Region Of Gene Research Articles

Untargeted Mutation Triggered by Ribonucleoside Embedded in DNA

DNA polymerases frequently misincorporate ribonucleoside 5′-triphosphates into nascent DNA strands. This study examined the effects of an incorporated ribonucleoside on untargeted mutations in human cells. Riboguanosine (rG) was introduced into the downstream region of the supF gene to preferentially detect the untargeted mutations. The plasmid containing rG was transfected into U2OS cells and the replicated DNA was recovered after 48 h. The mutation analysis using the indicator Escherichia coli RF01 strain showed the frequent induction of untargeted base substitutions at the G bases of 5′-GpA-3′ dinucleotides, similar to action-at-a-distance mutations induced by an oxidatively damaged base, 8-oxo-7,8-dihydroguanine, and an apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3 (APOBEC3) cytosine deaminase. APOBEC3B was then knocked down by RNA interference and the plasmid bearing rG was introduced into the knockdown cells. The untargeted mutations at 5′-GpA-3′ sites were reduced by ~80%. These results suggested that ribonucleosides embedded in DNA induce base substitution mutations at G bases in the same strand by an APOBEC3B-dependent mechanism, implying that ribonucleosides contribute to APOBEC3-dependent cancer initiation events.

Effects of Sequential Antimicrobial Phases on Root Canal Microbiome Dynamics in Two-Visit Treatment of Primary Apical Periodontitis: A Longitudinal Experimental Study.

Effective management of primary apical periodontitis depends on understanding the dynamic interactions within the root canal microbiome. This study aimed to investigate the effect of sequential antimicrobial phases on the root canal microbiome during a two-visit treatment approach, with a focus on calcium hydroxide medication. Samples were collected from three teeth across four treatment phases: initial infection (S1), after chemomechanical preparation (S2), after intracanal medication (S3), and after a final flush (S4). DNA was extracted, and the V3-V4 regions of the 16S rRNA gene were sequenced using Illumina MiSeq. Sequencing data were analyzed with QIIME 2, and differentially abundant taxa were identified using linear discriminant analysis effect size (LEfSe). While microbial community composition did not differ significantly between phases, the Firmicutes/Bacteroidetes ratio decreased after the antimicrobial stages. LEfSe analysis revealed higher abundances of Lactobacillales, Arthrobacter, and Veillonella in the untreated (CMP) group. Bifidobacterium longum was relatively more abundant in the intracanal medication (ICM) phase, and Dorea formicigenerans was more abundant in the final-flush (FF) phase. Although calcium hydroxide treatment did not induce statistically significant changes in overall root canal microbial composition, trends such as a reduction in the Firmicutes/Bacteroidetes ratio and a relative increase in Bifidobacterium longum numbers suggest potential ecological shifts. The observed relative increase in Bifidobacterium longum numbers may represent a hypothesis-driven observation reflecting indirect ecological effects rather than direct pH modulation. While visual patterns (e.g., PCA clustering) were observed, they lacked statistical support. Further studies with larger sample sizes are needed to validate these observations and assess the potential role of beneficial bacteria in root canal treatments.

SS18-SSX drives TYK2 expression to activate STAT3/Bcl2 axis, facilitating apoptosis evasion and advancing synovial sarcoma progression

Synovial sarcoma (SS) is a rare soft tissue sarcoma characterized by high-grade malignancy and poor prognosis. Preliminary research indicates that apoptosis evasion is a key factor in SS progression, primarily attributed to the overexpression of anti-apoptotic genes. However, the mechanisms underlying this phenomenon are still not fully understood. This study aims to investigate the factors responsible for apoptosis evasion, evaluate their potential as targets for anti-apoptotic interventions, and analyze their mechanisms in detail. Our findings reveal that tyrosine kinase 2 (TYK2) is upregulated in highly malignant SS. Through in vitro as well as in vivo functional analyses, we have demonstrated that, TYK2 significantly accelerates SS cells progression. Mechanistically, TYK2 activates STAT3, which promotes the expression of BCL2, an anti-apoptotic gene. Inhibition of STAT3 activation using specific inhibitors can disrupt the TYK2-enhanced expression of Bcl2, indicating that the TYK2/STAT3/Bcl2 axis is a key regulatory pathway mediating apoptosis evasion in SS. Furthermore, our investigation into the upstream regulation of TYK2 reveals that the fusion protein SS18-SSX enhances the transcriptional activity of TYK2 by binding to the promoter region of the TYK2 gene, thereby increasing its expression levels. Thus, the TYK2/STAT3/Bcl2 axis is a crucial mechanism through which SS18-SSX mediates apoptosis evasion in SS cells. In conclusion, our findings contribute to understanding how SS18-SSX-driven TYK2 expression mediates apoptosis evasion mechanisms and propose targeting TYK2 as a strategy to induce apoptosis in SS.Graphical

