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Singh, H.

Publications and source records attributed to Singh, H..

At least 55 records · Page 3Linked to original sources

A Drosophila model for Costello Syndrome caused by Ras mutation K117R

Germline mutations that increase signaling through the Ras pathway can cause developmental disorders called RASopathies. The RASopathy Costello syndrome has been described to present with hallmarks that include short stature, intellectual disability, cardiac issues, and characteristic facial abnormalities and has been associated with gain-of-function mutations in HRas. The most common HRas mutations in Costello Syndrome occur at G12 and G13, but there are also other rare mutation sites such as K117 including HRasK117R. RasK117R mutations are also found in colorectal cancer. Drosophila studies modeling gain-of-function in Ras primarily utilize the common cancer-associated mutation G12V, and previous Drosophila RASopathy models assessing Ras gain-of-function mutations have used human sequences for KRas G12D and HRas G12S. To augment these studies, we characterized the phenotype of engineering the rare gain-of-function mutation K117R in the Drosophila Ras sequence. We report here that constitutive low-level expression of RasK117R increased lethality and reduced body size while also causing rough eye and ectopic wing vein phenotypes in those flies that survived to adulthood. Ras pathway inhibitors Trametinib and Rigosertib suppressed the lethality but not the reduced size phenotypes. Trametinib strongly suppressed the K117R wing vein phenotype whereas Rigosertib had only subtle effects. Trametinib is a direct MEK inhibitor. Rigosertib has been reported to have strong effects on PI3K signaling and to indirectly inhibit the Raf-ERK branch. Therefore, this data is consistent with an interpretation that some lethality in the fly RasK117R model depends on elevated signaling through the Raf-ERK branch and potentially some lethality depends on the PI3K branch. In contrast, the lack of effects on the reduced size phenotypes would be consistent with small stature resulting from Raf- and PI3K-independent processes. We propose that this model can be useful for future mechanistic analysis and pharmacological screening and evaluation.

developmental biology↗

Pseudomonas aeruginosa-mediated cardiac dysfunction is driven by extracellular vesicles released during infection

Pseudomonas aeruginosa (P.a.) is a gram-negative, opportunistic bacterium abundantly present in the environment. Often P.a. infections cause severe pneumonia, if left untreated. Surprisingly, up to 30% of patients admitted to the hospital for community- acquired pneumonia develop adverse cardiovascular complications such as myocardial infarction, arrhythmia, left ventricular dysfunction, and heart failure. However, the underlying mechanism of infection-mediated cardiac dysfunction is not yet known. Recently, we demonstrated that P.a. infection of the lungs led to severe cardiac electrical abnormalities and left ventricular dysfunction with limited P.a. dissemination to the heart tissue. To understand the mechanism of cardiac dysfunction during P.a. infection, we utilized both in vitro and in vivo models. Our results revealed that inflammatory cytokines contribute but are not solely responsible for severe contractile dysfunction in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Instead, exposure of hiPSC-CMs with conditioned media from P.a. infected human monocyte-derived macrophages (hMDMs) was sufficient to cause severe contractile dysfunction and arrhythmia in hiPSC-CMs. Specifically, exosomes released from infected hMDMs and bacterial outer membrane vesicles (OMVs) are the major drivers of cardiomyocyte contractile dysfunction. By using LC-MS/MS, we identified bacterial proteins, including toxins that are packaged in the exosomes and OMVs, which are responsible for contractile dysfunction. Furthermore, we demonstrated that systemic delivery of bacterial OMVs to mice caused severe cardiac dysfunction, mimicking the natural bacterial infection. In summary, we conclude that OMVs released during infection enter circulation and drive cardiac dysfunction.

immunology↗

Epromoters bind key stress-related transcription factors to regulate clusters of stress response genes

