Biology subjects

Patel, J.

Publications and source records attributed to Patel, J..

At least 73 records · Page 4Linked to original sources

bioRxiv2022

Long-term NAD+ supplementation prevents the progression of age-related hearing loss in mice

Age-related hearing loss (ARHL) is the most common sensory disability associated with human aging. Yet, there are no approved measures for preventing or treating this debilitating condition. With its slow progression, continuous and safe approaches are critical for ARHL treatment. Nicotinamide Riboside (NR), a NAD+ precursor, is well tolerated even for long-term use and is already shown effective in various disease models including Alzheimers and Parkinsons Disease. It has also been beneficial against noise induced hearing loss and in hearing loss associated with premature aging. However, its beneficial impact on ARHL is not known. Using two different wild-type mouse strains, we show that long-term NR administration prevents the progression of ARHL. Through transcriptomic and biochemical analysis, we find that NR administration restores age-associated reduction in cochlear NAD+ levels, upregulates biological pathways associated with synaptic transmission and PPAR signaling, and reduces the number of orphan ribbon synapses between afferent auditory neurons and inner hair cells. We also find that NR targets a novel pathway of lipid droplets in the cochlea by inducing the expression of CIDEC and PLIN1 proteins that are downstream of PPAR signaling and are key for lipid droplet growth. Taken together, our results demonstrate the therapeutic potential of NR treatment for ARHL and provide novel insights into its mechanism of action.

animal behavior and cognition↗

bioRxiv2022

Development of amidase-dependent pyrazinoic acid prodrugs with activity against pyrazinamide resistant Mycobacterium tuberculosis

Rapid emergence of drug resistance in Mycobacterium tuberculosis (Mtb) is one of the most significant healthcare challenges of our time. The cause of drug resistance is multifactorial, with the long course anti-tubercular therapy required to treat tuberculosis (TB) constituting a major contributing factor. Introduction of pyrazinamide (PZA) resulted in shortening of TB treatment from twelve to six months and consequently played a critical role in curbing drug resistance that developed over long course therapy. Nevertheless, because PZA is a prodrug activated by a nonessential amidase, PncA, resistance to PZA develops and frequently results in treatment failure. Here, we leveraged a whole cell drug screening approach to identify anti-tuberculars with unconventional mechanisms of action or activation that could be further developed into compounds effective at killing Mtb resistant to PZA. We discovered an amide containing prodrug, DG160, that was activated by the amidase, Rv2888c (AmiC). This amidase was capable of metabolizing a variety of amide containing compounds including a novel pyrazinoic acid-isoquinolin-1-amine prodrug, JSF-4302, which we developed as a potential PncA-independent replacement for PZA. As predicted, AmiC activation of JSF-4302 led to the generation of POA in Mtb including in a PZA resistant clinical isolate, thereby successfully delivering the active component of PZA while bypassing the need for activation by PncA. This work provides a framework for a new approach to drug development and prodrug activation in Mtb. SIGNIFICANCEPyrazinamide (PZA) is a vital component of Mycobacterium tuberculosis (Mtb) treatment since its inclusion shortened tuberculosis therapy by six months. However, PZA is a prodrug and resistance develops at a high frequency due to mutations in its activator PncA. Here, we present the discovery of amide-containing anti-tubercular prodrugs that are activated intracellularly by the Mtb amidase, AmiC. Taking advantage of this finding, we successfully designed and synthesized pyrazinoic acid (POA) prodrugs that were activated by AmiC and found that these compounds delivered intracellular POA to PZA- resistant Mtb isolates that contained a nonfunctional PncA. This new approach to prodrug development provides a method for delivering conjugated drugs into Mtb with the potential to overcome clinical drug resistance.

microbiology↗

bioRxiv2022

Establishing Novel Doxorubicin-Loaded Polysaccharide Hydrogel for Controlled Drug Delivery for Treatment of Pediatric Brain Tumors

