differential expression analysis, we identified numerous mRNA transcripts responsive to LDL, small LDL, and large LDL. Subsequent eQTL analysis revealed a rich landscape of eQTL-mRNA associations, including a subset of eQTL reported in GWAS studies of LDL and related traits. The study serves as a testament to the important role of integrative genomics in unraveling the enigmatic GWAS relationships between genetic variants and the complex fabric of human traits and diseases.

Protective Association of APOC1/rs4420638 with Risk of Obesity: A case-control Study in Portuguese Children

The association of the rs4420638 polymorphism, near the APOC1 gene, was examined with the risk of obesity among Portuguese children. A sample of 446 Portuguese individuals (231 boys and 215 girls) of European descent, aged 3.2 to 13.7 years old (mean age: 7.98 years), were selected to conduct a case-control study. Body mass index (BMI), BMI Z-scores, and waist circumference were calculated. Genotyping was performed by real time PCR using a pre-designed TaqMan probe. Logistic regression and the nonparametric Mann-Whitney test were used to test the associations. The association results revealed a significant protective effect from the minor G-allele of SNP rs4420638 against obesity, with an odds ratio (OR) of 0.619 (95% CI 0.421-0.913; p = 0.0155) in the additive model, and OR of 0.587 (95% CI 0.383-0.9; p = 0.0145) in the dominant model. Moreover, comparing genotype groups (AA vs. AG + GG), significantly lower values (p < 0.05) for the anthropometric traits weight, height, BMI, BMI Z-score and waist circumference, were observed in the carriers of allele G. The present study provides further evidence for the APOE/APOC1 candidate-region association with the risk of obesity. This was the first study to describe the protective association of the rs4420638 minor G-allele against obesity in childhood exclusively.

SORCS2 activity in pancreatic α-cells safeguards insulin granule formation and release from glucose-stressed β-cells

Sorting receptor SORCS2 is a stress-response factor protecting neurons from acute insults, such as during epilepsy. SORCS2 is also expressed in the pancreas, yet its action in this tissue remains unknown. Combining metabolic studies in SORCS2-deficient mice with ex vivo functional analyses and single-cell transcriptomics of pancreatic tissues, we identified a role for SORCS2 in protective stress response in pancreatic islets, essential to sustain insulin release. We show that SORCS2 is predominantly expressed in islet alpha cells. Loss of expression coincides with inability of these cells to produce osteopontin, a secreted factor that facilitates insulin release from stressed beta cells. In line with diminished osteopontin levels, beta cells in SORCS2-deficient islets show gene expression patterns indicative of aggravated cell stress, and exhibit defects in insulin granule maturation and a blunted glucose response. These findings corroborate a function for SORCS2 in protective stress response that extends to metabolism.

Genetic history of Cambridgeshire before and after the Black Death

The extent of the devastation of the Black Death pandemic (1346-1353) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at the local scale. Here, we report 275 ancient genomes, including 109 with coverage >0.1×, from later medieval and postmedieval Cambridgeshire of individuals buried before and after the Black Death. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. While we detect long-term shifts in local genetic ancestry in Cambridgeshire, we find no evidence of major changes in genetic ancestry nor higher differentiation of immune loci between cohorts living before and after the Black Death.

VLDL Biogenesis and Secretion: It Takes a Village

The production and secretion of VLDLs (very-low-density lipoproteins) by hepatocytes has a direct impact on liver fat content, as well as the concentrations of cholesterol and triglycerides in the circulation and thus affects both liver and cardiovascular health, respectively. Importantly, insulin resistance, excess caloric intake, and lack of physical activity are associated with overproduction of VLDL, hepatic steatosis, and increased plasma levels of atherogenic lipoproteins. Cholesterol and triglycerides in remnant particles generated by VLDL lipolysis are risk factors for atherosclerotic cardiovascular disease and have garnered increasing attention over the last few decades. Presently, however, increased risk of atherosclerosis is not the only concern when considering today's cardiometabolic patients, as they often also experience hepatic steatosis, a prevalent disorder that can progress to steatohepatitis and cirrhosis. This duality of metabolic risk highlights the importance of understanding the molecular regulation of the biogenesis of VLDL, the lipoprotein that transports triglycerides and cholesterol out of the liver. Fortunately, there has been a resurgence of interest in the intracellular assembly, trafficking, degradation, and secretion of VLDL by hepatocytes, which has led to many exciting new molecular insights that are the topic of this review. Increasing our understanding of the biology of this pathway will aid to the identification of novel therapeutic targets to improve both the cardiovascular and the hepatic health of cardiometabolic patients. This review focuses, for the first time, on this duality.

