Biology subjects

Kumar, D.

Publications and source records attributed to Kumar, D..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

HIF1α and HIF2α mRNA Expression in Oral Squamous Cell Carcinoma does not correlate with protein expression

BackgroundOral cancer is one of the common cancers among men, its presentation is usually late. Tumor growth leads to hypoxia, and HIF1 and HIF2 are important regulators of hypoxia induced pathways, inducing angiogenesis and tumor growth. This study compares the expression levels of HIF1 and HIF2 mRNA in OSCC tissues to adjacent normal mucosa. MethodsRNA was isolated from 85 OSCC tissues and adjacent normal mucosa followed by real-time (RT) PCR to quantify HIF1 and HIF2 expression using GAPDH and {beta}-actin respectively as reference genes. ResultsHIF1 overexpression was detected in 76.47% of case and 71.76% of controls (p=0.4906), whereas HIF2 overexpression occurred in 91.76% of cases 94.11% of controls (p=0.35). HIF1 and HIF2 expression level were not significantly different in OSCC tissues compared to adjacent normal mucosa. ConclusionHIF1 and HIF2 play important role in hypoxia induced pathways and tumor progression, yet this study found no significant variation in expression between OSCC tissues and surrounding normal tissues. This suggest that their expression may be due to physiological adaptability to hypoxia or stress, or may be due to use of adjacent tissue as control and loss of protein expression could be due to post translational modifications.

cancer biology↗

bioRxiv2025

GenDiS3 database: census on prevalence of protein domain superfamilies of known structure in the entire sequence database

Despite the vast amount of sequence data available, a significant disparity exists between the number of protein sequences identified and the relatively few structures that have been resolved. This disparity highlights the challenge in structural biology to bridge the gap between sequence information and three-dimensional structural data, and the necessity for robust databases capable of linking distant homologues to known structures. Studies have indicated that there is a limited number of structural folds, despite the vast diversity of proteins. Hence, computational tools can enhance our ability to classify protein sequences, much before their structures are determined or their functions characterised, thereby bridging the gap between sequence and structural data. GenDiS is a repository with information on Genomic Distribution of protein domain superfamilies, involving a one-time computational exercise to search for trusted homologues of protein domains of known structures against the vast sequence database. We have updated this database employing advanced bioinformatics tools, including DELTA-BLAST for initial detection of hits and HMMSCAN for validation, significantly improving the accuracy of domain identification. Using these tools, over 151 million sequence homologues for 2060 superfamilies (SCOPe) were identified and 116 million out of them were validated as true positives. Through a case study on glycolysis-related enzymes, variations in domain architectures of these enzymes are explored, revealing evolutionary changes and functional diversity amongst these essential proteins. We present another case, LoG gene, where there one can tune-in and find significant mutations across the evolutionary lineage. The GenDiS database, GenDiS3, and the associated tools made available at https://caps.ncbs.res.in/gendis3/, offer a powerful resource for researchers in functional annotation and evolutionary studies. Database URL: https://caps.ncbs.res.in/gendis3/

bioinformatics↗

bioRxiv2025

THE CORRELATION BETWEEN REDOX ACTIVITY AND ANTIMICROBIAL PROPERTIES OF PYOCYANIN FROM Pseudomonas aeruginosa

Pseudomonas aeruginosa, a metabolically versatile gram-negative bacterium, has garnered attention for its ability to thrive in diverse environments and its capacity to produce pyocyanin, a secondary metabolite with multifunctional properties. Pyocyanin, a redox-active phenazine compound, plays a critical role in mediating the ecological competitiveness of P. aeruginosa through its antimicrobial, biofilm-modulating, and reactive oxygen species (ROS)-generating activities. Beyond its contributions to bacterial virulence, pyocyanin demonstrates significant potential in various industrial and biomedical applications due to its redox properties and ability to function under diverse environmental conditions. This study investigates the electrochemical behaviour and pH-dependent antimicrobial activity of pyocyanin to evaluate its applicability in environmental and medical fields. Soil-derived P. aeruginosa isolates were cultured for pyocyanin (PYO) production, and the pigment was characterized using UV-visible spectroscopy to get its spectral integrity. Electrochemical analysis through cyclic voltammetry revealed enhanced redox activity in acidic environments and stable functionality in alkaline conditions. Antimicrobial assays demonstrated that pyocyanin exhibited optimal activity at neutral to slightly alkaline pH, effectively inhibiting bacterial and fungal growth, while extreme acidic conditions reduced its efficacy. The findings highlight pyocyanins versatility as both a redox mediator and an antimicrobial agent. In medical contexts, its pH-sensitive activity aligns well with physiological conditions, offering promise for combating multidrug-resistant pathogens. Future optimization of pyocyanin biosynthesis, particularly through cost-effective and scalable methods, could unlock its full potential in biotechnological and therapeutic innovations.