According to the National Cancer Institute, of the more than 10 million cancer survivors alive in the United States at least 270,000 were originally diagnosed under the age of 21. While the 5-year survival rates for most childhood cancers appear very promising, the long-term survival rates are still very dismal. There is significant long-term morbidity and mortality associated with treatment of childhood cancer, and the risk of these effects continues to increase years after completion of therapy. Among childhood cancer survivors the cumulative incidence of a chronic health condition is 73.4% 30 years after the original cancer diagnosis, with a cumulative incidence of 42.4% for severe, disabling, life-threatening, or death due to a chronic condition caused by the chemotherapy used to treat the initial malignancy. Brain tumors are the most prevalent solid tumor diagnosed in children, and account for 20 percent of all childhood cancer deaths. The efficacy of all chemotherapy agents can be limited by their toxicity, their instability, and their ability to be formulated into practical drug products for use in the clinical setting To address this gap, our group has developed a novel carbohydrate-based hydrogel, Amygel, that is capable of being loaded with drugs and injected directly into the site of disease. Local drug delivery using Amygel has potential to improve childhood cancer treatment outcomes and prevent the devastating effects of systemic chemotherapy exposure. Development of Amygel for clinical use has three focus areas including: increasing drug concentration at the target site; improving chemotherapy penetration through tumor tissue, and; establishing chemotherapy dosage forms for pediatric use. For this study, we formulated Amygel with dimethyl sulfoxide and integrated the chemotherapy doxorubicin (DOX). High-performance liquid chromatography (HPLC) was used to confirm the quality of DOX after hydrogel synthesis, rheology and syringability tests to characterize the mechanical properties, and performed an in vitro cytotoxicity test against the pediatric medulloblastoma cell line DAOY. On HPLC, we found that after integrating DOX into the Amygel matrix the drug maintained a strong band on the chromatograph at the same point with the same intensity as the control free drug, indicating there were no changes in the structural properties of DOX. The mechanical tests showed that there was a proportionate increase in the storage modulus of the drug-loaded hydrogels as the concentration of amylopectin increased from 3 wt% to 20 wt%, but even at 20 wt% the hydrogel remained below the medical standard for injectables that the burst force should not exceed 40 N and the sliding force below 20 N. Correlating with the rheology findings, as the concentration of amylopectin increased, and therefore the strength of the hydrogel, there was an increase in the magnitude of force required for gel injection. These mechanical studies additionally provide evidence that the mechanical stability of the gel is not dampened by the incorporation of DOX. Drug release and cytotoxicity studies demonstrated a sufficient release of DOX from the hydrogels, and that the DOX released was able to achieve significant (p<0.01) cell death.

bioengineering↗

bioRxiv2022

Apurinic/apyrimidinic nuclease 1 drives genomic evolution contributing to chemoresistance and tumorigenesis in solid tumor

Genomic instability fuels genomic alterations that befit cancer cells with necessary adaptations to keep proliferating and overcome the impact of host anti-tumor immunity and cytotoxic therapy. Since DNA breaks are required for genomic rearrangements to take place, we hypothesized that dysregulated nuclease activity mediates genomic instability in cancer. Using an integrated genomics protocol, we identified a four gene deoxyribonuclease signature correlating with genomic instability in six human cancers which included adenocarcinomas of esophagus (EAC), lung, prostate, stomach, pancreas and triple negative breast cancer. Functional screens confirmed the role of these nucleases in genomic instability and growth of cancer cells. Apurinic/apyrimidinic nuclease 1 (APE1), identified as top nuclease in functional screen, was further investigated in five cell lines representing four solid tumors (EAC, lung, prostate and breast cancer). We demonstrate that chemical as well as transgenic suppression of APE1 impaired growth/colony formation and increased cytotoxicity of chemotherapeutic agent, whereas inhibited spontaneous as well as chemotherapy-induced DNA breaks, homologous recombination (HR) activity and genomic instability in all cancer cell types tested. Treatment with APE1 inhibitor also impaired tumor growth and significantly increased efficacy of a chemotherapeutic agent in a subcutaneous mouse model of EAC. Overexpression of APE1 in normal esophageal epithelial cells increased DNA breaks and HR activity, leading to massive mutational, copy number as well as karyotypic instability. Evaluation of by whole genome sequencing identified HR as the top mutational process activated by APE1. Normal cells overexpressing APE1 grew as tumors in mice and tumors removed from mice displayed additional karyotypic changes, providing evidence of genomic instability in vivo. Overall, our data demonstrate that elevated APE1 dysregulates HR activity, G2/M checkpoint and genome stability thus contributing to tumorigenesis and chemoresistance in cancer. Therefore, inhibitors of APE1 have potential to inhibit growth and increase cytotoxicity of chemotherapeutic agents while minimizing spontaneous as well as chemotherapy-induced genomic damage and instability in EAC and other solid tumors.

