Identification and validation of key non-coding RNAs and mRNAs using co-expression network analysis in pre-eclampsia

An integrated strategy to identify COVID-19 causal genes and characteristics represented by LRRC37A2

Genome-wide association study (GWAS) could identify host genetic factors associated with coronavirus disease 2019 (COVID-19). The genes or functional DNA elements through which genetic factors affect COVID-19 remain uncharted. The expression quantitative trait locus (eQTL) provides a path to assess the correlation between genetic variations and gene expression. Here, we firstly annotated GWAS data to describe genetic effects, obtaining genome-wide mapped genes. Subsequently, the genetic mechanisms and characteristics of COVID-19 were investigated by an integrated strategy that included three GWAS-eQTL analysis approaches. It was found that 20 genes were significantly associated with immunity and neurological disorders, including prior and novel genes such as OAS3 and LRRC37A2. The findings were then replicated in single-cell datasets to explore the cell-specific expression of causal genes. Furthermore, associations between COVID-19 and neurological disorders were assessed as a causal relationship. Finally, the effects of causal protein-coding genes of COVID-19 were discussed using cell experiments. The results revealed some novel COVID-19-related genes to emphasize disease characteristics, offering a broader insight into the genetic architecture underlying the pathophysiology of COVID-19.

Metabolomic analysis-identified 2-hydroxybutyric acid might be a key metabolite of severe preeclampsia

This study set out to determine the key metabolite changes underlying the pathophysiology of severe preeclampsia (PE) using metabolic analysis. We collected sera from 10 patients with severe PE and from 10 healthy pregnant women of the same trimester and analyzed them using liquid chromatography mass spectrometry. A total of 3,138 differential metabolites were screened, resulting in the identification of 124 differential metabolites. Kyoto encyclopedia of genes and genomes pathway analysis revealed that they were mainly enriched in the following metabolic pathways: central carbon metabolism in cancer; protein digestion and absorption; aminoacyl-transfer RNA biosynthesis; mineral absorption; alanine, aspartate, and glutamate metabolism; and prostate cancer. After analysis of 124 differential metabolites, 2-hydroxybutyric acid was found to be the most critical differential metabolite, and its use allowed the differentiation of women with severe PE from healthy pregnant women. In summary, our analysis revealed that 2-hydroxybutyric acid is a potential key metabolite for distinguishing severe PE from healthy controls and is also a marker for the early diagnosis of severe PE, thus allowing early intervention.

Identification of Key Genes and Pathways Associated with Preeclampsia by a WGCNA and an Evolutionary Approach

Preeclampsia (PE) is the serious obstetric-related disease characterized by newly onset hypertension and causes damage to the kidneys, brain, liver, and more. To investigate genes with key roles in PE’s pathogenesis and their contributions, we used a microarray dataset of normotensive and PE patients and conducted a weighted gene co-expression network analysis (WGCNA). Cyan and magenta modules that are highly enriched with differentially expressed genes (DEGs) were revealed. By using the molecular complex detection (MCODE) algorithm, we identified five significant clusters in the cyan module protein–protein interaction (PPI) network and nine significant clusters in the magenta module PPI network. Our analyses indicated that (i) human accelerated region (HAR) genes are enriched in the magenta-associated C6 cluster, and (ii) positive selection (PS) genes are enriched in the cyan-associated C3 and C5 clusters. We propose these enriched HAR and PS genes, i.e., EIF4E, EIF5, EIF3M, DDX17, SRSF11, PSPC1, SUMO1, CAPZA1, PSMD14, and MNAT1, including highly connected hub genes, HNRNPA1, RBMX, PRKDC, and RANBP2, as candidate key genes for PE’s pathogenesis. A further clarification of the functions of these PPI clusters and key enriched genes will contribute to the discovery of diagnostic biomarkers for PE and therapeutic intervention targets.

NAPSB as a predictive marker for prognosis and therapy associated with an immuno-hot tumor microenvironment in hepatocellular carcinoma

Background

Napsin B Aspartic Peptidase, Pseudogene (NAPSB) was associated with CD4 + T cell infiltration in pancreatic ductal adenocarcinoma. However, the biological role of NAPSB in hepatocellular carcinoma (HCC) remains to be determined.

Methods

The expression of NAPSB in HCC as well as its clinicopathological association were analyzed using data from several public datasets. qRT-PCR was used to verify the relative expression of NAPSB in patients with HCC using the Zhongnan cohort. Kaplan–Meier analyses, and univariate and multivariate Cox regression were conducted to determine the prognosis value of NAPSB on patients with HCC. Then enrichment analyses were performed to identify the possible biological functions of NAPSB. Subsequently, the immunological characteristics of NAPSB in the HCC tumor microenvironment (TME) were demonstrated comprehensively. The role of NAPSB in predicting hot tumors and its impact on immunotherapy and chemotherapy responses was also analyzed by bioinformatics methods.

