Allele-specific expression of mutated in colorectal cancer (MCC) gene and alternative susceptibility to colorectal cancer in schizophrenia

A compendium of methods: Searching allele specific expression via RNA sequencing

Diploid mammalian genome has paired alleles for each gene; typically allowing for equal expression of the two alleles within the cell/tissue. However, genetic regulatory elements and epigenetic modifications can disrupt this equality, leading to preferential expression of one allele. Examining high-confidence allele-specific expression (ASE) is vital for understanding genetic variations and their impact on major diseases like cancers and diabetes. ASE analysis not only aids in disease prognosis and diagnosis but also helps to identify regulatory mechanisms operating within the genome. While advances in sequencing technologies have greatly improved our understanding of ASE, challenges remain in estimating it accurately. In this article, we reviewed methods for detecting ASE using both bulk RNASeq and single-cell RNASeq data to provide deeper insights beyond the mere prediction of ASE genes. Fundamentally, ASE detection methods are data-driven and can be classified according to type of data used. Some methods utilize both, DNA genotyping information and RNASeq while others rely solely on RNASeq data. This article offers a comparative analysis of these methods and compilation of repositories providing valuable insights.

PheMIME: an interactive web app and knowledge base for phenome-wide, multi-institutional multimorbidity analysis

OBJECTIVES

To address the need for interactive visualization tools and databases in characterizing multimorbidity patterns across different populations, we developed the Phenome-wide Multi-Institutional Multimorbidity Explorer (PheMIME). This tool leverages three large-scale EHR systems to facilitate efficient analysis and visualization of disease multimorbidity, aiming to reveal both robust and novel disease associations that are consistent across different systems and to provide insight for enhancing personalized healthcare strategies.

MATERIALS AND METHODS

PheMIME integrates summary statistics from phenome-wide analyses of disease multimorbidities, utilizing data from Vanderbilt University Medical Center, Mass General Brigham, and the UK Biobank. It offers interactive and multifaceted visualizations for exploring multimorbidity. Incorporating an enhanced version of associationSubgraphs, PheMIME also enables dynamic analysis and inference of disease clusters, promoting the discovery of complex multimorbidity patterns. A case study on schizophrenia demonstrates its capability for generating interactive visualizations of multimorbidity networks within and across multiple systems. Additionally, PheMIME supports diverse multimorbidity-based discoveries, detailed further in online case studies.

RESULTS

The PheMIME is accessible at https://prod.tbilab.org/PheMIME/. A comprehensive tutorial and multiple case studies for demonstration are available at https://prod.tbilab.org/PheMIME_supplementary_materials/. The source code can be downloaded from https://github.com/tbilab/PheMIME.

DISCUSSION

PheMIME represents a significant advancement in medical informatics, offering an efficient solution for accessing, analyzing, and interpreting the complex and noisy real-world patient data in electronic health records.

CONCLUSION

PheMIME provides an extensive multimorbidity knowledge base that consolidates data from three EHR systems, and it is a novel interactive tool designed to analyze and visualize multimorbidities across multiple EHR datasets. It stands out as the first of its kind to offer extensive multimorbidity knowledge integration with substantial support for efficient online analysis and interactive visualization.

The causal relationship of colorectal cancer on schizophrenia: A Mendelian randomization study

Comorbidities associated with psychiatric disorders often occur in patients with cancer. A causal effect of schizophrenia on cancer was observed using Mendelian randomization (MR) analysis. However, the causal effect of colorectal cancer on schizophrenia has not been studied using MR analysis. Therefore, we performed MR analysis to investigate the causal effects of colorectal cancer on schizophrenia. We performed "two-sample summary-data Mendelian randomization" using publicly available genome-wide association studies data to investigate the causal relationship between colorectal cancer (as exposure) and schizophrenia (as outcome). The inverse variance weighted method was used to calculate causal estimates. In 2 TSMR analyses, we reported that the odds ratios for schizophrenia per log odds increase in colorectal cancer risk were 6.48 (95% confidential interval [CI] of OR 1.75-24.03; P = .005) and 9.62 × 106 (95% CI of OR 1.13-8.22 × 1013; P = .048). Pleiotropic tests and sensitivity analysis demonstrated minimal horizontal pleiotropy and robustness of the causal relationship. We provide evidence for a causal relationship between the incidence of colorectal cancer and the development of schizophrenia through TSMR analysis.