microbiology↗

bioRxiv2024

EEG data quality in large scale field studies in India and Tanzania

There is a growing imperative to understand the neurophysiological impact of our rapidly changing and diverse technological, social, chemical, and physical environments. To untangle the multidimensional and interacting effects requires data at scale across diverse populations, taking measurement out of a controlled lab environment and into the field. Electroencephalography (EEG), which has correlates with various environmental factors as well as cognitive and mental health outcomes, has the advantage of both portability and cost-effectiveness for this purpose. However, with numerous field researchers spread across diverse locations, data quality issues and researcher idle time due to insufficient participants can quickly become unmanageable and expensive problems. In programs we have established in India and Tanzania, we demonstrate that with appropriate training, structured teams, and daily automated analysis and feedback on data quality, non-specialists can reliably collect EEG data alongside various survey and assessments with consistently high throughput and quality. Over a 30-week period, research teams were able to maintain an average of 25.6 subjects per week, collecting data from a diverse sample of 7,933 participants ranging from Hadzabe hunter-gatherers to office workers. Furthermore, data quality, computed on the first 2,400 records using two common methods, PREP and FASTER, was comparable to benchmark datasets from controlled lab conditions. Altogether this resulted in a cost per subject of under $50, a fraction of the cost typical of such data collection, opening up the possibility for large-scale programs particularly in low- and middle-income countries. Significance StatementWith wide human diversity, a rapidly changing environment and growing rates of neurological and mental health disorders, there is an imperative for large scale neuroimaging studies across diverse populations that can deliver high quality data and be affordably sustained. Here we demonstrate, across two large-scale field data acquisition programs operating in India and Tanzania, that with appropriate systems it is possible to generate high throughput EEG data of quality comparable to controlled lab settings. With effective costs of under $50 per subject, this opens new possibilities for low- and middle-income countries to implement large-scale programs, and to do so at scales that previously could not be considered.

neuroscience↗

bioRxiv2024

HelD is a Global Transcription Factor Enhancing Gene Expression in Rapidly Growing Mycobacteria

HelD protein, also named HelR (encoded by MSMEG_2174 in Mycobacterium smegmatis), interacts with mycobacterial RNA polymerase (RNAP) and affects rifampicin resistance in Mycobacterium abscessus. Here, we provide data on rifampicin resistance and helD presence in the genomes of other clinically relevant nontuberculous mycobacteria. We show that helD is primarily found in rapidly growing mycobacteria, such as M. smegmatis, where we detected HelD at a subset of promoters that can also associate with CarD and RbpA. Transcriptome analysis of a helD deletion strain using RNA-seq revealed that HelD enhances gene expression during exponential growth and decreases it in stationary phase, during which we observed reduced levels of CarD, RbpA, and GTP, the initiation nucleotide for the majority of M. smegmatis transcripts. We propose a model in which HelD releases abortive RNAP complexes and confirm that HelD dissociates RNAP from the promoter in vitro. HelD not only helps mycobacteria overcome rifampicin treatment but also supports efficient transcription during rapid growth, which indicates a dual role of this transcription regulator.

microbiology↗

bioRxiv2024

A clinical mutation in uvrA, a DNA repair gene, confers survival advantage to Mycobacterium tuberculosis in the host