Stress insults trigger the rapid and global reprogramming of gene transcription by coordinated recruitment of a limited number of key inducible transcription factors to cis-regulatory elements. Here, we performed a comprehensive analysis of different stress models and observed that co-induced genes are generally located in close genomic proximity. By integrating gene expression and transcription factor binding resources in different stress models, we found an enrichment for clusters whereby only one of the promoters of the cluster recruits the key transcription factors, reminiscent of Epromoters, a type of cis-regulatory elements displaying both promoter and enhancer function. Epromoter-regulated clusters were frequently found irrespectively of the stress or inflammatory response. Predicted Epromoters displayed enhancer activity and regulated clusters of stress-response genes independently of their genomic location. These findings have significant implications for understanding complex gene regulation following the response to acute perturbations. TeaserWhen cells face stress, they undergo rapid changes in gene expression, orchestrated by a handful of key transcription factors. But how do these factors coordinate such a complex response? Our study reveals that "Epromoters"--cis-regulatory elements that combine the functions of both promoters and enhancers help organize stress-response genes into tightly regulated clusters. This discovery not only deepens our understanding of gene regulation in the face of stress but also offers exciting implications for studying inflammation and other acute cellular responses.

genomics↗

Drivers of antibiotic resistance in two monsoon-impacted Indian urban rivers receiving untreated wastewater

Rivers in India receive 78.7% of untreated sewage from cities and towns making it a potential global "hotspot" for AMR. During monsoon, flooding is common in most Indian cities bringing in fecal contamination in storm runoff. Identifying the major driving factors contributing to the elevated levels of AMR in these rivers is essential to combat AMR proliferation. Determining whether the introduction of ARBs and ARGs through fecal pollution or subsequent (co-) selection for ARGs through chemical pollutants is responsible for the rise and spread of AMR is important in mitigation efforts. To achieve this, we targeted two rivers in northern India which received untreated wastewater and assessed the level of two fecal indicators (E. coli and intI1) and wastewater-associated ARGs (ermF, sul1, sul2, and tetW) along with heavy metals (Ag, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn). Water and sediment samples were collected in triplicates at 5-6 locations for each river. Consequently, to evaluate how seasonality affects the ARG levels as well as their drivers in these heavily polluted rivers, sampling campaigns were carried out during three seasons: in summer (pre-monsoon), during monsoon, and post-monsoon in winter. We here demonstrate that the main source for the river resistome in the Bindal and Rispana is the constant inflow of untreated wastewater throughout the year and not the co-selection of ARGs due to the presence of heavy metals. This may be true for many Indian rivers that receive untreated or partially treated wastewater. The rainfall adds to the ARG abundance of the river instead of diluting it. MGE intI1 is more reliable than E. coli as an indicator for fecal pollution and horizontal gene transfer. Heavy metals, despite being present in the river in higher concentrations than the MCSC, no evidence for co-selection was observed.

molecular biology↗

Altered AP-1, RUNX, and EGR chromatin dynamics drive fibrotic lung disease

Pulmonary fibrosis, including systemic sclerosis-associated interstitial lung disease (SSc-ILD), involves myofibroblasts and SPP1hi macrophages as drivers of fibrosis. Single-cell RNA sequencing has delineated fibroblast and macrophages transcriptomes, but limited insight into transcriptional control of profibrotic gene programs. To address this challenge, we analyzed multiomic snATAC/snRNA-seq on explanted SSc-ILD and donor control lungs. The neural network tool ChromBPNet inferred increased TF binding at single base pair resolution to profibrotic genes, including CTHRC1 and ADAM12, in fibroblasts and SPP1 and CCL18 in macrophages. The novel algorithm HALO confirmed AP-1, RUNX, and EGR TF activity controlling profibrotic gene programs and established TF-regulatory element-gene networks. This TF action atlas provides comprehensive insights into the transcriptional regulation of fibroblasts and macrophages in healthy and fibrotic human lungs.

systems biology↗

Comparative analysis of Endoxifen, Tamoxifen and Fulvestrant: A Bioinformatics Approach to Uncover Mechanisms of Action in Breast Cancer