Unlocking the mysteries of VLDL: exploring its production, intracellular trafficking, and metabolism as therapeutic targets

Reducing circulating lipid levels is the centerpiece of strategies for preventing and treating atherosclerotic cardiovascular disease (ASCVD). Despite many available lipid-lowering medications, a substantial residual cardiovascular risk remains. Current clinical guidelines focus on plasma levels of low-density lipoprotein (LDL). Recent attention has been given to very low-density lipoprotein (VLDL), the precursor to LDL, and its role in the development of coronary atherosclerosis. Preclinical investigations have revealed that interventions targeting VLDL production or promoting VLDL metabolism, independent of the LDL receptor, can potentially decrease cholesterol levels and provide therapeutic benefits. Currently, methods, such as mipomersen, lomitapide, and ANGPTL3 inhibitors, are used to reduce plasma cholesterol and triglyceride levels by regulating the lipidation, secretion, and metabolism of VLDL. Targeting VLDL represents an avenue for new lipid-lowering strategies. Interventions aimed at reducing VLDL production or enhancing VLDL metabolism, independent of the LDL receptor, hold promise for lowering cholesterol levels and providing therapeutic benefits beyond LDL in the management of ASCVD.

Utilizing Human Genetics to Develop Chemoprevention for Cancer-Too Good an Opportunity to be Missed

Large-scale genetic studies are reliably identifying many risk factors for disease in the general population. Several of these genetic risk factors encode potential drug targets, and genetics has already helped to introduce targeted agents for some diseases, an example being lipid-lowering drugs to reduce the incidence of cardiovascular disease. Multiple drugs have been developed to treat cancers based on somatic mutations and genomics, but in stark contrast, there seems to be a reluctance to use germline genetic data to develop drugs to prevent malignancy, despite the large numbers of people who could benefit, the potential for lowering cancer rates, and the widespread current use of non-pharmaceutical measures to reduce cancer risk factors such as tobacco, alcohol, and infectious diseases. We argue that concerted efforts for cancer prevention based on genetics, including genes influenced by common polymorphisms that modulate cancer risk, are urgently needed. There are enormous, yet underutilized, opportunities to develop novel targeted agents for chemoprevention of cancer based on human germline genetics. Such efforts are likely to require the support of a dedicated funding program by national and international agencies. See related commentary by Winham and Sherman, p. 13.

Causal effect of beta-blockers on the risk of lung cancer: a Mendelian randomization study

Background

It remains uncertain whether there is a causal association of the use of beta-blockers (BBs) on lung cancer risk. We used a two-sample Mendelian randomization (MR) approach to identify the causal association of BBs and lung cancer risk.

Methods

Twenty-two BB-related single-nucleotide polymorphisms (SNPs) were obtained from the UK Biobank as the instrumental variables (IVs). Genetic summary data information of lung cancer was extracted from the International Lung Cancer Consortium, with a total of 11,348 cases and 15,861 controls. We adopted the inverse-variance weighted (IVW) approach to conduct the MR analyses. Egger-intercept analysis was further performed as sensitivity analysis for pleiotropy evaluation. Additionally, we investigated whether BBs could causally affect the risk of lung cancer through their pharmacological effects.

Results

The current IVW analysis suggested a decreased lung cancer risk in BB users [odds ratio (OR) =0.83; 95% confidence interval (CI): 0.73-0.95; P<0.01]. Results of Egger-intercept analysis demonstrated that no pleiotropy was found (P=0.94), which suggested the robustness of the causality. However, there was little evidence that pharmacological effects mediate the association between BBs and lung cancer.

Conclusions

The current analysis suggested that BBs could decrease the risk of lung cancer but may be not via its pharmacological effects. Further research is in need for elucidating the underlying mechanisms.

