Gene Reports最新文献

The genus Mustelus comprises demersal smoothhound sharks, including M. canis and M. norrisi. Despite their economic value and known conservation concerns, only a few genetic and no genomic resources exist for these two species. In this study, we assembled and described the complete mitochondrial genomes of Mustelus canis and M. norrisi. The mitochondrial genomes of M. canis and M. norrisi are 16,758 bp and 16,769 bp in length, respectively. Both mitogenomes are A + T rich and contain 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region (CR) 1122 bp and 1121 bp in length, respectively. Mitochondrial synteny observed in M. canis and M. norrisi is identical to that previously reported for congeneric species. In the studied mitochondrial genomes, all PCGs experienced purifying selection. In both species, 21 of the 22 tRNA genes exhibited a typical ‘cloverleaf’ secondary structure, except trnS1 that lacked a complete D-arm. The CR of the studied species lacked tandem repeats, but abundant A + T rich dinucleotide microsatellites were detected. Maximum likelihood and Bayesian inference phylogenetic analyses based on translated PCGs supported the monophyly of the family Triakidae. The same analyses indicated that the genus Mustelus was not monophyletic considering that all representatives of the genus Mustelus clustered together with Triakis megalopterus in a fully supported clade. The assembled mitochondrial genomes will aid with the accurate identification of specimens belonging to the genus Mustelus and support biomonitoring programs based on environmental DNA (eDNA).

Background

Circular RNAs (circRNAs) have emerged as potential clinical targets in cancer therapy, since they have been shown to play a crucial role in tumor development by acting as competitive endogenous RNAs (ceRNAs) that regulate downstream mRNA expression by sequestering microRNAs (miRNAs). The present study, aimed to identify novel ceRNA networks involving circRNAs, miRNAs, and mRNAs in using a combination of Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets and explore the function of circ_0000518 in the malignancy of colorectal cancer (CRC).

Methods

Raw data related to CRC, including circRNAs, miRNAs and mRNAs, were downloaded from GEO and TCGA databases. A circRNA/miRNA/mRNA network was established by differential analysis and multiple databases were used to predict downstream targets. The role of this network in the development of CRC was further validated by a series of cellular experiments including dual luciferase assay, migration assay and flow apoptosis assay.

Results

Differential expression analysis of two GEO datasets (GSE142837 and GSE126094) revealed four circRNAs, which were used to predict downstream miRNAs and mRNAs based on several databases. These predictions, combined with TCGA analysis, were used to construct a ceRNA network composed of 4 circRNAs, 9 miRNAs, and 52 mRNAs. The circ_0000518/miR-326/ephrin type-B receptor 3 (EPHB3) axis was eventually selected for functional validation in two CRC cell lines. Subsequently, it was experimentally verified that circ_0000518 was highly expressed in CRC; meanwhile, it was found that the proliferation and migration of CRC cells were significantly weakened by knocking down circ_0000518, while apoptosis of tumors was promoted.

Conclusion

The data demonstrated the identification of a novel circRNA/miRNA/mRNA competitive endogenous network in CRC. The regulatory role of the circ_0000518/miR-326/EPHB3 axis in this network was preliminarily validated by cellular experiments exploring CRC tissue samples and two CRC cell lines.

Rotavirus A (RVA) possesses a genome of 11-segmented, double-stranded RNAs, each of which is classified into genotypes. A variety of genotype constellations have been generated through reassortment, but reassortment does not appear to occur randomly. Here genomic sequences for 281 RVA strains with distinct genotype constellations retrieved from the International Nucleotide Sequence Database were analyzed to identify shared clusters between phylogenetic trees for genomic segments. The largest numbers of shared clusters were observed between the genomic segments encoding viral protein 1 (VP1) and VP2 as well as VP2 and VP3, suggesting that not only VP1 but also VP3 may interact with VP2 inside the core. Larger numbers were also associated with the segment encoding non-structural protein 5/6 (NSP5/6), which may be a hub for bundling genomic segments. Although VP7 and VP4 segments were associated with smaller numbers, reassortments between these segments as well as VP7 and VP6 segments appeared to be restricted due to interactions in constructing the virion. For VP4 segment, the number with NSP1 segment was significantly greater than those with other segments, possibly reflecting that specificities in receptor binding and interferon antagonism may define host range restriction. Overall, no cluster was shared by all genomic segments, supporting that RVA constituted a single species.

Background

Repute in the widely-used compounds in H. pylori eradication regimen, mainly in the communities sustained with the pattern of Clarithromycin and Metronidazole MDRs, are the critical criterias focused on in molecular medication for therapeutic revision. 23S rRNA mutations are the leading cause of Clarithromycin suboptimal efficacy, and Lgt, RdxA preliminary stop codon formats result in Metronidazole lesser activity. In the present study, phenotypic resistance patterns of commonly used compounds in combination therapy, as well as identify predominant MDR patterns, were deeply analyzed.

