Biology subjects

Agrawal, N.

Publications and source records attributed to Agrawal, N..

18 recordsLinked to original sources

bioRxiv2026

Glial Mutant Huntingtin Expression Initiates a Progressive Pathological Cascade Toward Neuronal Involvement in Drosophila

The mechanisms of involvement of glial cells in the progression of Huntingtons disease remain sparingly elucidated. Using the Drosophila melanogaster model, we investigated the temporal course of the disease pathogenesis induced by pan-glial expression of HTTex1pQ93 in comparison to the temporal course of pathology induced by pan-neuronal expression. Our behavioural data were supported by quantitative confocal microscopy, quantification of aggregate formation and its morphometry, Manders M2 colocalization index, and correlative holotomography. Expression of mHTT in glial cells led to developmental defects and subsequent delayed onset of motor dysfunction and death with increasing amounts of HTT and changes in the immunoreactivity of glial cells. In spite of the progressive increase in HTT accumulation, glial aggregates showed stability after their initial formation, while neuronal mHTT revealed distinct age-dependent remodelling of its aggregates. Importantly, there was an initial preference of glial mHTT for glial compartments followed by a progressively increasing number of HTT in the neurons with aging. Correlative holotomography provided spatial evidence of the neuronal association of HTT. Together, these findings demonstrate that glial mHTT establishes a distinct progressive pathological trajectory characterised by evolving glial pathology, increasing neuronal involvement, and delayed functional decline, highlighting glia as an active component of HD-like disease progression.

neuroscience↗

bioRxiv2026

Integrated analysis of stemness-associated immune modulatory circuits in squamous cell carcinomas

Emerging evidence indicates that a subset of cancer cells enriched for stemness-related gene signatures possess distinct immunomodulatory capacities, enabling these tumor-initiating stem cells (tSCs) to more effectively evade or resist anti-tumor immunity. Despite these advances, the tSC-specific molecular circuits orchestrating their specialized immune privilege program are not well defined. Here, in squamous cell carcinomas of the skin and oral cavity, we comprehensively delineate the unique immune-evasive properties of tSCs and dissect the transcriptional regulation shaping their immunomodulatory programs. By integrating transcriptome profiling, chromatin landscape mapping, genetic perturbation, and single-cell RNA sequencing, we found that the tSC-specific immune program is broadly governed by SOX2, a stemness-associated transcription factor. We demonstrate that SOX2 enables tSCs to sustain immature tumor-associated neutrophils (TANs) and subsequently trigger these myeloid cells to foster the development of tumor-associated macrophages (TAMs). This SOX2-directed tSC-TAN-TAM axis establishes a localized immunosuppressive niche for protecting tSC. SIGNIFICANCEHere, we uncover SOX2 as a master regulator that orchestrates conserved immune modulatory circuits in tSCs to sustain pro-tumor myeloid cell states. These findings place tSCs at the apex of immune landscape remodeling, asserting a central role of stemness-associated program in organizing the immunosuppressive tumor microenvironment.

cancer biology↗

bioRxiv2025

Hepatocyte-like cells die via steroid hormone and nuclear receptor E75-mediated apoptosis

Metabolic organs must sustain physiological function while retaining the capacity for timely cell death. Systemic hormones play a key role in coordinating this balance, yet how they regulate cell death in vivo remains unclear. Here, we investigate hormone-regulated cell death in a metabolically specialised organ using Drosophila oenocytes, polyploid hepatocyte-like cells, as a tractable in vivo model. Using non-invasive longitudinal live imaging combined with oenocyte-specific genetic manipulation, we directly visualise larval oenocyte death during metamorphosis. We show that larval oenocyte loss is a dynamic, multistep process controlled by the steroid hormone ecdysone. We further identify the ecdysone-induced nuclear receptor E75 as a key regulator of the timing of cell death, as loss of E75 triggers premature oenocyte death. Oenocyte-specific manipulation of cell death pathways, together with live imaging using genetically encoded caspase reporters, provides direct evidence that larval oenocytes die by apoptosis. Together, this work defines how systemic hormonal signals regulate the timing of apoptosis in metabolically specialised polyploid cells and establishes oenocytes as a powerful in vivo system for studying cell death in metabolic organs.