Development and Comprehensive Evaluation of Culture-Independent, Long Amplicon-Based Targeted Next-Generation Sequencing Methods for Predicting Antimicrobial Resistance in Tuberculosis.

The great variety of antimicrobial resistance (AMR) profiles among tuberculosis (TB) patients necessitates a comprehensive detection method. This study developed culture-independent, long amplicon-based targeted next-generation sequencing (tNGS) methods for predicting AMR across 16 drugs within the Mycobacterium tuberculosis complex (MTBC). Multiplex PCR amplification was employed to enrich 20 gene regions, with sequencing performed on either the Oxford Nanopore Technologies (ONT) or Illumina platforms. Customized bioinformatics pipelines provide a streamlined process from raw data to clinician-friendly reports. The ONT tNGS method has been optimized, and its performance has been thoroughly evaluated, utilizing Q20+ chemistry in combination with the R10.4.1 flow cell. It requires only 15 high-quality reads per target gene to accurately identify all variants, with the turnaround time taking 4 h and 50 min. Studies confirmed that this method effectively identifies Mycobacterium species and was highly resistant to interference from other clinical pathogens. To ensure optimal coverage, it is recommended to input at least 500 copies of the genome and sequence 500MB of high-quality FASTQ data. Diagnostic performance evaluations demonstrate that this method achieves 98.35% concordance with phenotypic drug susceptibility testing (pDST) and is consistent with the results obtained from Xpert MTB/RIF assays. The design of long amplicons not only ensures comprehensive coverage of target regions but also simplifies primer design, facilitating compatibility with various sequencing platforms. Compared with previous studies, the optimized ONT tNGS method in this study significantly improves turnaround time, detection accuracy, and the comprehensive coverage of mutations associated with AMR.

Genetic Investigation of Regulatory Regions of MKRN3 and DLK1 Genes in Children with Central Precocious Puberty.

Most of the loss-of-function mutations described in children with central precocious puberty (CPP) is located into the coding regions of MKRN3 or DLK1 genes. Notably, potential abnormalities in the regulatory regions of these CPP-genes are rarely explored. To search for pathogenic variants in the regulatory regions of MKRN3 and DLK1 genes in patients with familial or idiopathic CPP. A cohort of 217 individuals with CPP (205 girls and 12 boys; 143 sporadic cases and 74 familial cases) was investigated. Rare and potentially pathogenic variants in the coding regions of both genes were previously excluded. Analyses of the regulatory regions of MKRN3 and DLK1 were performed using polymerase chain reaction and direct automated sequencing (Sanger method). Circulating serum levels of MKRN3 and DLK1 proteins were measured using ELISA assay. We identified a heterozygous allelic variant (c.-265G>A), previously associated with CPP, located in the promoter region of the MKRN3 gene in three girls from two unrelated families. In silico prediction analysis indicated that the c.-265G>A variant was in the ZNF384 binding region. ZNF384 gene encodes a C2H2-type zinc finger protein, which might act as a transcription factor. MKRN3 serum levels varied from 197.5 pg/mL to 1,907 pg/mL and were relatively lower in patients with CPP who carried the c.-265G>A variant. No pathogenic allelic variant was found in the regulatory region of the DLK1 gene. Pathogenic variants in the regulatory region of MKRN3 gene are rare and can be associated with the CPP phenotype.

Rapid Sex Identification in Spotted Knifejaw (Oplegnathus punctatus) Using tmem88 Gene Structural Variation Markers.