Evaluation of input data modality choices on functional gene embeddings

Functional gene embeddings, numerical vectors capturing gene function, provide a promising way to integrate functional gene information into machine learning models. These embeddings are learnt by applying self-supervised machine-learning algorithms on various data types including quantitative omics measurements, protein-protein interaction networks and literature. However, downstream evaluations comparing alternative data modalities used to construct functional gene embeddings have been lacking. Here we benchmarked functional gene embeddings obtained from various data modalities for predicting disease-gene lists, cancer drivers, phenotype-gene associations and scores from genome-wide association studies. Off-the-shelf predictors trained on precomputed embeddings matched or outperformed dedicated state-of-the-art predictors, demonstrating their high utility. Embeddings based on literature and protein-protein interactions inferred from low-throughput experiments outperformed embeddings derived from genome-wide experimental data (transcriptomics, deletion screens and protein sequence) when predicting curated gene lists. In contrast, they did not perform better when predicting genome-wide association signals and were biased towards highly-studied genes. These results indicate that embeddings derived from literature and low-throughput experiments appear favourable in many existing benchmarks because they are biased towards well-studied genes and should therefore be considered with caution. Altogether, our study and precomputed embeddings will facilitate the development of machine-learning models in genetics and related fields.

Missense variants in SORT1 are associated with LDL-C in an Amish population

Common noncoding variants at the human 1p13.3 locus associated with SORT1 expression are among those most strongly associated with low-density lipoprotein cholesterol (LDL-C) in human genome-wide association studies. However, validation studies in mice and cell lines have produced variable results regarding the directionality of the effect of SORT1 on LDL-C. This, together with the fact that the 1p13.3 variants are associated with expression of several genes, has raised the question of whether SORT1 is the causal gene at this locus. Using whole exome sequencing in members of an Amish population, we identified coding variants in SORT1 that are associated with increased (rs141749679, K302E) and decreased (rs149456022, Q225H) LDL-C. Further, analysis of plasma lipoprotein particle subclasses by ion mobility in a subset of rs141749679 (K302E) carriers revealed higher levels of large LDL particles compared to noncarriers. In contrast to the effect of these variants in the Amish, the sortilin K302E mutation introduced into a C57BL/6J mouse via CRISPR/Cas9 resulted in decreased non-high-density lipoprotein cholesterol, and the sortilin Q225H mutation did not alter cholesterol levels in mice. This is indicative of different effects of these mutations on cholesterol metabolism in the two species. To our knowledge, this is the first evidence that naturally occurring coding variants in SORT1 are associated with LDL-C, thus supporting SORT1 as the gene responsible for the association of the 1p13.3 locus with LDL-C.

High Expression of PSRC1 Predicts Poor Prognosis in Lung Adenocarcinoma

Background: The incidence of lung cancer is increasing annually, but the mechanism of its occurrence and development requires further study. This study aimed to investigate the biological function and prognostic value of proline- and serine-rich coiled-coil 1 (PSRC1) in lung cancer. Methods: We used data from The Cancer Genome Atlas (TCGA) to analyze the association between clinical features and PSRC1 expression in non-small cell carcinoma. The relationship between PSRC1 expression and prognosis in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) was analyzed using Kaplan-Meier curves. The function of PSRC1 was identified using enrichment analysis, and the relationship between PSRC1 expression and immune cell infiltration was studied. In addition, the expression of PSRC1 in 150 patients with non-small cell carcinoma was detected using immunohistochemistry, and its clinical significance was analyzed. Results: It was found that the expression level of PSRC1 was higher in LUAD and LUSC tumor tissues than in normal tissues, and the results were confirmed by immunohistochemistry in 150 patients. TCGA data showed that high PSRC1 expression in LUAD was associated with poorer overall survival (p = 0.003) and progression-free interval (p = 0.012). Multivariable analysis showed that PSRC1 was an independent risk factor for LUAD. Functional enrichment analysis showed that PSRC1 is related to tumor development. Conclusion: High PSRC1 expression is significantly associated with LUAD survival and may be a promising prognostic biomarker.

