In this study, we propose reclassification of 5 out of 16 PROC VUS (variants of uncertain significance): C238S, I243T, G403R, P405S, and S421N, as pathogenic variants, associated with thrombophilia due to PROC deficiency. The obtained results are based on in silico analysis, which enables a detailed assessment of variants' impact, despite limited clinical evidence. In particular, the G403R substitution, next to the S402-active site, is expected to reduce the flexibility of the local coil domain, affecting the catalytic activity of serine protease. The P405S substitution may imply B-factor gain (P = 0.24; p-value=0.040). On the other hand, the S421N variant causes phosphorylation site disruption at S421, which serves as a target for CK2 phosphorylation. C238S substitution alters metal binding, while the I243T variant may alter transmembrane properties (P = 0.27, P-value=0.00071). All five PROC variants hold promise as diagnostic markers for protein C deficiency and may also serve as potential drug targets for therapeutic intervention.

Hygromycin B (HygB), a broad-spectrum antibiotic, is widely used in molecular biology, agriculture, and veterinary medicine. It inhibits protein synthesis by binding to ribosomes, and its plasmid-borne resistance gene serves as a selectable marker for applications in gene manipulation technologies. The binding site of the P1 phage-borne toxin Doc, which induces bacterial apoptosis, overlaps with the binding site of HygB in helix h44 of 16S rRNA. Hence isolation and characterization of chromosomal HygB resistance would largely serve as gateway to understand the less studied but imperative and emerging modes of drug resistance like bacterial multicellularity and heteroresistance. In this study we have investigated the chromosomal origin of HygB resistance in E. coli through a combination of classical genetics and whole-genome sequencing. Eight HygB-resistant mutants were analyzed, and co-transduction experiments revealed a narrow region (71.8-75.8 min) to have conferred resistance. Whole-genome sequencing confirmed a single base pair change in the fusA gene (A1754 to G1754) as the cause. This is a maiden report on a missense mutation of fusA leading to HygB resistance and these findings provide valuable insights into the mechanisms of HygB resistance.

Dysregulation of m6A modification has significant implications in human carcinogenesis. METTL3, a crucial m6A writer, acts as an oncogenic driver in non-small cell lung cancer (NSCLC). Here, we explored its mechanisms in driving NSCLC development.

Ubiquitin-specific protease 7 (USP7) is one of deubiquitinases and has been reported to regulate cancer cell biological processes through removing ubiquitin modifications from protein substrates. Myosins of class VI (MYO6) is shown to be highly expressed in many of cancers, and is associated with tumor progression in several cancers by affecting cell survival. Moreover, USP7 and MYO6 have been revealed to be involved in colorectal cancer (CRC) progression. Here, we aimed to investigate the intricate interplay between MYO6 and USP7 in CRC, and whether their interaction was associated with deubiquitination.

Recent research has discovered a connection between the AAA+ ATPase PSMC4 (Proteasome 26S Subunit, ATPase 4) and several forms of cancer. However, a detailed analysis of the oncogenic potential of PSMC4 was elusive. In this study, we anticipate PSMC4's potential as a cancer biomarker. We aimed to comprehensively assess the expression profiles, prognostic significance, and relevant cellular pathways associated with it. Through our examination of various types of cancers, PSMC4 is found to be overexpressed. Interestingly, our result finds a positive correlation between PSMC4 overexpression and unfavourable overall survival rates in cancer. Further, we looked into the mutations and copy number amplifications of PSMC4 across various cancers. Our study reveals that missense mutations plays a great role behind the oncogenic potential of PSMC4. Several possible mutation sites are predicted. Interestingly, we found fifteen hotspot mutations in the ATPase domain of PSMC4. Additionally, PSMC4 has shown a high amplification percentage in various cancers. We are additionally attentive to the functional characteristics of the protein PSMC4 across various types of cancer. In the protein-protein interaction analyses, it was found that multiple oncoproteins were directly interacting with PSMC4. The top signaling pathways of PSMC4 also indicate that it plays a crucial role in cancer development. Overall, this study reveals that PSMC4 could be a potential diagnostic and prognostic marker for cancer, making it a promising biomarker and target.

Hepatitis B is a widespread viral infection and a major global public health concern. The human sodium taurocholate co-transporter polypeptide (NTCP) serves as a key receptor for the hepatitis B virus (HBV), enabling its entry into hepatocytes. Understanding how specific NTCP mutations influence its stability and interaction with HBV is critical for elucidating mechanisms of viral infectivity and resistance. This study evaluates the impact of seven non-synonymous NTCP mutations on receptor stability and HBV binding using a comprehensive bioinformatics approach. Mutant NTCP/HBsAg complexes were generated via HADDOCK, and binding affinities were predicted using PRODIGY. Molecular dynamics simulations with GROMACS further assessed the stability and behavior of NTCP/PreS1 complexes. Our findings reveal that V160M and S267F significantly reduce complex stability and binding affinity, suggesting a potential role in natural resistance to HBV infection. Mutations I88T and R84W moderately affect NTCP-HBV interactions, while V200M, I223T, and I279T show minimal impact, maintaining wild-type reference complex characteristics. This study highlights the differential effects of NTCP mutations on HBV infectivity, providing insights into host susceptibility and resistance. The integrative computational strategy offers a robust framework for understanding HBV-host interactions and may aid in identifying novel therapeutic targets.