Spotted knifejaw (Oplegnathus punctatus) is an economically important marine cultured species exhibiting a unique complex sex chromosome system (X1X1X2X2 in females and X1X2Y in males), with males possessing one fewer chromosome (2n = 47) than females (2n = 48) and an abnormally large Y chromosome. Additionally, males demonstrate significant growth advantages over females. Rapid and accurate sex identification is essential for effective culture management, selective breeding, and population control. In this study, we identified a homologous region of the tmem88 gene containing large DNA insertion markers on the X and Y chromosomes through whole-genome sequencing of O. punctatus. The X1 chromosome harbors a 278bp DNA fragment, whereas the Y chromosome contains a 1472bp fragment, resulting in a 1194bp size difference indicative of structural variation in the non-coding region of the tmem88 gene. We developed a rapid detection method based on this variation, utilizing a pair of primers that amplify two distinct bands (278bp and 1472bp) in male (X1X2Y) individuals and a single 278bp band in female (X1X1X2X2) individuals when analyzed by agarose gel electrophoresis. This method enables efficient and accurate sex differentiation in O. punctatus, significantly reducing the time required for identification and enhancing detection efficiency. This study provides a valuable tool for the rapid identification of sex in O. punctatus, facilitating improved breeding strategies and supporting the large-scale production of high-quality fry.

Microbial and proteomic signatures of type 2 diabetes in an Arab population

BackgroundThe rising prevalence of Type 2 diabetes mellitus (T2D) in the Qatari population presents a significant public health challenge, highlighting the need for innovative approaches to early detection and management. While most efforts are centered on using blood samples for biomarker discovery, the use of saliva remains underexplored.MethodsUsing noninvasive saliva samples from 2974 Qatari subjects, we analyzed the microbial communities from diabetic, pre-diabetic, and non-diabetic participants based on their HbA1C levels. The salivary microbiota was assessed in all subjects by sequencing the V1–V3 regions of 16S rRNA gene. For the proteomics profiling, we randomly selected 50 gender and age-matched non-diabetic and diabetic subjects and compared their proteome with SOMAscan. Microbiota and proteome profiles were then integrated to reveal candidate biomarkers for T2D.ResultsOur results indicate that the salivary microbiota of pre-diabetic and diabetic individuals differs significantly from that of non-diabetic subjects. Specifically, a significant increase in the abundance of Campylobacter, Dorea, and Bacteroidales was observed in the diabetic subjects compared to their non-diabetic controls. Metabolic pathway prediction analysis for these bacteria revealed a significant overrepresentation of genes associated with fatty acid and lipid biosynthesis, as well as aromatic amino acid metabolism in the diabetic group. Additionally, we observed distinct differences in salivary proteomic profiles between diabetic and non-diabetic subjects. Notably, levels of Haptoglobin, Plexin-C1, and MCL-1 were elevated, while Osteopontin (SPP1), Histone1H3A (HIST3H2A), and Histone H1.2 were reduced in diabetic individuals. Furthermore, integrated correlation analysis of salivary proteome and microbiota data demonstrated a strong positive correlation between HIST1H3A and HIST3H2A with Porphyromonas sp., all of which were decreased in the diabetic group.ConclusionThis is the first study to assess the salivary microbiota in T2D patients from a large cohort of the Qatari population. We found significant differences in the salivary microbiota of pre-diabetic and diabetic individuals compared to non-diabetic controls. Our study is also the first to assess the salivary proteome using SOMAScan in diabetic and non-diabetic subjects. Integration of the microbiota and proteome profiles revealed a unique signature for T2D that can be used as potential T2D biomarkers.

Genetic Diversity of Cultured Rainbow Trout (Oncorhynchus mykiss) Populations in Turkey Based on Mitochondrial DNA Cytochrome b (cyt-b) Sequence Analysis