cancer biology↗

bioRxiv2022

An innovative hematopoietic stem cell gene therapy approach benefits CLN1 disease in the mouse model

Hematopoietic stem and progenitor cells (HSPCs) can lead to the establishment of a long-lasting microglia-like progeny in the brain of properly myeloablated hosts. We exploited this approach to treat the severe CLN1 neurodegenerative disorder, which is the most aggressive form of neuronal ceroid lipofuscinoses, due to deficiency of palmitoyl-protein thioesterase 1 (hPPT1). We here provide first evidence that: i) transplantation of wild type HSPCs exerts a partial but long-lasting mitigation of the symptoms; ii) transplantation of HSPCs over-expressing hPPT1 by lentiviral gene transfer enhances therapeutic benefit as compared to wild type cell transplant, with first demonstration of such a dose-effect benefit for a purely neurodegenerative condition like CLN1 disease; iii) transplantation of hPPT1 over-expressing HSPCs by a novel intracerebroventricular (ICV) approach is sufficient to transiently ameliorate CLN1 disease symptomatology in the absence of hematopoietic tissue engraftment of the transduced cells; and iv) the combinatorial transplantation of transduced HSPCs intravenously and ICV results in the most robust therapeutic benefit among the tested approaches on both pre-symptomatic as well as symptomatic animals. Overall, these findings provide first evidence of the efficacy and feasibility of this novel approach to treat CLN1 disease and possibly other neurodegenerative conditions, paving the way for its future clinical application.

neuroscience↗

bioRxiv2022

Hand Gesture Prediction via Transient-phase sEMG using Transfer Learning of Dilated Efficient CapsNet: Towards Generalization for Neurorobotics

There has been an accelerated surge to utilize the deep neural network for decoding central and peripheral activations of the humans nervous system to boost up the spatiotemporal resolution of neural interfaces used in neurorobotics. Such algorithmic solutions are motivated for use in human-centered robotic systems, such as neurorehabilitation, prosthetics, and exoskeletons. These methods are proved to achieve higher accuracy on individual data when compared with the conventional machine learning methods but are also challenged by their assumption of having access to massive training samples. ObjectiveIn this letter, we propose Dilated Efficient CapsNet to improve the predictive performance when the available individual data is very minimum and not enough to train an individualized network for controlling a personalized robotic system. MethodWe proposed the concept of transfer learning using a new design of the dilated efficient capsular neural network to relax the need of having access to massive individual data and utilize the field knowledge which can be learned from a group of participants. In addition, instead of using complete sEMG signals, we only use the transient phase, reducing the volume of training samples to 20% of the original and maximizing the agility. ResultsIn experiments, we validate our model performance with various amounts of injected personalized training data (25%-100% of transient phase) that is segmented once by time and once by repetition. The results of this paper support the use of transfer learning using a dilated capsular neural network and show that with the use of such a model, the knowledge domain learned on a small number of subjects can be utilized to minimize the need for new data of new subjects while focusing only on the transient phase of contraction (which is a challenging neural interfacing problem).

bioengineering↗

bioRxiv2022

TP53 knockout in MCF7 breast cancer cells induces sensitivity to fluoropyrimidine drugs.

TP53 mutations are present in all molecular subtypes of breast cancer and often correlate with decreased survival; however, few therapeutic options exist for patients with TP53-mutant breast cancers. To discover therapeutic strategies for these patients, we investigated the sensitivity of 129 FDA-approved chemotherapies to TP53-KO and TP53-WT MCF7 breast adenocarcinoma cells and found p53 loss to confer sensitivity to 5-fluorouracil (5-FU). We then treated the p53-null cells and isogenic controls with F10, a second-generation polymeric fluoropyrimidine, and found this preferential cytotoxicity of TP53-KO cells to be significantly magnified. F10 killing could only minimally be rescued by addition of exogenous uridine, whereas it was completely abrogated by addition of exogenous thymidine, suggesting DNA incorporation to be central to the cytotoxic mechanism of action. Furthermore, F10 killing of p53-null cells was persistent even in heterogeneous cellular mixtures more reflective of natural tumor evolution. Together, our results suggest F10 may widen the therapeutic window for TP53-mutant breast cancer by enhancing genotoxicity in cells resistant to apoptosis.

