Biology subjects

Nanda, R.

Publications and source records attributed to Nanda, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Confluent growth state dependent transcriptomic adaptation in A549 lung cancer cells

Cell confluency is a major determinant of cell-cell communication, protein interactions, access to nutrients, and signalling dynamics, thereby significantly impacting biological outcomes. Lung cancer cells like A549 are widely used as screening models for scientific studies wherein their growth in vitro progress from non-confluent to confluent growth. In this study, we investigated the transcriptomic adaptations associated with the transition of A549 cells from baseline non-confluent to confluent growth. Comparative transcriptomic analysis between confluent and cells at baseline identified 815 upregulated and 671 downregulated transcripts. Pathway enrichment analysis of deregulated transcripts in confluent cells revealed enhanced cholesterol and sterol biosynthetic pathways, along with suppression of chromosomal segregation and mitotic pathways. At confluency, an increased expression of glucose transporters (SLC2, SLC60, and SL37 families) and glycolytic pathways, and a decrease in amino acid transporters (SLC1, SLC7, SLC38, and SLC36) and amino acid metabolic pathways is observed. A reduced one-carbon metabolic signature (SHMT2, DHFR, and MTHFD2) and enhanced fatty acid precursor synthesis (HMGCLL1, ALDH6A1, and AASS) were also observed at confluency. 1H NMR profiling of culture media revealed higher glucose and glutamine utilisation with lactate accumulation during culture maturation. Collectively, the data suggest transcriptome-level rewiring in A549 cells with preferential biosynthesis of lipids and sterols at confluency and underscore the importance of considering culture maturity in cancer biology, metabolism, and therapeutic studies.

systems biology↗

bioRxiv2025

Lipid-mediated GPR32 signaling reprograms macrophage metabolism to impair anti-tuberculous immunity

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), has evolved strategies to evade innate immunity and establish persistent infection. However, the mechanisms by which M. tuberculosis reprograms human macrophage metabolism remain incompletely defined. Tuberculous pleural effusion (TB-PE), a common extrapulmonary manifestation that frequently coexists with pulmonary TB, offers a unique, clinically relevant immunometabolic window into the TB microenvironment. Here, using patient-derived TB-PE samples, we demonstrate that this microenvironment induces a metabolic state in human macrophages that compromises their antimicrobial function. Lipidomic analysis identified an enrichment of the specialized pro-resolving mediator Resolvin D5 (RvD5), which signals through GPR32 to suppress macrophage microbicidal activity. The acellular fraction of TB-PE was sufficient to induce RvD5 secretion by monocytes, correlating with increased expression of RvD5 biosynthetic enzymes in pleural monocytes from TB patients. Mechanistically, RvD5-GPR32 signaling inhibited glycolysis without promoting oxidative phosphorylation, reducing HIF-1 activity and impairing intracellular M. tuberculosis control. HIF-1 stabilization restored antimicrobial function. These findings uncover the RvD5-GPR32-HIF-1 axis as a mechanism of metabolic immune suppression and a potential target for host-directed TB therapy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/663524v3_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@64feceorg.highwire.dtl.DTLVardef@948ab0org.highwire.dtl.DTLVardef@1d387forg.highwire.dtl.DTLVardef@682f72_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Pre-exposure to time-restricted feeding reduces tissue CD4+ T cells with limited effect on Mycobacterium tuberculosis clearance

Time-restricted feeding (TRF) in human and animal models positively impacts metabolic health by improving glucose homeostasis and reducing adiposity. However, limited studies have investigated the impact of TRF on the host immune response and upon bacterial infection. In this study, C57BL/6 mice (6-8 weeks old, male) were subjected to 8 hours of dark-phase TRF for 30 days, and aerosol infected with a low dose (100-400 colony-forming units) of Mycobacterium tuberculosis (Mtb) H37Rv. The body weight gain, multi-tissue metabolome, and proteome changes and distribution of immune cells in these study groups were monitored. In the first 15 days of TRF, mice showed better glucose tolerance with marginal weight loss. The serum and liver metabolome of TRF mice demonstrated perturbed fatty acid biosynthesis and degradation, steroid hormone biosynthesis pathways and tyrosine metabolism. Liver proteome data of TRF mice indicated an increased fatty acid oxidation which might affect the host immune cell frequency and functionality. The Mtb-infected TRF and control mice had similar tissue (lung, spleen and liver) bacterial burden at 21 days post-infection. The bone marrow of Mtb-infected TRF mice had significantly lower CD3+ T cells, and CD4+ T cells were low both in the bone marrow and lungs. This study reports that mice undergoing 8 hours of TRF had an improved metabolic phenotype, and discontinuing TRF limits its positive impact on handling Mtb infection at an early point.