DNA repair pathways play an essential role in maintaining the genomic integrity of bacteria, and a perturbation in their biological activity helps bacteria survive under duress. In drug-resistant clinical strains, we identified a Q135K mutation in the uvrA gene, a DNA repair pathway gene. To delineate the role of uvrA and the Q135K mutation, we generated the gene replacement mutant of UvrA (Rv{Delta}uvrA) in Mycobacterium tuberculosis H37Rv (Mtb-Rv). While the lack of UvrA function in Rv{Delta}uvrA could be restored upon complementation with uvrA, the uvrA-Q135K mutant identified in clinical drug-resistant strains failed to do so. This was reflected in higher mutation rates in Rv{Delta}uvrA and Rv{Delta}uvrA::uvrAQ135A, compared with wild-type Rv or Rv{Delta}uvrA::uvrA complemented strains in the presence and absence of oxidative stress. Killing kinetics experiments with anti-TB drugs showed increased survival of Rv{Delta}uvrA and Rv{Delta}uvrA::uvrAQ135K, strains compared with Rv or Rv{Delta}uvrA::uvrA. Importantly, Rv{Delta}uvrA and Rv{Delta}uvrA::uvrAQ135K showed enhanced survival in peritoneal macrophages and murine infection model of infection. Together, data suggests that acquiring Q135K mutation benefits the pathogen, which helps enhance the hosts survival adaptability. Author SummaryDNA repair mechanisms in an organism are necessary for correcting the errors generated during replication or when it is damaged/modified due to insults. As a GC organism, Mtb is highly prone to host-mediated attacks on its genome, which, if uncorrected, can impact its genome integrity. The drug-resistant clinical strains of Mtb harbor Q135K mutation in uvrA, the first enzyme in the nucleotide excision repair pathway. With the help of genetic, molecular, and murine challenge experiments, we show that the UvrA-Q135K mutation abrogates the enzymes activity, compromising the Mtb strain harboring the mutation in the oxidative and nitrosative stress. On the contrary, the mutation in UvrA imparts survival advantage in activated macrophages and murine infection models. Results presented argue that identified mutation helps in better adaptability in the host, which may include faster acquisition of drug resistance.

microbiology↗

bioRxiv2024

SARS-CoV-2 ORF3a Protein Impairs Syncytiotrophoblast Maturation, Alters ZO-1 Localization, and Shifts Autophagic Pathways in Trophoblast Cells and 3D Organoids

SARS-CoV-2 infection poses a significant risk to placental physiology, but its impact on placental homeostasis is not well understood. We and others have previously shown that SARS-CoV-2 can colonize maternal and fetal placental cells, yet the specific mechanisms remain unclear. In this study, we investigate ORF3a, a key accessory protein of SARS-CoV-2 that exhibits continuous mutations. Our findings reveal that ORF3a is present in placental tissue from pregnant women infected with SARS-CoV-2 and disrupts autophagic flux in placental cell lines and 3D stem-cell-derived trophoblast organoids (SC-TOs), impairing syncytiotrophoblast differentiation and trophoblast invasion. This disruption leads to protein aggregation in cytotrophoblasts (CTB) and activates secretory autophagy, increasing CD63+ extracellular vesicle secretion, along with ORF3a itself. ORF3a also compromises CTB barrier integrity by disrupting tight junctions via interaction with ZO-1, mediated by its PDZ-binding motif, SVPL. Colocalization of ORF3a and ZO-1 in SARS-CoV-2-infected human placental tissue supports our in vitro findings. Deleting the PDZ binding motif in the ORF3a protein (ORF3a-noPBM mutant) restored proper ZO-1 localization at the cell junctions in an autophagy-independent manner. Lastly, we demonstrate that constitutive ORF3a expression induces SC-TOs to transition towards a secretory autophagy pathway likely via the PBM motif, as the ORF3a-NoPBM mutants showed a significant lack of CD63 expression. This study demonstrates the functional impact of ORF3a on placental autophagy and reveals a new mechanism for the activation of secretory autophagy, which may lead to increased extracellular vesicle secretion. These findings provide a foundation for exploring therapeutic approaches targeting ORF3a, specifically focusing on its PBM region to block its interactions with host cellular proteins and limiting placental impact.