Breast cancer remains a significant health challenge, with estrogen receptor positive (ER+) subtypes being particularly prevalent forms of breast cancer. Current anti-estrogen therapies, such as tamoxifen and fulvestrant, have limitations, including partial agonist activity and resistance development, which evidence the need for more potent alternatives. Endoxifen, a metabolite of tamoxifen, has emerged as a promising breast cancer therapeutic candidate due to its superior anti-estrogenic effects and side effect profile. The omics signatures for endoxifen, tamoxifen and fulvestrant, obtained from publicly available datasets, were aggregated and harmonized by means of the PandaOmics platform, a commercially available target-discovery platform using multiple AI engines including generative pretrained transformers. Pathway enrichment analyses provided insight into these agents mechanisms of action (MOA) in breast cancer. The analyses revealed unexpected variances in several key pathways from expected interactions via estrogen-dependent and independent effects. All three drugs downregulated estrogen signaling and cell cycle-related pathways, such as E2F targets, G2-M checkpoints, Myc targets, and mitotic spindle, and stimulated apoptosis. Fulvestrant and tamoxifen activated pro-inflammatory and immune pathways and perturbed epithelial-mesenchymal transition (EMT). Endoxifen perturbed the PI3K/Akt/mTORC1 pathway, pursuant to distinct molecular mechanisms compared to its parent compound, tamoxifen, and fulvestrant. In summary, advanced AI-driven methodologies demonstrate the capacity to analyze multi-omics data in a comparative way to advance the understanding of endocrine therapy mechanisms in breast cancer. This insight into the distinct effects of endoxifen, tamoxifen, and fulvestrant may aid in selecting the most effective therapies for specific indications and in identifying drug-specific biomarkers.

cancer biology↗

Multiomic Insights into Human Health: Gut Microbiomes of Hunter-Gatherer, Agropastoral, and Western Urban Populations

Societies with exposure to preindustrial diets exhibit improved markers of health. Our study used a comprehensive multi-omic approach to reveal that the gut microbiome of the Ju/hoansi hunter-gatherers, one of the most remote KhoeSan groups, exhibit a higher diversity and richness, with an abundance of microbial species lost in the western population. The Ju/hoansi microbiome showed enhanced global transcription and enrichment of complex carbohydrate metabolic and energy generation pathways. The Ju/hoansi also show high abundance of short-chain fatty acids that are associated with health and optimal immune function. In contrast, these pathways and their respective species were found in low abundance or completely absent in Western populations. Amino acid and fatty acid metabolism pathways were observed prevalent in the Western population, associated with biomarkers of chronic inflammation. Our study provides the first in-depth multi-omic characterization of the Ju/hoansi microbiome, revealing uncharacterized species and functional pathways that are associated with health.

genomics↗

Combining Scalable Organ Chip Platform with Deep Learning-Based Imaging Analysis for Cancer Therapeutic Screening

Functional precision oncology represents an emerging approach to genomic approaches by testing treatment options directly on patient-derived models. Current assays, including the use of patient-derived xenograft (PDX) and patient-derived organoid (PDOs), faces major barriers in clinical use due to technical challenges, such as standardization, cost, assay time, scalability, and faithful mimicry of patient tumor microenvironment (TME). Here, we introduce an Organ Chip (OC) device constructed entirely from thermoplastic materials, free of porous membrane or other barrier structures, and optimized for high-content imaging (HCI). This automation-compatible device supports tissue-specific extracellular matrices and coculture for a wide spectrum of organ and disease types, including the TME. As a proof-of-concept, we demonstrate the growth of pancreatic, lung, and colon cancer cell lines and primary lung cancer cells and the testing of cancer drugs in these models. HCI-based phenotypic profiling enabled accurate quantification of drug response, with better performance than traditional biochemical assays. Moreover, we developed a deep-learning method for assessing drug responses using bright field images. The integration of a low-cost, scalable, and faithful OC models with automatic high-content image analysis represents a significant stride towards functional precision oncology and cancer drug discovery.

