Studying the Genetics of Complex Disease With Ancestry-Specific Human Phenotype Networks: The Case of Type 2 Diabetes in East Asian Populations

Sex differences in the genetics of sarcoidosis across European and African ancestry populations

Background

Sex differences in the susceptibility of sarcoidosis are unknown. The study aims to identify sex-dependent genetic variations in two clinical sarcoidosis phenotypes: Löfgren's syndrome (LS) and non-Löfgren's syndrome (non-LS).

Methods

A meta-analysis of genome-wide association studies was conducted on Europeans and African Americans, totaling 10,103 individuals from three population-based cohorts, Sweden (n = 3,843), Germany (n = 3,342), and the United States (n = 2,918), followed by an SNP lookup in the UK Biobank (UKB, n = 387,945). A genome-wide association study based on Immunochip data consisting of 141,000 single nucleotide polymorphisms (SNPs) was conducted in the sex groups. The association test was based on logistic regression using the additive model in LS and non-LS sex groups independently. Additionally, gene-based analysis, gene expression, expression quantitative trait loci (eQTL) mapping, and pathway analysis were performed to discover functionally relevant mechanisms related to sarcoidosis and biological sex.

Results

We identified sex-dependent genetic variations in LS and non-LS sex groups. Genetic findings in LS sex groups were explicitly located in the extended Major Histocompatibility Complex (xMHC). In non-LS, genetic differences in the sex groups were primarily located in the MHC class II subregion and ANXA11. Gene-based analysis and eQTL enrichment revealed distinct sex-specific gene expression patterns in various tissues and immune cell types. In LS sex groups, a pathway map related to antigen presentation machinery by IFN-gamma. In non-LS, pathway maps related to immune response lectin-induced complement pathway in males and related to maturation and migration of dendritic cells in skin sensitization in females were identified.

Conclusion

Our findings provide new evidence for a sex bias underlying sarcoidosis genetic architecture, particularly in clinical phenotypes LS and non-LS. Biological sex likely plays a role in disease mechanisms in sarcoidosis.

Visceral adiposity index outperforms conventional anthropometric assessments as predictor of diabetes mellitus in elderly Chinese: a population-based study

Background

This study assessed the performance of visceral adiposity index and body shape index in predicting diabetes mellitus (DM) risk and compared their predictive ability to that of body mass index and waist circumference.

Methods

Among 8249 consecutive subjects who attended the Nationwide Health Check Up System for Senior Citizens (≥ 65 years) between 2008 and 2018, we examined the associations of several adiposity indices with DM risk and explored gender differences.

Results

Among all adiposity indicators, Chinese visceral adiposity index (CVAI) demonstrated the highest discriminatory ability for diabetes mellitus with area under receiver operating characteristic curves (AUC) of 0.65, 0.68, and 0.66 for men, women, and all participants, respectively, and optimal cut-offs set as 126.09 in men and 117.77 in women. Compared with body shape index (ABSI), both CVAI and VAI were strongly associated with baseline DM (adjusted OR: 4.85, 95% CI: 4.05–5.82 and 4.22, 95% CI: 3.53–5.05 for 4th vs 1st quartile groups by CVAI and VAI, P < 0.001), which was more pronounced in older adult women (P_interaction < 0.05). Over a median of 5.25 years (IQR: 3.07–6.44 years) follow-up, Cox regression models showed higher predictive ability of CVAI and VAI compared to ABSI. Further, both CVAI and VAI independently predicted new-onset DM (adjusted HR: 1.29, 95% CI: 1.22–1.37 and 1.16, 95% CI: 1.11–1.21 by CVAI and VAI) and composite endpoint of new DM and death among those without baseline DM.

Conclusions

Our population-based data demonstrated that Chinese visceral adiposity index may serve as a superior clinical indicator of diabetes when compared with conventional anthropometric indices among older adult Chinese, especially in women.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12986-021-00608-6.

Presentation and outcome of chronic kidney disease in Italian and immigrant citizens: results from the Emilia-Romagna PIRP project

INTRODUCTION

In recent decades, high income countries (HIC) have been exposed to huge human migratory flows. Consistent with this influx, there has been a dramatic increase in the number of chronic kidney disease (CKD) patients in the immigrant population. In Italy, comparisons between Italian and immigrant CKD patients are still lacking, thus we aimed to describe the baseline clinical characteristics and the main outcomes of CKD patients who immigrated to Italy and reside in the Emilia Romagna region.

METHODS

This is a retrospective cohort study based on CKD patients from the Prevenzione Insufficienza Renale Progressiva (PIRP) project, which included 963 (3.1%) immigrants among the 30,702 patients seen by nephrologists between April 1st, 2004 and June 30th, 2020. We sub-divided the immigrants into seven groups based on their area of origin, and compared their baseline characteristics, CKD progression and time to end-stage kidney disease (ESKD) to those of Italian CKD patients.