cancer biology↗

bioRxiv2022

Ehrlichia SLiM ligand mimetic activates Notch signaling in human monocytes

Ehrlichia chaffeensis evades innate host defenses by reprogramming the mononuclear phagocyte through mechanisms that involve exploitation of multiple evolutionarily conserved cellular signaling pathways including Notch. This immune evasion strategy is directed in part by tandem repeat protein (TRP) effectors. Specifically, the TRP120 effector activates and regulates Notch signaling through interactions with the Notch receptor and the negative regulator, F-Box and WD repeat domain-containing 7 (FBW7). However, the specific molecular interactions and motifs required for E. chaffeensis TRP120-Notch receptor interaction and activation have not been defined. To investigate the molecular basis of TRP120 Notch activation, we compared TRP120 with endogenous canonical/non-canonical Notch ligands and identified a short region of sequence homology within the tandem repeat (TR) domain. TRP120 was predicted to share biological function with Notch ligands, and a function-associated sequence in the TR domain was identified. To investigate TRP120-Notch receptor interactions, colocalization between TRP120 and endogenous Notch-1 was observed. Moreover, direct interactions between full length TRP120, the TRP120 TR domain containing the putative Notch ligand sequence, and the Notch receptor LBR were demonstrated. To molecularly define the TRP120 Notch activation motif, peptide mapping was used to identify an 11-amino acid short linear motif (SLiM) located within the TRP120 TR that activated Notch signaling and downstream gene expression. Peptide mutants of the Notch SLiM or anti-Notch SLiM antibody reduced or eliminated Notch activation and NICD nuclear translocation. This investigation reveals a novel molecularly defined pathogen encoded Notch SLiM mimetic that activates Notch signaling consistent with endogenous ligands. ImportanceE. chaffeensis infects and replicates in mononuclear phagocytes, but how it evades innate immune defenses of this indispensable primary innate immune cell is not well understood. This investigation reveals the molecular details of a ligand mimicry cellular reprogramming strategy that involves a short linear motif (SLiM) which enables E. chaffeensis to exploit host cell signaling to establish and maintain infection. E. chaffeensis TRP120 is a moonlighting effector that has been associated with cellular activation and other functions including ubiquitin ligase activity. Herein, we identify and demonstrate that a SLiM present within each tandem repeat of TRP120 activates Notch signaling. Notch is an evolutionarily conserved signaling pathway responsible for many cell functions including cell fate, development, and innate immunity. The proposed study is significant because it reveals the first molecularly defined pathogen encoded SLiM that appears to have evolved de novo to mimic endogenous Notch ligands. Understanding Notch activation during E. chaffeensis infection provides a model in which to study pathogen exploitation of signaling pathways and will be useful in developing molecularly-targeted countermeasures for inhibiting infection by a multitude of disease-causing pathogens that exploit cell signaling through molecular mimicry. Author SummaryE. chaffeensis is a small, obligately intracellular, Gram-negative bacterium that has evolved cellular reprogramming strategies to subvert innate defenses of the mononuclear phagocyte. Ehrlichial TRP effectors interface with the host cell and are involved in pathogen-host interplay that facilitates exploitation and manipulation of cellular signaling pathways; however, the molecular interactions and functional outcomes are not well understood. This study provides molecular insight into a eukaryotic mimicry strategy whereby secreted effectors of obligately intracellular pathogens activate the evolutionarily conserved Notch signaling pathway through a short linear motif ligand mimetic to promote intracellular infection and survival.

pathology↗

bioRxiv2021

A CRISPR toolbox for generating intersectional genetic mice for functional, molecular, and anatomical circuit mapping