Genome-wide association meta-analysis identifies 17 loci associated with nonalcoholic fatty liver disease

Nonalcoholic fatty liver disease (NAFLD) is common and partially heritable and has no effective treatments. We carried out a genome-wide association study (GWAS) meta-analysis of imaging (n = 66,814) and diagnostic code (3,584 cases versus 621,081 controls) measured NAFLD across diverse ancestries. We identified NAFLD-associated variants at torsin family 1 member B (TOR1B), fat mass and obesity associated (FTO), cordon-bleu WH2 repeat protein like 1 (COBLL1)/growth factor receptor-bound protein 14 (GRB14), insulin receptor (INSR), sterol regulatory element-binding transcription factor 1 (SREBF1) and patatin-like phospholipase domain-containing protein 2 (PNPLA2), as well as validated NAFLD-associated variants at patatin-like phospholipase domain-containing protein 3 (PNPLA3), transmembrane 6 superfamily 2 (TM6SF2), apolipoprotein E (APOE), glucokinase regulator (GCKR), tribbles homolog 1 (TRIB1), glycerol-3-phosphate acyltransferase (GPAM), mitochondrial amidoxime-reducing component 1 (MARC1), microsomal triglyceride transfer protein large subunit (MTTP), alcohol dehydrogenase 1B (ADH1B), transmembrane channel like 4 (TMC4)/membrane-bound O-acyltransferase domain containing 7 (MBOAT7) and receptor-type tyrosine-protein phosphatase δ (PTPRD). Implicated genes highlight mitochondrial, cholesterol and de novo lipogenesis as causally contributing to NAFLD predisposition. Phenome-wide association study (PheWAS) analyses suggest at least seven subtypes of NAFLD. Individuals in the top 10% and 1% of genetic risk have a 2.5-fold to 6-fold increased risk of NAFLD, cirrhosis and hepatocellular carcinoma. These genetic variants identify subtypes of NAFLD, improve estimates of disease risk and can guide the development of targeted therapeutics.

Genetic predisposition to nonalcoholic fatty liver disease: insights from ANGPTL8 gene variants in Iranian adults

Nonalcoholic fatty liver disease (NAFLD) is a prevalent chronic liver disease with a global prevalence, and modulation of ANGPTL8 expression has emerged as a promising predictor of NAFLD susceptibility. This research was conducted to scrutinize ANGPTL8 protein expression in NAFLD patients and elucidate the interplay between ANGPTL8 gene polymorphisms and their lipid profiles, thus shedding new light on the pathophysiology of this complex disease. The study comprised 423 unrelated participants, including 222 healthy controls and 201 individuals with NAFLD, screened using FibroScan/ultrasonography and laboratory tests. The main goal focused on the genotype and allele frequency distribution in the ANGPTL8 gene, specifically analyzing two genetic variations: rs737337 (T/C) and rs2278426 (C/T). The participants diagnosed with NAFLD were slightly younger (P ≥ 0.05) and had a higher body mass index (BMI) than the individuals in the control group. Notably, there was a significant difference in the occurrence of the rs737337 polymorphism between the NAFLD and control groups, with a lower frequency observed in the NAFLD group. Our results indicated that individuals with the TC + CC genotype and C allele of rs737337 (T/C) had a decreased risk of higher levels of ALT and AST. Conversely, those with the CT, CT + TT genotype, and T allele of rs2278426 (C/T) exhibited an increased risk of higher levels of ALT and AST. The results imply that the rs2278426 (C/T) variant of the ANGPTL8 gene is more strongly linked to an increased risk of NAFLD compared to the rs737337 polymorphism. However, additional research is needed to understand the specific molecular mechanisms responsible for the upregulation of ANGPTL8 in individuals with NAFLD.

Leveraging Genetics to Address the Role of GALNT2 on Atherogenic Dyslipidemia

Several studies have shown that downregulation of GALNT2 (Polypeptide N-Acetylgalactosaminyltransferase 2), encoding polypeptide N-acetylgalactosaminyltransferase 2, decreases high-density lipoprotein cholesterol (HDL-C) and increases triglycerides levels by glycosylating key enzymes of lipid metabolism, such as angiopoietin like 3, apolipoprotein C-III, and phospholipid transfer protein. GALNT2 is also a positive modulator of insulin signaling and action, associated with in vivo insulin sensitivity and during adipogenesis strongly upregulates adiponectin. Thus, the hypothesis that GALNT2 affects HDL-C and triglycerides levels also through insulin sensitivity and/or circulating adiponectin, is tested. In 881 normoglycemic individuals the G allele of rs4846914 SNP at the GALNT2 locus, known to associate with GALNT2 downregulation, is associated with low HDL-C and high values of triglycerides, triglycerides/HDL-C ratio, and theHomeostatic Model Assessment of insulin resistance HOMAIR (p-values = 0.01, 0.027, 0.002, and 0.016, respectively). Conversely, no association is observed with serum adiponectin levels (p = 0.091). Importantly, HOMAIR significantly mediates a proportion of the genetic association with HDL-C (21%, 95% CI: 7-35%, p = 0.004) and triglyceride levels (32%, 95% CI: 4-59%, p = 0.023). The results are compatible with the hypothesis that, besides the effect on key lipid metabolism enzymes, GALNT2 alters HDL-C and triglyceride levels also indirectly through a positive effect on insulin sensitivity.