RESULTS

At presentation, Italian subjects were on average older (73.1 years) and had less preserved kidney function (eGFR 34.3 ml/min), while South and East Asians had the highest proportion of diabetes and obesity (approximately 45% and 30%, respectively). At 4-year follow-up, about 20% of patients from South Asia, Eastern Europe and Arab Countries were diagnosed with ESKD, compared to only 11% of Italians and Latin Americans.

CONCLUSIONS

We found important differences between Italian and immigrant CKD patients, as well as among immigrant subgroups. First clinical encounters with nephrologists revealed that immigrants had varied patterns of clinical presentation and of nephropathy. During follow-up, immigrants showed faster kidney function decline which led to a higher risk of disease evolution and progression towards ESKD.

Type 2 diabetes-associated polymorphisms correlate with SIRT1 and TGF-β1 gene expression

The polymorphisms rs3758391 and rs1800470 located in SIRT1 and TGF-β1 have been associated with type 2 diabetes in different populations but its functional effect is not clear. In this study, we evaluated their effect on the expression of SIRT1 and TGF-β1 in peripheral blood as well as their participation in the formation of DNA-protein complexes in a pancreas-derived cell line. It has been described that SIRT1 and TGF-β1 participate in cell growth and regulation of production and secretion of insulin in the pancreas. Anthropometric and biochemical profiles of 127 adults were measured. Genotypes for rs3758391 and rs1800470 were determined using TaqMan assays. Expression analysis of SIRT1 and TGF-β1 were performed using real-time PCR. Gene expression of these genes increased 1.8 ± 0.6- and 1.3 ± 0.6-fold in patients carrying the TT genotype of rs3758391 and rs1800470 when compared to carriers of the CC genotype. Then, we tested whether these single-nucleotide polymorphisms (SNPs) (and rs932658, which is in linkage disequilibrium with rs3758391) are located in regulatory DNA-protein binding sites by electrophoretic mobility shift assays using nuclear extract from the pancreas-derived cell line BxPC-3. The electrophoretic mobility shift assay showed no binding of nuclear proteins to DNA. In conclusion, the genotypes of rs3758391 and rs1800470 are associated with modifications in the expression of the genes SIRT1 and TGF-β1, respectively, but none of the tested SNPs are located in regulatory DNA-protein binding sites.

Propylthiouracil-induced organizing pneumonia: A case report

RATIONALE

Propylthiouracil (PTU) is a common antithyroid drug which can treat hyperthyroidism effectively. PTU is, however, associated to multiple adverse effects. In rare case, PTU can cause interstitial pneumonia.

PATIENT CONCERNS

A 40-year-old woman presented with dyspnea and was diagnosed with pulmonary infection at the first time. After the treatment with moxifloxacin, her symptoms still got worse.

DIAGNOSIS

The lung tissues biopsy confirmed the diagnosis of organizing pneumonia (OP) and the administration of PTU suggested the diagnosis of PTU-induced OP.

INTERVENTION

Withdrawal of PTU and the administration of methylprednisolone.

OUTCOMES

The patient's symptoms relieved significantly 1 month later and lung computed tomography (CT) scan also demonstrated significant reduction of lung lesions.

LESSONS

Here we report the first case of histologically confirmed OP induced by PTU and conduct a literature review of the cases of PTU-induced interstitial pneumonia. The awareness of PTU-induced OP can help physicians reduce the possibility of misdiagnosis.

Kill two birds with one stone: making multi-transgenic pre-diabetes mouse models through insulin resistance and pancreatic apoptosis pathogenesis

BACKGROUND

Type 2 diabetes is characterized by insulin resistance accompanied by defective insulin secretion. Transgenic mouse models play an important role in medical research. However, single transgenic mouse models may not mimic the complex phenotypes of most cases of type 2 diabetes.

METHODS

Focusing on genes related to pancreatic islet damage, peripheral insulin resistance and related environmental inducing factors, we generated single-transgenic (C/EBP homology protein, CHOP) mice (CHOP mice), dual-transgenic (human islet amyloid polypeptide, hIAPP; CHOP) mice (hIAPP-CHOP mice) and triple-transgenic (11β-hydroxysteroid dehydrogenase type 1, 11β-HSD1; hIAPP; CHOP) mice (11β-HSD1-hIAPP- CHOP mice). The latter two types of transgenic (Tg) animals were induced with high-fat high-sucrose diets (HFHSD). We analyzed the diabetes-related symptoms and histology features of the transgenic animals.