This study aimed to investigate the genetic diversity and structure of rainbow trout (Oncorhynchus mykiss) cultured populations in different provinces of Turkey, based on the cytochrome b (cyt-b) gene region of mitochondrial DNA (mtDNA). Tissue samples were collected from a total of 98 fish (seven fish per province) across 14 provinces, followed by DNA isolation. The mtDNA cyt-b gene region (754 bp) was amplified using PCR. Genetic diversity indices, genetic structure, and phylogenetic analyses were calculated from the cyt-b gene sequence data. The average nucleotide frequencies of the four nucleotides cytosine (C), thymine (T), adenine (A), and guanine (G) were found to be 26.2%, 24.9%, 26.2%, and 22.8%, respectively, with a higher A + T content (51%) compared to G + C content (49%). A total of 645 polymorphic loci were identified across the 14 populations, and 50 distinct haplotypes were defined. Haplotypic diversity ranged from 0.91 to 0.48, while nucleotide diversity (π) varied between 0.26 and 0.00. The highest genetic diversity was observed in the Tokat and Van populations, whereas the lowest was recorded in the Elazığ and Kahramanmaraş populations. AMOVA analyses revealed that 71.1% of the genetic diversity was found between populations, while 28.9% was found within populations. Pairwise FST values ranged from 0.38 to 0.99, with an average FST of 0.71. Phylogenetic analyses indicated that the populations clustered into two main groups, with further sub-groupings within these clusters. Notably, the Kahramanmaraş and Elazığ populations were found to be significantly differentiated from other populations. In conclusion, despite rainbow trout not being a native species in Turkey, the findings of this study indicate that the genetic diversity of the populations is at a good level. However, in order to preserve the genetic diversity of cultured rainbow trout populations and to increase effective population size, it is recommended that breeders engage in fry exchanges and import new rainbow trout specimens to enhance genetic diversity.

Histone variant H3.5 in testicular cell differentiation and its interactions with histone chaperones

Testicular cell differentiation is a highly regulated process, essential for male reproductive health. The histone variant H3.5 is apparently a critical player in this intricate orchestra of cell types, but its regulation and function remains poorly understood. To elucidate its role, we fractionized testicular cells using c-Kit/CD117 as a separation marker and analyzed H3.5 expression. Further, we investigated the regulation of H3.5 expression using public data repositories. We explored DNA methylation patterns in specific regions of the H3-5 gene and assessed H3-5 copy number gain in seminoma specimens. Additionally, we examined the testicular localization of H3.5 and its histone chaperone interactions to understand its regulation at the protein level. We used qRT-PCR, MeDIP, and qPCR to study H3.5 expression and DNA methylation in various cell types. H3-5 copy number gain was analyzed using qPCR. Protein interactions were investigated through fluorescence-2-hybrid assays in baby hamster kidney cells. H3.5 is primarily enriched in spermatocytes. DNA methylation of a CpG island overlapping the H3-5 promoter appeared to be involved in the tissue-specific regulation of H3.5 expression. Elevated H3.5 expression was observed in seminoma specimens, suggesting a potential link to testicular tumors. H3-5 copy number gain was associated with elevated H3.5 expression in seminoma specimens. Furthermore, we identified physical interactions between H3.5 and histone chaperones Asf1a and Asf1b, HIRA, CAF p150 and DAXX, shedding light on the protein-level regulation of H3.5. These findings provide valuable insights into the molecular mechanisms governing testicular cell differentiation and the potential role of H3.5 in testicular pathologies.

Denatonium inhibits RANKL-induced osteoclast differentiation and rescues the osteoporotic phenotype by blocking p65 signaling pathway

BackgroundBone remodeling is a critical process that maintains skeletal integrity, orchestrated by the balanced activities of osteoclasts, which resorb bone, and osteoblasts, which form bone. Osteoclastogenesis, the formation of osteoclasts, is primarily driven by NFATc1, a process activated through c-Fos and NF-κB signaling pathways in response to receptor activator of nuclear factor κB ligand (RANKL). Dysregulation of RANKL signaling is a key contributor to pathological bone loss, as seen in conditions such as osteoporosis.MethodsWe investigated the effects of denatonium, a known bitter compound, on RANKL-induced osteoclast differentiation. We used RNA sequencing (RNA-seq) to analyze gene expression profiles in osteoclast precursors treated with denatonium. Transcription factor prediction analysis was conducted to identify key targets of denatonium action. Additionally, we performed Western blotting to examine the phosphorylation status of AKT and p65, crucial components of the NF-κB pathway. Chromatin immunoprecipitation (ChIP) assays were employed to assess the binding of p65 to promoter regions of osteoclast-related genes. Finally, we tested the therapeutic potential of denatonium in a mouse model of osteoporosis.ResultsOur findings demonstrated that denatonium significantly inhibited RANKL-induced osteoclastogenesis by targeting the p65 pathway. RNA-seq analysis revealed a downregulation of osteoclast-related genes following denatonium treatment, corroborated by transcription factor prediction analysis, which highlighted p65 as a key target. Denatonium effectively blocked the phosphorylation of AKT and p65, key steps in NF-κB activation. ChIP assays further confirmed that denatonium reduced the enrichment of p65 at promoter regions critical for osteoclast differentiation. In vivo, denatonium treatment in an osteoporosis animal model led to a significant restoration of bone health, demonstrating its potential as a therapeutic agent.ConclusionsThis study identifies denatonium as an inhibitor of RANKL-induced osteoclast differentiation, potentially acting through suppression of the p65 signaling pathway. The ability of denatonium to downregulate osteoclast-related genes and inhibit key signaling events highlights its potential as a candidate for further investigation in the context of bone loss and osteoporosis.

