Clinically significant missense variants in human GALNT3, GALNT8, GALNT12, and GALNT13 genes: intriguing in silico findings

Expression of GALNT8 and O-glycosylation of BMP receptor 1A suppress breast cancer cell proliferation by upregulating ERα levels

BACKGROUND

Mucin-type O-glycosylation is one of the most abundant types of O-glycosylation and plays important roles in various human carcinomas, including breast cancer. A large family of polypeptide N-acetyl-α-galactosaminyltransferases (GALNTs) initiate and define sites of mucin-type O-glycosylation. However, the specific mechanisms underlying GALNT8 expression and its roles in tumorigenesis remain poorly characterized.

METHODS

GALNT8 expression was assessed in 140 breast cancer patients. Immunofluorescence, immunoprecipitation, lectin blot and quantitative real-time PCR were used to investigate the expression of GALNT8 and its role in regulating estrogen receptor α (ERα) via bone morphogenetic protein (BMP) signaling.

RESULTS

The expression of GALNT8 was associated with breast cancer patient survival. GALNT8 downregulation was associated with a reduction in ERα levels, while GALNT8 overexpression elevated the transcription and protein levels of ERα and suppressed colony formation, suggesting an important role of GALNT8 in cancer cell proliferation. Conversely, GALNT8 knockdown led to the inhibition of BMP/SMAD/RUNX2 axis, which decreased ERα transcription. Further analysis suggested that BMP receptor 1A (BMPR1A) was O-GalNAcylated. Sites mutation of BMPR1A indicated that Thr137 and Ser37/Ser39/Ser44/Thr49 of BMPR1A were the main O-glycosylation sites. Although we cannot exclude the indirect effect of GALNT8, our results demonstrated that the expression of GALNT8 and O-glycosylation of BMPR1A play key roles in regulating the activity of BMP/SMAD/RUNX2 signaling and ERα expression.

CONCLUSION

These findings suggest that GALNT8 expression and abnormal O-GalNAcylation of BMPR1A increase ERα expression and suppress breast cancer cell proliferation by modulating the BMP signaling pathway.

GENERAL SIGNIFICANCE

Our results identify the involvement of GALNT8 in regulating ERα expression.

National recommendations of the French Genetics and Cancer Group - Unicancer on the modalities of multi-genes panel analyses in hereditary predispositions to tumors of the digestive tract

In case of suspected hereditary predisposition to digestive cancers, next-generation sequencing can analyze simultaneously several genes associated with an increased risk of developing these tumors. Thus, "Gastro Intestinal" (GI) gene panels are commonly used in French molecular genetic laboratories. Lack of international recommendations led to disparities in the composition of these panels and in the management of patients. To harmonize practices, the Genetics and Cancer Group (GGC)-Unicancer set up a working group who carried out a review of the literature for 31 genes of interest in this context and established a list of genes for which the estimated risks associated with pathogenic variant seemed sufficiently reliable and high for clinical use. Pancreatic cancer susceptibility genes have been excluded. This expertise defined a panel of 14 genes of confirmed clinical interest and relevant for genetic counseling: APC, BMPR1A, CDH1, EPCAM, MLH1, MSH2, MSH6, MUTYH, PMS2, POLD1, POLE, PTEN, SMAD4 and STK11. The reasons for the exclusion of the others 23 genes have been discussed. The paucity of estimates of the associated tumor risks led to the exclusion of genes, in particular CTNNA1, MSH3 and NTHL1, despite their implication in the molecular pathways involved in the pathophysiology of GI cancers. A regular update of the literature is planned to up-grade this panel of genes in case of new data on candidate genes. Genetic and epidemiological studies and international collaborations are needed to better estimate the risks associated with the pathogenic variants of these genes either selected or not in the current panel.

Evaluation of GALNT16 polymorphisms to breast cancer risk in Chinese population

BACKGROUND

Polypeptide N-acetylgalactosaminyltransferase 16 (GALNT16) is an N-acetylgalactosaminyltransferase gene that alters protein O-glycosylation, which plays a role in tumor development. This study aims to explore the association of eight GALNT16 polymorphisms with susceptibility to breast cancer (BC).

METHODS

This case-control study included 563 BC patients and 552 age-matched healthy controls from the Chinese Han population. The genotypes of GALNT16 polymorphisms were detected using the Agena MassARRAY. The relationship between GALNT16 polymorphisms and BC risk was evaluated using a chi-squared test with an odds ratio (OR) and 95% confidence intervals (CI) under five genetic models.

RESULTS

We observed that rs2105269 and rs72625676 were associated with higher BC risk in younger patients with age ≤51 (rs2105269, codominant: p = .006; recessive: p = .005 additive: p = .018; and allele: p = .012; rs72625676, codominant: p = .038; recessive: p = .037). For rs1275678 polymorphism, there was a significantly decreased risk of BC among elder patients (codominant: p = .017; dominant: p = .019; additive: p = .030; and allele: p = .029). Further analysis by clinical characteristics showed rs2105269 was associated with tumor size and lymph node metastasis.