RESULTS

Comparing symptoms on the spot-checked points, we determined that the triple-transgene mice were more suitable for systematic study. The results of intraperitoneal glucose tolerance tests (IPGTT) of triple-transgene animals began to change 60 days after induction (p < 0.001). After 190 days of induction, the body weights (p < 0.01) and plasma glucose of the animals in Tg were higher than those of the animals in Negative Control (Nc). After sacrificed, large amounts of lipid were found deposited in adipose (p < 0.01) and ectopically deposited in the non-adipose tissues (p < 0.05 or 0.01) of the animals in the Tg HFHSD group. The weights of kidneys and hearts of Tg animals were significantly increased (p < 0.01). Serum C peptide (C-P) was decreased due to Tg effects, and insulin levels were increased due to the effects of the HFHSD in the Tg HFHSD group, indicating that damaged insulin secretion and insulin resistance hyperinsulinemia existed simultaneously in these animals. The serum corticosterone of Tg was slightly higher than those of Nc due to the effects of the 11βHSD-1 transgene and obesity. In Tg HFHSD, hepatic adipose deposition was more severe and the pancreatic islet area was enlarged under compensation, accompanying apoptosis. In the transgenic control diet (Tg ControlD) group, hepatic adipose deposition was also severe, pancreatic islets were damaged, and their areas were decreased (p < 0.05), and apoptosis of pancreatic cells occurred. Taken together, these data show the transgenes led to early-stage pathological changes characteristic of type 2 diabetes in the triple-transgene HFHSD group. The disease of triple-transgenic mice was more severe than that of dual or single-transgenic mice.

CONCLUSION

The use of multi-transgenes involved in insulin resistance and pancreatic apoptosis is a better way to generate polygene-related early-stage diabetes models.

A new approach to disentangle genetic and epigenetic components on disease comorbidities: studying correlation between genotypic and phenotypic disease networks

Disease comorbidity is a result of complex epigenetic interplay. A disease is rarely a consequence of an abnormality in a single gene; complex pathways to disease patterns emerge from gene-gene interactions and gene-environment interactions. Understanding these mechanisms of disease and comorbidity development, breaking down them into clusters and disentangling the epigenetic - actionable - components, is of utter importance from a public health perspective. With the increase in the average life expectancy, healthy aging becomes a primary objective, from both an individual (i.e. quality of life) and a societal (i.e. healthcare costs) standpoint. Many studies have analyzed disease networks based on common altered genes, on protein-protein interactions, or on shared disease comorbidites, i.e. phenotypic disease networks. In this work we aim at studying the relations between genotypic and phenotypic disease networks, using a large statewide cohort of individuals (100, 000+ from California, USA) with linked clinical and genotypic information, the Genetic Epidemiology Research on Adult Health and Aging (GERA). By comparing their phenotypic and genotypic networks, we try to disentangle the epigenetic component of disease comorbidity.

Characterization of the Asian Phenotype - An Emerging Paradigm with Clinicopathological and Human Research Implications

Background: Modern medicine recognizes that salient, inherent variations between Caucasians and Asians exist. Radical changes are occurring in the health scene with increasing emphasis centered on the recognition of inter-individual variations unique to Asians that impact on medical management and outcomes. Aim: This review analyzes distinct features or outcomes in terms of epidemiology, disease thresholds, diagnostic cutoffs and treatment responses of Asian people compared with non-Asians. Methods: This review is based on a literature search via PubMed and MEDLINE for relevant articles related to the Asian phenotype and its impact on health and disease. Results: An 'Asian phenotype' could be characterized across the spectrum of biomedical disciplines and underscores the major challenges clinicians must face in their daily management of a cosmopolitan population and their extrapolation of research outcomes. Conclusion: Interventions for various ailments that have traditionally ignored population differences have now entered the age of personalized, stratified or precision medicine requiring an individualized approach being adopted as a new standard of care. Factoring in Asian phenotypes is essential for the medical research community and the development of improved clinical practice guidelines across a continuum of disciplines that will ultimately translate to better human health round the world.

AN INTEGRATED NETWORK APPROACH TO IDENTIFYING BIOLOGICAL PATHWAYS AND ENVIRONMENTAL EXPOSURE INTERACTIONS IN COMPLEX DISEASES

Complex diseases are the result of intricate interactions between genetic, epigenetic and environmental factors. In previous studies, we used epidemiological and genetic data linking environmental exposure or genetic variants to phenotypic disease to construct Human Phenotype Networks and separately analyze the effects of both environment and genetic factors on disease interactions. To better capture the intricacies of the interactions between environmental exposure and the biological pathways in complex disorders, we integrate both aspects into a single "tripartite" network. Despite extensive research, the mechanisms by which chemical agents disrupt biological pathways are still poorly understood. In this study, we use our integrated network model to identify specific biological pathway candidates possibly disrupted by environmental agents. We conjecture that a higher number of co-occurrences between an environmental substance and biological pathway pair can be associated with a higher likelihood that the substance is involved in disrupting that pathway. We validate our model by demonstrating its ability to detect known arsenic and signal transduction pathway interactions and speculate on candidate cell-cell junction organization pathways disrupted by cadmium. The validation was supported by distinct publications of cell biology and genetic studies that associated environmental exposure to pathway disruption. The integrated network approach is a novel method for detecting the biological effects of environmental exposures. A better understanding of the molecular processes associated with specific environmental exposures will help in developing targeted molecular therapies for patients who have been exposed to the toxicity of environmental chemicals.