Common variants on 17q25 and gene-gene interactions conferring risk of schizophrenia in Han Chinese population and regulating gene expressions in human brain

Cell communication pathway prognostic model identified detrimental neurodevelopmental pathways in neuroblastoma

Neurodevelopmental cell communication plays a crucial role in neuroblastoma prognosis. However, determining the impact of these communication pathways on prognosis is challenging due to limited sample sizes and patchy clinical survival information of single cell RNA-seq data. To address this, we have developed the cell communication pathway prognostic model (CCPPM) in this study. CCPPM involves the identification of communication pathways through single-cell RNA-seq data, screening of prognosis-significant pathways using bulk RNA-seq data, conducting functional and attribute analysis of these pathways, and analyzing the post-effects of communication within these pathways. By employing the CCPPM, we have identified ten communication pathways significantly influencing neuroblastoma, all related to axongenesis and neural projection development, especially the BMP7-(BMPR1B-ACVR2B) communication pathway was found to promote tumor cell migration by activating the transcription factor SMAD1 and regulating UNK and MYCBP2. Notably, BMP7 expression was higher in neuroblastoma samples with distant metastases. In summary, CCPPM offers a novel approach to studying the influence of cell communication pathways on disease prognosis and identified detrimental communication pathways related to neurodevelopment.

rvTWAS: identifying gene-trait association using sequences by utilizing transcriptome-directed feature selection

Toward the identification of genetic basis of complex traits, transcriptome-wide association study (TWAS) is successful in integrating transcriptome data. However, TWAS is only applicable for common variants, excluding rare variants in exome or whole-genome sequences. This is partly because of the inherent limitation of TWAS protocols that rely on predicting gene expressions. Our previous research has revealed the insight into TWAS: the 2 steps in TWAS, building and applying the expression prediction models, are essentially genetic feature selection and aggregations that do not have to involve predictions. Based on this insight disentangling TWAS, rare variants' inability of predicting expression traits is no longer an obstacle. Herein, we developed "rare variant TWAS," or rvTWAS, that first uses a Bayesian model to conduct expression-directed feature selection and then uses a kernel machine to carry out feature aggregation, forming a model leveraging expressions for association mapping including rare variants. We demonstrated the performance of rvTWAS by thorough simulations and real data analysis in 3 psychiatric disorders, namely schizophrenia, bipolar disorder, and autism spectrum disorder. We confirmed that rvTWAS outperforms existing TWAS protocols and revealed additional genes underlying psychiatric disorders. Particularly, we formed a hypothetical mechanism in which zinc finger genes impact all 3 disorders through transcriptional regulations. rvTWAS will open a door for sequence-based association mappings integrating gene expressions.

Pan-Cancer Analysis Reveals SH3TC2 as an Oncogene for Colorectal Cancer and Promotes Tumorigenesis via the MAPK Pathway

Simple Summary

SH3 domain and tetrapeptide repeat 2 (SH3TC2) is a protein-encoding gene and has previously been described as a critical signaling hub for neurological disorders, but no systematic analysis of SH3TC2 is available in cancer research. We analyzed SH3TC2 in various kinds of cancer to find its tumorigenic role in one or more specific cancers and further explored the mechanism of SH3TC2 in colorectal cancer (CRC). Our research revealed that higher expression of SH3TC2 indicated poor disease-free survival and promoted CRC progression and invasion via the MAPK signaling pathway.