Methods

Columbia blood agar was used for MICs evaluation of Mzt, Cam, Amx, and Tet. 23S rRNA at NL: 1939‐2380 was amplified and sequenced. Lgt and its neighboring gene rdxA at NL: 561‐1666 were tagged to extract nucleotide mismatches by PCR-sequencing.

Results

In total, 42 out of 348 (12.06%) were found to have H. pylori related disease. Beyond the MICs, resistance rates to Mzt, Cam, Amx, and Tet were 42.85%, 19.04%, 7.14%, 4.76%. Quote of MDRs, evaluated patients with a rate of 9/42 (21.42%); relevant forms of MDRs were the pattern of Metronidazole and Clarithromycin for 8/42 (19.04%), while Metronidazole and Amoxicillin MDRs addressed a minimum. Given the tagged sequences, 2/8 (25%) of Cam-resistant patients could be isolated with the mutations A2142G and G2097A. For Mzt, 7/18 (38.88%) of resistant patients detected by lgt mutations at 808‐919, disseminated with Lgt coding site at 233‐242, p = 0.006. rdxA stop codons at 211 (495) and 205 (489) detected in 3/18 (16.66%). Overall, within 5 out of 8 (62.5%) Metronidazole-associated MDRs, accumulation of lgt mutations or mutated Lgt residues was impressively detected in Mzt full level of resistance, Odds Ratios: 37.3.

Conclusions

It is assumed that mutations inside lgt that caused Lgt termination sites can facilitate Metronidazole-resistant patient probing and be related to potent MDRs with Metronidazole resistance centrality.

Background

Lung cancer ranks as the second most prevalent cancer in both men and women and stands as one of the most prevalent and lethal malignancies globally. In recent decades, the therapeutic potential of bacteria has gained recognition in pharmaceutical and therapeutic research. While bacteria have historically been associated with cancer causation, recent studies have unveiled their potential as efficacious agents for targeted cancer therapy. However, limited data exist on the characterization and impact of Staphylococcus aureus (S. aureus) extract on lung cancer cell lines. Consequently, this study aims to investigate the effect of S. aureus extract on inducing apoptosis in A549, a lung cancer cell line, and MRC-5, a lung normal cell line, by evaluating the expression levels of the bax and bcl-2 genes.

Methods

Initially, cytoplasmic extract of S. aureus was prepared using the sonication technique. The protein concentration was determined via the Bradford assay, and the presence of proteins was confirmed using SDS-PAGE. A549, representing a lung cancer cell line, and MRC-5, representing a lung normal cell line, were exposed to varying concentrations of bacterial extract, and cell viability was assessed using the MTT assay. Subsequently, the expression levels of the bax and bcl-2 genes were quantified utilizing the Real-Time PCR method.

Results

Cytoplasmic extract derived from S. aureus demonstrated the ability to modulate the expression levels of apoptotic genes. Relative to the control group, the bax gene exhibited a fivefold overexpression, while the expression of the bcl-2 gene decreased by more than half compared to the control. Furthermore, the results of the MTT assay indicated that the bacterial cytoplasmic extract exhibited concentration-dependent cytotoxicity on cancer cells, highlighting a significant increase in cell death with escalating concentrations.

Conclusions

This research highlights the potential of S. aureus extract for targeted lung cancer therapy by promoting cancer cell apoptosis while sparing normal cells. These findings open up exciting possibilities for innovative cancer treatments and improved patient outcomes, emphasizing the promise of S. aureus extract in the fight against lung cancer.

Background

Obesity in children is a major worldwide concern that has several negative health consequences in both the short and long term. The objective of this study was to evaluate the expression level of microRNA-122 in obese Egyptian children and investigate its potential associations with insulin resistance and cardiovascular diseases.

Methods

The study included 70 obese and 30 age-matched normal-weight control children. Anthropometric measurements, systolic, and diastolic blood pressures were assessed, and quantitative real-time polymerase chain reaction was used to determine the expression of circulating microRNA-122. Pancreatic beta cell function (HOMA2-%B), insulin resistance (HOMA2-IR), and insulin sensitivity (HOMA2-%S) was assessed by the homeostasis model assessment version 2 (HOMA2). McAuley index and single-point insulin sensitivity estimator (SPISE) was used to further evaluate insulin sensitivity. Levels of serum biochemical parameters were measured.

Results

The obese group showed significantly higher levels of microRNA-122, fasting blood glucose, triglycerides, total cholesterol, LDL, VLDL, non-HDL cholesterol, cardiac risk ratios, atherogenic coefficient, atherosclerotic index, insulin levels, HOMA2-%B, and HOMA2-IR compared to the control group. In obese children, microRNA-122 exhibited a significant negative correlation with HDL while a significant positive correlation with the cardiac risk ratio 1 and the atherogenic coefficient. MicroRNA-122 had predictive ability for insulin resistance and cardiovascular diseases risk in obese children. However, a significant decrease in HDL levels, HOMA2-%S, McAuley, and SPISE insulin sensitivity indices was found in obese children.