BackgroundA full understanding of circuits and cellular mechanisms governing health and disease requires the dissection and multi-faceted study of discrete cell subtypes in developing and adult animal models. Recombinase-driven expression of transgenic response alleles represents a significant and powerful approach to delineate cell populations for functional, molecular, and anatomical study. In addition to single recombinase systems, the expression of two recombinases in distinct, but partially overlapping, populations allow for more defined target expression. Although the application of this method is becoming increasingly popular, the expense and difficulty associated with production of customized intersectional mouse lines have limited widespread application to more common allele manipulations that are often commercially produced at great expense. ResultsWe present a simplified CRISPR toolkit for rapid, inexpensive, and facile intersectional allele production. Briefly, we produced 7 intersectional mouse lines using a dual recombinase system, one mouse line with a single recombinase system, and three embryonic stem (ES) cell lines that are designed to study how functional, molecular, and anatomical features relate to each other in building circuits that underlie physiology and behavior. As a proof-of-principle, we applied three of these lines to different neuronal populations for anatomical mapping and functional in vivo investigation of respiratory control. We also generated a mouse line with a single recombinase-responsive allele that controls the expression of the calcium sensor Twitch-2B. This mouse line was applied globally to study the effects of follicle stimulating hormone (FSH) and luteinizing hormone (LH) on calcium release in the ovarian follicle. ConclusionsLines presented here are representative examples of outcomes possible with the successful application of our genetic toolkit for the facile development of diverse, modifiable animal models. This toolkit will allow labs to create single or dual recombinase effector lines easily for any cell population or subpopulation of interest when paired with the appropriate Cre and FLP recombinase mouse lines or viral vectors. We have made our tools and derivative intersectional mouse and ES cell lines openly available for non-commercial use through publicly curated repositories for plasmid DNA, ES cells, and transgenic mouse lines.

genetics↗

bioRxiv2021

Convergent, functionally independent signaling by mu and delta opioid receptors in hippocampal parvalbumin interneurons

Functional interactions between G protein-coupled receptors are poised to enhance neuronal sensitivity to neuromodulators and therapeutic drugs. Mu and Delta opioid receptors (MORs and DORs) can interact when overexpressed in the same cells, but whether co-expression of endogenous MORs and DORs in neurons leads to functional interactions is unclear. Here, we show that both MORs and DORs inhibit parvalbumin-expressing basket cells (PV-BCs) in hippocampal CA1 through partially occlusive signaling pathways that terminate on somato-dendritic potassium channels and presynaptic calcium channels. Using photoactivatable opioid neuropeptides, we find that DORs dominate the response to enkephalin in terms of both ligand-sensitivity and kinetics, which may be due to relatively low expression levels of MOR. Opioid-activated potassium channels do not show heterologous desensitization, indicating that MORs and DORs signal independently. In a direct test for heteromeric functional interactions, the DOR antagonist TIPP-Psi does not alter the kinetics or potency of either the potassium channel or synaptic responses to photorelease of the MOR agonist DAMGO. Thus, despite largely redundant and convergent signaling, MORs and DORs do not functionally interact in PV-BCs. These findings imply that crosstalk between MORs and DORs, either in the form of physical interactions or synergistic intracellular signaling, is not a preordained outcome of co-expression in neurons.

neuroscience↗

bioRxiv2021

Human primed endothelial colony forming cells exert neuroprotective effects in the growth restricted newborn piglet

The fetal brain is particularly vulnerable to the detrimental effects of fetal growth restriction (FGR) with subsequent abnormal neurodevelopment being common. There are no current treatments to protect the FGR newborn from lifelong neurological disorders. This study examines whether pure fetal mesenchymal stem cells and endothelial colony forming cells (ECFC) from the human term placenta are neuroprotective through modulating neuroinflammation and supporting the brain vasculature. We determined that one dose of these primed ECFCs (pECFC) on the first day of life to the newborn FGR piglet improved damaged vasculature, restored the neurovascular unit, reduced brain inflammation and improved adverse neuronal and white matter changes present in the FGR newborn piglet brain. These findings could not be reproduced using mesenchymal stromal cells alone. These results demonstrate pECFC treatment exerts beneficial effects on multiple cellular components in the FGR brain and act as a neuroprotectant. One Sentence SummaryStem cell treatment improves brain outcomes in the growth restricted newborn

neuroscience↗

bioRxiv2020

Communicating Regulatory High Throughput Sequencing Data Using BioCompute Objects

