Association of gene coding variation and resting metabolic rate in a multi-ethnic sample of children and adults

Integrating bulk and single-cell RNA sequencing reveals SH3D21 promotes hepatocellular carcinoma progression by activating the PI3K/AKT/mTOR pathway

As a novel genetic biomarker, the potential role of SH3D21 in hepatocellular carcinoma remains unclear. Here, we decipher the expression and function of SH3D21 in human hepatocellular carcinoma. The expression level and clinical significance of SH3D21 in hepatocellular carcinoma patients, the relationship between SH3D21 and the features of tumor microenvironment (TME) and role of SH3D21 in promoting hepatocellular carcinoma progression were analyzed based on the bulk samples obtained from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. Single-cell sequencing samples from Gene Expression Omnibus (GEO) database were employed to verify the prediction mechanism. Additionally, different biological effects of SH3D21 on hepatocellular carcinoma cells were investigated by qRT-PCR, CCK-8 assay, colony forming assay and Western blot analysis. Bioinformatics analysis and in vitro experiments revealed that the expression level of SH3D21 was up-regulated in hepatocellular carcinoma and correlated with the poor prognosis in hepatocellular carcinoma patients. SH3D21 effectively promoted the proliferation, invasion, and migration as well as the formation of immunosuppressive microenvironment of hepatocellular carcinoma. In addition, SH3D21 can activate the PI3K/AKT/mTOR signaling pathway. SH3D21 stimulates the progression of hepatocellular carcinoma by activating the PI3K/AKT/mTOR signaling pathway, and SH3D21 can serve as a prognostic biomarker and therapeutic target for hepatocellular carcinoma.

Gene-deficient mouse model established by CRISPR/Cas9 system reveals 15 reproductive organ-enriched genes dispensable for male fertility

Since the advent of gene-targeting technology in embryonic stem cells, mice have become a primary model organism for investigating human gene function due to the striking genomic similarities between the two species. With the introduction of the CRISPR/Cas9 system for genome editing in mice, the pace of loss-of-function analysis has accelerated significantly. This has led to the identification of numerous genes that play crucial roles in male reproductive processes, including meiosis, chromatin condensation, flagellum formation in the testis, sperm maturation in the epididymis, and fertilization in the oviduct. Despite the advancements, the functions of many genes, particularly those enriched in male reproductive tissues, remain largely unknown. In our study, we focused on 15 genes and generated 13 gene-deficient mice [4933411K16Rik, Adam triple (Adam20, Adam25, and Adam39), BC048671, Cfap68, Gm4846, Gm4984, Gm13570, Nt5c1b, Ppp1r42, Saxo4, Sh3d21, Spz1, and Tektl1] to elucidate their roles in male fertility. Surprisingly, all 13 gene-deficient mice exhibited normal fertility in natural breeding experiments, indicating that these genes are not essential for male fertility. These findings have important implications as they may help prevent other research laboratories from duplicating efforts to generate knockout mice for genes that do not demonstrate an apparent phenotype related to male fertility. By shedding light on the dispensability of these genes, our study contributes to a more efficient allocation of research resources in the exploration of male reproductive biology.

Sweet swell of burning fat: emerging role of high-density lipoprotein in energy homeostasis

PURPOSE OF REVIEW

Metabolism of lipids and lipoproteins, including high-density lipoprotein (HDL), plays a central role in energy homeostasis. Mechanisms underlying the relationship between energy homeostasis and HDL however remain poorly studied.

RECENT FINDINGS

Available evidence reveals that HDL is implicated in energy homeostasis. Circulating high-density lipoprotein-cholesterol (HDL-C) levels are affected by energy production, raising with increasing resting metabolic rate. Lipolysis of triglycerides as a source of energy decreases plasma levels of remnant cholesterol, increases levels of HDL-C, and can be cardioprotective. Switch to preferential energy production from carbohydrates exerts opposite effects.

SUMMARY

Low HDL-C may represent a biomarker of inefficient energy production from fats. HDL-C-raising can be beneficial when it reflects enhanced energy production from burning fat.