immunology↗

bioRxiv2025

Inflammasome activation dictates the efficacy of antimycobacterial activity of frontline TB drugs

Recent developments in TB treatment have identified an enormous potential of host targeting entities (host directed therapies-HDT) in achieving better and faster control of infection. We have previously demonstrated the synergistic effect of sertraline with frontline TB drugs in clearing infection in murine tissues. We surmised that understanding the mechanism of sertraline mediated enhancement of antibiotic efficacy would help identify novel pathways of pathogen control. Here, we have used sertraline as a probe to identify host signaling pathways that are important for bacterial control. We identify a role for sertraline mediated modulation of macrophage mitochondrial physiology in this process. We show that the resultant ROS generated in cells acts as the secondary signal for host cell inflammasome activation catalyzing the greater release of IL1beta; and significant efflux of K+ from the SRT treated macrophages. We thus highlight an important relationship between mitochondrial physiology in regulating the activation of the inflammasome to achieve better control of Mtb by infected macrophages.

microbiology↗

bioRxiv2025

VDR-calcium axis regulates the diet-driven metabolic shift during weaning

Weaning in mammals is associated with a shift in the metabolism, driven by the differences in the macronutrient composition of milk and post-weaning diet. Milk has a higher fat content compared with the carbohydrate-enriched solid food. Malnutrition during this stage could affect this transition with long-term adverse effects. The role of micronutrients during this transition is not well understood. Mice lacking a functional vitamin D receptor (VDR) progressively develop severe skeletal muscle and adipose atrophy after weaning, suggesting a role for vitamin D signaling in the metabolic transition during weaning. Here, we demonstrate that after weaning, VDR knock-out mice exhibit systemic energy deprivation and higher lipolysis in inguinal white adipose tissue, probably due to increased norepinephrine signaling via protein kinase A (PKA) and extracellular signalling-regulated kinase (ERK) pathways. Energy deprivation in vdr-/- mice is associated with defective liver glycogenolysis, characterized by increased expression of protein phosphatase-1 and decreased phosphorylation of glycogen phosphorylase. However, restoration of serum calcium levels by a rescue diet is sufficient to restore energy metabolism in vdr-/- mice. Interestingly, maintaining a high-fat-containing milk-based diet post-weaning could prevent the onset of energy deprivation, liver glycogen storage defect, and adipose atrophy in these mice without restoring serum calcium levels. Our data show that the vitamin D-calcium axis is essential for the adaptation of mice to the dietary shift from high-fat-containing milk to post-weaning carbohydrate-enriched diets. It also reveals a novel macronutrient-micronutrient interaction that shapes the metabolic flexibility of the individual based on the dietary composition of nutrients.

physiology↗

bioRxiv2024

Isotopic tracing in Mycobacterium tuberculosis-infected alveolar epithelial cells indicates metabolic specificity to their virulence and drug-resistance status

