Size matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development

Hirschsprung disease (HSCR) is a complex genetic disease characterized by absence of ganglia in the intestine. HSCR etiology can be explained by a unique combination of genetic alterations: rare coding variants, predisposing haplotypes and Copy Number Variation (CNV). Approximately 18% of patients have additional anatomical malformations or neurological symptoms (HSCR-AAM). Pinpointing the responsible culprits within a CNV is challenging as often many genes are affected. Therefore, we selected candidate genes based on gene enrichment strategies using mouse enteric nervous system transcriptomes and constraint metrics. Next, we used a zebrafish model to investigate whether loss of these genes affects enteric neuron development in vivo.

This study included three groups of patients, two groups without coding variants in disease associated genes: HSCR-AAM and HSCR patients without associated anomalies (HSCR-isolated). The third group consisted of all HSCR patients in which a confirmed pathogenic rare coding variant was identified. We compared these patient groups to unaffected controls. Predisposing haplotypes were determined, confirming that every HSCR subgroup had increased contributions of predisposing haplotypes, but their contribution was highest in isolated HSCR patients without RET coding variants. CNV profiling proved that specifically HSCR-AAM patients had larger Copy Number (CN) losses. Gene enrichment strategies using mouse enteric nervous system transcriptomes and constraint metrics were used to determine plausible candidate genes located within CN losses. Validation in zebrafish using CRISPR/Cas9 targeting confirmed the contribution of UFD1L, TBX2, SLC8A1, and MAPK8 to ENS development. In addition, we revealed epistasis between reduced Ret and Gnl1 expression and between reduced Ret and Tubb5 expression in vivo. Rare large CN losses—often de novo—contribute to HSCR in HSCR-AAM patients. We proved the involvement of six genes in enteric nervous system development and Hirschsprung disease.

Hirschsprung disease is a congenital disorder characterized by the absence of intestinal neurons in the distal part of the intestine. It is a complex genetic disorder in which multiple variations in our genome combined, result in disease. One of these variations are Copy Number Variations (CNVs): large segments of our genome that are duplicated or deleted. Patients often have Hirschsprung disease without other symptoms. However, a proportion of patients has additional associated anatomical malformations and neurological symptoms. We found that CNVs, present in patients with associated anomalies, are more often larger compared to unaffected controls or Hirschsprung patients without other symptoms. Furthermore, Copy Number (CN) losses are enriched for constrained coding regions (CCR; genes usually not impacted by genomic alterations in unaffected controls) of which the expression is higher in the developing intestinal neurons compared to the intestine. We modelled loss of these candidate genes in zebrafish by disrupting the zebrafish orthologues by genome editing. For several genes this resulted in changes in intestinal neuron development, reminiscent of HSCR observed in patients. The results presented here highlight the importance of Copy Number profiling, zebrafish validation and evaluating all CCR expressed in developing intestinal neurons during diagnostic evaluation.

Association of hepatitis B surface antigen seropositivity and hepatitis B surface antibody seropositivity with diabetes: a cross-sectional study based on two Chinese populations in Guangdong, China

OBJECTIVES

To examine whether hepatitis B surface antigen (HBsAg) seropositivity and hepatitis B surface antibody (HBsAb) seropositivity were associated with the presence of diabetes in two population-based studies in southern China, the Guangzhou Biobank Cohort Study (GBCS) and the Major Infectious Disease Prevention and Control (MIDPC) study.

DESIGN

A cross-sectional study.

SETTING

The GBCS was conducted among a community social and welfare organisation with branches in all 10 districts of Guangzhou. The MIDPC was conducted among the community residents in two districts of Guangzhou and three districts of Zhongshan.

PARTICIPANTS

4947 participants from the GBCS and 4357 participants from the MIDPC were included in this study.

PRIMARY AND SECONDARY OUTCOME MEASURES

Type 2 diabetes was the main study outcome, which was diagnosed by fasting blood glucose ≥7.0 mmol/L, and/or self-reported history of diabetes.

RESULTS

After adjusting for age, sex, education, occupation, smoking status, alcohol use, physical activity and body mass index, we found no association of HBsAg seropositivity in GBCS or MIDPC (OR=1.12, 95% CI 0.74 to 1.69, and OR=0.83, 95% CI 0.59 to 1.17, respectively), and HBsAb seropositivity (OR=0.85, 95% CI 0.65 to 1.12, OR=1.00, 95% CI 0.86 to 1.16, respectively) with the presence of diabetes. Null associations were found for analysis pooling GBCS and MIDPC data after similar adjustment. The adjusted OR for the associations of HBsAg seropositivity and HBsAb seropositivity with the presence of diabetes in the pooled sample was 0.91 (95% CI 0.70 to 1.19) and 0.98 (95% CI 0.86 to 1.12), respectively.

