MTHFR C677T and MTR A2756G Gene Polymorphism in Neural Tube Defect Patients and Its Association with Red Blood Cell Folate Level in Eastern Indian Population

Identification of amino acid metabolism‑related genes as diagnostic and prognostic biomarkers in sepsis through machine learning

Previous research has highlighted the critical role of amino acid metabolism (AAM) in the pathophysiology of sepsis. The present study aimed to explore the potential diagnostic and prognostic value of AAM-related genes (AAMGs) in sepsis, as well as their underlying molecular mechanisms. Gene expression profiles from the Gene Expression Omnibus (GSE65682, GSE185263 and GSE154918 datasets) were analyzed. Based on weighted gene co-expression network analysis and machine learning algorithms, hub AAMGs were identified in the GSE65682 database. Subsequently, hub AAMGs were evaluated for their expression levels and diagnostic and prognostic significance in sepsis, as well as their interactions with regulatory pathways and role in immune cell infiltration. Additionally, trends in AAMG expression were validated using clinical samples, and their functions in sepsis were confirmed through an in vitro model. In total, four AAMGs were identified, two of which, methionine synthase (MTR) and methionine-R-isomerase 1 (MRI1), demonstrated significant differential expression in the GSE65682, GSE185263 and GSE154918 datasets, which was further validated using clinical samples. A diagnostic nomogram based on MTR and MRI1 expression demonstrated strong diagnostic effectiveness across the three aforementioned databases. Moreover, the expression of both genes were negatively correlated with sepsis prognosis and showed stratified prognostic capabilities. Newly identified pathways included KRAS and IL-2/STAT5 signaling. MTR and MRI1 negatively correlated with the infiltration of inflammatory cells, such as M1 macrophages and neutrophils, and positively correlated with anti-inflammatory cells, such as CD8+ T and dendritic cells. In vitro experiments further demonstrated that overexpression of MTR could mitigate the inhibition of cloning and proliferation induced by LPS and ATP in RAW 264.7 cells. These findings highlighted the potential of MTR and MRI1 as biomarkers for diagnosing and prognosticating sepsis, potentially acting through the regulation of methionine in the pathophysiology of this disease. The present study provided new insights into the role of AAM in the mechanisms underlying sepsis and in the potential development of future targeted therapies.

Exploring research hotspots and future directions in neural tube defects field by bibliometric and bioinformatics analysis

Background

Neural tube defects (NTDs) is the most common birth defect of the central nervous system (CNS) which causes the death of almost 88,000 people every year around the world. Much efforts have been made to investigate the reasons that contribute to NTD and explore new ways to for prevention. We trawl the past decade (2013-2022) published records in order to get a worldwide view about NTDs research field.

Methods

7,437 records about NTDs were retrieved from the Web of Science (WOS) database. Tools such as shell scripts, VOSviewer, SCImago Graphica, CiteSpace and PubTator were used for data analysis and visualization.

Results

Over the past decade, the number of publications has maintained an upward trend, except for 2022. The United States is the country with the highest number of publications and also with the closest collaboration with other countries. Baylor College of Medicine has the closest collaboration with other institutions worldwide and also was the most prolific institution. In the field of NTDs, research focuses on molecular mechanisms such as genes and signaling pathways related to folate metabolism, neurogenic diseases caused by neural tube closure disorders such as myelomeningocele and spina bifida, and prevention and treatment such as folate supplementation and surgical procedures. Most NTDs related genes are related to development, cell projection parts, and molecular binding. These genes are mainly concentrated in cancer, Wnt, MAPK, PI3K-Akt and other signaling pathways. The distribution of NTDs related SNPs on chromosomes 1, 3, 5, 11, 14, and 17 are relatively concentrated, which may be associated with high-risk of NTDs.

Conclusion

Bibliometric analysis of the literature on NTDs field provided the current status, hotspots and future directions to some extant. Further bioinformatics analysis expanded our understanding of NTDs-related genes function and revealed some important SNP clusters and loci. This study provided some guidance for further studies. More extensive cooperation and further research are needed to overcome the ongoing challenge in pathogenesis, prevention and treatment of NTDs.

Double whammy: the genetic variants in CECR2 and high Hcy on the development of neural tube defects

Introduction: Neural tube defects (NTDs) are serious congenital malformations. The etiology of NTDs involves both genetic and environmental factors. Loss of CECR2 in mice has been shown to result in NTDs. Our previous study indicated that high homocysteine (HHcy) levels could further reduced the expression level of CECR2. This investigation aims to explore the genetic influence of the chromatin remodeling gene, CECR2, in humans and determine if HHcy can have a synergistic effect on protein expression. Methods: We conducted Next-Generation Sequencing (NGS) of the CECR2 gene in 373 NTD cases and 222 healthy controls, followed by functional assay application to select and evaluate CECR2 missense variants and subsequent Western blotting to identify protein expression levels. Results: From the analysis, we identified nine rare, NTD-specific mutations within the CECR2 gene. Significantly, four missense variants (p.E327V, p.T521S, p.G701R, and p.G868R) were selected via functional screening. The E9.5 mouse ectodermal stem cell line NE-4C, transfected with plasmids expressing p.E327V, p.T521S, p.G868R variants or a recombinant harboring all four (named as 4Mut), exhibited notable reductions in CECR2 protein expression. Furthermore, exposure to homocysteine thiolactone (HTL), an extremely reactive homocysteine metabolite, amplified the reduction in CECR2 expression, accompanied by a significant increase in the apoptotic molecule Caspase3 activity, a potential NTD inducer. Importantly, folic acid (FA) supplementation effectively counteracted the CECR2 expression decline induced by CECR2 mutation and HTL treatment, leading to reduced apoptosis. Discussion: Our observations underscore a synergistic relationship between HHcy and genetic variations in CECR2 concerning NTDs, thereby reinforcing the concept of gene-environment interaction phenomena in NTD etiology.