Mycobacterium tuberculosis (Mtb), the causative organism of tuberculosis (TB), infects different host cells; however, studies on its metabolic impact on the type 2 alveolar epithelial cells are limited. In this study, comparative metabolic insights of A549 cells infected with laboratory (H37RV, H37Ra) and clinical isolates (drug-resistant: S6, S11 and sensitive: S4, S5) were derived from read out of the 13C-based proteinogenic amino acid kinetics. Mtb H37Rv (virulent) exhibited higher growth kinetics within A549 cells compared to H37Ra (avirulent), whereas drug-resistant clinical isolate S6 showed the highest intracellular growth. The viability of H37Rv-infected A549 cells was significantly low. Interestingly, the drug-resistant clinical Mtb isolates maintained better cell viability over time. A [13C6] glucose tracer and mass isotopomer distributions revealed that A549 cells infected with virulent Mtb strains exhibited higher dependency on the central carbon metabolism like glycolysis, the pentose phosphate pathway and the tricarboxylic acid cycle for de novo amino acid biosynthesis. Drug-resistant Mtb isolates infected A549 cells showed robust 13C incorporation in the proteinogenic Threonine, Methionine and Lysine, derived from the tricarboxylic acid cycle. A549 cells infected with Mtb, irrespective of their drug resistance status, showed 13C incorporation in the essential amino acids (lysine, methionine, threonine, valine), underlining the dependencies of the pathogen on the de novo host metabolic precursors. These findings elucidate the importance of deciphering the strain-specific host-pathogen metabolic interactions to develop targeted therapies against drug-resistant Mtb infections.

biochemistry↗

bioRxiv2024

Diabetes-Tuberculosis Comorbidity Characterized by Reduced Type-II Interferon and Elevated Th17 Responses.

Understanding the perturbed lung immune cells distribution and its functionality in tuberculosis (TB) is well documented; however, limited reports have covered their disruption, if any, in diabetes-tuberculosis (DM-TB) comorbid conditions. Here, we employed single-cell RNA-seq to investigate the molecular mechanisms that govern the heterogeneity in host immune response in DM-TB comorbid conditions. Diabetes is associated with chronic hyperinflammation and reduced lung-infiltrating immune cells, which delays the immune response to Mycobacterial infection. scRNA-seq of lung CD3 and CD11c cells revealed compromised adaptive and innate immunity, with decreased Th1 and M1 macrophage populations in DM-TB mice. A dampened immune response, marked by increased IL-16 signaling and reduced TNF and IFN-II responses, was observed in DM-TB. This study highlights chronic inflammation, hyperglycemia, and dyslipidemia associated with diabetes impairing anti-TB immunity. Selective inhibition of aberrant IL-16 secretion and Th17 cell activation might provide strategies for better managing DM-TB comorbidity.

immunology↗

bioRxiv2024

Copy number variation analysis of 9,482 Mycobacterium tuberculosis isolates identifies lineage-specific molecular determinants.

BackgroundClinical manifestations of tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) show lineage-specific differences contributed by genetic polymorphism such as phylo-single nucleotide variations (PhyloSNPs) and insertion or deletions (INDELs). Intragenomic rearrangement events, such as gene duplications and deletions, may cause gene copy number differences in Mtb, contributing to lineage-specific phenotypic variations, if any, which need better understanding. ResultsThe relative gene copy number differences in high-quality publicly available whole genome sequencing datasets of 9,482 clinical Mtb isolates were determined by repurposing and modifying an RNA-seq data analysis pipeline. The pipeline included various steps, viz., alignment of reads, sorting by coordinate, GC bias correction, and variant stabilising transformation. The strategy showed maximum separation of lineage-specific clusters in two principal components, capturing [~]54% variability. Unsupervised hierarchical clustering of the top 100 genes and pairwise comparisons between Mtb lineages revealed an overlapping subset of genes (n=42) having significantly perturbed copy numbers (Benjamin Hochberg adjusted P-value < 0.05 and log2(drug-resistant/sensitive) > {+/-} 1). These 42 genes formed multiple tandem gene clusters and are known to be involved in virulence, pathogenicity and defence response to invading phages. A separate comparison showed a significantly high copy number of phage genes and a recently reported druggable target Rv1525 in pre- and extensively drug-resistant (Pre-XDR, XDR) compared to drug-sensitive clinical Mtb isolates. ConclusionThe identified gene sets in Mtb clinical isolates may be useful targets for lineage-specific therapeutics and diagnostics development.

genomics↗

bioRxiv2024

Phosphoglucomutase A mediated regulation of carbon flux is essential for antibiotic and disease persistence in Mycobacterium tuberculosis