developmental biology↗

bioRxiv2025

A novel Parvimonas OTU is inversely associated with having caries or fillings in children

BackgroundDental caries is the most common chronic oral disease in children, but its etiology is complex and multifactorial. The association of the oral microbiota with caries is underexplored in children. We investigated saliva microbiota in Finnish children and aimed to identify microbial biomarkers associated with the risk of having caries or fillings (CF). MethodsWe examined 400 Finnish children (180 girls, 220 boys) aged 7-9 years who provided stimulated saliva samples and underwent clinical oral examinations at baseline of the Physical Activity and Nutrition in Children study. Of these children, 261 (65%) were with CF and 139 (35%) were without CF. We characterized the saliva microbiota using the 16S rRNA gene sequencing, examined differences in the abundance and composition at the phylum and genus level between these two groups, and studied the associations of selected Operational Taxonomic Units (OTUs) with the risk of having CF in crude and adjusted (OTUs, age, Silness-Loe plaque index) models. ResultsAlpha diversity and richness did not differ between the groups (p>0.1 for Shannon, inverse Simpson, and Chao1 indices) in the total sample nor when analyzed among girls and boys separately. Beta diversity differed between the groups in the total sample, and when girls and boys were analyzed separately (p corrected by false discovery rate method [pcorr] [~] 0.001). In total, 80 OTUs differed between the groups at the genus level (pcorr<0.01). Two OTUs were independently associated with the risk of having CF. A novel Parvimonas OTU was inversely associated with having CF (odds ratio [ORcrude] 0.49, 95% confidence interval [CI] 0.32 to 0.75). In addition, an OTU of probably Streptococcus mutans was positively associated with having CF (ORcrude 6.01, 95% CI 3.49 to 10.36). ConclusionA Parvimonas species represented by a novel OTU is independently and inversely associated with the risk of having CF in children.

microbiology↗

bioRxiv2025

mRNA-based tuberculosis vaccines BNT164a1 and BNT164b1 are immunogenic, well-tolerated and efficacious in rodent models

We designed and preclinically tested two mRNA-LNP-based vaccine candidates to protect against tuberculosis (TB). BNT164a1 and BNT164b1 encode the same eight Mycobacterium tuberculosis (Mtb) antigens expressed across different infection stages: Ag85A, Hrp1, ESAT-6, RpfD, RpfA, HbhA, M72, and VapB47. BNT164a1 utilizes nucleoside-unmodified mRNA, while BNT164b1 utilizes N1-methyl pseudouridine-modified mRNA. Prime-boost immunization with BNT164 candidates elicited antibody and/or T-cell responses against all antigens in three mouse strains (C57BL/6, BALB/c, and HLA-A2.1/DR1 humanized mice). The candidates demonstrated favorable safety profiles in a rat toxicity study and significantly reduced bacterial burdens of two Mtb strains in murine aerosol challenge models. BNT164 protection correlated with granuloma infiltration by CD8+ T cells with memory precursor phenotypes. In conclusion, BNT164a1 and BNT164b1 were immunogenic, well tolerated and efficacious in preclinical models and are the first mRNA-based TB vaccines to enter phase I/II clinical trials (NCT05537038, NCT05547464).

immunology↗

bioRxiv2025

Mechanistic Insights into Cross-β Sheet Formation in the HIV-Associated Amyloidogenic Peptide PAP248-286 from Unbiased All-Atom Molecular Dynamics Simulation

Semen-derived enhancer of viral infection (SEVI) fibrils, assembled from the peptide fragment PAP248-286, enhance HIV transmission by promoting viral attachment to host cells. However, the molecular basis of SEVI nucleation and early aggregation remains unclear. Here, we conducted 80 independent all-atom molecular dynamics (MD) simulations spanning a total of 40 s, together with 100 independent steered MD and umbrella sampling runs, to explore the dimerization and dissociation of PAP248-286 Our results show that hydrogen bonding is the dominant stabilizing force driving {beta}-sheet formation during peptide association. Residue-level analyses identified Arg10, Val17, Glu19, and Ile20 as key contributors to inter-peptide binding, consistent with steric zipper motifs described in other amyloid systems. Steered MD revealed mechanically resilient dimers with average rupture forces of [~]20 kcal/mol/[A] and multi-barrier unbinding behavior. Umbrella sampling estimated a peptide dissociation free energy of [~]8.7 kcal/mol, highlighting a clear thermodynamic separation between bound and unbound states. Together, these findings suggest that small {beta}-sheet nuclei in PAP248-286 dimers act as cooperative intermediates that seed the formation of full-length cross-{beta} structures, providing atomistic insights into the earliest steps of SEVI fibril assembly.