Genetic and metabolic aspects of non-alcoholic fatty liver disease (NAFLD) pathogenicity

Background

Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease showing a rising prevalence globally. Genetic predisposition plays a key role in the development and progression of the disease pathogenicity.

Main body

This paper summarizes genetic associations based on their influence on several metabolic aspects such as lipid metabolism, glucose metabolism, hepatic iron accumulation and cholesterol metabolism toward the NAFLD pathogenicity. Furthermore, we present variations in some epigenetic characters and the microRNA profile with regard to NAFLD.

Conclusion

As reported in many studies, the PNPLA3 rs738409 variant seems to be significantly associated with NAFLD susceptibility. Other gene variants like TM6SF2 rs58542926, MBOAT7 rs641738 and GCKR variants also appear to be more prevalent among NAFLD patients. We believe these genetic variants may provide insights into new trends in developing noninvasive biomarkers and identify their suitability in clinical practice in the future.

Graphical abstract

Sortilin Is Upregulated in Osteoarthritis-Dependent Cartilage Calcification and Associated with Cellular Senescence

Osteoarthritis (OA) is a chronic joint disease characterized by articular cartilage calcification, loss of articular cartilage, bone changes, pain, and disability. Cartilage calcification is one hallmark of OA and is predominantly caused by basic calcium crystals formed due to an imbalance of the pyrophosphate pathway. Sortilin is a transmembrane protein that contributes to vascular calcification in atherosclerosis by externalizing alkaline phosphatase (ALP)-containing vesicles. Calcification in atherosclerosis and osteoarthritis has been associated with cellular senescence. The aim of this study was to investigate the potential role of sortilin and senescence in osteoarthritis-dependent cartilage calcification. Osteoarthritic cartilage from human knee joints was collected after joint replacement, and samples were analyzed by immunohistochemistry and quantitative RT-PCR analysis. Human chondrocytes were treated with osteogenic medium for up to 21 days to induce calcification. Western blots for sortilin and ALP, as well as an ALP activity assay, were performed. Human chondrocytes were treated with mitomycin C to induce senescence, and sortilin expression was quantified at the protein and gene levels. Sections of knee joints from a murine model of osteoarthritis were stained for sortilin and p16 and analyzed by immunohistochemistry. Treatment of wild-type chondrocytes using an osteogenic medium similar to human chondrocytes was performed. Osteoarthritic cartilage from mouse and human knee joints showed an increased number of sortilin and p16-positive chondrocytes compared to healthy cartilage. This observation was corroborated by increased gene expression of sortilin and p16 in mild and moderate osteoarthritic cartilage samples. To investigate the mechanism of sortilin regulation, human chondrocytes were treated with osteogenic medium to induce calcification. Sortilin protein levels and expression were increased after 7 days of stimulation, whereas ALP levels and activity were upregulated after 21 days of stimulation. Similar observations were made in a murine osteoarthritis model. Mechanistically, senescent chondrocytes induced by mitomycin C showed an upregulation of sortilin and ALP gene expression compared to non-senescent chondrocytes. Our data indicate that sortilin and ALP are upregulated during cartilage calcification, which is associated with chondrocyte senescence and thus might contribute to the pathogenesis of osteoarthritis. Cellular senescence seems to induce sortilin expression.

An adult-based genetic risk score for liver fat associates with liver and plasma lipid traits in children and adolescents

BACKGROUND & AIMS

Genome-wide association studies have identified steatogenic variants that also showed pleiotropic effects on cardiometabolic traits in adults. We investigated the effect of eight previously reported genome-wide significant steatogenic variants, individually and combined in a weighted genetic risk score (GRS), on liver and cardiometabolic traits, and the predictive ability of the GRS for hepatic steatosis in children and adolescents.