Cyto-, gene, and multireceptor architecture of the early postnatal mouse hippocampal complex.

Neurotransmitter receptors are key molecules in signal transmission in the adult brain, and their precise spatial and temporal balance expressions also play a critical role in normal brain development. However, the specific balance expression of multiple receptors during hippocampal development is not well characterized. In this study, we used quantitative in vivo receptor autoradiography to measure the distributions and densities of 18 neurotransmitter receptor types in the mouse hippocampal complex at postnatal day 7, and compared them with the expressions of their corresponding encoding genes. We provide a novel and comprehensive characterization of the cyto-, gene, and multireceptor architecture of the developing mouse hippocampal and subicular regions during the developmental period, which typically differs from that in the adult brain. High-density receptor expressions with distinct regional and laminar distributions were observed for AMPA, Kainate, mGluR2/3, GABAA, GABAA/BZ, α2, and A1 receptors during this specific period, whereas NMDA, GABAB, α1, M1, M2, M3, nicotinic α4β2, 5-HT1A, 5-HT2, D1 and D2/D3 receptors exhibited relatively low and homogeneous expressions. This specific balance of multiple receptors aligns with regional cytoarchitecture, neurotransmitter distributions, and gene expressions. Moreover, contrasting with previous findings, we detected a high α2 receptor density, with distinct regional and laminar distribution patterns. A non-covariation differentiation phenomenon between α2 receptor distributions and corresponding gene expressions is also demonstrated in this early developmental period. The multimodal data provides new insights into understanding the hippocampal development from the perspective of cell, gene, and multireceptor levels, and contributes important resources for further interdisciplinary analyses.

Genomic analyses revealed low genetic variation in the intron-exon boundary of the doublesex gene within the natural populations of An. gambiae s.l. in Burkina Faso

BackgroundThe recent success of a population control gene drive targeting the doublesex gene in Anopheles gambiae paved the way for developing self-sustaining and self-limiting genetic control strategies targeting the sex determination pathway to reduce and/or distort the reproductive capacity of insect vectors. However, targeting these genes for genetic control requires a better understanding of their genetic variation in natural populations to ensure effective gene drive spread. Using whole genome sequencing (WGS) data from the Ag1000G project (Ag3.0, 3.4 and 3.8), and Illumina pooled amplicon sequencing, we investigated the genetic polymorphism of the intron-4–exon-5 boundary of the doublesex gene in the natural populations of An. gambiae sensu lato (s.l.).ResultsThe analyses showed a very low variant density at the gRNA target sequence of the Ag(QFS)1 gene drive (previously called dsxFCRISPRh) within the populations of West and East Africa. However, populations from the forest area in Central Africa exhibited four SNP at frequencies ranging from 0.011 to 0.26. The SNP (2R:48714641[C > T]) at high frequencies, i.e. 0.26 is identified within the An. coluzzii population from Angola. The analyses also identified 90 low frequency (1 − 5%) SNPs in the genomic region around the gRNA target sequence (intron-4–exon-5 boundary). Three of these SNPs (2R:48714472 A > T; 2R:48714486 C > A; 2R:48714516 C > T) were observed at frequencies higher than 5% in the UTR region of the doublesex gene. The results also showed a very low variant density and constant nucleotide diversity over a five-year survey in natural An. gambiae s.l. populations of Burkina Faso.ConclusionThese findings will guide the implementation of doublesex-targeted gene drives to support the current control tools in malaria elimination efforts. Our methods can be applied to efficiently monitor the evolution of any sequence of interest in a natural population via pooled amplicon sequencing, surpassing the need for WGS.

Persistent elite controllers as the key model to identify permanent HIV remission.