bioengineering↗

Targeting mitochondrial metabolism with CPI-613 in chemoresistant ovarian tumors

BackgroundThere is evidence indicating that chemoresistance in tumor cells is mediated by the reconfiguration of the tricarboxylic acid cycle, leading to heightened mitochondrial activity and oxidative phosphorylation (OXPHOS). Previously, we have shown that ovarian cancer cells that are resistant to chemotherapy display increased OXPHOS, mitochondrial function, and metabolic flexibility. To exploit this weakness in chemoresistant ovarian cancer cells, we examined the effectiveness of the mitochondrial inhibitor CPI-613 in treating preclinical ovarian cancer. MethodsChemosensitive OVCAR3, and chemoresistant CAOV3 and F2 ovarian cancer cells lines and their xenografts in nude mice were used. Functional metabolic studies were performed using Seahorse instrument. Metabolite quantification was performed using LC/MS/MS. ResultsMice treated with CPI-613 exhibited a notable increase in overall survival and a reduction in tumor development and burden in OVCAR3, F2, and CAOV3 xenografts. CPI-613 suppressed the activity of pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase complex, which are two of its targets. This led to a reduction in OXPHOS and tricarboxylic acid cycle activity in all 3 xenografts. The addition of CPI-613 enhanced the responsiveness of chemotherapy in the chemoresistant F2 and CAOV3 tumors, resulting in a notable improvement in survival rates and a reduction in tumor size as compared to using chemotherapy alone. CPI-613 reduced the chemotherapy-induced OXPHOS in chemoresistant tumors. The study revealed that the mechanism by which CPI-613 inhibits tumor growth is through mitochondrial collapse. This is evidenced by an increase in superoxide production within the mitochondria, a decrease in ATP generation, and the release of cytochrome C, which triggers mitochondria-induced apoptosis. Our study demonstrates the translational potential of CPI-613 against chemoresistant ovarian tumors.

cancer biology↗

Heat Stable and Intrinsically Sterile Liquid Protein Formulations

Over 80% of biologic drugs, and 90% of vaccines, require temperature-controlled conditions throughout the supply chain to minimize thermal inactivation and contamination. This cold chain is costly, requires stringent oversight, and is impractical in remote environments. Here, we report chemical dispersants that non-covalently solvate proteins within fluorous liquids to alter their thermodynamic equilibrium and reduce conformational flexibility. This generates non-aqueous, fluorine-based liquid protein formulations that biochemically rigidify protein structure to yield thermally stable biologics at extreme temperatures (up to 90{degrees}C). These non-aqueous formulations are impervious to contamination by microorganismal pathogens, degradative enzymes, and environmental impurities, and display comparable pre-clinical serum half-life and safety profiles to standard saline protein samples. As a result, we deliver a fluorochemical formulation paradigm that may limit the need for cold chain logistics of protein reagents and biopharmaceuticals.

biophysics↗

Expression of Plasmodium Major Facilitator Superfamily Protein in Transporters-Delta Candida Identifies a Drug Transporter

AimTo assess the functional relevance of a putative Major Facilitator Superfamily (MFS) protein (PF3D7_0210300; "PfMFS_DT") as a drug transporter, using Candida glabrata for orthologous protein expression. MethodsCDS encoding PfMFS_DT was integrated into the genome of genetically engineered C. glabrata strain MSY8 via homologous recombination, followed by assessing its functional relevance as a drug transporter. Results and ConclusionThe modified C. glabrata strain exhibited plasma membrane localization of PfMFS_DT and characteristics of an MFS transporter, conferring resistance to antifungals, ketoconazole and itraconazole. The nanomolar inhibitory effects of the drugs on the intra-erythrocytic growth of P. falciparum highlight their antimalarial properties. This study proposes PfMFS_DT as a drug transporter, expanding the repertoire of the currently known antimalarial "resistome".

cell biology↗

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

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

biochemistry↗

Development and Outcomes of an International Certificate Program in Science Policy and Advocacy for STEM PhD Students and Postdocs

