Biology subjects

Awasthi, S.

Publications and source records attributed to Awasthi, S..

18 recordsLinked to original sources

bioRxiv2026

Estrogen receptor alpha regulates alcohol craving in females: convergent evidence from mouse models and human genetics

Alcohol craving and consumption fluctuate across the reproductive cycle in females with alcohol use disorder (AUD), suggesting that estrogen signaling contributes to disease vulnerability. Here, we investigated the role of estrogen receptor alpha (ER; Esr1; ESR1) in alcohol seeking using complementary mouse and human approaches, as this receptor was previously identified as a risk factor for AUD. Female mice were characterized in an IntelliCage-based multidimensional AUD paradigm that stratifies individuals into AUD-prone and AUD-resistant phenotypes. Transcriptomic profiling of the amygdala revealed that Esr1 is a top transcription factor for differentially expressed genes in mice drinking alcohol, and the estrogen signaling pathway was deregulated specifically in AUD-prone mice. Although alcohol exposure did not alter overall Esr1/ER mRNA or protein abundance, both transcript and protein levels positively correlated with cue-induced alcohol seeking, indicating that inter-individual variation in ER signaling predicts relapse-like behavior. Causal manipulations confirmed a functional role of ER. Local knockdown of Esr1 in the basolateral amygdala reduced excitatory synaptic transmission, attenuated alcohol motivation, cue-induced seeking, and relapse drinking, and impaired cue-associated memory recall without affecting anxiety-like behavior. Similarly, ovariectomy decreased amygdala ER expression, altered synaptic protein markers, and reduced alcohol-seeking behaviors, supporting regulation by endogenous ovarian hormones. Extending these findings to humans, ESR1 gene polymorphisms (rs6902771, rs11155819 and rs6557171) were associated with the probability of alcohol binge drinking and alcohol consumption days as well as craving and loss of control in real world in a longitudinal clinical cohort, while ESR1 mRNA blood levels were increased in women with AUD diagnosis. Together, these convergent molecular, circuit, behavioral, and genetic data identify ER signaling in the amygdala as an important modulator of alcohol-seeking behavior induced by alcohol cue and relapse vulnerability, highlighting estrogen pathways as potential therapeutic targets and markers for AUD.

neuroscience↗

bioRxiv2026

Genome-resolved house microbiome exhibits location-specific metabolic partitioning, and harbors hosts with clinically relevant antibiotic resistance genes

Residential indoor surfaces are recognized as diverse microbial ecosystems, while their genome-based organization and functional repertoires remain understudied. We recovered 2304 metagenome-assembled genomes (MAGs) from shotgun metagenomic sequencing of 10 houses in New Delhi, India. Genome-resolved analysis revealed a highly structured microbial community and substantial unexplored diversity, with 60% Species-level Genome Bins (SGBs) (629/1014) unclassified at the species level. Metabolism reveals a conserved metabolic core, along with spatial functional enrichment: the living area was significantly different from the bathroom and kitchen areas. The prevalent MAG species of the house microbiome, Paracoccus marcusii, Ottowia sp. 018060485, and Kocuria palustris, showed strain-level diversity with no stratification by house, but a subtle location-wise grouping. Potential pathogens, along with a wide range of antimicrobial resistance genes (ARGs), were identified across the MAGs, with 64 ARGs associated with mobile elements. Phylogenomic analysis of Escherichia coli MAGs indicated a split between commensal-like fecal lineages and pathotype-associated clusters, like Intestinal Pathogenic E. coli (InPEC). These results suggest that residential house microbiomes harbor microbial communities with both diverse metabolic capacity and clinical relevance. Together, these findings establish a reference for future indoor microbiome research and provide a foundation for antimicrobial resistance surveillance and the development of bio-informed building-infrastructures.

microbiology↗

bioRxiv2025

Selective and Controllable Trapping of Single Proteins in Nanopores using Reversible Covalent Bonds