To summarize the heterogeneity in the elite controllers population with the aim to identify a compatible profile with a persistent HIV remission, making distinction between persistent elite controllers, people with HIV (PWHIV) who permanently maintain virological control in the absence of antiretroviral treatment (ART), and transient elite controllers, PWHIV who eventually lose virological control. For this purpose, it is important to consider the mechanisms and biomarkers that have previously been associated with the maintenance and loss of the natural virological control. Transient elite controllers, before losing virological control, exhibit a distinct metabolomic, proteomic, microRNAs (miRNA), immunological and virological profile compared to persistent elite controllers. In addition to a reduced and less polyfunctional HIV-specific T-cell response, transient elite controllers show a greater proportion of intact proviruses integrated into genic regions. In contrast, persistent elite controllers display a privileged HIV-1 reservoir profile with absence of detected intact proviruses or low proportion of clonal intact proviruses preferentially integrated into genomic features associated with HIV-1 transcriptional repression. According to previous studies, the comprehensive characterization of persistent elite controllers might be crucial to identify other PWHIV with this distinct profile as spontaneously cured.

Single-cell analysis of a bi-clonal chronic lymphocytic leukemia reveals two clones with distinct gene expression pattern

Dual productive B-cell receptor (BCR) rearrangements have been repeatedly reported for chronic lymphocytic leukemia (CLL), but the standard population-based PCR analyses cannot distinguish whether these are bi-clonal CLL, or a monoclonal CLL with bi-allelic productive rearrangements. We investigated CLL cells by combined single-cell RNA and BCR sequencing. We identified two CLL clones using different immunoglobulin (Ig) heavy-chain V region genes (IGHV) genes and distinct Ig λ light chains. One clone is classified as Ig unmutated the other as mutated. The two CLL clones have distinct transcriptomes: Numerous genes were differentially expressed, with genes typical for unmutated or mutated CLL showing the expected representation in the two clones. Using PCR, cloning and Sanger sequencing of the IGHV rearrangements we detected both CLL clones over a period of three years without clinical progression of the CLL and thus giving insights into the disease biology of multi-clonal CLL.

Single-cell RNA-sequencing of BK polyomavirus replication in primary human renal proximal tubular epithelial cells identifies specific transcriptome signatures and a novel mitochondrial stress pattern.

BK polyomavirus (BKPyV) contributes to premature renal failure in 10%-20% of kidney transplant recipients. Current treatment relies on reducing immunosuppression to regain BKPyV-specific immune control. Subsequently, declining allograft function may result from persisting viral cytopathology, BKPyV-specific immune reconstitution, or alloimmunity/rejection, all being poorly distinguishable by current histological or molecular approaches. To reduce the complexity encountered in BKPyV-replicating kidneys, we analyzed differentially expressed genes (DEGs) in primary human renal proximal tubular epithelial cells at 24 and 48 h post-infection (hpi) using single-cell RNA-sequencing (10x-Genomics-3´ kit). At 24 hpi, viral transcript reads predominantly mapped to the early viral gene region (EVGR) and shifted to >100-fold higher late viral gene region (LVGR) levels at 48 hpi, matching the sequential bi-directional viral protein expression from the circular double-stranded BKPyV-DNA genome. Besides expected coverage "hills" at viral 3´-poly-A sites, unexpected "spike" and "pulse" reads resulted from off-target TSO priming. "Spike" and "pulse" patterns were rare for the mostly unidirectional reads mapping to the circular mitochondrial genome. Bioinformatic curation removed "spikes" and "pulses" and reclassified 10% of DEGs in renal proximal tubular epithelial cells (RPTECs). Up-regulated gene ontologies included S and G2/M phase, double-stranded DNA repair, proximal tubulopathy, and renal tubular dysfunction, whereas allograft rejection, antigen presentation, innate immunity, translation, and autophagy were down-regulated. BKPyV-LVGR expression induced a novel mitochondrial cell stress pattern consisting of discordant up-regulation and down-regulation of mitochondria-encoded and nucleus-encoded mitochondrial genes, respectively. We explored which top-scoring gene sets of late-phase BKPyV-replicating RPTECs can identify BKPyV-associated nephropathy in kidney transplant biopsies. The results should facilitate distinguishing BKPyV-associated pathology from other entities in kidney transplant biopsies.IMPORTANCEBK polyomavirus (BKPyV) infects more than 90% of the general population and then persists in the reno-urinary tract. Subsequently, low-level urinary shedding is seen in 10% of healthy BKPyV-seropositive persons, indicating that BKPyV replication occurs despite the presence of virus-specific cellular and humoral immunity. Notably, transplantation of donor kidneys with low-level BKPyV replication is a risk factor for progression to high-level BKPyV viruria, new-onset BKPyV-DNAemia and biopsy-proven BKPyV nephropathy. Here, we identify a short list of robust up- and down-regulated nucleus-encoded differentially expressed genes potentially allowing to discriminate viral from allograft immune damage. By carefully curating viral and mitochondrial transcriptomes, we identify a novel virus-associated mitochondrial stress pattern of up-regulated mitochondria-encoded and down-regulated nucleus-encoded mitochondrial transcripts which heralds the BKPyV-agnoprotein-mediated immune escape by breakdown of the mitochondrial membrane potential and network and mitophagy. The results may prove useful when assessing the role of BKPyV replication in kidney transplant patients with suspected acute rejection and/or BKPyV nephropathy.