Comorbidity of Novel CRHR2 Gene Variants in Type 2 Diabetes and Depression

The corticotropin-releasing hormone receptor 2 (CRHR2) gene encodes CRHR2, contributing to the hypothalamic-pituitary-adrenal stress response and to hyperglycemia and insulin resistance. CRHR2-/- mice are hypersensitive to stress, and the CRHR2 locus has been linked to type 2 diabetes and depression. While CRHR2 variants confer risk for mood disorders, MDD, and type 2 diabetes, they have not been investigated in familial T2D and MDD. In 212 Italian families with type 2 diabetes and depression, we tested 17 CRHR2 single nucleotide polymorphisms (SNPs), using two-point parametric-linkage and linkage-disequilibrium (i.e., association) analysis (models: dominant-complete-penetrance-D1, dominant-incomplete-penetrance-D2, recessive-complete-penetrance-R1, recessive-incomplete-penetrance-R2). We detected novel linkage/linkage-disequilibrium/association to/with depression (3 SNPs/D1, 2 SNPs/D2, 3 SNPs/R1, 3 SNPs/R2) and type 2 diabetes (3 SNPs/D1, 2 SNPs/D2, 2 SNPs/R1, 1 SNP/R2). All detected risk variants are novel. Two depression-risk variants within one linkage-disequilibrium block replicate each other. Two independent novel SNPs were comorbid while the most significant conferred either depression- or type 2 diabetes-risk. Although the families were primarily ascertained for type 2 diabetes, depression-risk variants showed higher significance than type 2 diabetes-risk variants, implying CRHR2 has a stronger role in depression-risk than type 2 diabetes-risk. In silico analysis predicted variants' dysfunction. CRHR2 is for the first time linked to/in linkage-disequilibrium/association with depression-type 2 diabetes comorbidity and may underlie the shared genetic pathogenesis via pleiotropy.

RMR-Related MAP2K6 Gene Variation on the Risk of Overweight/Obesity in Children: A 3-Year Panel Study

From a pilot GWAS, seven MAP2K6 (MEK6) SNPs were significantly associated with resting metabolic rate (RMR) in obese children aged 8-9 years. The aim of this study was to investigate how RMR-linked MEK6 variation affected obesity in Korean children. With the follow-up students (77.9%) in the 3-year panel study, the changes of the variables associated with obesity (such as anthropometrics, blood biochemistry, and dietary intake) were collected. After the MEK6 SNPs were screened by Affymetrix Genome-Wide Human SNP array 6.0, the genotyping of the seven MEK6 SNPs was performed via SNaPshot assay. As the prevalence of obesity (≥85th percentile) increased from 19.4% to 25.5%, the rates of change of the variables RMR, body mass index (BMI), waist circumference (WC), systolic blood pressure (SBP), and dietary intake (energy and carbohydrate intakes) increased. The rate of overweight/obesity was higher in all mutant alleles of the seven MEK6 SNPs than it was in the matched children without mutant alleles. However, over the 3-year study period, RMRs were only significantly increased by the mutants of two single nucleotide polymorphisms (SNPs), rs996229 and rs756942, mainly related to male overweight/obesity as both WC and SBP levels increased. In the mutants of two of the SNPs, the odds ratio of overweight/obesity risk was six times higher in the highest tercile of fat intake and SBP than those of the lowest tercile. For personalized medicine to prevent pediatric obesity, SBP, WC, and dietary fat intake should be observed, particularly if boys have mutants of MEK6 SNPs, rs9916229, or rs756942.

Exome Sequencing Identifies A Nonsense Variant in DAO Associated With Reduced Energy Expenditure in American Indians

BACKGROUND

Obesity and energy expenditure (EE) are heritable and genetic variants influencing EE may contribute to the development of obesity. We sought to identify genetic variants that affect EE in American Indians, an ethnic group with high prevalence of obesity.

METHODS

Whole-exome sequencing was performed in 373 healthy Pima Indians informative for 24-hour EE during energy balance. Genetic association analyses of all high-quality exonic variants (≥5 carriers) was performed, and those predicted to be damaging were prioritized.

RESULTS

Rs752074397 introduces a premature stop codon (Cys264Ter) in DAO and demonstrated the strongest association for 24-hour EE, where the Ter allele associated with substantially lower 24-hour EE (mean lower by 268 kcal/d) and sleeping EE (by 135 kcal/d). The Ter allele has a frequency = 0.5% in Pima Indians, whereas is extremely rare in most other ethnic groups (frequency < 0.01%). In vitro functional analysis showed reduced protein levels for the truncated form of DAO consistent with increased protein degradation. DAO encodes D-amino acid oxidase, which is involved in dopamine synthesis which might explain its role in modulating EE.

CONCLUSION

Our results indicate that a nonsense mutation in DAO may influence EE in American Indians. Identification of variants that influence energy metabolism may lead to new pathways to treat human obesity.

CLINICAL TRIAL REGISTRATION NUMBER

NCT00340132.

A genome-scale CRISPR/Cas9 knockout screening reveals SH3D21 as a sensitizer for gemcitabine

Gemcitabine, 2',2'-difluoro-2'-deoxycytidine, is used as a pro-drug in treatment of variety of solid tumour cancers including pancreatic cancer. After intake, gemcitabine is transferred to the cells by the membrane nucleoside transporter proteins. Once inside the cells, it is converted to gemcitabine triphosphate followed by incorporation into DNA chains where it causes inhibition of DNA replication and thereby cell cycle arrest and apoptosis. Currently gemcitabine is the standard drug for treatment of pancreatic cancer and despite its widespread use its effect is moderate. In this study, we performed a genome-scale CRISPR/Cas9 knockout screening on pancreatic cancer cell line Panc1 to explore the genes that are important for gemcitabine efficacy. We found SH3D21 as a novel gemcitabine sensitizer implying it may act as a therapeutic target for improvement of gemcitabine efficacy in treatment of pancreatic cancer.