Search bioRxiv⌕ Search

Biology subjects

Iyer, V.

Publications and source records attributed to Iyer, V..

17 recordsLinked to original sources

Mesoscale Soft Robotics for Mechanically Perturbing and Functionally Monitoring Responses in Human Organoids

Human organoids represent promising models for studies of significance to the biology and medical communities. Of the existing approaches for monitoring organoids, none offers the ability to apply programmable mechanical forces while simultaneously recording multi-modal physiological responses, of relevance to phenomena spanning from traumatic brain injuries to cardiac rhythm disorders. Here, we present a mesoscale soft robotic organoid interface that enables programmable delivery of forces to organoids of diverse shapes, and to map electrophysiological activity and mechanical responses. The platform combines actuation elements with integrated sensors for quantitative measurement and control. Studies using this technology reveal that spheroidal cortical organoids exhibit distinct responses to mechanical trauma, including silencing, recovery, and changes in neuronal firing patterns. Additional experiments on cardiac ring tissues demonstrate that sustained stretching induces beat-to-beat rhythm variability and altered conduction. The results establish a framework for investigating force-triggered transitions between physiological and disease-like states in human tissue models.

bioengineering↗

RTTN moonlights beyond the centrosome to control ribosome biogenesis and tRNA modification in human brain organoids

RTTN (rotatin) is a centrosomal protein mutated in severe malformations of cortical development, yet how its dysfunction disrupts human corticogenesis has remained unclear. Here, we show that RTTN has an unrecognized function at the core of the translation machinery. Using human telencephalic and hippocampal organoids carrying distinct RTTN alleles, together with single-cell and bulk transcriptomics, polysome profiling, and tRNA pseudouridine sequencing, we find that RTTN is enriched in cycling first-trimester neural progenitors and physically associates with ribosome-biogenesis and RNA-processing factors. RTTN mutations impair rRNA biogenesis and polysome assembly, reduce cytoplasmic ribosome density and nascent protein synthesis, and remodel the tRNA pseudouridylation landscape through both a PUS7L-dependent variable-arm signature and a broader RTTN-specific defect. These translational deficits are accompanied by prolonged mitosis, reduced entry into S-phase, and impaired interkinetic nuclear migration in mutant progenitors. Our findings redefine RTTN as a regulator of ribosome homeostasis and mRNA translation and implicate defective translational capacity as a driver of RTTN-associated microcephaly. Graphical AbstractRTTN sustains ribosome and tRNA homeostasis in human neural progenitors; its mutation disrupts mRNA translation, stalling progenitor proliferation and interkinetic nuclear migration, and driving cortical malformation and growth failure. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/744412v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@16124aaorg.highwire.dtl.DTLVardef@ae23f7org.highwire.dtl.DTLVardef@bb588forg.highwire.dtl.DTLVardef@1b35028_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

In vivo screening reveals new regulators of Natural Killer cell development and functional response to acute cytomegalovirus infection

Natural killer (NK) cells are critical innate immune effectors in antiviral and antitumour responses. However, the factors governing NK cell development and function remain incompletely understood. To address this, we adopted an in vivo screening approach, generating a panel of mice deficient in genes differentially expressed across NK cell maturation stages or following viral infection. We performed a combinational screen comprising baseline immunophenotyping and mouse cytomegalovirus (MCMV) challenge. We identified novel regulators of NK cell development, including transcriptional regulators and proteins with putative trafficking functions. MCMV challenge studies additionally identified proteins that impacted antiviral immunity independently of NK cell phenotypes, including a novel regulator of NK cell degranulation, Synaptotagmin-like protein 3. Identified genes exhibited reduced tolerance to loss-of-function in large scale human sequencing studies and evidence for reduced NK cell numbers in a cohort of immunodeficiency patients. Together, these findings provide a resource of NK-expressed genes important for NK cell maturation and function, with relevance to human health. SummaryPring et al. conduct an in vivo screen in mice identifying novel regulators of natural killer (NK) cell development and/or antiviral functionality. Large-scale human sequencing and human immunodeficiency patients revealed evidence for the relevance of identified genes in human health.