For regulatory submissions of next generation sequencing (NGS) data it is vital for the analysis workflow to be robust, reproducible, and understandable. This project demonstrates that the use of the IEEE 2791-2020 Standard, (BioCompute objects [BCO]) enables complete and concise communication of NGS data analysis results. One arm of a clinical trial was replicated using synthetically generated data made to resemble real biological data. Two separate, independent analyses were then carried out using BCOs as the tool for communication of analysis: one to simulate a pharmaceutical regulatory submission to the FDA, and another to simulate the FDA review. The two results were compared and tabulated for concordance analysis: of the 118 simulated patient samples generated, the final results of 117 (99.15%) were in agreement. This high concordance rate demonstrates the ability of a BCO, when a verification kit is included, to effectively capture and clearly communicate NGS analyses within regulatory submissions. BCO promotes transparency and induces reproducibility, thereby reinforcing trust in the regulatory submission process.

scientific communication and education↗

bioRxiv2020

Strengthening the BioCompute Standard by Crowdsourcing on PrecisionFDA

BackgroundThe field of bioinformatics has grown at such a rapid pace that a gap in standardization exists when reporting an analysis. In response, the BioCompute project was created to standardize the type and method of information communicated when describing a bioinformatic analysis. Once the project became established, its goals shifted to broadening awareness and usage of BioCompute, and soliciting feedback from a larger audience. To address these goals, the BioCompute project collaborated with precisionFDA on a crowdsourced challenge that ran from May 2019 to October 2019. This challenge had a beginner track where participants submitted BCOs based on a pipeline of their choosing, and an advanced track where participants submitted applications supporting the creation of a BCO and verification of BCO conformance to specifications. ResultsIn total, there were 28 submissions to the beginner track (including submissions from a bioinformatics masters class at George Washington University) and three submissions to the advanced track. Three top performers were selected from the beginner track, while a single top performer was selected for the advanced track. In the beginner track, top performers differentiated themselves by submitting BCOs that included more than the minimally compliant content. Advanced track submissions were very impressive. They included a complete web application, a command line tool that produced a static result, and a dockerized container that automatically created the BCO as the tool was run. The ability to harmonize the correct function, a simple user experience, and the aesthetics of the tool interface differentiated the tools. ConclusionsDespite being new to the concept, most beginner track scores were high, indicating that most users understood the fundamental concepts of the BCO specification. Novice bioinformatics students were an ideal cohort for this Challenge because of their lack of familiarity with BioCompute, broad diversity of research interests, and motivation to submit high-quality work. This challenge was successful in introducing the BCO to a wider audience, obtaining feedback from that audience, and resulting in a tool novices may use for BCO creation and conformance. In addition, the BCO specification itself was improved based on feedback illustrating the utility of a "wisdom of the crowd" approach to standards development.

bioinformatics↗

bioRxiv2020

Enhanced specificity of high sensitivity somatic variant profiling in cell-free DNA via paired normal sequencing: design, validation, and clinical experience of the MSK-ACCESS liquid biopsy assay

Circulating cell-free DNA (cfDNA) from blood plasma of cancer patients can be used to interrogate somatic tumor alterations non-invasively or when adequate tissue is unavailable. We have developed and clinically implemented MSK-ACCESS (Analysis of Circulating cfDNA to Evaluate Somatic Status), an NGS assay for detection of very low frequency somatic alterations in select exons and introns of 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 98% for a priori mutation profiling. To evaluate the performance and utility of MSK-ACCESS, we report results from the first 681 prospective blood samples (617 patients) that underwent clinical analysis to guide patient management. Somatic mutations, copy number, and/or structural variants were detected in 73% of the samples, and 56% of these circulating-tumor DNA (ctDNA) positive samples had clinically actionable alterations. The utilization of matched white blood cell sequencing allowed retention of somatic alterations while filtering out over 10,000 germline and clonal hematopoiesis variants, thereby greatly enhancing the specificity of the assay. Taken together, our experience illustrates the importance of analyzing a matched normal sample when interpreting cfDNA results and highlights the potential of cfDNA profiling to guide treatment selection, monitor treatment response, and identify mechanisms of treatment resistance.