Analysis of individual proteins using nanopores makes it possible to determine their size and shape in a label-free approach, within minutes, and from L sample volumes. Short residence times of proteins in the nanopore, high electrical current noise, and bandwidth limitations of the recording electronics during resistive pulse recordings, however, limit the accuracy of size and shape analysis of individual proteins. The work presented here introduces a polymer surface coating of solid-state nanopores to minimize non-specific interactions of proteins with the nanopore wall while functionalizing it covalently with phenylboronic acid (PBA) groups. These PBA groups make it possible to trap selectively glycated proteins by taking advantage of the formation of reversible covalent bonds between PBA and vicinal diol groups of glycated amino acid residues on proteins. Dwell time analysis revealed two populations of resistive pulses: short pulses with dwell times td below 0.4 ms from free translocation of proteins and resistive pulses that we term "long events" that last from 0.4 ms to 2 s and result from intended transient covalent bonds between glycated proteins and PBA groups in the nanopore lumen. The choice of applied potential differences during nanopore recordings or the pH value of the recording buffer makes it possible to control and extend the most probable trapping time of proteins in the nanopore within one to two orders of magnitude. This approach provides the highest accuracy for the determination of protein volume and shape achieved to date with solid-state nanopores and reveals that a trapping time of 1 to 20 ms is ideal to achieve reliable volume and shape analysis while retaining high throughput of the analysis. This approach, hence, extends the residence time of natively glycated proteins or of proteins that are intentionally glycated by straightforward incubation in a glucose solution, thereby providing selectivity and improving the accuracy of nanopore-based characterization of single proteins.

biophysics↗

bioRxiv2025

Deep learning-based classification of complex intracellular calcium concentration patterns

Intracellular calcium ion (Ca2+) exhibits diverse dynamical behaviors, including complex oscillations such as bursting and chaos. The distinction of diverse dynamical patterns in time series data holds significant biochemical and biophysical implications, as these patterns are intimately related to physiological cellular states associated with health and disease. In this work, we introduce a deep learning framework based on a large kernel convolutional neural network (LKCNN) for the classification of dynamical states of intracellular Ca2+ dynamics. We use a chemical Langevin equation to generate synthetic data for training the LKCNN, simulating intracellular Ca2+ concentration patterns mimicking real experimental traces. We show that the LKCNN framework reliably classifies diverse intracellular Ca2+ dynamical regimes, achieving near 90% accuracy across all dynamical states. To this end, we propose an optimized kernel size for the LKCNN classifier, which captures both short-lived fluctuations and long-range correlations. While steady states, bursting, and simple oscillations are robustly distinguished with near-perfect accuracy, the performance slightly degrades for chaotic and multiple periodicity states under realistic levels of intrinsic fluctuations, reflecting genuine overlap in their temporal signatures. We validate our classifier with experimental Ca2+ concentration data, showing strong agreement with manual labeling and confirming generalizability beyond synthetic datasets. These results establish LKCNNs as flexible and scalable tools for systematic classification of cellular dynamics, with broad potential applications to other oscillatory biological processes.

biophysics↗

bioRxiv2025

Pneumolysin nanopores with 20 nm inner diameter to characterize the size and shape of Tau oligomers

Protein nanopores are emerging as versatile tools to fingerprint biomolecules due to their capability to characterize single molecules without the requirement for labeling. A long-standing challenge with biological nanopores is, however, that large biomolecules in their native state are often too large to enter these pores. Here, we report the self-assembly of approximately 35 {+/-} 5 pneumolysin (PLY) toxins to a stable transmembrane pore with a diameter of 20 {+/-} 3 nm, an effective length of 9.5 nm, and excellent low noise characteristics in the context of nanopore-based resistive pulse recordings. The exceptionally large pore diameter enables the characterization of the size and shape of individual proteins and protein complexes ranging in molecular weight from 50 kDa to 0.8 MDa. Moreover, PLY pores make it possible to follow the time course of the formation of oligomers of tau protein in solution by revealing the size, monomer number, approximate shape, and abundance of these oligomers. At least four characteristics make PLY pores well suited for the characterization of heterogeneous amyloid oligomer samples: First, they are not prone to clogging. Second, they provide label-free single particle analysis. Third, their large diameters make it possible to characterize a wide range of amyloid oligomer sizes with high resolution. And fourth, resistive pulse recordings from these pores provide stable open pore current baselines with low electrical noise.

biophysics↗

bioRxiv2025

Therapeutic Potential of PRMT1 as a Critical Survival Dependency Target in Multiple Myeloma