Short-Term Changes in Fecal Bacteriobiome of Healthy Laboratory Mice After Antiviral Preparation Administration

Backgound/Objective: Novel compounds for mitigating globally growing microbial resistance to antibiotics have been recently more actively researched. Triviron is a polycationic amphiphile synthetic compound with a ribonuclease activity and is used as an antiviral in veterinary medicine. Methods: We studied the effect of triviron on the mouse (line Balb/c) fecal bacteriobiome at different time points (0, 5, 25, and 120 h after a single intragastrical administration) by using amplicon sequence diversity of the V3/V4 region of 16S rRNA genes. Results: Most of the operational taxonomic units (OTUs) belonged to Bacillota (1168 OTUs, i.e., 56% of the total number of OTUs in the study) and Bacteroidota (354, i.e., 17%), with the phyla together accounting for more than 90% of the total number of sequence reads. We found changed relative abundance of some bacterial taxa with time, including the dominating Bacteroidota and Bacillota phyla; some of the changes were sex-related, although at the start of the experiment, there were no difference between the sexes in their fecal bacteriobiome composition and structure. Conclusions: The results unequivocally demonstrated that in mice, feces bacterial community structure was affected by a one-time triviron administration, even at the highest hierarchical level of phyla. The finding that the core dominant phyla can be affected, with the effect lasting at least for five days, implies that some major and important functions of the gut microbiota can be affected as well.

DNMT3a Downregulation Ttriggered Upregulation of GABAA Receptor in the mPFC Promotes Paclitaxel-Induced Pain and Anxiety in Male Mice.

Chemotherapeutic agents, such as paclitaxel (PTX), induce neuroplastic changes and alter gene expression in the prefrontal cortex (PFC), which may be associated with chemotherapy-induced pain and negative emotions. Notably, DNA methylation undergoes adaptive changes in neurological disorders, emerging as a promising target for neuromodulation. In this study, systemic administration of PTX leads to a decrease in the expression of the DNA methyltransferase DNMT3a, while concurrently upregulating the expression of Gabrb1 mRNA and its encoded GABAARβ1 protein in the medial PFC (mPFC) of male mice. Overexpression of DNMT3a in the mPFC alleviates PTX-induced pain hypersensitivity, and anxiety-like behavior in these mice. Additionally, it reverses the PTX-induced increase in inhibitory synaptic transmission in the pyramidal neurons of the mPFC. Mechanistically, the upregulation of GABAARβ1 in the mPFC is linked to the reduced expression of DNMT3a and DNA hypomethylation at the promoter region of the Gabrb1 gene. Furthermore, a long-term diet rich in methyl donors alleviates PTX-induced pain hypersensitivity and anxiety-like behavior in mice. These findings suggest that the DNMT3a-mediated upregulation of GABAARβ1 in the mPFC contributes to PTX-induced neuropathic pain and anxiety, highlighting DNA methylation-dependent epigenetic regulation as a potential therapeutic target for addressing chemotherapy-induced cortical dysfunction.

Integrative functional screen of genomic loci uncovers CCND2 and its genetic regulatory mechanism in colorectal cancer development.