immunology↗

Anthropogenic habitats shape gut microbiome composition in Southern Indian bats

BackgroundAnthropogenic habitat modification and associated resources can exert selection pressures on wildlife and their microbiomes, altering their diversity, resulting in homogenization and making them resemble the human microbiome. Diet is an important predictor of the microbiomes of volant vertebrates, mainly for birds, but for bats, results remain inconclusive. In spite of Indias exceptional bat diversity, there is little understanding of how their microbiomes respond to anthropogenic habitats. Therefore, we investigated the trends of taxonomic and functional diversity and their relationships with host feeding-guild and phylogeny for six wide-ranging bat species across six anthropogenically modified sites in Southern India by generating 16S barcode sequences from their fecal samples. ResultsEubacteria dominated samples with diet-specific taxonomic composition. Frugivore microbiomes contained large proportions of Cyanobacteria, possibly sourced from consumed plant matter or polluted drinking-water sources, and Lactobacillales dominated insectivore microbiomes, while Gammaproteobacteria were abundant regardless of host feeding guild. We found human pathogens in our samples possibly transferred from polluted water to the guts of bats foraging in nearby areas. We observed diet-specific taxonomic, phylogenetic, and functional composition. However, functional composition incorporating abundances displayed a high degree of overlap across feeding-guilds, suggesting functional homogenisation of microbiomes across feeding guilds, possibly due to anthropogenicity. Sample-wise diversity indices were significantly different with respect to diet only when samples from the same roost were not pooled together. However, in all cases, microbiomes from the same diet types displayed significant taxonomic and phylogenetic similarity to each other. Lastly, we observed limited concordance of microbiome diversity with chiropteran phylogeny. ConclusionsBecause of these potential signatures of pollution on bat microbiomes such as pathogens, we recommend their monitoring, especially because Cyanobacteria play a known role in bat and human disease. Our study is one of the first to study microbiome composition and function from bat species common around human inhabitation in South India, and establishes baselines in this region.

evolutionary biology↗

WxS-QC - a quality control pipeline for human Whole-Genome and Whole Exome sequencing cohorts

MotivationWhole-exome (WES) and whole-genome (WGS) sequencing are rapidly becoming preferred methods for population-scale analysis of the human genetic landscape. However, there are currently no standardized quality control (QC) pipelines for human WES and WGS datasets. Moveover, there are no open datasets that can be used to test QC pipelines, because most projects (like 1000 genomes and gnomAD) publish only post-QC results. ResultsWe present WxS-QC, a powerful, scalable, and convenient pipeline for the QC of human WGS and WES cohorts, developed at the Wellcome Sanger Institute (WSI). Our pipeline is based on a deep refactoring of the gnomAD quality control pipeline code and is aligned with current best practices in WGS/WES cohort data QC. It offers a set of novel QC techniques, automatic export of resulting graphs and summary tables, excellent performance and scalability, and incorporates comprehensive documentation. To test our pipeline and similar solutions, we also assembled an open dataset with all required metadata. Availability and implementationThe pipeline code is written in Python using the Hail library and is freely available under the BSD-3 license here: https://github.com/wtsi-hgi/wxs-qc. It can run in any UNIX-like environment and has been able to efficiently process cohorts of up to 200,000 whole-exome samples with the potential to handle bigger datasets, depending on the available hardware. The detailed description of the pipeline, resources and test data is available in the pipeline documentation: https://github.com/wtsi-hgi/wxs-qc/blob/main/README.md The open test dataset is available to download from https://wxs-qc-data.cog.sanger.ac.uk/wxs-qc_public_dataset_v3.tar. An example of test dataset analysis is available in the supplementary materials.