microbiology↗

bioRxiv2024

Microbiota drives the sexually dimorphic infection outcomes in mealworm beetles

Sexually dimorphic responses to pathogenic infections in animals may stem from sex-specific differences in their life history and immune investment. Recent evidence highlights that such sex-specific variations in immune responses can also be critically regulated by microbiota. However, direct experiments to test how microbiota jointly impacts sex-specific immunity and vulnerability to pathogens are still limited. To this end, we used Tenebrio molitor beetles to first establish that sexes appear to differ in their microbiota composition and infection responses. Females were more vulnerable to bacterial infections and carried a higher bacterial load than males. When we depleted the microbiome, only females improved their post-infection survival, leading to a loss of sex-specific infection outcomes. Males, on the other hand, remained unaffected. Microbiota reconstitution (via feeding on faecal matter) of microbiota-depleted females increased their susceptibility to infection again, restoring the sexual dimorphism. We thus found a causal association between microbiome and infection responses. We also found reduced expression of an antimicrobial peptide tenecin 1 in females, which could be associated with their higher infection susceptibility, but such immune gene-vs-phenotypic associations were not consistent across microbiota manipulations. Immune strategies that are required to mediate the causal links between microbiome and infection response might thus vary with microbiota manipulations, warranting future investigations.

evolutionary biology↗

bioRxiv2024

Dose-dependent regulation of immune memory responses against HIV by saponin monophosphoryl lipid A nanoparticle adjuvant

The induction of durable protective immune responses is the main goal of prophylactic vaccines, and adjuvants play an important role as drivers of such responses. Despite advances in vaccine strategies, a safe and effective HIV vaccine remains a significant challenge. The use of an appropriate adjuvant is crucial to the success of HIV vaccines. Here we assessed the saponin/MPLA nanoparticle (SMNP) adjuvant with an HIV envelope (Env) trimer, evaluating the safety and impact of multiple variables including adjuvant dose (16-fold dose range), immunization route, and adjuvant composition on the establishment of Env-specific memory T and B cell responses (TMem and BMem) and long-lived plasma cells in non-human primates. Robust BMem were detected in all groups, but a 6-fold increase was observed in the highest SMNP dose group vs. the lowest dose group. Similarly, stronger vaccine responses were induced in the highest SMNP dose for CD40L+OX40+ CD4 TMem (11-fold), IFN{gamma}+ CD4 TMem (15-fold), IL21+ CD4 TMem (9-fold), circulating TFH (3.6-fold), bone marrow plasma cells (7-fold), and binding IgG (1.3-fold). Substantial tier-2 neutralizing antibodies were only observed in the higher SMNP dose groups. These investigations highlight the dose-dependent potency of SMNP in non-human primates, which are relevant for human use and next-generation vaccines.

immunology↗

bioRxiv2024

Effect of developmental and adult diet composition on reproductive aging in Drosophila melanogaster

Diet significantly affects reproductive outcomes across species, yet the precise effects of macronutrient compositions beyond caloric intake on reproductive aging are understudied. Existing literature presents conflicting views on the fertility impacts of nutrient-rich versus nutrient-poor developmental diets, underscoring a notable research gap. This study addresses these gaps by examining effects of isocaloric diets with varied protein-to-carbohydrate ratios during both developmental and adult stages on reproductive aging of a large, outbred Drosophila melanogaster population (n = [~]2100). Our results clearly demonstrate an age-dependent dietary impact on reproductive output, initially dominated by the developmental diet, then by a combination of developmental and adult diets in early to mid-life, and ultimately by the adult diet in later life. Importantly, we found that the effects of developmental and adult diets on reproductive output are independent, with no significant interaction. Further investigations into the mechanisms revealed that the effect of developmental diet on fecundity is regulated via ovarioles formation and vitellogenesis; while, the effect of adult diet on fecundity is mostly regulated only via vitellogenesis. These insights resolve disputes in the literature about dietary impacts on fertility and offer valuable perspectives for optimizing fertility strategies in improving public health and conservation efforts in this changing world. HighlightsO_LIEffect of developmental and adult diet composition on reproduction is age-dependent C_LIO_LIDevelopmental diet affects early-life; adult diet late-life; and both affect mid-life C_LIO_LIBut the effect of developmental and adult diets do not interact with each other C_LIO_LIDevelopmental diet regulates reproduction via ovarioles formation and vitellogenesis C_LIO_LIWhereas, adult diet regulates reproduction via differential vitellogenesis across age C_LI

ecology↗

bioRxiv2024

Analysis of Amblyomma americanum microRNAs in response to Ehrlichia chaffeensis infection and their potential role in vectorial capacity