Results

NAPSB was downregulated in patients with HCC and high NAPSB expression showed an improved survival outcome. Enrichment analyses showed that NAPSB was related to immune activation. NAPSB was positively correlated with immunomodulators, tumor-infiltrating immune cells, T cell inflamed score and cancer-immunity cycle, and highly expressed in immuno-hot tumors. High expression of NAPSB was sensitive to immunotherapy and chemotherapy, possibly due to its association with pyroptosis, apoptosis and necrosis.

Conclusions

NAPSB was correlated with an immuno-hot and inflamed TME, and tumor cell death. It can be utilized as a promising predictive marker for prognosis and therapy in HCC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12876-022-02475-8.

Characterization of the MG828507 lncRNA Located Upstream of the FLT1 Gene as an Etiology for Pre-Eclampsia

Background: FLT1 is one of the significantly overexpressed genes found in a pre-eclamptic placenta and is involved with the etiology of this disease. Methods: We conducted genome-wide expression profiling by RNA-seq of placentas from women with pre-eclampsia and those with normotensive pregnancy. Results: We identified a lncRNA gene, MG828507, located ~80 kb upstream of the FLT1 gene in a head-to-head orientation, which was overexpressed in the pre-eclamptic placenta. MG828507 and FLT1 are located within the same topologically associated domain in the genome. The MG828507 mRNA level correlated with that of the FLT1 in placentas from pre-eclamptic women as well as in samples from uncomplicated pregnancies. However, neither the overexpression nor knockdown of MG828507 affected the expression of FLT1. Analysis of pre-eclampsia-linking genetic variants at this locus suggested that the placental genotype of one variant was associated with the expression of MG828507. The MG828507 transcript level was not found to be associated with maternal blood pressure, but showed a relationship with birth and placental weights, suggesting that this lncRNA might be one of the pivotal placental factors in pre-eclampsia. Conclusion: Further characterization of the MG828507 gene may elucidate the etiological roles of the MG828507 and FLT1 genes in pre-eclampsia in a genomic context.

EZH2 enhances proliferation and migration of trophoblast cell lines by blocking GADD45A-mediated p38/MAPK signaling pathway

Impaired activity of the trophoblasts is a major contributor to the progression of pregnancy pathologies including preeclampsia (PE). This research probed the function of enhancer of zeste homolog 2 (EZH2) in activity of trophoblast cells and its correlation with growth arrest and DNA damage inducible alpha (GADD45A). EZH2 was predicted to be downregulated in placental tissues in PE according to a gene chip analysis, and reduced expression of EZH2 was detected in the placental tissues of patients with PE. Overexpression of EZH2 augmented proliferation and invasiveness of two trophoblast cell lines HTR-8/SVneo and JEG3 cells. EZH2 catalyzed trimethylation of lysine 27 on histone 3 (H3K27me3) in GADD45A promoter to suppress its transcription. GADD45A silencing increased the activity of the trophoblast cell lines and inactivated the p38/mitogen-activated protein kinase (MAPK) signaling pathway. Rescue experiments confirmed that either inhibition of GADD45A or p38 restored the proliferation, migration, and invasiveness of the trophoblast cell lines suppressed by EZH2 silencing. In conclusion, this work suggests that EZH2 enhances activity of trophoblast cell lines by suppressing GADD45A-mediated p38/MAPK signaling pathway.

Clinical tools and biomarkers to predict preeclampsia

Preeclampsia is pregnancy-specific, and significantly contributes to maternal, and perinatal morbidity and mortality worldwide. An effective predictive test for preeclampsia would facilitate early diagnosis, targeted surveillance and timely delivery; however limited options currently exist. A first-trimester screening algorithm has been developed and validated to predict preterm preeclampsia, with poor utility for term disease, where the greatest burden lies. Biomarkers such as sFlt-1 and placental growth factor are also now being used clinically in cases of suspected preterm preeclampsia; their high negative predictive value enables confident exclusion of disease in women with normal results, but sensitivity is modest. There has been a concerted effort to identify potential novel biomarkers that might improve prediction. These largely originate from organs involved in preeclampsia's pathogenesis, including placental, cardiovascular and urinary biomarkers. This review outlines the clinical imperative for an effective test and those already in use and summarises current preeclampsia biomarker research.