Scientists must play a significant role in enacting societal change by educating and advising policymakers on relevant policy topics. To fill the identified gap in science policy and advocacy training, during the pandemic years, we piloted and offered the online Science Policy & Advocacy for STEM Scientists Certificate Program starting in 2020. Over three cohorts, the program was focused on practical skills and concepts, networking, and career development opportunities, and providing pathways for PhD students and postdoctoral researchers to learn about and in many cases fully transition into science policy and advocacy roles and careers. Program participants were exposed to many important aspects of what it means to be involved in science policy and advocacy, and many chose to enter the field through subsequent opportunities facilitated by the program training. We sought to reduce a number of barriers to program participation, and additionally provided resources for others to develop similar programs at their university. We believe this training model is innovative and can be recapitulated, and sincerely hope to see more universities create similar programs in the US and internationally in order to serve trainees interested in science policy and advocacy and facilitate their building impactful careers in the field for years to come.

scientific communication and education↗

2-bromo-2',5'-dihydroxychalcone analogue Inhibits Endothelial Migration by Targeting VEGF-induced ERK 1/2 Phosphorylation

Angiogenesis, the process of new blood vessel formation, is characterized by three essential hallmarks: endothelial proliferation, migration, and differentiation. Each is integral in angiogenesis related diseases, especially cancer. With drug efficacy stagnated due to acquired drug resistance and off target side effects, the need for combinatorial therapy is ever more present. To identify new compounds that could aid current antiangiogenic therapies, we report the preliminary mechanistic evaluation of a 2-bromo-25-dihydroxychalcone analogue and its antimigratory effects on endothelial cells. After the synthesis and validation of the 2-bromo-25-dihydroxychalcone analogue (AH9), its effect was tested in vitro using human umbilical vein endothelial cells (HUVEC). Initial investigations into 2-bromo-25-dihydroxychalcone effect in vitro was conducted with a cell proliferation assay including MTT, afterward endothelial migration was measured with the scratch assay in subsequent functional studies. For mechanistic evaluation, vascular endothelial growth factor (VEGF) induced ERK phosphorylation using western blot was implemented. AH9 inhibited VEGF-induced ERK [1/2] phosphorylation similar to that of known antiangiogenic drug Sorafenib at all three concentrations 100 M (46%, p = 0.003), 30 M (64%, p = 0.0002) and 10 M (91%, p = 0.0001). In a scratch assay model, whilst sorafenib at 3 M was not able to limit migration after 8-hr compared to an untreated control (p = 0.0978), AH9 did (17.41%, p = 0.0079). Furthermore, AH9 was able to inhibit ERK [1/2] phosphorylation in a concentration dependent manner 100 M (46%, p = 0.003), 30 M (64%, p = 0.0002) and 10 M (91%, p = 0.0001) compared to the VEGF control. These preliminary findings support that AH9 could be exerting antimigratory effects through the inhibition of the VEGF induced MAPK/ERK pathway. This forms the foundation for further studies to explore chalcone analogues in hope to aid current antiangiogenic therapeutic strategies as potential angiogenic inhibitors.

pharmacology and toxicology↗

Temporal dynamics and genomic programming of plasma cell fates

Affinity-matured plasma cells (PCs) of varying lifespans are generated through a germinal center (GC) response. The developmental dynamics and genomic programs of antigen-specific PC precursors remain to be elucidated. Using a model antigen, we demonstrate biphasic generation of PC precursors, with those generating long-lived bone marrow PCs preferentially produced in the late phase of GC response. Clonal tracing using scRNA-seq+BCR-seq in spleen and bone marrow compartments, coupled with adoptive transfer experiments, reveal a novel PC transition state that gives rise to functionally competent PC precursors. The latter undergo clonal expansion, dependent on inducible expression of TIGIT. We propose a model for the proliferation and programming of precursors of long-lived PCs, based on extended antigen encounters followed by reduced antigen availability.

immunology↗

Rapid Prototyping of Thermoplastic Microfluidic 3D Cell Culture Devices by Creating Regional Hydrophilicity Discrepancy