miRNAs are small RNA molecules that regulate gene expression and play important roles in various biological processes in cells. The discovery of miRNAs is also of great importance in cancer research. miRNAs enable the development of new approaches in cancer treatment by regulating gene expression in cancer cells and have an important place in cancer development, treatment, and diagnosis. Multidrug resistance (MDR) in cancer is associated with the overexpression of ATP-binding cassette (ABC) transporter proteins in cancer cells. MDR contributes to the dysregulation of ABC transporter proteins, and miRNAs mediate MDR in various cancers, resulting in drug resistance. In this study, it was aimed to identify new miRNA sequences in genes associated with multidrug resistance in cancer using in silico method. After obtaining the mature human miRNA sequences in the miRBASE database, BLAST analyses were performed with these sequences for five multidrug resistance genes (ABCB1, ABCC3, ABCC10, ABCC11, ABCG2) known to be associated with cancer. The RNAhybrid tool was used to find the minimum free energy hybridization of gene and miRNA. The target genes of pre-miRNAs and the metabolic pathways in which the target genes play a role were identified with GeneMANIA, SRplot, miRTargetLink programs. Phylogenetic trees of miRNAs belonging to genes were created using the MEGA X software. Secondary structures of pre-miRNA sequences were determined using the RNAfold Web Server program. According to the data obtained from the study, 107 miRNAs associated with multidrug resistance were identified in human cancers. Transmembrane transporter, drug transport and response to drug functions, and metabolic activities of miRNA-related pathways of MDR genes in various cancer types were determined. Multidrug resistance (MDR) in cancer is often associated with overexpression of ABC transporter proteins, which can lead to failure of cancer treatments. Additionally, the relationship of miRNAs with ABC transporter proteins constitutes an important research area to understand the mechanisms of drug resistance and develop new treatment strategies.

Angiogenesis assumes an essential role in tumor development and is a fundamental condition for tumor growth. Yin Yang 1 (YY1) is highly expressed in various types of cancers and is a key player in tumor angiogenesis, but its role in ovarian cancer (OC) has not been fully elucidated. Therefore, this study will delve into the mechanism of YY1 in OC angiogenesis.

Somatic mutations in the telomerase reverse transcriptase promoter (TERTp) region are common in many cancers, including in liver cancers. Detection of TERTp mutations in tumor tissue DNAs and cell-free tumor DNAs is useful for diagnosing and monitoring cancers. Since the most common TERTp hotspot mutations, C228T and C250T, are difficult to identify using Sanger sequencing, we tested an easy and highly sensitive alternative method that targets these two sites using droplet digital PCR. Using this method, both the sensitivity and specificity for detecting these two mutations were 100 % in DNA samples derived from cell lines and liver cancer tissues, including hepatocellular carcinoma (HCC) and hepatoblastoma (HB). The detection limit for the allele frequencies of these mutations was approximately 0.1 %. This method is also widely applicable; for instance, it can be applied to DNA derived from FFPE (formalin-fixed paraffin embedded) samples. In addition, we applied this method to detecting TERTp mutations in cell-free DNA samples of patients with TERTp-mutated tumors. Finally, we found that outcomes for HB patients with TERTp mutations were significantly worse than in those without mutations, indicating the importance of this method for improving patient outcomes. In light of this, we discuss the advantages of this method for clinical implementation in the detection and monitoring of cancers.

Non-small cell lung cancer (NSCLC) is a lethal disease with high morbidity and mortality rates. HIF-1α is confirmed to be involved in NSCLC. However, the detailed mechanism of its role remains unclear. NCI-H226 and SK-MES-1 cell lines were used to explore the mechanisms by which hypoxia affects the progression of NSCLC in vitro. The cellular functions were detected by transwell. The expressions of key biomarkers were examined by Real-time quantitative reverse transcription PCR (qRT-PCR) and Western Blot assays. The RNA sequencing analysis was used to explore the downstream targets of HIF-1α. Luciferase and Chromatin immunoprecipitation (ChIP) assays confirmed the interaction between HIF-1α and GAB2. What's more, the xenograft model was used to investigate the effect of GAB2 in vivo. Hypoxia promoted the migration and invasion capabilities of NCI-H226 and SK-MES-1 cells. RNA sequencing analysis revealed that the expression of GAB2 is dramatically altered under a hypoxic environment. The bioinformatics analysis implied that the differentially expressed genes (DEGs) were enriched in the MEK/ERK signaling pathway and the significantly expressed GAB2 was associated with HIF-1α. Functionally, GAB2 regulated migration and invasion capabilities in vitro and facilitated tumor growth and lung metastasis of NSCLC in vivo. What's more, luciferase and ChIP assays further demonstrated that HIF-1α could bind to GAB2. Hypoxia-induced HIF-1α enhanced tumor growth and lung metastasis in NSCLC by targeting GAB2, which might provide novel insights into GAB2 as a potential therapeutic target for NSCLC.