Development and External Validation of a Novel Immune Checkpoint-Related Gene Signature for Prediction of Overall Survival in Hepatocellular Carcinoma

Objective: The purpose of this study was to develop and validate a novel immune checkpoint-related gene signature for prediction of overall survival (OS) in hepatocellular carcinoma (HCC). Methods: mRNA expression profiles and clinical follow-up information were obtained in the International Cancer Genome Consortium database. An external dataset from The Cancer Genome Atlas (TCGA) Liver Hepatocellular Carcinoma database was used to validate the results. The univariate and multivariate Cox regression analyses were performed based on the differentially expressed genes. We generated a four-mRNA signature to predict patient survival. Furthermore, the reliability and validity were validated in TCGA cohort. An integrated bioinformatics approach was performed to evaluate its diagnostic and prognostic value. Results: A four-gene (epidermal growth factor, mutated in colorectal cancer, mitogen-activated protein kinase kinase 2, and NRAS proto-oncogene, GTPase) signature was built to classify patients into two risk groups using a risk score with different OS in two cohorts (all P < 0.0001). Multivariate regression analysis demonstrated the signature was an independent predictor of HCC. Furthermore, the signature presented an excellent diagnostic power in differentiating HCC and adjacent tissues. Immune cell infiltration analysis revealed that the signature was associated with a number of immune cell subtypes. Conclusion: We identified a four-immune checkpoint-related gene signature as a robust biomarker with great potential for clinical application in risk stratification and OS prediction in HCC patients and could be a potential indicator of immunotherapy in HCC. The diagnostic signature had been validated to accurately distinguish HCC from adjacent tissues.

Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes

Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770 K bp). After quality control, 820 SNPs showed at least one sample with ASE. These SNPs were widespread among all autosomal chromosomes, being 32.01% found in 3'UTR and 31.41% in coding regions. We observed a considerable variation of ASE profile among individuals, which highlighted the need for biological replicates in ASE studies. Functional analysis revealed that ASE genes play critical biological functions in the development and maintenance of muscle tissue. Additionally, some of these genes were previously reported as associated with beef production and quality traits in livestock, thus indicating a possible source of bias on genomic predictions for these traits.

Sex-specific effects of a microsatellite polymorphism on human growth hormone receptor gene expression

Growth hormone (GH) binds to its specific receptor (GHR) at the surface of target cells activating multiple signaling pathways implicated in growth and metabolism. Dysregulation of GHRs leads to pathophysiological states that most commonly affect stature. We previously showed the association of a polymorphic (n = 15-37) GT microsatellite in the human GHR gene promoter with short stature in a sex-specific manner. In the present study we evaluated the functional relevance of this polymorphism in regulating GHR expression. Using luciferase reporter assays, we found that the GT repeat had a significant cis regulatory effect in response to HIF1α and a potential repressor role following C/EBPβ stimulation. Using a digital PCR application to measure allelic imbalance (AI), we showed a high prevalence of AI (∼76%) at the GHR locus in lymphoblastoid cell lines (LCLs), with a significantly higher degree of imbalance in LCLs derived from males. Examination of expression of GHR as well as other members of the GH-IGF1 axis in the LCLs revealed significant associations of GHR, IGF1 and BCL2 expression with GT genotype in a sex-specific manner. Our results suggest that this GT microsatellite exerts both cis and trans effects in a sex-specific context, revealing a new mechanism by which GHR gene expression is regulated.