biochemistry↗

bioRxiv2025

Tumor-Initiating Cells Fine-tune the Plasticity of Neutrophils to Sculpt a Protective Niche

The abundant accumulation of neutrophils in various solid cancers has been well recognized, but the functions of tumor-associated neutrophils (TANs) remain controversial. TANs have long been believed to be immune suppressive and have thus been referred to as "myeloid-derived suppressor cells". However, effective tumor control induced by immunotherapy was recently found to be associated with strong neutrophil signatures. These seemingly contradictory findings highlight the unexpected degree of plasticity and heterogeneity unique to TANs. How the cellular plasticity and functional heterogeneity of TANs are regulated remains unknown. Here, we show that, while anti-PDL1/CD40 agonist immunotherapy can induce interferon responses to reprogram many TANs, allowing them to become plastic and regain anti-tumor activities in squamous cell carcinomas, a subset of TANs residing at the tumor-stroma interface can preserve their immune suppressive state. Importantly, by designing a reverse genetic screening, we identified a group of Sox2Hi tumor-initiating cells (TICs) at the tumor-stroma interface that could upregulate Fatty Acid Desaturase 1 (Fads1) to produce arachidonic acid. This TIC-specific pathway can disrupt the interferon responsive potentials of TANs, preventing the interferon-mediated reprogramming. Thus, by fine-tuning the plasticity of neutrophils, TICs shape neutrophil heterogeneity and sculpt a protective micro-niche to survive from immunotherapy and drive cancer relapse.

cancer biology↗

bioRxiv2024

HisCl1 regulates gustatory habituation in sweet taste neurons and mediates sugar ingestion in Drosophila

Similar to other animals, the fly, Drosophila melanogaster, reduces its responsiveness to tastants with repeated exposure, a phenomenon called gustatory habituation. Previous studies have focused on the circuit basis of gustatory habituation in the fly chemosensory system 1,2. However, gustatory neurons reduce their firing rate during repeated stimulation 3, suggesting that cell-autonomous mechanisms also contribute to habituation. Here, we used deep learning-based pose estimation and optogenetic stimulation to demonstrate that continuous activation of sweet taste neurons causes gustatory habituation in flies. We conducted a transgenic RNAi screen to identify genes involved in this process and found that knocking down Histamine-gated chloride channel subunit 1 (HisCl1) in the sweet taste neurons significantly reduced gustatory habituation. Anatomical analysis showed that HisCl1 is expressed in the sweet taste neurons of various chemosensory organs. Using single sensilla electrophysiology, we showed that sweet taste neurons reduced their firing rate with prolonged exposure to sucrose. Knocking down HisCl1 in sweet taste neurons suppressed gustatory habituation by reducing the spike frequency adaptation observed in these neurons during high-concentration sucrose stimulation. Finally, we showed that flies lacking HisCl1 in sweet taste neurons increased their consumption of high-concentration sucrose solution at their first meal bout compared to control flies. Together, our results demonstrate that HisCl1 tunes spike frequency adaptation in sweet taste neurons and contributes to gustatory habituation and food intake regulation in flies. Since HisCl1 is highly conserved across many dipteran and hymenopteran species, our findings open a new direction in studying insect gustatory habituation.

neuroscience↗

bioRxiv2023

Investigating the effect of POPC-POPG Lipid Bilayer Composition on PAP248-286 Binding using CG Molecular Dynamics Simulations