bioinformatics↗

Species synonyms depict changing but taxon-independent taxonomic praxis

What constitutes a single species is ultimately arbitrary, resulting in idiosyncrasies in taxonomic praxis determining species counts. One consequence of this arbitrariness is taxonomic synonymization, wherein variation determined not unique enough to constitute distinct species gets merged into one. Synonymization is non-random and subject to taxon and trait-specific biases. We explore these trends using a comprehensive dataset of the worlds marine species for all large phyla and Animalia. We match all accepted species-names from the present day with their synonyms and calculate metrics of synonymization including the time lag between the years of descriptions of a species and its newest synonym. We find that although species description trends across phyla show no consistent, discernible trends, the fraction of names that gets synonymised remains initially constant across phyla, with a subsequent gradual decrease. Most accepted species described around the early 20th century possess synonyms created in the same year, indicating synonyms arising due to new name combinations, suggesting a distinct period of taxonomic praxis. This period was followed by a period of most species descriptions lacking synonyms on moving towards the present. Across taxa, we find the mean lag to be strongly negatively correlated to time, with time not being a limiting factor determining this trend. We also find the number of synonyms per accepted name to also be strongly negatively correlated to time in a taxon-independent manner. Our study considers when the diversity characterising species in the form of once-unique species-names becomes known to science. Our results suggest that across taxa, species described more recently encompass less biological variability, indicating a gradual change in how morphologically delineated species which comprise the vast majority of species described across time are described.

ecology↗

Immunogenicity and Structural Features of a Stabilized Clade-C HIV-1 Env Derived from a Pediatric Elite-neutralizer

The envelope (Env) glycoprotein derived from circulating viruses in elite-neutralizers (who naturally develop broadly neutralizing antibodies (bNAbs)), serves as potential template for HIV-1 vaccine design. Herein, we report the structure and immunogenicity of soluble clade-C HIV-1 Env trimer (330) derived from a pediatric elite-neutralizer (AIIMS_330). Using SOSIP, NFL and ferritin-nanoparticle (NP) platforms, we engineered immunogens that preserved native-like Env conformation, exhibited high thermostability and nanomolar affinity for diverse bNAbs, with minimal reactivity to non-neutralizing antibodies. Cryo-EM structure solved at 5 [A] resolution of 330-SOSIP trimer-autologous bNAb 44m complex revealed interactions at GDIR motif, N332 supersite along with additional contacts at E293, K337, K446 and glycans N326, N442, N448, as compared to our previously reported BG505-44m structure. Rabbit immunizations with soluble and NP-displayed formats elicited autologous, and heterologous neutralization of tier-1 clade-C viruses. Herein we define a structurally resolved HIV-1 clade C Env that supports multivalent vaccine strategies and provides mechanistic insights toward rational HIV-1 immunogen design.

immunology↗

Tropical island endemic birds' demographic responses to climate are modulated by habitat availability and species traits

Climate change and associated habitat fluctuations can expedite the diversification of insular lineages or lead to isolation and extinction. Tropical island birds are a model system to assess responses to climate change owing to their insular nature and ability to diversify rapidly. While there is some understanding of the diversification of tropical island avian clades, we are yet to understand the vulnerability of these species to climate change. Long-term species genetic diversity and historical demography are critical predictors of this. Therefore, we investigated the sensitivity of tropical island endemic birds to climate change and analysed how species traits determine these responses by comparing species traits with demographic histories and paleohabitat fluctuations during the Last Glacial Period (LGP). From publicly available whole genome and paleoclimatic datasets, we reconstructed tropical island endemics past demographic histories (effective population size (Ne)) using Pairwise Sequential Markovian Coalescent (PSMC) (n = 23) and suitable habitat (n = 29) during the LGP and the Holocene. We observed that most species experienced an increase in suitable habitat between the Last Interglacial and the Last Glacial Maximum. However, a concomitant increase in Ne was only observed in the hyper-diverse passerine clade, attesting to their ability to rapidly diversify. Overall, diet specialists and large-bodied species showed a decrease in Ne during the LGP. Our results indicate that species traits dictate tropical island endemics demographic responses to climate, and a plastic response to habitat availability could be a consequence of clades abilities to rapidly occupy new niches and diversify. Further, our analyses revealed that most species entered the Holocene with low effective population sizes. Given that tropical island endemics have small geographic ranges and are groups vulnerable to climate change, special efforts are necessary to conserve them. We recommend that conservation management policies add components like historical demography and species traits while assessing extinction threats for island populations.