APPROACH & RESULTS

Children and adolescents with overweight (including obesity) from an obesity clinic group (n = 1768) and a population-based group (n = 1890) were included. Cardiometabolic risk outcomes and genotypes were obtained. Liver fat was quantified using 1 H-MRS in a subset of 727 participants. Variants in PNPLA3, TM6SF2, GPAM and TRIB1 were associated with higher liver fat (p < .05) and with distinct patterns of plasma lipids. The GRS was associated with higher liver fat content, plasma concentrations of alanine transaminase (ALT), aspartate aminotransferase (AST) and favourable plasma lipid levels. The GRS was associated with higher prevalence of hepatic steatosis (defined as liver fat ≥5.0%) (odds ratio per 1-SD unit: 2.17, p = 9.7E-10). A prediction model for hepatic steatosis including GRS alone yielded an area under the curve (AUC) of 0.78 (95% CI 0.76-0.81). Combining the GRS with clinical measures (waist-to-height ratio [WHtR] SDS, ALT, and HOMA-IR) increased the AUC up to 0.86 (95% CI 0.84-0.88).

CONCLUSIONS

The genetic predisposition for liver fat accumulation conferred risk of hepatic steatosis in children and adolescents. The liver fat GRS has potential clinical utility for risk stratification.

Association of single nucleotide polymorphisms with dyslipidemia and risk of metabolic disorders in the State of Qatar

BACKGROUND

Dyslipidemia is recognized as one of the risk factors of cardiovascular diseases (CVDs), type 2 diabetes mellitus (T2DM), and non-alcoholic fatty liver disease (NAFLD).

OBJECTIVE

The study aimed to investigate the association between selected single nucleotide polymorphisms (SNPs) with dyslipidemia and increased susceptibility risks of CVD, NAFLD, and/or T2DM in dyslipidemia patients in comparison with healthy control individuals from the Qatar genome project.

METHODS

A community-based cross-sectional study was conducted among 2933 adults (859 dyslipidemia patients and 2074 healthy control individuals) from April to December 2021 to investigate the association between 331 selected SNPs with dyslipidemia and increased susceptibility risks of CVD, NAFLD and/or T2DM, and covariates.

RESULTS

The genotypic frequencies of six SNPs were found to be significantly different in dyslipidemia patients subjects compared to the control group among males and females. In males, three SNPs were found to be significant, the rs11172113 in over-dominant model, the rs646776 in recessive and over-dominant models, and the rs1111875 in dominant model. On the other hand, two SNPs were found to be significant in females, including rs2954029 in recessive model, and rs1801251 in dominant and recessive models. The rs17514846 SNP was found for dominant and over-dominant models among males and only the dominant model for females. We found that the six SNPs linked to gender type had an influence in relation to disease susceptibility. When controlling for the four covariates (gender, obesity, hypertension, and diabetes), the difference between dyslipidemia and the control group remained significant for the six variants. Finally, males were three times more likely to have dyslipidemia in comparison with females, hypertension was two times more likely to be present in the dyslipidemia group, and diabetes was six times more likely to be in the dyslipidemia group.

CONCLUSION

The current investigation provides evidence of association for a common SNP to coronary heart disease and suggests a sex-dependent effect and encourage potential therapeutic applications.

Polymorphisms of TRIB1 Genes for Coronary Artery Disease and Stroke Risk: A Systematic Review and Meta-analysis

BACKGROUND AND AIMS

In recent years, the results of the association between Tribbles Pseudokinase 1 (TRIB1) gene polymorphism and the risk of coronary artery disease (CAD) and stroke are inconsistent. This study aimed to systematically review the literature on TRIB1 gene polymorphisms and susceptibility to coronary atherosclerotic heart disease (CAD) and stroke.

METHODS

This study collected studies published until May 2022 through a systematic search of PubMed, Web of Science, and Google Scholar databases. After a systematic literature search, pooled odds ratio (OR) and their corresponding 95% confidence interval (CI) were used to assess the strength of the association.

RESULTS

We identified 6 studies on rs17321515, including 12892 controls and 4583 patients, and 3 on rs2954029, including 1732 controls and 1305 patients. In different genetic models, the rs2954029 genetic polymorphism significantly increased the risk of CAD and stroke. In the codominant model, the AA genotype increased the risk of CAD and stroke (OR=1.74, 95% CI=1.39-2.17, P<0.001); the TA genotype also increased the prevalence of CAD and stroke risk (OR=1.39, 95% CI=1.18-1.64, P<0.001). Compared with the control group, the TT+TA genotype increased the risk of CAD and stroke in the dominant genetic model (OR=1.46, 95%CI=1.25-1.71, P<0.001), and in the recessive model, the TA+AA genotype increased the risk of CAD and stroke (OR=1.41, 95% CI=1.15-1.72, P<0.001). In addition, the TRIB1 rs17321515 polymorphism was not found to be associated with the risk of CAD and stroke, which may be related to other factors such as race.