BackgroundMicroRNAs (miRNAs) represent a subset of small noncoding RNAs and carry tremendous potential for regulating gene expression at the post-transcriptional level. They play pivotal roles in distinct cellular mechanisms including inhibition of bacterial, parasitic, and viral infections via immune response pathways. Intriguingly, pathogens have developed strategies to manipulate the hosts miRNA profile, fostering environments conducive to successful infection. Therefore, changes in an arthropod hosts miRNA profile in response to pathogen invasion could be critical in understanding host-pathogen dynamics. Additionally, this area of study could provide insights into discovering new targets for disease control and prevention. The main objective of the present study is to investigate the functional role of differentially expressed miRNAs upon Ehrlichia chaffeensis, a tick-borne pathogen, infection in tick vector, Amblyomma americanum. MethodsSmall RNA libraries from uninfected and E. chaffeensis-infected Am. americanum midgut and salivary gland tissues were prepared using the Illumina Truseq kit. Small RNA sequencing data was analyzed using miRDeep2 and sRNAtoolbox to identify novel and known miRNAs. The differentially expressed miRNAs were validated using a quantitative PCR assay. Furthermore, a miRNA inhibitor approach was used to determine the functional role of selected miRNA candidates. ResultsThe sequencing of small RNA libraries generated >147 million raw reads in all four libraries and identified a total of >250 miRNAs across the four libraries. We identified 23 and 14 differentially expressed miRNAs in salivary glands, and midgut tissues infected with E. chaffeensis, respectively. Three differentially expressed miRNAs (miR-87, miR-750, and miR-275) were further characterized to determine their roles in pathogen infection. Inhibition of target miRNAs significantly decreased the E. chaffeensis load in tick tissues, which warrants more in-depth mechanistic studies. ConclusionsThe current study identified known and novel miRNAs and suggests that interfering with these miRNAs may impact the vectorial capacity of ticks to harbor Ehrlichia. This study identified several new miRNAs for future analysis of their functions in tick biology and tick-pathogen interaction studies.

systems biology↗

bioRxiv2024

Large-pore connexin hemichannels function as molecule transporters independently of ion conduction

Connexin hemichannels were identified as the first members of the eukaryotic large-pore channel family that mediate permeation of both atomic ions and small molecules between the intracellular and extracellular environments. The conventional view is that their pore is a large passive conduit through which both ions and molecules diffuse in a similar manner. In stark contrast to this notion, we demonstrate that the permeation of ions and of molecules in connexin hemichannels can be uncoupled and differentially regulated. We find that human connexin mutations that produce pathologies and were previously thought to be loss-of-function mutations due to the lack of ionic currents are still capable of mediating the passive transport of molecules with kinetics close to those of wild-type channels. This molecular transport displays saturability in the micromolar range, selectivity, and competitive inhibition, properties that are tuned by specific interactions between the permeating molecules and the N-terminal domain that lies within the pore -- a general feature of large-pore channels. We propose that connexin hemichannels and, likely, other large-pore channels, are hybrid channel/transporter-like proteins that might switch between these two modes to promote selective ion conduction or autocrine/paracrine molecular signaling in health and disease processes.

biophysics↗

bioRxiv2024

A Mycobacterium tuberculosis secreted virulence factor disrupts host snRNP biogenesis