PAP248-286 is a fusogenic peptide derived from prostatic acid phosphatase, commonly found in human semen, and is known to mediate HIV fusion with cell membranes. In this study, we performed 120 independent coarse-grained molecular dynamics simulations to investigate the spontaneous binding of PAP248-286 monomers, considering both charged and neutral histidine (His) residues, to membrane bilayers composed of different lipid compositions: 100% POPC, 70% POPC-30% POPG, and 50% POPC-50% POPG. Our simulations revealed that PAP248-286 displayed spontaneous binding to the membrane, with increased binding observed in the presence of anionic lipid POPG. Specifically, in systems containing 30% and 50% POPG lipids, monomer residues, particularly in the systems containing charged histidine (His) residues, exhibited prolonged binding with the membrane. Furthermore, our simulations indicated that PAP248-286 adopted a parallel orientation with the membrane, exposing its positively charged residues to the lipid bilayer. Interestingly, systems containing charged His residues showed higher lipid occupancy around the peptide. These findings are consistent with previous experimental data, suggesting that PAP248-286 binding is enhanced in membranes with charged His residues, resembling the conditions found in the acidic vaginal pH environment. The results of our study provide further insights into the molecular mechanisms underlying the membrane binding of PAP248-286, contributing to our understanding of its potential role in HIV fusion and infection.

biochemistry↗

bioRxiv2023

Detergent induced structural perturbations in peanut agglutinin: Insights from spectroscopic and molecular dynamic simulation studies

The three dimensional structure of a protein is very important for its structure. Studies relating to protein structure have been numerous and the effect of denaturants on proteins can help understand the process of protein folding and misfolding. Detergents are important denaturants and play important roles in various fields. Here we explored the effect of sodium dodecyl sulphate (SDS) and cetyltrimethylammonium bromide (CTAB) on the structure of peanut agglutinin (PNA). The protein was purified from its natural source and impact of SDS and CTAB was studied by circular dichroism, intrinsic fluorescence, 8-anilino-1-napthalenesulfonic acid, molecular docking and molecular dynamics simulation. Pure peanut agglutinin showed a trough at 220 nm and positive ellipticity peak at 195 nm, specific for lectins. Results from the experimental and simulation studies suggest how oppositely charged detergents can interact differently and lead to varied structural perturbations in PNA. Both the surfactants induce all protein-like circular dichroism in the protein, above its critical micelle concentrations, with significant change in accessible surface area that became more hydrophobic upon the treatment. Major interactions between the surfactants and protein, resulting in PNA conformational rearrangement, are electrostatic and van der Waals interactions. However, CTAB, like a cationic surfactant, has similar effects as anionic surfactant (SDS) but at significantly very low concentration. Though the effects followed same pattern in both the surfactant treatment, i.e. above respective CMC, the surfactants were inducing -helix/coil like conformation in PNA.

biochemistry↗

bioRxiv2023

Impact of water models on structure and dynamics of ligand-transport tunnels in enzymes derived from molecular dynamics simulations

Protein hydration plays a vital role in many biological functions and molecular simulations are frequently used to study the effect of protein hydration at the atomic level. However, the accuracy of these simulations has often been highly sensitive to the water model used, a phenomenon best known in the case of intrinsically disordered proteins. In the present study, we investigated the extent to which the choice of water model alters the behavior of complex networks of transport tunnels. Tunnels are essential because they allow substrates and products to access and exit the active sites of enzymes that are otherwise deeply embedded within the protein structure. The ability of these tunnels to regulate access directly affects enzyme efficiency and selectivity, making their study crucial for understanding enzyme function and inhibition at a mechanistic level. By performing all-atom molecular dynamics simulations of the wild-type haloalkane dehalogenase LinBWT and its two variants, LinB32 and LinB86, with synthetically engineered tunnel networks in TIP3P and OPC water models, we investigated the effects of these models on the overall tunnel topology. We also analyzed the properties of the main tunnels, such as their conformation, bottleneck dimensions, sampling efficiency, and duration of the tunnel opening. Our data demonstrate that all three proteins exhibited similar conformational behavior in both water models and differed in the geometrical characteristics of their auxiliary tunnels, in line with experimental observations. Interestingly, the results indicate that the stability of the open tunnels is sensitive to the water model and the system under question. Our findings suggest that the 3-point TIP3P model can provide comparable inference on the overall topology of the networks of primary tunnels and their geometry, and thus may be a desirable choice when computational resources are limited or when compatibility issues impede usage of OPC with certain protein force fields. However, when a more thorough investigation is performed, such as the calculation of ligand unbinding rates via such tunnel networks, where precision and intricate details are paramount, the more costly 4-point OPC model would be more suited. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/537534v2_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1d9a56eorg.highwire.dtl.DTLVardef@1fbe3f7org.highwire.dtl.DTLVardef@336f2corg.highwire.dtl.DTLVardef@c7b8fc_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2022