Conclusions

Modifications in blood levels of microRNA-122 in obese children may indicate a possible role in the etiology of childhood obesity and its associated consequences. As a result, it could function as a preliminary biomarker and potential indicator of further metabolic diseases.

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer and the limiting efficacy is achieved for TNBC patients with immunotherapy. The role of malignant cells in the tumor microenvironment (TME) is still complicated. Here, we firstly identified and characterized the malignant cells in the TME of TNBC based on single-cell and bulk RNA sequencing. Then a high score of gene copy number variation (CNV) was found in the malignant cells. And 2507 up-regulated genes and 830 down-regulated genes were obtained based on a difference analysis between the malignant cells and other epithelial cells. Furthermore, KLF3-targeted genes were identified as being associated with the development of breast cancer. Finally, an immunosuppressive role of the malignant cells was identified in the TME of TNBC as the strong interactions between tumor cells and CD8-positive exhausted T cells. Together, these findings provide new insights into the malignant cells of TME and a new idea to develop therapeutic strategy for immunotherapy of TNBC.

In the case of consanguineous families, comorbidity cannot be ruled out. Here, we reported a child of eleven years-old who presented profound congenital hearing impairment and progressive visual defect who was suspected to have Usher syndrome. We searched for mutations in Usher syndrome genes but we failed to detect any. We then performed whole exome sequencing to identify the causality of their phenotype. Interestingly, we found two homozygous missense variants, p.(Arg84Trp) in TMIE, responsible for deafness and p.(His337Arg) in PDE6B, responsible for retinitis pigmentosa. The combination of both variants mimics Usher syndrome. This article highlights the importance of genetics in avoiding clinical misdiagnosis, which is important for genetic counseling and in the perspective of gene therapy.

High-resolution genomic studies can help understanding the predisposition to cancer by identifying constitutional genetic variants of differential penetrance and pathogenicity in a family. We present a case report of whole exome analysis in a case (62/Female) with a history of pancreatic, intestinal, and prostate cancers in the paternal side and her unaffected son from Gujarat, India. Proband showed germline alterations in BRCA2 and NOS3 genes and in NTHL1 gene in her son. BRCA2 c.8954-3C > G has conflicting interpretations being characterized as likely pathogenic and variant of unknown significance (VUS) in 2018 and 2021, while our findings in 2022 classifies it as likely pathogenic. Novel germline genetic variants NOS3 c.1246_1255del (p. Ile417Thrfster9) and NTHL1 c.374dup (p. Val127GlyfsTer43) have been classified as VUS. In-silico analysis of the BRCA2 c.8954-3C > G indicates the location of the genetic variant at the splice site. Proband and her son show co-segregation of 9 constitutional genetic variants; 8 are likely benign and one is benign according to ClinVar. Identification of germline variants and studies on functional evidence will facilitate curated genetic counselling for the family and focussed risk-reduction strategies.

The current study was conducted to assess the relationship between the STAT3 gene variants rs744166 and rs2293152 and autoimmune thyroid disorder in the Pakhtun population of the province, of Khyber Pakhtunkhwa, Pakistan. Blood was collected from 100 healthy individuals and 400 thyroid-disordered patients. Of these, one hundred were diagnosed with Hashimoto's thyroiditis (HT), while 32 were confirmed as Grave's disease (GD) patients. T3, T4, and TSH serum levels were checked to diagnose thyroid disorders. The blood was analyzed for anti-thyroid peroxidase antibodies (Anti-TPOAb) (AESKULISA- ATPO - elisa kit), (Germany), and thyroid stimulating hormone receptor antibodies (TSHRAb), TSHR Ab elisa kit (Diametra Italy), respectively. PCR was used to amplify the targeted STAT3 gene polymorphisms from rs744166 (301 bp) and rs2293152 (365 bp) sequences and then digested by specific restriction endonucleases (AluI) and AciI respectively. The disease displayed a female predominance. The genotype TC and CC of rs744166 showed a significant relationship with Grave's disease (p = 0.002, OR = 0.28, 95 % CI = 0.11–0.77) in patients. The C allele contributed significantly to the disease in GD patients. The SNP rs2293152 significantly differed between GD patients and control (p = 0.032, OR = 0.29, 95 % CI = 0.09–0.86). Similarly, the G and C alleles showed a significant (p = 0.02) difference between GD patients and the control. No significant association was found for both SNPs in Hashimoto's thyroiditis disease. It is concluded that the STAT3 gene (rs744166 and rs2293152) was found to have a potential role in autoimmunity in GD patients. Still, it needs further studies with larger sample sizes in the Pakhtun population to understand this relationship.