The long-term survival of Mtb mandates judicious utilization of the available resources inside the host. Uninterrupted access to host-derived nutrients holds the key to the success of Mtb. Phosphoglucomutase enzyme besides synthesizing glycogen, which serves as a nutrient reservoir, also helps modulate the carbon flux in different pathogens. Studies on the role of glycogen metabolism in disease progression, reactivation, and drug susceptibility in tuberculosis are severely lacking. To investigate this, we generated an Mtb strain ({Delta}pgmA) devoid of the gene that encodes for the enzyme phosphoglucomutase A (pgmA). The absence of pgmA impedes the ability of the pathogen to survive under nutrient-limiting and reactivation conditions. In the current study, we demonstrate that the absence of cell membrane-associated glycolipids in {Delta}pgmA compromised the cell wall integrity and increased the susceptibility of {Delta}pgmA to various stresses. Interestingly, in comparison to the wild type, low cAMP levels in {Delta}pgmA imparted an enhanced growth phenotype on cholesterol. Differential gene expression and carbon flux analysis suggest that stored carbon in the form of glycogen is essential for the survival of Mtb under nutrient-limiting conditions. Finally, we demonstrate that the pgmA gene of Mtb is essential for the growth of Mtb inside the host. Overall, this study unveils the significance of pgmA-mediated regulation of membrane glycolipids and its implication on antibiotic and disease persistence in tuberculosis. Additionally, information derived from this study will help design anti-TB strategies that are novel, short, and more efficient.

microbiology↗

bioRxiv2024

Lung Mycobacterium tuberculosis infection perturbs metabolic pathways in non-pulmonary tissues

Mycobacterium tuberculosis (Mtb), through aerosol, reaches the lungs to cause pulmonary tuberculosis (TB); however, it may also affect the metabolism of other tissues in age-specific ways. In this study, female C57BL/6 mice (2 and 5 months old; M) were infected with a low aerosol dose (100-200 cfu) of Mtb H37Rv to monitor tissue mycobacterial load and multi-tissue metabolite profiling using gas chromatography and mass spectrometry (GC-MS). 5M C57BL/6 mice showed separate tissue metabolic phenotype with significantly higher lung aspartic acid, fecal oxalic acid and tryptophan levels with lower liver lysine and aspartic acid and fecal phenylalanine levels (log2FC: 5M/2M> {+/-}1.0, p<0.1) compared to 2M young controls. Upon Mtb infection, the lung mycobacterial load of 2M and 5M mice were similar till 6 weeks post-infection. However, significantly higher lung phosphoric acid, malonic acid and lower mannose levels (log2FC: Mtb infected/healthy> {+/-}1.0, p<0.1) were observed in Mtb-infected 5M C57BL/6 mice. Meanwhile, Mtb-infected 2M mice showed higher liver xylose and lower lysine levels. The thigh muscles of Mtb-infected 2M and 5M mice showed increased malic acid and oxalic acid and decreased glycine, serine, and glycerol levels. Fecal aspartic acid level was higher in Mtb-infected 5M mice, while a decreased abundance of fecal lysine was observed in Mtb-infected 2M mice. Overall, this study demonstrates a deregulated tissue-specific amino acid metabolism in Mtb-infected mice groups of different age groups, which might be targeted for managing TB infection-related adverse effects.

biochemistry↗

bioRxiv2023

Hypothetical gene Rv0495c regulates redox homeostasis in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) has evolved sophisticated surveillance mechanisms to regulate and neutralize redox imbalances and associated lethal consequences. Failing this, the accumulated ROS induces toxicity by oxidizing a variety of biological molecules including proteins, nucleic acids and lipids. In the present study we identified Mtbs Rv0495c gene as an important regulator of oxidized cytosolic environment. Compared to wild type Mtb strain lacking the Rv0495c gene, {Delta}Rv0495c, had increased ROS and NAD+/NADH ratio creating a highly oxidized intracellular environment. {Delta}Rv0495c strain demonstrated slow growth phenotype under in vitro and ex-vivo growth conditions and demonstrated enhanced susceptibility to drugs, oxidative, nitrosative and hypoxic growth conditions. In addition, the increase in the superoxide radicals triggered a Fenton-like reaction rendering the {Delta}Rv0495c susceptible to free iron. The increase in the intracellular ROS levels of the {Delta}Rv0495c was further corroborated by an increase in the expression of proteins involved in antioxidant defense and enhanced ROS-mediated oxidation and degradation of mycobacterial lipids. This superoxide-induced lipid degradation resulted in altered colony morphology and loss of membrane integrity in the {Delta}Rv0495c. Surprisingly, despite showing a growth defect phenotype in an ex-vivo macrophage infection model, the absence of the Rv0495c gene in Mtb enhanced the pathogenicity and augmented the ability of the Mtb to grow inside the host. Gene expression analysis revealed a Rv0495c mediated immunomodulation of the host controls inflammation and helps creates a favorable niche for long-term survival of Mtb inside the host. In summary, the current study underscores the fact that the truce in the war between the host and the pathogen favors long-term disease persistence in tuberculosis. We believe targeting Rv0495c could potentially be explored as a strategy to potentiate the current anti-TB regimen.