Abstract

SH3 domain and tetrapeptide repeat 2 (SH3TC2) is a protein-encoding gene and has previously been described as a critical signaling hub for neurological disorders. Although increasing evidence supports a vital role of SH3TC2 in the tumorigenesis of various kinds of cancer, no systematic analysis of SH3TC2 is available. The function and mechanism of SH3TC2 in other cancers remain unknown. Thus, this study aimed to analyze SH3TC2 in various kinds of cancer to find its tumorigenic role in one or more specific cancers. In the current study, we analyzed the expression level and prognostic value of SH3TC2 in different tumors in the TCGA-GTEx pan-cancer dataset. Subsequently, the prognostic role and mechanism of SH3TC2 in colorectal cancer (CRC) were further explored via clinical samples and in vitro and in vivo experiments. We observed differential expression of SH3TC2 in colon adenocarcinoma (COAD), acute myeloid leukemia (LAML), READ (rectum adenocarcinoma), SKCM (skin cutaneous melanoma), and TGCT (testicular germ cell tumors). Subsequently, SH3TC2 showed a significant effect on the clinical stage and prognostic value in CRC, LAML, and SKCM. Moreover, we found in the TCGA database and seven GEO datasets that SH3TC2 was significantly highly expressed in tumor tissue. Through enrichment analysis of SH3TC2 and its co-expressed genes, we found that SH3TC2 may play a role in the MAPK signaling pathway. Correlation analysis indicated that SH3TC2 was significantly associated with multiple key factors in the MAPK signaling pathway. Additionally, higher expression of SH3TC2 was found in tumor tissue in our cohort including 40 CRC patients. Overexpression of SH3TC2 may imply poor prognosis. Knockdown of SH3TC2 significantly inhibited tumor invasion, migration, and proliferation. More importantly, knockdown of SH3TC2 inhibited tumor growth in a CRC mouse model. The study preliminarily conducted a pan-cancer study of SH3TC2 and further explored the mechanism of SH3TC2 in CRC. Our research revealed that higher expression of SH3TC2 may promote CRC progression and invasion via the MAPK signaling pathway.

Insights into Interactions of Human Cytochrome P450 17A1: Review

Abstract:

Cytochrome P450s are a widespread and vast superfamily of hemeprotein monooxygenases that metabolize physiologically essential chemicals necessary for most species' survival, from protists to plants to humans. They catalyze the synthesis of steroid hormones, cholesterol, bile acids, and arachidonate metabolites and the degradation of endogenous compounds such as steroids, fatty acids, and other catabolizing compounds as an energy source and detoxifying xenobiotics such as drugs, procarcinogens, and carcinogens. The human CYP17A1 is one of the cytochrome P450 genes located at the 10q chromosome. The gene expression occurs in the adrenals and gonads, with minor amounts in the brain, placenta, and heart. This P450c17 cytochrome gene is a critical steroidogenesis regulator which performs two distinct activities: 17 alpha-hydroxylase activity (converting pregnenolone to 17-hydroxypregnenolone and progesterone to 17-hydroxyprogesterone, these precursors are further processed to provide glucocorticoids and sex hormones) and 17, 20-lyase activity (which converts 17-hydroxypregnenolone to DHEA). Dozens of mutations within CYP17A1 are found to cause 17-alpha-hydroxylase and 17, 20-lyase deficiency. This condition affects the function of certain hormone-producing glands, resulting in high blood pressure levels (hypertension), abnormal sexual development, and other deficiency diseases. This review highlights the changes in CYP17A1 associated with gene-gene interaction, drug-gene interaction, chemical-gene interaction, and its biochemical reactions; they have some insights to correlate with the fascinating functional characteristics of this human steroidogenic gene. The findings of our theoretical results will be helpful to further the design of specific inhibitors of CYP17A1.

Identification of genetic variants influencing methylation in brain with pleiotropic effects on psychiatric disorders

Psychiatric disorders affect 29% of the global population at least once in the lifespan, and genetic studies have proved a shared genetic basis among them, although the underlying molecular mechanisms remain largely unknown. DNA methylation plays an important role in complex disorders and, remarkably, enrichment of common genetic variants influencing allele-specific methylation (ASM) has been reported among variants associated with specific psychiatric disorders. In the present study we assessed the contribution of ASM to a set of eight psychiatric disorders by combining genetic, epigenetic and expression data. We interrogated a list of 3896 ASM tagSNPs in the brain in the summary statistics of a cross-disorder GWAS meta-analysis of eight psychiatric disorders from the Psychiatric Genomics Consortium, including more than 162,000 cases and 276,000 controls. We identified 80 SNPs with pleiotropic effects on psychiatric disorders that show an opposite directional effect on methylation and gene expression. These SNPs converge on eight candidate genes: ZSCAN29, ZSCAN31, BTN3A2, DDAH2, HAPLN4, ARTN, FAM109B and NAGA. ZSCAN29 shows the broadest pleiotropic effects, showing associations with five out of eight psychiatric disorders considered, followed by ZSCAN31 and BTN3A2, associated with three disorders. All these genes overlap with CNVs related to cognitive phenotypes and psychiatric traits, they are expressed in the brain, and seven of them have previously been associated with specific psychiatric disorders, supporting our results. To sum up, our integrative functional genomics analysis identified eight psychiatric disease risk genes that impact a broad list of disorders and highlight an etiologic role of SNPs that influence DNA methylation and gene expression in the brain.