We earlier reported that Mycobacterium tuberculosis (Mtb) alters host RNA splicing to help its intracellular growth. Here, we report an unprecedented mechanism whereby a secreted virulence factor from Mtb interferes with the biogenesis of key spliceosomal components, causing an altered RNA splicing pattern. A high-throughput yeast-2-hybrid screen identified several Mtb-secreted proteins that can interact with the host RNA splicing factors (SFs). Through custom-designed in-cell assays, we show that one of those proteins, Rv1435c, targets specific exon-skipping events to alter RNA splicing. We show that Rv14345c or host splicing regulator 1 (hsr1) facilitates direct interaction between Mtb phagosomes and U5 snRNA and SNRPF, key components of the snRNPs. Genetic deletion of hsr1 reverses the specific exon-skipping events caused by WT Mtb infection. The{Delta} hsr1 strain shows compromised growth during ex vivo infection in the macrophages and in vivo infection in the mice. Tissue sections from the WT Mtb or{Delta} hsr1-infected mice showed significant hsr1-dependent SNRPF staining, a phenomenon also noted in the human intestinal tuberculosis (ITB) biopsies. We infer that hsr1 is a virulence factor which alters RNA splicing by interacting with U5snRNA and SNRPF. The splicing regulators from the host and pathogen are novel targets for anti-tuberculosis therapy.

molecular biology↗

bioRxiv2024

PPARγ mediated enhanced lipid biogenesis fuels Mycobacterium tuberculosis growth in hepatocytes.

Mycobacterium tuberculosis (Mtb) infection of the lungs, besides producing prolonged cough with mucus, also causes progressive fatigue and cachexia with debilitating loss of muscle mass. While anti-tuberculosis (TB) drug therapy is directed toward eliminating bacilli, the treatment regimen ignores the systemic pathogenic derailments that probably dictate TB-associated mortality and morbidity. Presently, it is not understood whether Mtb spreads to metabolic organs and brings about these impairments. Here we show that Mtb creates a replication-conducive milieu of lipid droplets in hepatocytes by upregulating transcription factor PPAR{gamma} and scavenging lipids from the host cells. In hepatocytes, Mtb shields itself against the common anti-TB drugs by inducing drug-metabolizing enzymes. Infection of the hepatocytes in the in vivo aerosol mice model can be consistently observed post-week 4 along with enhanced expression of PPAR{gamma} and drug-metabolizing enzymes. Moreover, histopathological analysis indeed shows the presence of Mtb in hepatocytes along with granuloma-like structures in human biopsied liver sections. Hepatotropism of Mtb during the chronic infectious cycle results in immuno-metabolic dysregulation that could magnify local and systemic pathogenicity, altering clinical presentations.

microbiology↗

bioRxiv2023

Unravelling Silicon's Transcriptomic Armor in Soybean against Macrophomina phaseolina causing Charcoal Rot Disease

The Glycine max L. has been affected by more than 100 diseases, including Macrophomina phaseolina producing charcoal rot disease, which reduces production by 70%. In this investigation, RNA-Seq analysis is used for the first time to explore role of silicon in preventing soybean charcoal rot. The study explores the molecular mechanism underlying soybeans resilience to charcoal rot when treated with potassium silicon. It was meticulously investigated how Macrophomina phaseolina entered the roots. The SEM, which showed a strong link between potassium silicate accumulation and disease resistance. Further investigation indicates that a potassium silicate concentration of 1.7mM lowers disease incidence. Using Illumina HiSeq NGS data, we present a transcriptome analysis revealing genes associated with charcoal rot resistance, highlighting 3,106 genes with distinct expression patterns. The strong enrichment of pathways including "Biosynthesis of ansamycins" and "Flavone and flavonol biosynthesis," which contribute to resistance against charcoal rot, is highlighted by KEGG enrichment analysis. The ERF transcription factor and NB leucine-rich repeats stands out among the differentially expressed genes as being particularly connected to resistance. The crucial functions that many other important transcription factors, including as MYB, NAC, and proteins from the FAR1 family, play in enhancing soybeans resistance to charcoal rot are also noted. This newly discovered information could help in developing tactics to strengthen soybeans resistance to Macrophomina phaseolina.

microbiology↗

bioRxiv2023

Conformational Dynamics and metal-ion interactions in human small Ubiquitin-like modifier (SUMO2)