microbiology↗

bioRxiv2023

Iron chelation by deferoxamine as useful adjunct therapeutics in murine tuberculosis.

Dysregulated iron metabolism is reported in tuberculosis patients; therefore, it represents an opportunity for developing host-directed therapeutics. This study monitored the antimycobacterial properties of an iron chelator, i.e., Deferoxamine (DFO/D), and its impact on the transcript and metabolite levels of Mycobacterium tuberculosis (Mtb) in vitro. For in vivo validation, a group of mice received ferric carboxymaltose to create an iron overload condition, and controls were aerosol-infected with Mtb H37Rv. Mtb-infected mice received isoniazid (INH/H) and rifampicin (RIF/R) in combination with or without DFO before tissue-specific CFU assay, liver metabolite screening and iron quantification using mass spectrometry. DFO showed antimycobacterial properties comparable to INH in vitro. DFO treatment deregulated (log2DFO/control>{+/-}1.0) Mtb transcript (n=137) levels, the majority of which encode for iron-containing proteins and proteins involved in stress response. DFO treatment up-regulated Rv3622c (PE32), Rv2353c (PPE39) and Rv3022A (PE29) genes and conditional knocking down of ABC transporter like irtA by anhydrotetracycline (Atc) inducible CRISPR interference (CRISPRi) approach compromised Mtb growth showing their potential involvement in iron metabolism. Global Mtb metabolite analysis using GC-MS identified a set of 5 deregulated metabolites indicating a perturbed pentose phosphate pathway and inositol phosphate metabolism in the host upon DFO treatment. Iron-overloaded mice exhibited significantly higher tissue mycobacterial burden at two weeks post-infection, and the efficacy of INH and RIF were compromised, corroborating with previous reports. Iron chelation by DFO or combined with/adjunct to RIF and INH significantly reduced the lung/tissue mycobacterial burden at four weeks post-treatment, specifically in the first ([~]0.5 log) and second weeks ([~]0.5 log) of treatment. The intracellular pro-inflammatory cytokine levels in the lung CD4+ T cells of INH and RIF-treated groups with or without DFO were similar, suggesting DFO has a direct role in Mtb survival and metabolism rather than improved infection, and the efficacy of INH and RIF were compromised, corroborating with previous reports. DFO adjunct to RIF and INH treatment significantly altered liver arginine biosynthesis, which directly neutralizes ammonia and is immune-supportive. Conventionally, DFO is used for treating acute iron toxicity that is common in thalassemic patients, and this study demonstrates DFO has potential as adjunct therapeutics for tuberculosis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/543389v3_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@5066fdorg.highwire.dtl.DTLVardef@99a292org.highwire.dtl.DTLVardef@80426dorg.highwire.dtl.DTLVardef@892436_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Splenic T follicular helper cells compromise Mycobacterium tuberculosis clearance in aged C57BL/6 mice