CONCLUSION

Our study suggests that GALNT16 polymorphisms are associated with BC susceptibility in Chinese population.

Comprehensive Computational Analysis of Protein Phenotype Changes Due to Plausible Deleterious Variants of Human SPTLC1 Gene

Genetic variations found in the coding and non-coding regions of a geneare known to influence the structure as well as the function of proteins. Serine palmitoyltransferase long chain subunit 1 a member of α-oxoamine synthase family is encoded by SPTLC1 gene which is a subunit of enzyme serine palmitoyltransferase (SPT). Mutations in SPTLC1 have been associated with hereditary sensory and autonomic neuropathy type I (HSAN-I). The exact mechanism through which these mutations elicit protein phenotype changes in terms of structure, stability and interaction with other molecules is unknown. Thus, we aimed to perform a comprehensive computational analysis of single nucleotide polymorphisms (SNPs) of SPTLC1 to prioritize a list of potential deleterious SNPs and to investigate the protein phenotype change due to functional polymorphisms. In this study, a diverse set of SPTLC1 SNPs were collected and scrutinized to categorize the potential deleterious variants. Our study concordantly identified 21 non- synonymous SNPs as pathogenic and deleterious that might induce alterations in protein structure, flexibility and stability. Moreover, evaluation of frameshift, 3’ and 5’ UTR variants shows c.*1302T> Gas effective. This comprehensive in silico analysis of systematically characterized list of potential deleterious variants could open avenues as primary filter to substantiate plausible pathogenic structural and functional impact of variants.

Screening key long non-coding RNAs in early-stage colon adenocarcinoma by RNA-sequencing

AIM

We aim to identify the key long noncoding RNAs (lncRNAs) in early-stage colon adenocarcinoma (COAD).

PATIENTS & METHODS

Compared with colonic intraepithelial neoplasia, differentially expressed lncRNAs (DElncRNAs) in early-stage COAD were obtained by RNA-sequencing. Our previous work has obtained the differentially expressed mRNAs and miRNAs (DEmRNAs and DEmiRNAs) in early-stage COAD. DEmiRNA-DElncRNA-DEmRNA interaction analysis and functional annotation were performed. Validation of expression and receiver-operating characteristic analyses were performed based on The Cancer Genome Atlas.

RESULTS

Seventy-nine significantly DElncRNAs in early-stage COAD were obtained. MiR-153-3p-TUG1-DAPK1/ARNT2/KLK3/PLD1/SMAD2 and miR-153-3p-SNHG17-COL11A1/IGFBP3/KLF6 interactions were associated with early-stage COAD. Five DElncRNAs (ELFN1-AS1, LINC01234, SNHG17, UCA1 and LOC101929549) involved in early-stage COAD with potential diagnostic value.

CONCLUSION

LncRNAs involve in early-stage COAD by interaction with COAD-regulated genes and miRNAs.

Charge and Polarity Preferences for N-Glycosylation: A Genome-Wide In Silico Study and Its Implications Regarding Constitutive Proliferation and Adhesion of Carcinoma Cells

The structural and functional diversity of the human proteome is mediated by N- and O-linked glycosylations that define the individual properties of extracellular and membrane-associated proteins. In this study, we utilized different computational tools to perform in silico based genome-wide mapping of 1,117 human proteins and unravel the contribution of both penultimate and vicinal amino acids for the asparagine-based, site-specific N-glycosylation. Our results correlate the non-canonical involvement of charge and polarity environment of classified amino acids (designated as L, O, A, P, and N groups) in the N-glycosylation process, as validated by NetNGlyc predictions, and 130 literature-reported human proteins. From our results, particular charge and polarity combinations of non-polar aliphatic, acidic, basic, and aromatic polar side chain environment of both penultimate and vicinal amino acids were found to promote the N-glycosylation process. However, the alteration in side-chain charge and polarity environment of genetic variants, particularly in the vicinity of Asn-containing epitope, may induce constitutive glycosylation (e.g., aberrant glycosylation at preferred and non-preferred sites) of membrane proteins causing constitutive proliferation and triggering epithelial-to-mesenchymal transition. The current genome-wide mapping of 1,117 proteins (2,909 asparagine residues) was used to explore charge- and polarity-based mechanistic constraints in N-glycosylation, and discuss alterations of the neoplastic phenotype that can be ascribed to N-glycosylation at preferred and non-preferred sites.

N-acetylgalactosaminyltransferases in cancer

Aberrant mucin-type O-glycosylation by glycosyltransferases is a well-described hallmark of many cancers and is also associated with additional non-cancerous developmental and metabolic disorders. The current review focuses on N-acetylgalactosaminyltransferase genes (GALNTs) and proteins (GalNAcTs) to illustrate their importance in cancer biology. Aberrant O-glycosylation by GalNAcTs activates a wide range of proteins that carry out interactions of sessile and motile cells affecting organogenesis, responses to agonists and stimulating hyperproliferation and metastatisation of neoplastic cells. As genome-wide analyses have provided abundant clues regarding under- or over-expressed genes that characterize different types of cancers, GALNTs and their transferase products have attracted attention by being unexpected actors in neoplastic contexts. We intend to review the current knowledge on GALNTs and their encoded transferases in cancer and suggest what could be the significance of such information in cancer pathogenesis and management.