A Coarse-Grained Molecular Dynamics Investigation on Spontaneous Binding of Aβ9-40 Fibril with Cholesterol-mixed DPPC Bilayer

Alzheimers disease is the most common form of dementia. Its aetiology is characterized by the misfolding and aggregation of amyloid-{beta} (A{beta}) peptides into {beta}-sheet-rich A{beta} oligomers/fibrils. Whereas experimental studies have suggested that A{beta} oligomers/fibrils interact with the cell membranes and perturb their structures and dynamics, the molecular mechanism of this interaction is still not fully understood. In the present work, we have performed a total of 120 s-long simulations to investigate the interaction between trimeric or hexameric A{beta}1-40 fibrils with either a 100% DPPC bilayer, a 70% DPPC-30% cholesterol bilayer or a 50% DPPC-50 % cholesterol bilayer. Our simulation data capture the spontaneous binding of the aqueous A{beta}1-40 fibrils with the membranes and show that the central hydrophobic amino acid cluster, the lysine residue adjacent to it and the C-terminal hydrophobic residues are all involved in the process. Moreover, our data show that while the A{beta}1-40 fibril does not bind to the 100% DPPC bilayer, its binding affinity for the membrane increases with the amount of cholesterol. Overall, our data suggest that two clusters of hydrophobic residues and one lysine help A{beta}1-40 fibrils establish stable interactions with a cholesterol-rich DPPC bilayer. These residues are likely to represent potential target regions for the design of inhibitors, thus opening new avenues in structure-based drug design against A{beta} oligomer/fibril-membrane interaction.

biochemistry↗

bioRxiv2022

Early Stages of Misfolding of PAP248-286 at two different pH values: An Insight from Molecular Dynamics Simulations

PAP248-286 peptides, which are highly abundant in human semen, aggregate and form amyloid fibrils that enhance HIV infection. Previous experimental studies have shown that the infection-promoting activity of PAP248-286 begins to increase well before amyloid formation takes place and that pH plays a key role in the enhancement of PAP248-286-related infection. Hence, understanding the early stages of misfolding of the PAP2482-86 peptide is crucial. To this end, we have performed 60 independent MD simulations for a total of 24 s at two different pH values (4.2 and 7.2). Our data shows that misfolding of the PAP248-286 peptide is a multistage process and that the first step of the process is a transition from an "I-shaped" structure to a "U-shaped" structure. We further observed that the structure of PAP248-286 at the two different pH values shows significantly different features. At pH 4.2, the peptide has less intra-molecular H-bonds and a reduced -helical content than at pH 7.2. Moreover, differences in intra-peptide residues contacts are also observed at the two pH values. Finally, free energy landscape analysis shows that there are more local minima in the energy surface of the peptide at pH 7.2 than at pH 4.2. Overall, the present study elucidates the early stages of misfolding of the PAP248-286 peptide at the atomic level, thus possibly opening new avenues in structure-based drug discovery against HIV infection.

biochemistry↗

bioRxiv2021

TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them

Information regarding pathways through voids in biomolecules and their roles in ligand transport is critical to our understanding of the function of many biomolecules. Recently, the advent of high-throughput molecular dynamics simulations has enabled the study of these pathways, and of rare transport events. However, the scale and intricacy of the data produced requires dedicated tools in order to conduct analyses efficiently and without excessive demand on users. To fill this gap, we developed the TransportTools, which allows the investigation of pathways and their utilization across large, simulated datasets. TransportTools also facilitates the development of custom-made analyses. TransportTools is implemented in Python3 and distributed as pip and conda packages. The source code is available at https://github.com/labbit-eu/transport_tools.

bioinformatics↗

bioRxiv2021

Management of altered metabolic activity in Drosophila model of Huntington's disease by curcumin