Immunosenescence increases susceptibility to infectious diseases like tuberculosis (TB) in older subjects ([≥]60 years) and may impact containment of Mycobacterium tuberculosis (Mtb) during therapeutic intervention. A deeper understanding of cellular and molecular changes with age could inform new strategies to improve therapeutic outcomes. Here, we monitored the immunopathology, frequency and functionality of immune cells across extreme age groups of C57BL/6 mice following low aerosol dose infection (100-120 cfu) with Mtb H37Rv and treatment with rifampicin and isoniazid (RIF-INH). Up to 6 weeks of infection, tissue (lung, spleen and liver) mycobacterial load in old (17-19 months; M) and aged (31M) C57BL/6 mice was similar compared to young (2-4M) mice. However, at two weeks post-treatment, older mice showed a slower rate of Mtb clearance in the lungs. Old Mtb-infected mice had higher splenic T-follicular cytotoxic (TFC)-like cells and proteomic analysis of flow-sorted CD4+CD44+ T cells revealed deregulated mitochondrial proteins (4-hydroxy-2-oxoglutarate aldolase, aspartate aminotransferase and prostaglandin E synthase), pointing to impaired mitochondrial function. Collectively, these findings suggest that age-associated immune alterations may impair immunometabolic processes contributing to delayed Mtb clearance. These results highlight the potential importance of targeting immunometabolic dysfunction to improve TB treatment outcomes in older populations and reduce morbidity. SummaryThe elderly population is particularly susceptible to tuberculosis (TB), making it crucial to understand the cellular and molecular mechanisms contributing to the decline in immune responses with age. Evaluating the immunopathology, frequency and functionality of immune cells and Mtb-specific antibody responses across different age groups is essential for developing adjunct therapies for geriatric TB patients.

immunology↗

bioRxiv2022

Dysregulated cysteine metabolism leads to worsened liver pathology in diabetes-tuberculosis comorbid mice.

Diabetes mellitus (DM) is a well-known risk factor for tuberculosis (TB). Interestingly, DM is growing to pandemic proportions in TB endemic South-East Asian countries. DM-TB comorbidity induced pathophysiological changes warrants a better understanding to develop effective therapeutics. Tissue metabolomic profiling of streptozotocin (STZ) induced diabetic animals, infected with Mycobacterium tuberculosis H37Rv, showed metabolic dysregulation in the lungs, liver, brain, kidney and thigh muscle. At 3 w.p.i., the tissue (lungs, spleen, liver) bacterial loads were similar between DM-TB and TB with worsened lung pathology. Enrichment analysis of the deregulated liver metabolites (n=20; log2DM-TB/TB>{+/-}1.0) showed major perturbation in the cysteine-methionine, glycine-serine, branched chain amino acid (BCAA) and fatty acid metabolism. Parallel relative quantification of liver proteome of DM-TB and control mice groups (TB, DM and healthy) identified 1833 proteins which showed group specific variations. Enrichment analysis of significantly altered proteins (n=60; log2DM-TB/TB>{+/-}1.0) showed major perturbations in cysteine-methionine metabolism corroborating the metabolomics data. In addition, amino acid biosynthesis, retinol metabolism and polyol biosynthetic process were also differentially enriched in DM-TB groups compared to controls. Furthermore, a global correlation analysis of liver metabolome and proteome data showed strong association between aspartic acid, pyruvic acid, leucine and isoleucine with Cyp450 enzymes (Cyp2a5, Cyp3a11, Cyp4a10, Cyp4a14) involved in retinol metabolism. Whereas iminodiacetic acid, isoleucine and {gamma}-aminobutyric acid strongly correlated to enzymes (Cth, Ahcy, Kyat3, Mat1a) involved in the cysteine metabolism. So, targeting the perturbed liver cysteine and retinol metabolism in DM-TB comorbid condition might improve therapeutic outcomes and prevent organ damage.

biochemistry↗

bioRxiv2022

Multimodal Prediction of Breast Cancer Recurrence Assays and Risk of Recurrence

Gene expression-based recurrence assays are strongly recommended to guide the use of chemotherapy in hormone receptor-positive, HER2-negative breast cancer, but such testing is expensive, can contribute to delays in care, and may not be available in low-resource settings. Here, we describe the training and independent validation of a deep learning model that predicts recurrence assay result and risk of recurrence using both digital histology and clinical risk factors. We demonstrate that this approach outperforms an established clinical nomogram (area under the receiver operating characteristic curve of 0.833 versus 0.765 in an external validation cohort, p = 0.003), and can identify a subset of patients with excellent prognoses who may not need further genomic testing.