CONCLUSIONS

Taking advantage of data from two large cross-sectional studies, we found no association of serological status of HBsAg and HBsAb with the presence of diabetes or glucose measures.

Trajectories of lipid profile with cognitive function: 12-year follow-up of Guangzhou Biobank cohort study

Studies on the trajectories of lipid profile with cognitive decline are scarce and inconsistent. We examined this association and explored potential effect modification. Lipid profiles including high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), triglycerides (TG) and total cholesterol (TC) were measured at baseline, first and second follow-ups, and classified into trajectory groups. Immediate, delayed memory recall and cognitive function were assessed by the immediate (IWRT) and delayed 10-word recall test (DWRT), and mini-mental state examination (MMSE), respectively, at baseline and follow-ups, and converted into standardized scores. Linear mixed-effect model was used. Results show that elevated HDL-C was associated with increasing annual change rates in DWRT and MMSE scores (β (95% confidence intervals) = 0.005 (-0.001 to 0.011) SD/year and 0.020 (0.014 to 0.027) SD/year, respectively), while LDL-C and TC were associated with a decrease in DWRT scores (-0.005 (-0.008 to -0.001) SD/year and - 0.009 (-0.011 to -0.006) SD/year, respectively). Moderate-increasing HDL-C, high-decreasing LDL-C or moderate-decreasing TC trajectories were associated with increases in DWRT, IWRT and MMSE scores. Stronger associations were identified for HDL-C with an increase in MMSE scores within the lower family income group and for LDL-C with a decrease in IWRT scores among individuals taking lipid-lowering drug. In conclusion, HDL-C was associated with improvements, while LDL-C and TC with decline in memory and cognitive function. Increasing HDL-C and decreasing LDL-C and TC trajectories predicted better memory and cognitive performance. The observed effect modifications highlight the importance of personalized approaches in lipid management to optimize cognitive outcomes.

Association of Measures of Glucose Metabolism with Colorectal Cancer Risk in Older Chinese: A 13-Year Follow-up of the Guangzhou Biobank Cohort Study-Cardiovascular Disease Substudy and Meta-Analysis

BACKGRUOUND

Abnormal glucose metabolism is a risk factor for colorectal cancer (CRC). However, association of glycosylated hemoglobin (HbA1c) with CRC risk remains under-reported. We examined the association between glycemic indicators (HbA1c, fasting plasma glucose, fasting insulin, 2-hour glucose, 2-hour insulin, and homeostasis model of risk assessment-insulin resistance index) and CRC risk using prospective analysis and meta-analysis.

METHODS

Participants (n=1,915) from the Guangzhou Biobank Cohort Study-Cardiovascular Disease Substudy were included. CRC events were identified through record linkage. Cox regression was used to assess the associations of glycemic indicators with CRC risk. A meta-analysis was performed to investigate the association between HbA1c and CRC risk.

RESULTS

During an average of 12.9 years follow-up (standard deviation, 2.8), 42 incident CRC cases occurred. After adjusting for potential confounders, the hazard ratio (95% confidence interval [CI]) of CRC for per % increment in HbA1c was 1.28 (95% CI, 1.01 to 1.63) in overall population, 1.51 (95% CI, 1.13 to 2.02) in women and 1.06 (95% CI, 0.68 to 1.68) in men. No significant association of other measures of glycemic indicators and baseline diabetes with CRC risk was found. Meta-analyses of 523,857 participants including our results showed that per % increment of HbA1c was associated with 13% higher risk of CRC, with the pooled risk ratio being 1.13 (95% CI, 1.01 to 1.27). Subgroupanalyses found stronger associations in women, colon cancer, Asians, and case-control studies.

CONCLUSION

Higher HbA1c was a significant predictor of CRC in the general population. Our findings shed light on the pathology of glucose metabolism and CRC, which warrants more in-depth investigation.