genomics↗

bioRxiv2020

HSP90 facilitates oncogenic alterations of metabolism in B-cell lymphomas

HSP90 is critical for maintenance of the cellular proteostasis. In cancer cells, HSP90 also becomes a nucleating site for the stabilization of multiprotein complexes including signaling pathways and transcription complexes. Here, we described a novel role of HSP90 in the cytosolic compartmentalization of metabolic pathways in proliferating cancer cells. We found that HSP90 assists in the organization of metabolic enzymes into non-membrane-bound functional compartments termed metabosomes. Under experimental conditions that conserved the cellular proteostasis, we demonstrated that the compartmentalizing activity of HSP90 is critical to sustain the coordinated synthesis of multiple metabolites required for energy production, maintenance of the cellular biomass and secretion of immunometabolites. Conversely, inhibition of the nucleating capacity of HSP90 modified the topology of cytosolic metabosomes before protein degradation was apparent decreasing the efficiency of MYC-driven metabolic pathways. Inhibition of HSP90 decreases cancer metabolism in B-cell lymphoma cells and patients providing a novel mechanism of activity for this class of drugs.

cancer biology↗

bioRxiv2020

Recapitulation of human embryonic heart beating to promote differentiation of hepatic endoderm to hepatoblasts

A microfluidic platform recapitulating human embryonic heart beat improves the functionalization state of hepatocytes derived from hepatic endoderm (HE). Mechanical stretching of mimicked heart beats was applied to HE cells cultured on the microfluidic platform. Stimulated HE-derived hepatoblasts increased cytochrome P450 3A (CYP3A) metabolic activities and hepatoblast functional markers expression, leading for advancement of regenerative medicine and drug screening.

bioengineering↗

bioRxiv2019

High-throughput identification of MHC class I binding peptides using an ultradense peptide array

Rational vaccine development and evaluation requires identifying and measuring the magnitude of epitope-specific CD8 T cell responses. However, conventional CD8 T cell epitope discovery methods are labor-intensive and do not scale well. Here, we accelerate this process by using an ultradense peptide array as a high-throughput tool for screening peptides to identify putative novel epitopes. In a single experiment, we directly assess the binding of four common Indian rhesus macaque MHC class I molecules - Mamu-A1*001, -A1*002, -B*008, and -B*017 - to approximately 61,000 8-mer, 9-mer, and 10-mer peptides derived from the full proteomes of 82 simian immunodeficiency virus (SIV) and simian-human immunodeficiency virus (SHIV) isolates. Many epitope-specific CD8 T cell responses restricted by these four MHC molecules have already been identified in SIVmac239, providing an ideal dataset for validating the array; up to 64% of these known epitopes are found in the top 192 SIVmac239 peptides with the most intense MHC binding signals in our experiment. To assess whether the peptide array identified putative novel CD8 T cell epitopes, we validated the method by IFN-{gamma} ELISPOT assay and found three novel peptides that induced CD8 T cell responses in at least two Mamu-A1*001-positive animals; two of these were validated by ex vivo tetramer staining. This high-throughput identification of peptides that bind class I MHC will enable more efficient CD8 T cell response profiling for vaccine development, particularly for pathogens with complex proteomes where few epitope-specific responses have been defined.

immunology↗

bioRxiv2019

Contrast invariant tuning in human perception of image content

Higher levels of visual processing are progressively more invariant to low-level visual factors such as contrast. Although this invariance trend has been well documented for simple stimuli like gratings and lines, it is difficult to characterize such invariances in images with naturalistic complexity. Here, we use a generative image model based on a hierarchy of learned visual features--a Generative Adversarial Network--to constrain image manipulations to remain within the vicinity of the manifold of natural images. This allows us to quantitatively characterize visual discrimination behaviour for naturalistically complex, non-linear image manipulations. We find that human tuning to such manipulations has a factorial structure. The first factor governs image contrast with discrimination thresholds following a power law with an exponent between 0.5 and 0.6, similar to contrast discrimination performance for simpler stimuli. A second factor governs image content with approximately constant discrimination thresholds throughout the range of images studied. These results support the idea that human perception factors out image contrast relatively early on, allowing later stages of processing to extract higher level image features in a stable and robust way.

neuroscience↗