In search of a function for the E3B1/Abi2/Argbp1/NESH family (Review)

A Potential Four-Gene Signature and Nomogram for Predicting the Overall Survival of Papillary Thyroid Cancer

Background. Although the prognosis of papillary thyroid cancer (PTC) is relatively good, some patients experience recurrence or distant metastasis after thyroidectomy and progress to radioactive iodine refractory stage. Therefore, accurate prediction of clinical outlook can aid to screen out the minority of patients with poorer prognosis and avoid excessive treatment in low-risk patients. Methods. The RNA-seq and clinical data of PTC patients was downloaded from the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) databases. Multivariate and Lasso Cox regression analyses were used to construct a prognostic nomogram to predict overall survival (OS). Thereafter, quantitative RT-PCR and Human Protein Atlas (HPA) database were employed to verify the expression of key genes. Results. A four-gene risk score comprising ABI3BP, DPT, MRO, and TENM1 was exhibited strong prognostic value. Moreover, an integrated nomogram was established based on the risk score, age, AJCC (American Joint Commission on Cancer) stage, tumor size, extrathyroidal extension, and history of neoadjuvant treatment, which exhibited significantly better predictive performance than TNM stage system ( $P<0.05$ ). GSEA (Gene Set Enrichment Analysis) and GSVA (Gene Set Variation Analysis) revealed that the different tumor-associated hallmarks, biological processes, and pathways were substantially enriched in the poor-prognosis group. In addition, a ceRNA network was constructed by including the four genes (ABI3BP, DPT, MRO, and TENM1), 54 lncRNAs, and 10 miRNAs. Finally, both the relative mRNA and protein expression of ABI3BP, DPT, MRO, and TENM1 were validated. Conclusion. The present study identified a four-gene risk signature and developed a novel nomogram, which could be regarded as a reliable prognostic model for PTC patients. The findings also revealed preliminary potential mechanisms that may influence the prognosis outcome. These results can be conducive to design personalized treatment and prognosis management in affected patients.

Gill and Liver Transcript Expression Changes Associated With Gill Damage in Atlantic Salmon (Salmo salar)

Gill damage represents a significant challenge in the teleost fish aquaculture industry globally, due to the gill's involvement in several vital functions and direct contact with the surrounding environment. To examine the local and systemic effects accompanying gill damage (which is likely to negatively affect gill function) of Atlantic salmon, we performed a field sampling to collect gill and liver tissue after several environmental insults (e.g., harmful algal blooms). Before sampling, gills were visually inspected and gill damage was scored; gill scores were assigned from pristine [gill score 0 (GS0)] to severely damaged gills (GS3). Using a 44K salmonid microarray platform, we aimed to compare the transcriptomes of pristine and moderately damaged (i.e., GS2) gill tissue. Rank Products analysis (5% percentage of false-positives) identified 254 and 34 upregulated and downregulated probes, respectively, in GS2 compared with GS0. Differentially expressed probes represented genes associated with functions including gill remodeling, wound healing, and stress and immune responses. We performed gill and liver qPCR for all four gill damage scores using microarray-identified and other damage-associated biomarker genes. Transcripts related to wound healing (e.g., neb and klhl41b) were significantly upregulated in GS2 compared with GS0 in the gills. Also, transcripts associated with immune and stress-relevant pathways were dysregulated (e.g., downregulation of snaclec 1-like and upregulation of igkv3) in GS2 compared with GS0 gills. The livers of salmon with moderate gill damage (i.e., GS2) showed significant upregulation of transcripts related to wound healing (i.e., chtop), apoptosis (e.g., bnip3l), blood coagulation (e.g., f2 and serpind1b), transcription regulation (i.e., pparg), and stress-responses (e.g., cyp3a27) compared with livers of GS0 fish. We performed principal component analysis (PCA) using transcript levels for gill and liver separately. The gill PCA showed that PC1 significantly separated GS2 from all other gill scores. The genes contributing most to this separation were pgam2, des, neb, tnnt2, and myom1. The liver PCA showed that PC1 significantly separated GS2 from GS0; levels of hsp70, cyp3a27, pparg, chtop, and serpind1b were the highest contributors to this separation. Also, hepatic acute phase biomarkers (e.g., serpind1b and f2) were positively correlated to each other and to gill damage. Gill damage-responsive biomarker genes and associated qPCR assays arising from this study will be valuable in future research aimed at developing therapeutic diets to improve farmed salmon welfare.

Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data

Simple Summary

Bohai Black cattle are one of the indigenous black coat cattle breeds in China, which are famous for their excellent meat quality. Whole-genome sequencing technology has been extensively developed to study species genome genetic diversity, population structure, selection pressure, demographic events, etc. However, a limited number of studies have reported genomic diversity and selection pressures in Bohai Black cattle. The purpose of this study is to analyze population structure and genomic differences between Bohai Black cattle and five “core” cattle populations from all over the world, mainly oriented on the identification of selection signatures using whole-genome sequencing data. In addition, we identify a series of candidate genes that can potentially be related to black coat color, meat quality, immunity, and reproduction in this breed. This study provides valuable genomic resources and theoretical basis for the future breeding of Bohai Black cattle.

Abstract

Bohai Black cattle are one of the well-known cattle breeds with black coat color in China, which are cultivated for beef. However, no study has conducted a comprehensive analysis of genomic diversity and selective pressures in Bohai Black cattle. Here, we performed a comprehensive analysis of genomic variation in 10 Bohai Black cattle (five newly sequenced and five published) and the published whole-genome sequencing (WGS) data of 50 cattle representing five “core” cattle populations. The population structure analysis revealed that Bohai Black cattle harbored the ancestry with European taurine, Northeast Asian taurine, and Chinese indicine. The Bohai Black cattle demonstrated relatively high genomic diversity from the other cattle breeds, as indicated by the nucleotide diversity (pi), the expected heterozygosity (H_E) and the observed heterozygosity (H_O), the linkage disequilibrium (LD) decay, and runs of homozygosity (ROH). We identified 65 genes containing more than five non-synonymous SNPs (nsSNPs), and an enrichment analysis revealed the “ECM-receptor interaction” pathways associated with meat quality in Bohai Black cattle. Five methods (CLR, θπ, F_ST, θπ ratio, and XP-EHH) were used to find several pathways and genes carried selection signatures in Bohai Black cattle, including black coat color (MC1R), muscle development (ITGA9, ENAH, CAPG, ABI2, and ISLR), fat deposition (TBC1D1, CYB5R4, TUSC3, and EPS8), reproduction traits (SPIRE2, KHDRBS2, and FANCA), and immune system response (CD84, SLAMF1, SLAMF6, and CDK10). Taken together, our results provide a valuable resource for characterizing the uniqueness of Bohai Black cattle.

The Extracellular Matrix Protein ABI3BP in Cardiovascular Health and Disease

ABI3BP is a relatively newly identified protein whose general biological functions are not yet fully defined. It is implicated in promoting cellular senescence and cell-extracellular matrix interactions, both of which are of vital importance in the cardiovascular system. ABI3BP has been shown in multiple studies to be expressed in the heart and vasculature, and to have a role in normal cardiovascular function and disease. However, its precise role in the cardiovascular system is not known. Because ABI3BP is present in the cardiovascular system and is altered in cardiovascular disease states, further investigation into ABI3BP's biological and biochemical importance in cardiovascular health and disease is warranted.

Tripartite motif protein 32 facilitates cell growth and migration via degradation of Abl-interactor 2

Tripartite motif protein 32 (TRIM32) mRNA has been reported to be highly expressed in human head and neck squamous cell carcinoma, but the involvement of TRIM32 in carcinogenesis has not been fully elucidated. In this study, we found by using yeast two-hybrid screening that TRIM32 binds to Abl-interactor 2 (Abi2), which is known as a tumor suppressor and a cell migration inhibitor, and we showed that TRIM32 mediates the ubiquitination of Abi2. Overexpression of TRIM32 promoted degradation of Abi2, resulting in enhancement of cell growth, transforming activity, and cell motility, whereas a dominant-negative mutant of TRIM32 lacking the RING domain inhibited the degradation of Abi2. In addition, we found that TRIM32 suppresses apoptosis induced by cis-diamminedichloroplatinum (II) in HEp2 cell lines. These findings suggest that TRIM32 is a novel oncogene that promotes tumor growth, metastasis, and resistance to anticancer drugs.