Although genome-wide association studies (GWASs) have identified dozens of loci associated with colorectal cancer (CRC) susceptibility, the causal genes or risk variants within these loci and their biological functions often remain elusive. Recently, the genomic locus 12p13.32, with the tag SNP rs10774214, was identified as a crucial CRC risk locus in Asian populations. However, the functional mechanism of this region has not been fully elucidated. Here, we applied a high-throughput RNA interference (RNAi) approach in CRC cell lines to interrogate the function of genes in this genomic region. Multiple genes were found to affect cell functions, with CCND2 having the most significant effect as an oncogene. Moreover, overexpressed CCND2 could promote CRC cell proliferation. Subsequently, by integrating a fine-mapping analysis and multi-ancestry large-scale population cohorts consisting of 14,358 CRC cases and 34,251 healthy controls, we identified a regulatory variant rs4477507-T that contributed to an increased CRC risk in populations from China (OR = 1.16, 95%CI = 1.11-1.22, P = 4.45×10-10) and Europe (OR = 1.17, 95%CI = 1.12-1.21, P = 1.65×10-14). Functional characterization of the variant demonstrated that it could act as an allele-specific enhancer to distally facilitate the expression of CCND2 mediated by the transcription factor TEAD4. Overall, our study underscores the essential role of CCND2 in CRC development and delineates its regulatory mechanism mediated by rs4477507, establishing an epidemiological and biological link between genetic variation and CRC pathogenesis.

Substantial Heritability Underlies Fairness Norm Adaptation Capability and its Neural Basis.

The present research uncovers the shared genetic underpinnings of fairness norm adaptation capability, its neural correlates, and long-term mental health outcomes. One hundred and eighty-six twins are recruited and played as responders in the Ultimatum Game (UG) while undergoing fMRI scanning in their early adulthood (Study-1) and are measured on depressive symptoms eight years later (Study-2). With computational modeling, the process of norm adaptation is differentiated from that of fairness valuation in UG. The two processes both have moderate levels of heritability. The anterior insula has a significant phenotypic correlation, whereas the Supplementary Motor Area/Medial Frontal Gyrus (SMA/mSFG) shows both a significant phenotypic correlation and a shared genetic influence with the learning rate, an index for norm adaptation. The dopaminergic DRD2 polymorphisms correlate with both the learning rate and the SMA/mSFG encoding of prediction error, constituting of their common genetic basis. Regional gene expression analysis reveals the high expression of dopamine-related genes in the SMA/mSFG. Moreover, the learning rate can predict depressive symptom severity eight years later, with the DRD2 polymorphisms constituting their shared genetic basis. This suggests that heritability is a non-negligible driving force behind norm adaptation, which facilitates the learning of social norms in changing environments and preserves long-term mental health.

Dysanapsis Genetic Risk Predicts Lung Function Across the Lifespan.

Rationale: Dysanapsis refers to a mismatch between airway tree caliber and lung size arising early in life. Dysanapsis assessed by computed tomography (CT) is evident by early adulthood and associated with chronic obstructive pulmonary disease (COPD) risk later in life. Objectives: By examining the genetic factors associated with CT-assessed dysanapsis, we aimed to elucidate its molecular underpinnings and physiological significance across the lifespan. Methods: We performed a genome-wide association study of CT-assessed dysanapsis in 11,951 adults, including individuals from two population-based and two COPD-enriched studies. We applied colocalization analysis to integrate genome-wide association study and gene expression data from whole blood and lung. Genetic variants associated with dysanapsis were combined into a genetic risk score that was applied to examine association with lung function in children from a population-based birth cohort (n = 1,278) and adults from the UKBiobank (n = 369,157). Measurements and Main Results: CT-assessed dysanapsis was associated with genetic variants from 21 independent signals in 19 gene regions, implicating HHIP (hedgehog interacting protein), DSP, and NPNT as potential molecular targets based on colocalization of their expression. A higher dysanapsis genetic risk score was associated with obstructive spirometry among 5-year-old children and among adults in the fifth, sixth, and seventh decades of life. Conclusions: CT-assessed dysanapsis is associated with variation in genes previously implicated in lung development, and dysanapsis genetic risk is associated with obstructive lung function from early life through older adulthood. Dysanapsis may represent an endophenotype link between the genetic variations associated with lung function and COPD.