evolutionary biology↗

Transfer RNA acetylation regulates in vivo mammalian stress signaling

Transfer RNA (tRNA) modifications are crucial for protein synthesis, but their position-specific physiological roles remain poorly understood. Here we investigate the impact of N4-acetylcytidine (ac4C), a highly conserved tRNA modification, using a Thumpd1 knockout mouse model. We find that loss of Thumpd1-dependent tRNA acetylation leads to reduced levels of tRNALeu, increased ribosome stalling, and activation of eIF2 phosphorylation. Thumpd1 knockout mice exhibit growth defects and sterility. Remarkably, concurrent knockout of Thumpd1 and the stress-sensing kinase Gcn2 causes penetrant postnatal lethality, indicating a critical genetic interaction. Our findings demonstrate that a modification restricted to a single position within type II cytosolic tRNAs can regulate ribosome-mediated stress signaling in mammalian organisms, with implications for our understanding of translation control as well as therapeutic interventions.

developmental biology↗

Negative allosteric modulation of cannabinoid CB1 receptor signaling suppresses opioid-mediated tolerance and withdrawal without blocking opioid antinociception

The direct blockade of CB1 cannabinoid receptors produces therapeutic effects as well as adverse side-effects that limit their clinical potential. CB1 negative allosteric modulators (NAMs) represent an indirect approach to decrease the affinity and/or efficacy of orthosteric cannabinoid ligands or endocannabinoids at CB1. We recently reported that GAT358, a CB1-NAM, blocked opioid-induced mesocorticolimbic dopamine release and reward via a CB1-allosteric mechanism of action. Whether a CB1-NAM dampens opioid-mediated therapeutic effects such as analgesia or alters other unwanted side-effects of opioids remain unknown. Here, we characterized the effects of GAT358 on nociceptive behaviors in the presence and absence of morphine. We examined the impact of GAT358 on formalin-evoked pain behavior and Fos protein expression, a marker of neuronal activation, in the lumbar dorsal horn. We also assessed the impact of GAT358 on morphine-induced slowing of colonic transit, tolerance, and withdrawal behaviors. GAT358 attenuated morphine antinociceptive tolerance without blocking acute antinociception. GAT358 also reduced morphine-induced slowing of colonic motility without impacting fecal boli production. GAT358 produced antinociception in the presence and absence of morphine in the formalin model of inflammatory nociception and reduced the number of formalin-evoked Fos protein-like immunoreactive cells in the lumbar spinal dorsal horn. Finally, GAT358 mitigated the somatic signs of naloxone-precipitated, but not spontaneous, opioid withdrawal following chronic morphine dosing in mice. Our results support the therapeutic potential of CB1-NAMs as novel drug candidates aimed at preserving opioid-mediated analgesia while preventing their unwanted side-effects. Our studies also uncover previously unrecognized antinociceptive properties associated with an arrestin-biased CB1-NAMs. HighlightsO_LICB1 negative allosteric modulator (NAM) GAT358 attenuated morphine tolerance C_LIO_LIGAT358 reduced morphine-induced slowing of colonic motility but not fecal production C_LIO_LIGAT358 was antinociceptive for formalin pain alone and when combined with morphine C_LIO_LIGAT358 reduced formalin-evoked Fos protein expression in the lumbar spinal cord C_LIO_LIGAT358 mitigated naloxone precipitated withdrawal after chronic morphine dosing C_LI

neuroscience↗

SAMHD1 controls innate immunity by regulating condensation of immunogenic self RNA

Recognition of pathogen-derived foreign nucleic acids is central to innate immune defense. This requires discrimination between structurally highly similar self and nonself nucleic acids to avoid aberrant inflammatory responses as in the autoinflammatory disorder Aicardi-Goutieres syndrome (AGS). How vast amounts of self RNA are shielded from immune recognition to prevent autoinflammation is not fully understood. Here we show that SAM domain and HD domain-containing protein 1 (SAMHD1), one of the AGS-causing genes, functions as a single-stranded RNA (ssRNA) 3exonuclease, the lack of which causes cellular RNA accumulation. Increased ssRNA in cells leads to dissolution of RNA-protein condensates, which sequester immunogenic double-stranded RNA (dsRNA). Release of sequestered dsRNA from condensates triggers activation of antiviral type I interferon via retinoic acid-inducible gene I-like receptors. Our results establish SAMHD1 as a key regulator of cellular RNA homeostasis and demonstrate that buffering of immunogenic self RNA by condensates regulates innate immune responses.