Islet-Resident Memory T Cells Orchestrate the Immunopathogenesis of Type 1 Diabetes through the FABP4-CXCL10 Axis

Type 1 diabetes (T1D) is a chronic disease characterized by self-destruction of insulin-producing pancreatic β cells by cytotoxic T cell activity. However, the pathogenic mechanism of T cell infiltration remains obscure. Recently, tissue-resident memory T (TRM) cells have been shown to contribute to cytotoxic T cell recruitment. TRM cells are found present in human pancreas and are suggested to modulate immune homeostasis. Here, the role of TRM cells in the development of T1D is investigated. The presence of TRM cells in pancreatic islets is observed in non-obese diabetic (NOD) mice before T1D onset. Mechanistically, elevated fatty acid-binding protein 4 (FABP4) potentiates the survival and alarming function of TRM cells by promoting fatty acid utilization and C-X-C motif chemokine 10 (CXCL10) secretion, respectively. In NOD mice, genetic deletion of FABP4 or depletion of TRM cells using CD69 neutralizing antibodies resulted in a similar reduction of pancreatic cytotoxic T cell recruitment, a delay in diabetic incidence, and a suppression of CXCL10 production. Thus, targeting FABP4 may represent a promising therapeutic strategy for T1D.

ImmuneMirror: A machine learning-based integrative pipeline and web server for neoantigen prediction

Neoantigens are derived from somatic mutations in the tumors but are absent in normal tissues. Emerging evidence suggests that neoantigens can stimulate tumor-specific T-cell-mediated antitumor immune responses, and therefore are potential immunotherapeutic targets. We developed ImmuneMirror as a stand-alone open-source pipeline and a web server incorporating a balanced random forest model for neoantigen prediction and prioritization. The prediction model was trained and tested using known immunogenic neopeptides collected from 19 published studies. The area under the curve of our trained model was 0.87 based on the testing data. We applied ImmuneMirror to the whole-exome sequencing and RNA sequencing data obtained from gastrointestinal tract cancers including 805 tumors from colorectal cancer (CRC), esophageal squamous cell carcinoma (ESCC) and hepatocellular carcinoma patients. We discovered a subgroup of microsatellite instability-high (MSI-H) CRC patients with a low neoantigen load but a high tumor mutation burden (> 10 mutations per Mbp). Although the efficacy of PD-1 blockade has been demonstrated in advanced MSI-H patients, almost half of such patients do not respond well. Our study identified a subset of MSI-H patients who may not benefit from this treatment with lower neoantigen load for major histocompatibility complex I (P < 0.0001) and II (P = 0.0008) molecules, respectively. Additionally, the neopeptide YMCNSSCMGV-TP53G245V, derived from a hotspot mutation restricted by HLA-A02, was identified as a potential actionable target in ESCC. This is so far the largest study to comprehensively evaluate neoantigen prediction models using experimentally validated neopeptides. Our results demonstrate the reliability and effectiveness of ImmuneMirror for neoantigen prediction.

Association of Testosterone and Sex Hormone-Binding Globulin With All-Cause and Cardiovascular Disease Mortality in Older Chinese Men

BACKGROUND

The associations of high and low testosterone with all-cause and cardiovascular disease (CVD) mortality risk in men are conflicting. Our objective was to examine associations of total testosterone, free testosterone, bioavailable testosterone, and sex hormone-binding globulin (SHBG) with all-cause and CVD mortality in older Chinese men.

METHODS

Total testosterone and SHBG were assayed, and free testosterone and bioavailable testosterone were calculated using Vermeulen formula. Cox proportional hazards regression was used to assess the associations with risks of all-cause and CVD mortality, giving hazard ratios (HRs) and 95% confidence intervals (CIs).

RESULTS

Of 3 948 men aged 50+ years, 949 deaths (312 CVD) occurred during an average 10.5-year follow-up. After multivariable adjustments, the highest, versus the third, quartile of total testosterone and free testosterone were associated with higher all-cause mortality risk (1.17 [0.97-1.41] and 1.45 [1.20-1.74], respectively), whereas free testosterone was associated with higher CVD mortality risk (1.88 [1.33-2.66]). Similar positive associations were found for bioavailable testosterone and all-cause mortality risk (1.27 [1.05-1.54]). Lower SHBG (quartile 1 vs quartile 3) was associated with higher all-cause and CVD mortality risk (1.25 [1.04-1.52] and 1.28 [1.08-1.52], respectively). Consistent associations were observed in relatively healthy men and men excluded death during the first year.

CONCLUSIONS

Higher total testosterone, free testosterone, and bioavailable testosterone were associated with higher all-cause mortality in older men, higher free testosterone was associated with higher CVD mortality whilst lower SHBG was associated with higher all-cause and CVD mortality. Clarification and confirmation of causality require further mechanistic studies.