CONCLUSIONS

The rs2954029 A allele was significantly associated with an increased risk of CAD and stroke, according to the present meta-analysis. However, the association of rs17321515 polymorphism with susceptibility to CAD and stroke has not been found in this study.

TM6SF2 Determines Both the Degree of Lipidation and the Number of VLDL Particles Secreted by the Liver

In 2014, exome-wide studies identified a glutamine176lysine (p.E167K) substitution in a protein of unknown function named transmembrane 6 superfamily member 2 (TM6SF2). The p.E167K variant was associated with increased hepatic fat content and reduced levels of plasma TG and LDL cholesterol. Over the next several years, additional studies defined the role of TM6SF2, which resides in the ER and the ER-Golgi interface, in the lipidation of nascent VLDL to generate mature, more TG-rich VLDL. Consistent results from cells and rodents indicated that the secretion of TG was reduced in the p.E167K variant or when hepatic TM6SF2 was deleted. However, data for secretion of APOB was inconsistent, either reduced or increased secretion was observed. A recent study of people homozygous for the variant demonstrated reduced in vivo secretion of large, TG-rich VLDL1 into plasma; both TG and APOB secretion were reduced. Here we present new results demonstrating increased secretion of VLDL APOB with no change in TG secretion in p.E167K homozygous individuals from the Lancaster Amish community compared to their wild-type siblings. Our in vivo kinetic tracer results are supported by in vitro experiments in HepG2 and McA cells with knock-down or Crispr-deletions of TM6SF2, respectively. We offer a model to potentially explain all of the prior data and our new results.

Insulin Regulation of Hepatic Lipid Homeostasis

The incidence of obesity, insulin resistance, and type II diabetes (T2DM) continues to rise worldwide. The liver is a central insulin-responsive metabolic organ that governs whole-body metabolic homeostasis. Therefore, defining the mechanisms underlying insulin action in the liver is essential to our understanding of the pathogenesis of insulin resistance. During periods of fasting, the liver catabolizes fatty acids and stored glycogen to meet the metabolic demands of the body. In postprandial conditions, insulin signals to the liver to store excess nutrients into triglycerides, cholesterol, and glycogen. In insulin-resistant states, such as T2DM, hepatic insulin signaling continues to promote lipid synthesis but fails to suppress glucose production, leading to hypertriglyceridemia and hyperglycemia. Insulin resistance is associated with the development of metabolic disorders such as cardiovascular and kidney disease, atherosclerosis, stroke, and cancer. Of note, nonalcoholic fatty liver disease (NAFLD), a spectrum of diseases encompassing fatty liver, inflammation, fibrosis, and cirrhosis, is linked to abnormalities in insulin-mediated lipid metabolism. Therefore, understanding the role of insulin signaling under normal and pathologic states may provide insights into preventative and therapeutic opportunities for the treatment of metabolic diseases. Here, we provide a review of the field of hepatic insulin signaling and lipid regulation, including providing historical context, detailed molecular mechanisms, and address gaps in our understanding of hepatic lipid regulation and the derangements under insulin-resistant conditions. © 2023 American Physiological Society. Compr Physiol 13:4785-4809, 2023.

Lipid-Associated GWAS Loci Predict Antiatherogenic Effects of Rosuvastatin in Patients with Coronary Artery Disease