immunology↗

Accelerating Minimap2 for accurate long read alignment on GPUs

Long read sequencing technology is becoming increasingly popular for Precision Medicine applications like Whole Genome Sequencing (WGS) and microbial abundance estimation. Minimap2 is the state-of-the-art aligner and mapper used by the leading long read sequencing technologies, today. However, Minimap2 on CPUs is very slow for long noisy reads. [~]60-70% of the run-time on a CPU comes from the highly sequential chaining step in Minimap2. On the other hand, most Point-of-Care computational workflows in long read sequencing use Graphics Processing Units (GPUs). We present minimap2-accelerated (mm2-ax), a heterogeneous design for sequence mapping and alignment where minimap2s compute intensive chaining step is sped up on the GPU and demonstrate its time and cost benefits. We extract better intra-read parallelism from chaining without loosing mapping accuracy by forward transforming Minimap2s chaining algorithm. Moreover, we better utilize the high memory available on modern cloud instances apart from better workload balancing, data locality and minimal branch divergence on the GPU. We show mm2-ax on an NVIDIA A100 GPU improves the chaining step with 5.41 - 2.57X speedup and 4.07 - 1.93X speedup : costup over the fastest version of Minimap2, mm2-fast, benchmarked on a Google Cloud Platform instance of 30 SIMD cores.

genomics↗

Long noncoding RNA VENTHEART is required for cardiomyocyte specification and function

RationaleLong noncoding RNAs (lncRNAs) control cardiac gene expression during heart development and disease. It is accordingly plausible for the same lncRNA to regulate both cardiac development, as well as play a role in adult heart disease progression. lncRNA regulators of early cardiomyocyte (CM) lineage commitment have been identified and characterised, however those controlling later CM specification remain unknown. ObjectivesIn this study we identified a novel lncRNA required for CM specification, maturation and function, and also discovered its suggested relevance to heart disease. Methods and ResultsWe performed single cell RNA-seq on human embryonic stem cell derived cardiomyocytes at 2, 6 and 12 weeks of differentiation. Weighted correlation network analysis (WGCNA) identified core gene modules, including lncRNAs highly abundant and uniquely expressed in the human heart. A lncRNA (we call VENTHEART, VHRT) co-expressed with cardiac maturation and ventricular-specific genes MYL2 and MYH7, as well as in adult human ventricular tissue. CRISPR-mediated excision of VHRT led to impaired CM sarcomere formation, and loss of the CM specification gene program. VHRT knockdown (KD) in hESC-CMs confirmed its regulatory role for key cardiac contraction, calcium hemostasis and heart development genes, including MYH6 and RYR2. Functional evaluation after VHRT KD using impedance-based technology and action potential recordings, proved reduced contraction amplitude and loss of the ventricular-like action potential in CM, respectively. Through an integrative analysis of genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) and gene co-expression network, we found VHRT to be co-regulated with core cardiac contractile genes, and the likely source of a heart failure genetic association signal overlapping the VHRT gene locus. Finally, VHRT KD and human failing heart transcriptome comparison validates the consistent downregulation again of cardiac contractile and calcium regulatory genes (P<0.05). ConclusionWe conclude that VHRT lncRNA is required for proper CM specification and function. Furthermore, reduced VHRT may contribute to the development or progression of human heart disease.

cell biology↗

A genome-wide screen in mice to identify cell-extrinsic regulators of pulmonary metastatic colonisation