Huntingtons disease (HD) is a devastating polyglutamine (polyQ) disorder characterized by extensive neurodegeneration and metabolic abnormalities at systemic, cellular and intracellular levels. Metabolic alterations in HD manifest as abnormal body weight, dysregulated biomolecule levels, impaired adipocyte functions and defective energy state which exacerbate disease progression and pose acute threat to the health of challenged individuals in form of insulin resistance, cardiovascular disease and energy crisis. To colossally mitigate disease symptoms, we tested the efficacy of curcumin in Drosophila model of HD. Curcumin is bioactive component of turmeric (Curcuma longa Linn), well-known for its ability to modulate metabolic activities. We found that curcumin effectively managed abnormal body weight, dysregulated lipid content and carbohydrate level in HD flies. In addition, curcumin administration lowered elevated reactive-oxygen-species (ROS) levels in adult adipose tissue of diseased flies, and improved survival and locomotor function in HD flies at advanced disease stage. Altogether, these findings clearly suggest that curcumin efficiently attenuates metabolic derangements in HD flies and can prove beneficial in alleviating the complexities associated with HD. Phytochemicals like curcumin that can regulate multiple targets in complex diseases like HD, with least side-effects and maximum benefits, provide a better hope for the treatment of terminally-ill HD patients.

neuroscience↗

bioRxiv2020

TMPRSS2, a SARS-CoV-2 internalization protease is downregulated in head and neck cancer patients.

ObjectivesTwo of the main target tissues of SARS-coronavirus 2 are the oral cavity pharynx-larynx epithelium, the main virus entry site, and the lung epithelium. The virus enters host cells through binding of the Spike protein to ACE2 receptor and subsequent S priming by the TMPRSS2 protease. Herein we aim to assess differences in both ACE2 and TMPRSS2 expression in normal tissues from oral cavity-pharynx-larynx and lung tissues as well as neoplastic tissues from the same histological areas. The information provided in this study may contribute to better understanding of SARS-coronavirus 2 ability to interact with different biological systems and contributes to cumulative knowledge on potential mechanisms to inhibit its diffusion. Materials and MethodsThe study has been conducted using The Cancer Genome Atlas (TCGA) and the Regina Elena Institute (IRE) databases and validated by experimental model in HNSCC and Lung cancer cells. Data from one COVID19 positive patient who was operated on for HNSCC was also included. We have analyzed 478 tumor samples and 44 normal samples from TCGA HNSCC cohort for whom both miRNA and mRNA sequencing was available. The dataset included 391 HPV- and 85 HPV+ cases, with 331 P53 mutated and 147 P53 wild type cases respectively. 352 out of 478 samples were male and 126 female. In IRE cohort we analyzed 66 tumor samples with matched normal sample for miRNA profiling and 23 tumor\normal matched samples for mRNA profiling. 45 out of 66 tumors from IRE cohort were male and 21 female, 38 were P53 mutated and 27 wild type. Most patients (63 of 66) in IRE cohort were HPV negative. Normalized TCGA HNSCC gene expression and miRNA expression data were obtained from Broad Institute TCGA Genome Data Analysis Center (http://gdac.broadinstitute.org/). mRNA expression data from IRE cohort used in this study has been deposited to NCBIs Gene Expression Omnibus and is accessible through GEO series accession number GSE107591. In order to inference about potential molecular modulation of TMPRSS2, we also included miRNAs expression for the 66 IRE cohort matched tumor and normal samples from Agilent platform. DNA methylation data for TCGA tumors were obtained from Wanderer (http://maplab.imppc.org/wanderer/). We used miRWalk and miRNet web tools for miRNA-target interaction prediction and pathway enrichment analysis. The correlation and regression analyses as well as the miRNA and gene modulation and the survival analysis were conducted using Matlab R2019. ResultsTMPRSS2 expression in HNSCC was significantly reduced compared to the normal tissues and had a prognostic value in HNSCC patients. Reduction of TMPRSS2 expression was more evident in women than in men, in TP53 mutated versus wild TP53 tumors as well as in HPV negative patients compared to HPV positive counterparts. Functionally, we assessed the multivariate effect on TMPRSS2 in a single regression model. We observed that all variables had an independent effect on TMPRSS2 in HNSCC patients with HPV negative, TP53 mutated status and with elevated TP53-dependent Myc-target genes associated with low TMPRSS2 expression. Investigation of the molecular modulation of TMPRSS2 in both HNSCC and lung cancers revealed that expression of microRNAs targeting TMPRSS2 anti-correlated in both TCGA and IRE HNSCC datasets, while there was not evidence of TMPRSS2 promoter methylation in both tumor cohorts. Interestingly, the anti-correlation between microRNAs and TMPRSS2 expression was corroborated by testing this association in a SARS-CoV-2 positive HNSCC patient. ConclusionsCollectively, these findings suggest that tumoral tissues, herein exemplified by HNSCC and lung cancers might be more resistant to SARS-CoV-2 infection due to reduced expression of TMPRSS2. The protective mechanism might occur, at least partially, through the aberrant activation of TMPRSS2 targeting microRNAs; thereby providing strong evidence on the role of non-coding RNA molecule in host viral infection. These observations may help to better assess the frailty of SARS-CoV-2 positive cancer patients.