SUMO (Small Ubiquitin-like Modifiers) proteins are involved in a crucial post-translational modification commonly termed as SUMOylation. Currently little is known about localisation and accumulation of SUMO2 conjugates in response to proteasome inhibitors. In this work, we have investigated a strong binding of Cu2+ ions in the C-terminal region of SUMO2 resulting in its aggregation and seems to interefere in its non-covalent interaction with a V/I-X-V/I-V/I based SIM. In Ubiquitin-proteasome system, SUMO2 controls many targets in regulation of all aspects of metabolism. The conformational flexibility of SUMO2 could play a crucial role, therefore we have also characterized native-state flexibility of human SUMO2. We show that compared to SUMO1, several amino acids in SUMO2 around 1-helix region access energetically similar near-native conformations. This could play a fundamental role in its non-covalent interactions with SUMO interaction motifs (SIMs).

biochemistry↗

bioRxiv2023

Decoding Prognostic Markers Bioinformatics Insights into PIH1D1 and p53 in Children's Brain Cancer

Genetic alterations in normal brain cells lead to the development of brain tumors (BT). The incidence of newly diagnosed cases is on the rise over time. Understanding the molecular biology of pediatric brain tumors is crucial for advancing novel therapeutic approaches to prevent or effectively manage this disease. The R2TP complex, a conserved co-chaperone from yeast to mammals, including RUVBL1, RUVBL2, PIH1D1, and RPAP3 in humans, plays a crucial role in the assembly and maturation of various multi-subunit complexes. This study evaluates the expression of PIH1D1 and p53 in pediatric brain cancers using The Cancer Genome Atlas (TCGA) data through the UALCAN platform--a novel, user-friendly resource for cancer OMICS data analysis. Our analysis revealed elevated expression levels of PIH1D1 in pediatric brain tumors across all age groups compared to normal tissues, suggesting its potential as an early detection marker and a prognostic indicator. Additionally, P53 emerged as a promising target for brain tumor treatment, warranting exploration for age-specific applications. The Venn Diagram analysis further delineated key genes within the PIH1D1 and P53 networks, providing insights into the genetic landscape of childhood brain cancer. Despite these findings, the study has limitations, primarily relying on bioinformatics databases. Future research will incorporate clinical tissues and cell lines in in vivo and in vitro experiments to unravel the mechanistic roles of PIH1D1 and p53 in brain tumors. This comprehensive approach bridges bioinformatics and clinical exploration, contributing to a holistic understanding of pediatric brain cancer molecular biology and paving the way for targeted therapeutic interventions.

bioinformatics↗

bioRxiv2023

A mitochondrial quality control mechanism reverses the phagosome maturation arrest caused by Mycobacterium tuberculosis

Phagosome maturation arrest (PMA) imposed by Mycobacterium tuberculosis (Mtb) is a classic tool that helps Mtb evade macrophage anti-bacterial responses. The exclusion of RAB7, a small GTPase, from Mtb-phagosomes causes PMA. Here, we report an unexpected mechanism that triggers crosstalk between the mitochondrial quality control (MQC) and the phagosome maturation pathways that reverses the PMA. CRISPR-mediated p62/SQSTM1 depletion (p62KD) does not appear to impact mitochondrial quality. The p62KD cells are restrictive to Mtb growth, triggered by an increasingly oxidative environment and increased lysosomal targeting. The lysosomal targeting of Mtb is facilitated by enhanced TOM20+ mitochondria-derived vesicles (MDVs) biogenesis, a key MQC mechanism. In p62KD cells, TOM20+-MDVs biogenesis is MIRO1/MIRO2-dependent and gets delivered to lysosomes for degradation in a RAB7-dependent manner. Upon infection in p62KD cells, TOM20+-MDVs get extensively targeted to Mtb-phagosomes, inadvertently facilitating RAB7 recruitment, PMA reversal and lysosomal targeting of Mtb; the phenotype also replicated in p62/SQSTM1 knockout cells. Triggering MQC collapse in p62KDcells further diminishes Mtb survival, signifying cooperation between redox- and lysosome-mediated mechanisms. The MQC-anti-bacterial pathway crosstalk could be exploited for host-directed anti-tuberculosis therapies.

microbiology↗