Metastatic colonisation, whereby a disseminated tumour cell is able to survive and proliferate at a secondary site, involves both tumour cell-intrinsic and -extrinsic factors. To identify tumour cell-extrinsic (microenvironmental) factors that regulate the ability of metastatic tumour cells to effectively colonise a tissue, we performed a genome-wide screen utilising the experimental metastasis assay on mutant mice. Mutant and wildtype (control) mice were tail vein-dosed with murine metastatic melanoma B16-F10 cells and 10 days later the number of pulmonary metastatic colonies were counted. Of the 1,300 genes/genetic locations (1,344 alleles) assessed in the screen 34 genes were determined to significantly regulate pulmonary metastatic colonisation (15 increased and 19 decreased; P<0.005 and genotype effect <-60 or >+60). Whilst several of these genes have known roles in immune system regulation (Bach2, Cyba, Cybb, Cybc1, Id2, Igh-6, Irf1, Irf7, Ncf1, Ncf2, Ncf4 and Pik3cg) most are involved in a disparate range of biological processes, ranging from ubiquitination (Herc1) to diphthamide synthesis (Dph6) to Rho GTPase-activation (Arhgap30 and Fgd4), with no previous reports of a role in the regulation of metastasis. Thus, we have identified numerous novel regulators of pulmonary metastatic colonisation, which may represent potential therapeutic targets.

cancer biology↗

Minimized double guide RNA libraries enable scale-limited CRISPR/Cas9 screens

Genetic screens based on CRISPR/Cas technology are a powerful tool for understanding cellular phenotypes. However, the coverage and replicate requirements result in large experiment sizes, which are limiting when samples are scarce, or the protocols are expensive and laborious. Here, we present an approach to reduce the scale of genome-wide perturbation screens up to fivefold without sacrificing performance. To do so, we deliver two randomly paired gRNAs into each cell, and rely on recent advances in gRNA design, as well as availability of gRNA effect measurements, to reduce the number of gRNAs per gene. We designed a human genome-wide library that has effective size of 30,000 constructs, yet targets each gene with three gRNAs. Our minimized double guide RNA library gives similar results to a standard single gRNA one, but using substantially fewer cells. We demonstrate that genome-wide screens can be optimized in a demanding model of induced pluripotent stem cells, reducing reagent cost 70% per replicate compared to conventional approach, while retaining high performance. The screen design and the reduction in scale it provides will enable functional genomics experiments across many possible combinations of environments and genetic backgrounds, as well as in hard to obtain and culture primary cells.

genetics↗

No unexpected CRISPR-Cas9 off-target activity revealed by trio sequencing of gene-edited mice

Introduction Introduction Results and Discussion Conclusion Author Contributions Competing Financial Interests 1. gRNA choices and... 2. Zygote injection 3. DNA extraction from... 4. Amplicon sequencing and... 5. Whole Genome Sequencing 6. Probability of detecting... 7. Variant calling, Trio... 8. Intersection of all... 9. Comparison of SNVs... 10. Validation with PCR... 11. Re-analysis of De... Supplementary Figure Supplementary tables References CRISPR-Cas technologies have transformed genome-editing of experimental organisms and have ...

bioengineering↗

A screen for combination therapies in BRAF/NRAS wild type melanoma identifies nilotinib plus MEK inhibitor as a synergistic combination

Despite recent therapeutic advances in the management of BRAFV600-mutant melanoma, there is still a compelling need for more effective treatments for patients who developed BRAF/NRAS wild type disease. Since the activity of single targeted agents is limited by innate and acquired resistance, we performed a high-throughput drug screen using 180 drug combinations to generate over 18,000 viability curves, with the aim of identifying agents that synergise to kill BRAF/NRAS wild type melanoma cells. From this screen we observed strong synergy between the tyrosine kinase inhibitor nilotinib and MEK inhibitors and validated this combination in an independent cell line collection. We found that AXL expression was associated with synergy to the nilotinib/MEK inhibitor combination, and that both drugs work in concert to suppress pERK. This finding was supported by genome-wide CRISPR screening which revealed that resistance mechanisms converge on regulators of the MAPK pathway. Finally, we validated the synergy of nilotinib/trametinib combination in vivo using patient-derived xenografts. Our results indicate that a nilotinib/MEK inhibitor combination may represent an effective therapy in BRAF/NRAS wild type melanoma patients.

cancer biology↗