Allelic Switching of DLX5, GRB10, and SVOPL during Colorectal Cancer Tumorigenesis

Allele-specific expression (ASE) is found in approximately 20-30% of human genes. During tumorigenesis, ASE changes due to somatic alterations that change the regulatory landscape. In colorectal cancer (CRC), many chromosomes show frequent gains or losses while homozygosity of chromosome 7 is rare. We hypothesized that genes essential to survival show allele-specific expression (ASE) on both alleles of chromosome 7. Using a panel of 21 recently established low-passage CRC cell lines, we performed ASE analysis by hybridizing DNA and cDNA to Infinium HumanExome-12 v1 BeadChips containing cSNPs in 392 chromosome 7 genes. The results of this initial analysis were extended and validated in a set of 89 paired normal mucosa and CRC samples. We found that 14% of genes showed ASE in one or more cell lines and identified allelic switching of the potential cell survival genes DLX5, GRB10, and SVOPL on chromosome 7, whereby the most abundantly expressed allele in the normal tissue is the lowest expressed allele in the tumor and vice versa. We established that this allelic switch does not result from loss of imprinting. The allelic switching of SVOPL may be a result of transcriptional downregulation, while the exact mechanisms resulting in the allelic switching of DLX5 and GRB10 remain to be elucidated. In conclusion, our results show that profound changes take place in allelic transcriptional regulation during the tumorigenesis of CRC.

Double-Edged Sword of Tumour Suppressor Genes in Schizophrenia

Schizophrenia (SCZ) is a common psychiatric disorder with polygenetic pathogenesis. Among the many identified candidate genes and loci, the group of tumour suppressor genes has drawn our interest. In this mini-review article, we describe evidence of a correlation between major tumour suppressor genes and SCZ development. Genetic mutations ranging from single nucleotide polymorphisms to large structural alterations have been found in tumour-related genes in patients with SCZ. Epigenetic mechanisms, including DNA methylation/acetylation and microRNA regulation of tumour suppressor genes, have also been implicated in SCZ. Beyond genetic correlations, we hope to establish causal relationships between tumour suppressor gene function and SCZ risk. Accumulating evidence shows that tumour suppressor genes may mediate cell survival and neural development, both of which contribute to SCZ aetiology. Moreover, converging intracellular signalling pathways indicate a role of tumour suppressor genes in SCZ pathogenesis. Tumour suppressor gene function may mediate a direct link between neural development and function and psychiatric disorders, including SCZ. A deeper understanding of how neural cell development is affected by tumour suppressors may lead to improved anti-psychotic drugs.

Association of VAMP5 and MCC genetic polymorphisms with increased risk of Hirschsprung disease susceptibility in Southern Chinese children

Hirschsprung disease (HSCR) is a genetic disorder characterized by the absence of neural crest cells in parts of the intestine. This study aims to investigate the association of vesicle-associated membrane protein 5 (VAMP5) and mutated in colorectal cancer (MCC) genetic polymorphisms and their correlated risks with HSCR. We examined the association in four polymorphisms (rs10206961, rs1254900 and rs14242 in VAMP5, rs11241200 in MCC) and HSCR susceptibility in a Southern Chinese population composed of 1473 cases and 1469 controls. Two variants in VAMP5 were replicated as associated with HSCR. Interestingly, we clarified SNPs rs10206961 and rs1254900 in VAMP5 are more essential for patients with long-segment aganglionosis (LHSCR). Relatively high expression correlation was observed between VAMP5 and MCC using data from public database showing there may exist potential genetic interactions. SNP interaction was cross-examined by logistic regression and multifactor dimensionality reduction analysis revealing that VAMP5 rs1254900 and MCC rs11241200 were interacting significantly, thereby contributing to the risk of HSCR. The results suggest that significant associations of the rs10206961 and rs14242 in VAMP5 with an increased risk of HSCR in Southern Chinese, especially in LHSCR patients. This study provided new evidence of epistatic association of VAMP5 and MCC with increased risk of HSCR.

Current Tissue Molecular Markers in Colorectal Cancer: A Literature Review

BACKGROUND

Colorectal cancer (CRC) is one of the most spread neoplasia types all around the world, especially in western areas. It evolves from precancerous lesions and adenomatous polyps, through successive genetic and epigenetic mutations. Numerous risk factors intervene in its development and they are either environmental or genetic.

AIM OF THE REVIEW

Alongside common screening techniques, such as fecal screening tests, endoscopic evaluation, and CT-colonography, we have identified the most important and useful biomarkers and we have analyzed their role in the diagnosis, prevention, and prognosis of CRC.

CONCLUSION

Biomarkers can become an important tool in the diagnostic and therapeutic process for CRC. But further studies are needed to identify a noninvasive, cost-effective, and highly sensible and specific screening test for their detection and to standardize their use in clinical practice.