We have shown that lipid-associated loci discovered by genome-wide association studies (GWAS) have pleiotropic effects on lipid metabolism, carotid intima-media thickness (CIMT), and CAD risk. Here, we investigated the impact of lipid-associated GWAS loci on the efficacy of rosuvastatin therapy in terms of changes in plasma lipid levels and CIMT. The study comprised 116 CAD patients with hypercholesterolemia. CIMT, total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG) were measured at baseline and after 6 and 12 months of follow-up, respectively. Genotyping of fifteen lipid-associated GWAS loci was performed by the MassArray-4 System. Linear regression analysis adjusted for sex, age, body mass index, and rosuvastatin dose was used to estimate the phenotypic effects of polymorphisms, and p-values were calculated through adaptive permutation tests by the PLINK software, v1.9. Over one-year rosuvastatin therapy, a decrease in CIMT was linked to rs1689800, rs4846914, rs12328675, rs55730499, rs9987289, rs11220463, rs16942887, and rs881844 polymorphisms (Pperm < 0.05). TC change was associated with rs55730499, rs11220463, and rs6065906; LDL-C change was linked to the rs55730499, rs1689800, and rs16942887 polymorphisms; and TG change was linked to polymorphisms rs838880 and rs1883025 (Pperm < 0.05). In conclusion, polymorphisms rs1689800, rs55730499, rs11220463, and rs16942887 were found to be predictive markers for multiple antiatherogenic effects of rosuvastatin in CAD patients.

Gene-environment interactions in the associations of PFAS exposure with insulin sensitivity and beta-cell function in a Faroese cohort followed from birth to adulthood

BACKGROUND

Exposure to perfluoroalkyl substances (PFAS) has been associated with changes in insulin sensitivity and pancreatic beta-cell function in humans. Genetic predisposition to diabetes may modify these associations; however, this hypothesis has not been yet studied.

OBJECTIVES

To evaluate genetic heterogeneity as a modifier in the PFAS association with insulin sensitivity and pancreatic beta-cell function, using a targeted gene-environment (GxE) approach.

METHODS

We studied 85 single-nucleotide polymorphisms (SNPs) associated with type 2 diabetes, in 665 Faroese adults born in 1986-1987. Perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) were measured in cord whole blood at birth and in participants' serum from age 28 years. We calculated the Matsuda-insulin sensitivity index (ISI) and the insulinogenic index (IGI) based on a 2 h-oral glucose tolerance test performed at age 28. Effect modification was evaluated in linear regression models adjusted for cross-product terms (PFAS*SNP) and important covariates.

RESULTS

Prenatal and adult PFOS exposures were significantly associated with decreased insulin sensitivity and increased beta-cell function. PFOA associations were in the same direction but attenuated compared to PFOS. A total of 58 SNPs were associated with at least one PFAS exposure variable and/or Matsuda-ISI or IGI in the Faroese population and were subsequently tested as modifiers in the PFAS-clinical outcome associations. Eighteen SNPs showed interaction p-values (PGxE) < 0.05 in at least one PFAS-clinical outcome association, five of which passed False Discovery Rate (FDR) correction (PGxE-FDR<0.20). SNPs for which we found stronger evidence for GxE interactions included ABCA1 rs3890182, FTO rs9939609, FTO rs3751812, PPARG rs170036314 and SLC12A3 rs2289116 and were more clearly shown to modify the PFAS associations with insulin sensitivity, rather than with beta-cell function.

DISCUSSION

Findings from this study suggest that PFAS-associated changes in insulin sensitivity could vary between individuals as a result of genetic predisposition and warrant replication in independent larger populations.

Pharmacogenomics of response to statin treatment and susceptibility to statin-induced adverse drug reactions in Asians: a scoping review

Background

Statins are the most widely used lipid-lowering agents for patients with hyperlipidemia. However, interindividual variations in efficacy and risk of adverse drug reactions to statin treatment have been widely reported. Ethnicity is well known to be one of the contributing factors to this variation, particularly among Asians.

Objectives

To identify genetic variants associated with statin treatment responses among Asian populations with a focus on four commonly prescribed statins: atorvastatin, rosuvastatin, simvastatin, and pravastatin.

Methods

A literature search was conducted in Medline and Embase databases. Studies published from 2008 to 2021 were included. The title and abstract of each article were screened by two reviewers and verified by another two reviewers. Data charted include information on authors, year of study, study population, statin studied, gene studied, study findings, and data of significant statistical value.

Results

A total of 35 articles were included from the 1,939 original studies related to treatment efficacy and 5 articles out of the 284 original studies related to adverse effects. Genetic variants in transmembrane transporters, cytochrome P450 isoenzymes, and apolipoproteins are the most extensively studied among Asian populations, with a main focus on ethnic Chinese. However, Asia consists of genetically different populations, and the results of this review indicated that there is a paucity of studies on other ethnic groups within Asia.

Conclusions

Considering the ethnicity of patients could provide a potential value to personalized medicine in statin therapy.