PPDPF Promotes the Progression and acts as an Antiapoptotic Protein in Non-Small Cell Lung Cancer

Resistance to radiotherapy is frequently observed in the clinic and leads to poor prognosis of non-small cell lung cancer (NSCLC). How to overcome resistance to radiotherapy is a challenge in the treatment of NSCLC. In this study, PPDPF was found to be upregulated in NSCLC tissues and cell lines, and its expression negatively correlated with the overall survival of patients with NSCLC. PPDPF promoted the growth, colony formation and invasion of lung cancer cells. Moreover, knockout of PPDPF inhibited tumorigenesis in the KL (Kras^G12D; LKB1^f/f) mouse model of lung cancer. Additionally, overexpression of PPDPF led to radioresistance in lung cancer cells, and knockdown of PPDPF sensitized lung cancer cells to radiotherapy. Mechanistically, PPDPF interacted with BABAM2 (an antiapoptotic protein) and blocked its ubiquitination by MDM2, thus stabilizing BABAM2 and promoting the radioresistance of lung cancer cells. Our present study suggested PPDPF as a therapeutic target in NSCLC.

The interaction of histone modification related H3F3B and NSD2 genes increases the susceptibility to schizophrenia in a Chinese population

The role of histone modifications in the pathogenesis of schizophrenia has been proposed previously. H3F3B is a member of the histone 3. NSD2 is a histone methyltransferase that mediates dimethylation of Histone 3 lysine 36 (H3K36me2). The aim of the current study was to explore the associations between SNPs within H3F3B gene (rs60700976, rs3214028) and NSD2 gene (rs13148597, rs75820801) and the susceptibility to schizophrenia in a Chinese population. A total of 810 patients and 490 healthy controls were recruited and genetic association analyses were performed. The H3F3B gene polymorphisms rs3214028 and rs60700976 were significantly associated with schizophrenia. Rs60700976 was also associated with psychotic symptoms in schizophrenia patients. Furthermore, we found the interaction between NSD2 gene and H3F3B gene was related to the susceptibility to schizophrenia. The corresponding best three-locus model was H3F3B (rs60700976) - NSD2 (rs75820801, rs13148597), and the high-risk genotype combination was rs13148597(CC)- rs60700976(GG)-rs75820801(TT) (OR = 1.388[1.091-1.766], P = .007). The low-risk genotype combination was rs13148597(CC)-rs60700976(GG)-rs75820801(CT) (OR = 0.57 [0.330-0.985], P = .042). Our findings provided the preliminary evidence that the histone modification related H3F3B and NSD2 genes may confer the susceptibility to schizophrenia in a Chinese population.

Zinc finger proteins in psychiatric disorders and response to psychotropic medications

Zinc finger proteins are a large family of abundantly expressed small motifs that play a crucial role in a wide range of physiological and pathophysiological mechanisms. Findings published so far support an involvement of zinc fingers in psychiatric disorders. Most of the evidence has been provided for the zinc finger protein 804A (ZNF804A) gene, which has been suggested to be implicated in schizophrenia and bipolar disorder. This evidence has been corroborated by a wide range of functional studies showing that ZNF804A regulates the expression of genes involved in cell adhesion and plays a crucial role in neurite formation and maintenance of dendritic spines. On the other hand, far less is known on other zinc finger proteins and their involvement in psychiatric disorders. In this review, we discussed studies exploring the role of zinc finger proteins in schizophrenia, bipolar disorder, and major depressive disorder as well as in pharmacogenetics of psychotropic drugs.