Microfluidic three-dimensional cell culture devices that enable the recapitulation of key aspects of organ structures and functions in vivo represent a promising preclinical platform to improve translational success during drug discovery. Essential to these engineered devices is the spatial patterning of cells from different tissue types within a confined microenvironment. Traditional fabrication strategies lack the scalability, cost-effectiveness, and rapid prototyping capabilities required for industrial applications, especially for processes involving thermoplastic materials. Here, we introduce an approach to pattern fluid guides inside microchannels by establishing differential hydrophilicity using pressure-sensitive adhesives as masks and a subsequent selective coating with a biocompatible polymer. We identified optimal coating conditions using polyvinylpyrrolidone, which resulted in rapid and consistent hydrogel flow in both the open-chip prototype and the fully bonded device containing additional features for medium perfusion. We tested the suitability of our device for dynamic 3D cell culture by growing human hepatocytes in the device under controlled fluid flow for a 14-day period. Additionally, we demonstrated the potential of using our device for pharmaceutical high-throughput screening applications, such as predicting drug-induced liver injury. Our approach offers a facile strategy of rapid prototyping thermoplastic microfluidic organ chips with varying geometries, microstructures, and substrate materials.

bioengineering↗

Overcoming migratory exhaustion: Expression of Matrix metalloproteinase-8 (MMP-8) promotes tumor infiltration and anti-tumor activity of CAR-T cells

Despite the encouraging success of chimeric antigen receptor (CAR) T-cell therapy in treating hematological malignancies, the translation of adoptive cell therapies to solid tumors remains a challenge. Several studies have attributed the inability of tumor-infiltrating T cells to traffic to solid tumors, primarily to the presence of the extracellular matrix (ECM) and immunosuppressive environment of solid tumors. The ability of the transferred T cells to infiltrate the tumor is an essential prerequisite for anti-tumor activity. We show here that upon activation and expansion, T cells quickly lose their migratory capacity, leading to migratory exhaustion. At the molecular level, migratory exhaustion could be attributed to the downregulation of matrix metalloproteinase 8 (MMP8). To overcome this, we hypothesized that T cells genetically modified to secrete the mature form of matrix metalloproteinase 8 (mMMP8) would facilitate migration across matrix barriers in vitro and in vivo. We demonstrated that CAR T cells that co-express mMMP8 demonstrate robust migration across Matrigel and can kill tumor cells embedded in Matrigel in vitro. We tested the efficacy of these mMMP8 engineered cells in both leukemic and ovarian cancer cell models embedded in Matrigel in xenograft mouse models. Our results illustrate that unlike parental CAR T cells that have minimal anti-tumor efficacy in these models, CAR T cells that secrete mMMP8 promote T-cell infiltration, leading to the eradication of the tumors and survival. We anticipate that the co-expression of mMMP8 can be broadly utilized to improve the infiltration and efficacy of CAR T cells targeting many different antigens.

cancer biology↗

Replicative stress in gastroesophageal adenocarcinoma is associated with chromosomal instability and sensitivity to DNA damage response inhibitors.

Gastroesophageal adenocarcinoma (GEA) is an aggressive, often lethal, malignancy that displays marked chromosomal instability (CIN). To understand adaptive responses that enable CIN, we analyzed paired normal, premalignant, and malignant gastric lesions from human specimens and a carcinogen-induced mouse model, observing activation of replication stress, DNA damage response (DDR), and cell cycle regulator p21 in neoplastic progression. In GEA cell lines, expression of DDR markers correlated with ploidy abnormalities, including high-level focal amplifications and whole-genome duplication (WGD). Moreover, high expression of DNA damage marker H2AX correlated with CIN, WGD, and inferior patient survival. By developing and implementing a composite diagnostic score that incorporates TP53 mutation status, ploidy abnormalities, and H2AX expression, among other genomic information, we can identify GEA cell lines with enhanced sensitivity to DDR pathway inhibitors targeting Chk1/2 and Wee1. Anti-tumor properties were further augmented in combination with irinotecan (SN38) but not gemcitabine chemotherapy. These results implicate specific DDR biomarkers and ploidy abnormalities as diagnostic proxy that may predict premalignant progression and response to DDR pathway inhibitors.

cancer biology↗