cancer biology↗

bioRxiv2020

The Impact of Digital Histopathology Batch Effect on Deep Learning Model Accuracy and Bias

The Cancer Genome Atlas (TCGA) is one of the largest biorepositories of digital histology. Deep learning (DL) models have been trained on TCGA to predict numerous features directly from histology, including survival, gene expression patterns, and driver mutations. However, we demonstrate that these features vary substantially across tissue submitting sites in TCGA for over 3,000 patients with six cancer subtypes. Additionally, we show that histologic image differences between submitting sites can easily be identified with DL. This site detection remains possible despite commonly used color normalization and augmentation methods, and we quantify the digital image characteristics constituting this histologic batch effect. As an example, we show that patient ethnicity within the TCGA breast cancer cohort can be inferred from histology due to site-level batch effect, which must be accounted for to ensure equitable application of DL. Batch effect also leads to overoptimistic estimates of model performance, and we propose a quadratic programming method to guide validation that abrogates this bias.

bioinformatics↗

bioRxiv2020

Acute radiofrequency electromagnetic radiation exposures cause neuronal DNA damage and impair neurogenesis in the young adolescent rat brain

Mobile phone is now a commonly used communication device in all age groups. Young adolescents use it for longer duration and effect of its radiofrequency electromagnetic radiation (RF-EMR) on their brain structure and function need detailed investigation. In the present study, we investigated the effect of RF-EMR emitted from mobile phones, on young adolescent rat brain. Wistar rats (5 weeks, male) were exposed to RF-EMR signal (2,115 MHz) from a mobile phone at a whole body averaged specific absorption rate (SAR) of 1.15 W/kg continuously for 8 h. Higher level of lipid peroxidation, carbon centered lipid radicals and DNA damage were observed in the brain of rat exposed to RF-EMR. Number of neural progenitor cells (NPCs) in dentate gyrus (DG) were found to be relatively low in RF-EMR exposed rats that may be due to reduced neurogenesis. Acute exposure to RF-EMR induced neuronal degeneration in DG region with insignificant variation in CA3, CA1 and cerebral cortex sub regions of hippocampus. Findings of this study, indicate that acute exposure of high frequency RF-EMR at relatively higher SAR may adversely impact the neurogenesis and function of adolescent rat brain. Generation of carbon centered lipid radicals, and nuclear DNA damage might be playing critical role in reduced neurogenesis and higher neuronal degeneration in the cortex and hippocampus of brain. Detailed understanding of RF-EMR induced alteration in brain function will be useful to develop appropriate interventions for reducing the impact caused by RF-EMR damage.

biochemistry↗

bioRxiv2020

Troxerutin acts on complement mediated inflammation to ameliorate arthritic symptoms in rats.

Troxerutin (TXR), is a phytochemical reported to possess anti-inflammatory and hepatoprotective effects. In this study, we aimed to exploit anti-arthritic properties of TXR using an adjuvant induced arthritic (AIA) rat model. AIA induced rats showed highest arthritis score at disease onset and by oral administration of TXR (50, 100, 200 mg/kg body weight), reduced to basal level in a dose dependent manner. Isobaric tag for relative and absolute quantitative (iTRAQ) proteomics tool was employed to identify deregulated joint homogenate proteins in AIA and TXR treated rats to decipher probable mechanism of the TXR action in arthritis. iTRAQ analysis identified a set of 434 joint homogenate proteins with 65 deregulated proteins (log2 case/control [≥]1.5) in AIA. Expressions of a set of important proteins (AAT, T-kininogen, vimentin, desmin, and nucleophosmin) that could classify AIA from healthy were validated using Western blot analysis. Western blot data corroborated proteomics findings. In silico protein-protein interaction study of joint homogenate proteome revealed that complement component 9, the major building blocks of the membrane attack complex (MAC) responsible for sterile inflammation, gets perturbed in AIA. Our dosimetry study suggests that a TXR dose of 200 mg/kg body weight for 15 days is sufficient to bring the arthritis score to basal levels in AIA rats. We have shown the importance of TXR as an anti-arthritis agent in AIA model and after additional investigation its arthritis ameliorating properties could be exploited for clinical usability.

biochemistry↗