Translational bioinformatics in mental health: open access data sources and computational biomarker discovery

Mental illness is increasingly recognized as both a significant cost to society and a significant area of opportunity for biological breakthrough. As -omics and imaging technologies enable researchers to probe molecular and physiological underpinnings of multiple diseases, opportunities arise to explore the biological basis for behavioral health and disease. From individual investigators to large international consortia, researchers have generated rich data sets in the area of mental health, including genomic, transcriptomic, metabolomic, proteomic, clinical and imaging resources. General data repositories such as the Gene Expression Omnibus (GEO) and Database of Genotypes and Phenotypes (dbGaP) and mental health (MH)-specific initiatives, such as the Psychiatric Genomics Consortium, MH Research Network and PsychENCODE represent a wealth of information yet to be gleaned. At the same time, novel approaches to integrate and analyze data sets are enabling important discoveries in the area of mental and behavioral health. This review will discuss and catalog into an organizing framework the increasingly diverse set of MH data resources available, using schizophrenia as a focus area, and will describe novel and integrative approaches to molecular biomarker discovery that make use of mental health data.

Replicated associations of FADS1, MAD1L1, and a rare variant at 10q26.13 with bipolar disorder in Chinese population

Genetic analyses of psychiatric illnesses, such as bipolar disorder (BPD), have revealed essential information regarding the underlying pathological mechanisms. While such studies in populations of European ancestry have achieved prominent success, understanding the genetic risk factors of these illnesses (especially BPD) in Chinese population remains an urgent task. Given the lack of genome-wide association study (GWAS) of BPD in Chinese population from Mainland China, replicating the previously reported GWAS hits in distinct populations will provide valuable information for future GWAS analysis in Han Chinese. In the present study, we have recruited 1146 BPD cases and 1956 controls from Mainland China for genetic analyses, as well as 65 Han Chinese brain amygdala tissues for mRNA expression analyses. Using this clinical sample, one of the largest Han Chinese BPD samples till now, we have conducted replication analyses of 21 single nucleotide polymorphisms (SNPs) extracted from previous GWAS of distinct populations. Among the 21 tested SNPs, 16 showed the same direction of allelic effects in our samples compared with previous studies; 6 SNPs achieved nominal significance (p < 0.05) at one-tailed test, and 2 additional SNPs showed marginal significance (p < 0.10). Aside from replicating previously reported BPD risk SNPs, we herein also report several intriguing findings: (1) the SNP rs174576 was associated with BPD in our Chinese sample and in the overall global meta-analysis, and was significantly correlated with FADS1 mRNA in diverse public RNA-seq datasets as well as our in house collected Chinese amygdala samples; (2) two (partially) independent SNPs in MAD1L1 were both significantly associated with BPD in our Chinese sample, which was also supported by haplotype analysis; (3) a rare SNP rs78089757 in 10q26.13 region was a genome-wide significant variant for BPD in East Asians, and this SNP was near monomorphic in Europeans. In sum, these results confirmed several significant BPD risk genes. We hope this Chinese BPD case-control sample and the current brain amygdala tissues (with continuous increasing sample size in the near future) will provide helpful resources in elucidating the genetic and molecular basis of BPD in this major world population.

Genetic association and meta-analysis of a schizophrenia GWAS variant rs10489202 in East Asian populations

Previous genome-wide association studies (GWAS) suggest that rs10489202 in the intron of MPC2 (mitochondrial pyruvate carrier 2) is a risk locus for schizophrenia in Han Chinese populations. To validate this discovery, we conducted a replication analysis in an independent case-control sample of Han Chinese ancestry (437 cases and 2031 controls), followed by a meta-analytic investigation in multiple East Asian samples. In the replication analysis, rs10489202 showed marginal association with schizophrenia (two-tailed P = 0.071, OR = 1.192 for T allele); in the meta-analysis using a total of 14,340 cases and 20,349 controls from ten East Asian samples, rs10489202 was genome-wide significantly associated with schizophrenia (two-tailed P = 3.39 × 10^-10, OR = 1.161 for T allele, under the fixed-effect model). We then performed an explorative investigation of the association between this SNP and bipolar disorder, as well as a major depressive disorder, and the schizophrenia-predisposing allele was associated with an increased risk of major depressive disorder in East Asians (two-tailed P = 2.49 × 10^-2, OR = 1.103 for T allele). Furthermore, expression quantitative trait loci (eQTL) analysis in lymphoblastoid cell lines from East Asian donors (N = 85 subjects) revealed that rs10489202 was specifically and significantly associated with the expression of TIPRL gene (P = 5.67 × 10^-4). Taken together, our data add further support for the genetic involvement of this genomic locus in the susceptibility to schizophrenia in East Asian populations, and also provide preliminary evidence for the underlying molecular mechanisms.