Mutations are responsible for the genetic origin of various diseases. Existing techniques for mutation identification often fails to detect the full spectrum of mutations in complex genomes hindering progress in diagnosis, treatment and prevention of diseases. Here we propose an algorithm to identify the location and type of mutation occurring in a mutated string with respect to a reference mRNA sequence. In addition to identifying insertion and deletion, by constructing suitable rational combinations of the prime numbers, our algorithm is able to classify point mutations in a novel way by distinguishing missense mutation from silent mutation. Amino acid transformation at each missense mutation site is identified. Moreover, the method allows to locate regions in the sequence undergoing frameshift. It turns out to be efficient when applied on sample dataset. Application of this framework to two haplotypes of the Plasmodium falciparum datasets exhibits different mutation profile to develop similar chloroquine resistance. Despite the overwhelming similarity between the β-globin genes of pygmy and common chimpanzees, our algorithm is able to pinpoint the minute details of the mutations occurring in them differentiating the two species. Additionally, in Alzheimer datasets, the method meticulously identifies true variations in related genes.

Effective mutant screening is critical for improving industrial microorganisms. This study was conducted to evaluate the effect of repeated mutagenesis with gamma rays on the experimental evolution of rhizobial high-temperature tolerance. Wild-type Bradyrhizobium diazoefficiens USDA110 cells grow optimally at 32-34 °C, but their growth is markedly retarded at 36 °C. Wild-type cells were subcultured in a 96-well deep-well plate for 76 or 83 days, with a gradual increase in temperature from 34.0 to 37.0 °C. Additionally, they were exposed to gamma radiation (1-120 Gy, 10 times in total) during the experimental period. The 40-Gy and 80-Gy treatments generated the most lines with high-temperature-tolerance. However, after extended subculturing without mutagenesis, tolerant lines obtained following the 80-Gy treatment produced smaller colonies than tolerant lines obtained after the 40-Gy treatment, suggesting the accumulation of deleterious mutations. These results imply that approximately 40 Gy is the appropriate dose for accumulating beneficial mutations under our experimental conditions. The two most tolerant lines obtained via the 30-Gy treatment commonly had a mutation in the 16S ribosomal RNA gene and the DNA-directed RNA polymerase subunit beta' gene (rpoC), possibly reflecting a strong relationship with high-temperature tolerance. The optimal mutagenesis conditions for accumulating beneficial mutations were discussed based on the number of induced mutations in the population.

Colorectal cancer (CRC) is the third most common cancer worldwide and causes more than 50,000 deaths in the United States each year. Due to the limited therapeutic options and poor prognosis in CRC, extensive research and development of novel therapeutic methods is essential. In this regard, the presence of cancer stem cells with unlimited division ability is the main reason for the therapeutic resistance in CRC. Tigecycline is a pharmacological mitochondria inhibitor and blocks mitochondria-related cell proliferation in cancer cells. This study investigated the effects of Tigecycline combined with radiotherapy on CRC cell apoptosis.

Cervical cancer (CC) is a major cause of morbidity and mortality in women, with complex etiology and progression. Diacylglycerol kinases (DGKs) are pivotal in lipid metabolism. Although diacylglycerol kinase beta (DGKβ) is well-studied in neurology, its role in cancer, especially CC, remains underexplored. This study aimed to explore DGKβ's role and mechanism in CC.

Cervical cancer (CC) is a common malignant tumor in women. M2 macrophages are associated with tumor growth, metastasis, and immunosuppression. Apolipoprotein C1 (APOC1) has been confirmed as an oncogene in CC. However, the role and mechanism of APOC1 in CC progression and M2 macrophages remain to be elucidated.

Prostate cancer (PCa) incidence increases as age advances and seriously endangers men's health worldwide. Arginase 2 (ARG2) has been identified as a potential diagnostic and prognostic marker for PCa. However, the molecular mechanisms underlying its function in PCa remain undefined.

Hepatocellular carcinoma (HCC) is the most common malignant tumor worldwide with a high mortality rate. Herein, this study aims to explore the molecular mechanisms of E2F transcription factor 1 (E2F1), ubiquitin specific peptidase 19 (USP19) and c-Myc in regulating HCC progression.

Many m6A methyltransferases have been identified to regulate colorectal cancer (CRC) progression. METTL14 has been confirmed to play a negative role in CRC process, but the molecular mechanism of METTL14 in regulating CRC progression needs to be further elucidated.

To investigate the mechanisms by which allyl isothiocyanate (AITC) exerts its anticancer effects, the present study investigated the cytotoxic effects of AITC and its metabolites on hepatocellular carcinoma HepG2 cells.

Forkhead box A2 (FOXA2) is found to be abnormally overexpressed in bladder cancer (BCa), but its role and underlying molecular mechanisms in BCa progression remain revealed.