Characterization of GALNTL5 gene sequence and expression in ovine testes and sperm

The polypeptide N-acetylgalactosaminyltransferase-like protein 5 (GALNTL5), which belongs to the polypeptide N-acetylgalactosaminyltransferase (pp-GalNAc-T) gene family, is a newly identified gene that is specifically expressed in testis and involved in spermatogenesis. However, there is no data showing the existence of GALNTL5 in ram testis at various developmental stages and its influence on sperm motility. Therefore, the objectives of the present study were to evaluate the presence of GALNTL5 in the testis of 3-24 months (M) ram and to investigate the expression of GALNTL5 in spermatozoa with different motilities. We detected a 1602 bp cDNA fragment of GALNTL5 that included a 1326 bp coding sequence, encoding 441 amino acids and 90 and 185 bp of the 5' and 3' untranslated regions, respectively. The GALNTL5 amino acid sequence showed 51.87-83.48% identity with the sequences of proteins from other species. It was detected exclusively in the testis and the levels of both the mRNA and protein were progressively increased with age. Immunohistochemistry further revealed that GALNTL5 specifically localized in the elongating spermatids and spermatozoa, and it was demonstrated to be strongly concentrated in the head, neck, and mid-piece region of spermatozoa by immunocytochemistry. The sperm density and the percentage of live sperm in the high motility group (≥80%) were significantly higher than in the low motility group (≤50%), and the reverse trend was observed with the abnormal sperm. Western blot analysis showed that the protein expression of PGK2, ALDOA, and GALNTL5 were significantly higher in the high motility group than in the low motility group. Overall, the data suggest that GALNTL5 is an important functional molecule during spermatogenesis. Moreover, it is the first to suggest that the expression level of GALNTL5 is positively correlated with the sperm motility.

Colorectal cancer: A review of the genome-wide association studies in the kingdom of Saudi Arabia

Genome-wise association studies (GWAS) identify risk variants and modifiers that can influence the pathophysiological processes involved in colorectal cancer (CRC) and thus are important to detect associations between disease phenotypes. Our literature review, performed as per PRISMA statement indicates a significant lack of GWAS functional studies in Saudi Arabia. Therefore, studies on sequencing and mapping are needed to identify gene variants that play a role in the pathophysiology of CRC in this specific population. Because it is not apt to generalize disease associations found in other racial and/or ethnic groups to the Arabic or Middle Eastern population, it is very important to conduct GWAS taking into account multiple ethnicities in this region. In addition, linkage studies and case-control studies that include the various confounding and epigenetic factors are needed for appropriate diagnosis of CRC. We recommend that studies in this region be conducted to understand the role of gene-environment interactions across the various ethnic groups, stages of cancer, tumor type, clinical variables, and the population risk to CRC.

BRAF gene: From human cancers to developmental syndromes

The BRAF gene encodes for a serine/threonine protein kinase that participates in the MAPK/ERK signalling pathway and plays a vital role in cancers and developmental syndromes (RASopathies). The current review discusses the clinical significance of the BRAF gene and other members of RAS/RAF cascade in human cancers and RAS/MAPK syndromes, and focuses the molecular basis and clinical genetics of BRAF to better understand its parallel involvement in both tumourigenesis and RAS/MAPK syndromes—Noonan syndrome, cardio-facio-cutaneous syndrome and LEOPARD syndrome.

First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene

GalNAc-T1, a key candidate of GalNac-transferases genes family that is involved in mucin-type O-linked glycosylation pathway, is expressed in most biological tissues and cell types. Despite the reported association of GalNAc-T1 gene mutations with human disease susceptibility, the comprehensive computational analysis of coding, noncoding and regulatory SNPs, and their functional impacts on protein level, still remains unknown. Therefore, sequence- and structure-based computational tools were employed to screen the entire listed coding SNPs of GalNAc-T1 gene in order to identify and characterize them. Our concordant in silico analysis by SIFT, PolyPhen-2, PANTHER-cSNP, and SNPeffect tools, identified the potential nsSNPs (S143P, G258V, and Y414D variants) from 18 nsSNPs of GalNAc-T1. Additionally, 2 regulatory SNPs (rs72964406 and #x26; rs34304568) were also identified in GalNAc-T1 by using FastSNP tool. Using multiple computational approaches, we have systematically classified the functional mutations in regulatory and coding regions that can modify expression and function of GalNAc-T1 enzyme. These genetic variants can further assist in better understanding the wide range of disease susceptibility associated with the mucin-based cell signalling and pathogenic binding, and may help to develop novel therapeutic elements for associated diseases.