cancer biology↗

bioRxiv2019

Functional interactions between post-translationally modified amino acids of methyl-coenzyme M reductase in Methanosarcina acetivorans

Methyl-coenzyme M reductase (MCR) plays an important role in mediating global levels of methane by catalyzing a reversible reaction that leads to the production or consumption of this potent greenhouse gas in methanogenic and methanotrophic archaea. In methanogenic archaea, the alpha subunit of MCR (McrA) typically contains four to six post-translationally modified amino acids near the active site. Recent studies have identified genes that install two of these modifications (thioglycine and 5-(S)-methylarginine), yet little is known about the installation and function of the remaining post-translationally modified residues. Here, we provide in vivo evidence that a dedicated SAM-dependent methyltransferase encoded by a gene we designated mcmA is responsible for formation of S-methylcysteine in Methanosarcina acetivorans McrA. Phenotypic analysis of mutants incapable of cysteine methylation suggests that the S-methylcysteine residue plays an important role in adaptation to a mesophilic lifestyle. To examine the interactions between the S-methylcysteine residue and the previously characterized thioglycine, 5-(S)-methylarginine modifications, we generated M. acetivorans mutants lacking the three known modification genes in all possible combinations. Phenotypic analyses revealed complex, physiologically relevant interactions between the modified residues, which alter the thermal stability of MCR in a combinatorial fashion that is not readily predictable from the phenotypes of single mutants. Surprisingly, high-resolution crystal structures of the various unmodified MCRs were indistinguishable from the fully modified enzyme, suggesting that interactions between the post-translationally modified residues do not exert a major influence on the physical structure of the enzyme, but rather serve to fine-tune the activity and efficiency of MCR.

microbiology↗

bioRxiv2019

Deep learning detects virus presence in cancer histology

Oncogenic viruses like human papilloma virus (HPV) or Epstein Barr virus (EBV) are a major cause of human cancer. Viral oncogenesis has a direct impact on treatment decisions because virus-associated tumors can demand a lower intensity of chemotherapy and radiation or can be more susceptible to immune check-point inhibition. However, molecular tests for HPV and EBV are not ubiquitously available.\n\nWe hypothesized that the histopathological features of virus-driven and non-virus driven cancers are sufficiently different to be detectable by artificial intelligence (AI) through deep learning-based analysis of images from routine hematoxylin and eosin (HE) stained slides. We show that deep transfer learning can predict presence of HPV in head and neck cancer with a patient-level 3-fold cross validated area-under-the-curve (AUC) of 0.89 [0.82; 0.94]. The same workflow was used for Epstein-Barr virus (EBV) driven gastric cancer achieving a cross-validated AUC of 0.80 [0.70; 0.92] and a similar performance in external validation sets. Reverse-engineering our deep neural networks, we show that the key morphological features can be made understandable to humans.\n\nThis workflow could enable a fast and low-cost method to identify virus-induced cancer in clinical trials or clinical routine. At the same time, our approach for feature visualization allows pathologists to look into the black box of deep learning, enabling them to check the plausibility of computer-based image classification.

cancer biology↗