Multivariate Pattern Analysis of Genotype-Phenotype Relationships in Schizophrenia

Genetic risk variants for schizophrenia have been linked to many related clinical and biological phenotypes with the hopes of delineating how individual variation across thousands of variants corresponds to the clinical and etiologic heterogeneity within schizophrenia. This has primarily been done using risk score profiling, which aggregates effects across all variants into a single predictor. While effective, this method lacks flexibility in certain domains: risk scores cannot capture nonlinear effects and do not employ any variable selection. We used random forest, an algorithm with this flexibility designed to maximize predictive power, to predict 6 cognitive endophenotypes in a combined sample of psychiatric patients and controls (N = 739) using 77 genetic variants strongly associated with schizophrenia. Tenfold cross-validation was applied to the discovery sample and models were externally validated in an independent sample of similar ancestry (N = 336). Linear approaches, including linear regression and task-specific polygenic risk scores, were employed for comparison. Random forest models for processing speed (P = .019) and visual memory (P = .036) and risk scores developed for verbal (P = .042) and working memory (P = .037) successfully generalized to an independent sample with similar predictive strength and error. As such, we suggest that both methods may be useful for mapping a limited set of predetermined, disease-associated SNPs to related phenotypes. Incorporating random forest and other more flexible algorithms into genotype-phenotype mapping inquiries could contribute to parsing heterogeneity within schizophrenia; such algorithms can perform as well as standard methods and can capture a more comprehensive set of potential relationships.

Progress in genome-wide association studies of schizophrenia in Han Chinese populations

Since 2006, genome-wide association studies of schizophrenia have led to the identification of numerous novel risk loci for this disease. However, there remains a geographical imbalance in genome-wide association studies, which to date have primarily focused on Western populations. During the last 6 years, genome-wide association studies in Han Chinese populations have identified both the sharing of susceptible loci across ethnicities and genes unique to Han Chinese populations. Here, we review recent progress in genome-wide association studies of schizophrenia in Han Chinese populations. Researchers have identified and replicated the sharing of susceptible genes, such as within the major histocompatibility complex, microRNA 137 (MIR137), zinc finger protein 804A (ZNF804A), vaccinia related kinase 2 (VRK2), and arsenite methyltransferase (AS3MT), across both European and East Asian populations. Several copy number variations identified in European populations have also been validated in the Han Chinese, including duplications at 16p11.2, 15q11.2-13.1, 7q11.23, and VIPR2 and deletions at 22q11.2, 1q21.1-q21.2, and NRXN1. However, these studies have identified some potential confounding factors, such as genetic heterogeneity and the effects of natural selection on tetraspanin 18 (TSPAN18) or zinc finger protein 323 (ZNF323), which may explain the population differences in genome-wide association studies. In the future, genome-wide association studies in Han Chinese populations should include meta-analyzes or mega-analyses with enlarged sample sizes across populations, deep sequencing, precision medicine treatment, and functional exploration of the risk genes for schizophrenia.

Replication of Han Chinese GWAS loci for schizophrenia via meta-analysis of four independent samples

Schizophrenia is a highly heritable psychiatric disorder with unclear aetiology. Recent genome-wide association studies (GWAS) in European populations have reported numerous susceptibility variants, while GWAS in East Asians also identified several risk loci but with fewer independent replications. Here we focus on nine single nucleotide polymorphisms (SNPs) which have shown genome-wide significant associations with schizophrenia in previous Han Chinese GWAS, and we tend to replicate the associations in four independent samples of East Asian origin including a total of 3977 cases and 5589 controls. The results showed that rs10489202 in MPC2 (BRP44) is significantly associated with schizophrenia in these East Asian replication samples (one-tailed P=5.75×10(-3), OR=1.12), and further meta-analysis after including previous GWAS data yielded a genome-wide significant association (two-tailed P=1.11×10(-10), OR=1.19), adding further support for the involvement of this locus in the genetic risk of schizophrenia, and future studies regarding the underlying molecular mechanisms of the risk association are necessary.