Multiple myeloma (MM) is a neoplasm of antibody-producing plasma cells and is the second most prevalent hematological malignancy worldwide. Development of drug resistance and disease relapse significantly impede the success of MM treatment, highlighting the critical need to discover novel therapeutic targets. In a custom CRISPR/Cas9 screen targeting 197 DNA damage response-related genes, Protein Arginine N-Methyltransferase 1 (PRMT1) emerged as a top hit, revealing it as a potential therapeutic vulnerability and survival dependency in MM cells. PRMT1, a major Type I PRMT enzyme, catalyzes the asymmetric transfer of methyl groups to arginine residues, influencing gene transcription and protein function through post-translational modification. Dysregulation or overexpression of PRMT1 has been observed in various malignancies including MM and is linked to chemoresistance. Treatment with the Type I PRMT inhibitor GSK3368715 resulted in a dose-dependent reduction in cell survival across a panel of MM cell lines. This was accompanied by reduced levels of asymmetric dimethylation of arginine (ADMA) and increased arginine monomethylation (MMA) in MM cells. Cell cycle analysis revealed an accumulation of cells in the G0/G1 phase and a reduction in the S phase upon GSK3368715 treatment. Additionally, PRMT1 inhibition led to a significant downregulation of genes involved in cell proliferation, DNA replication, and DNA damage response (DDR), likely inducing genomic instability and impairing tumor growth. This was supported by Reverse Phase Protein Array (RPPA) analyses, which revealed a significant reduction in levels of proteins associated with cell cycle regulation and DDR pathways. Overall, our findings indicate that MM cells critically depend on PRMT1 for survival, highlighting the therapeutic potential of PRMT1 inhibition in treating MM.

cancer biology↗

bioRxiv2023

Gene Set-Based Analysis of the Endosomal Sorting Processes Cargo Selection and Membrane Tubulation with Human Reward System Reactivity

Dysfunction of the dopaminergic reward system has been implicated in the pathophysiology of several neuropsychiatric disorders. The endosomal network encompasses important processes related to neurotransmission in dopamine neurons, e.g, endocytosis, sorting, recycling and degradation of receptors. In the present study, we investigated whether genetic variation influencing the endosomal sorting machinery, in particular cargo selection and membrane tubulation, may impact on the activation strength in key regions of the mesolimbic reward system, i.e. the ventral tegmental area (VTA) and the nucleus accumbens (NAc). To test our hypothesis, the VTA and NAc responses to conditioned reward stimuli were investigated using the desire-reason dilemma (DRD) paradigm during functional magnetic resonance imaging (fMRI). Association of these neural responses with a set of genetic variants related to endosomal sorting processes were tested in two independent samples (N = 182; N = 214). In the first sample, the gene set was associated with both VTA and NAc responses to conditioned reward stimuli [empirical P -values: R-VTA 0.0036; R-NAc 0.0016; L-NAc 0.0094], while the effect in the R-VTA could be replicated in the second sample [empirical P -value: R-VTA 0.0443] at the level of the gene set. For the NAc, an additional exploratory analysis of a patient-only subsample of the first sample (N = 64) suggested that the gene set may express its effect in this brain region predominantly in patients. These findings provide first evidence that the endosomal sorting processes cargo selection and membrane tubulation influence neural responses of the reward system to conditioned stimuli. Further studies are required to clarify the role of endosomal sorting processes in the pathophysiology of neuropsychiatric disorders.

genetics↗

bioRxiv2023

Simultaneous Determination of Size and Shape of Single alpha-Synuclein Oligomers in Solution

Soluble oligomers of amyloid-forming proteins are implicated as toxic species in the context of several neurodegenerative diseases. Since the size and shape of these oligomers influences their toxicity, their biophysical characterization is essential for a better understanding of the structure-toxicity relationship. Amyloid oligomers are difficult to characterize by conventional approaches due to their heterogeneity in size and shape, their dynamic aggregation process, and their low abundance. This paper demonstrates that resistive-pulse measurements using polymer-coated solid-state nanopores enable single-particle level characterization of the size and shape of individual Syn oligomers in solution within minutes. A comparison of the resulting size distribution with single-particle analysis by transmission electron microscopy and mass photometry reveals that nanopore-based characterization agrees well with both methods, while providing better size resolution and elucidating that Syn samples are composed of stable oligomer sub-populations that contain multiples of approximately 12 monomers (i.e., 12-, 24-, 48-, 60-, 84-mers). Applying the unique capability of nanopores to approximate particle size and shape to picomolar concentrations of Syn oligomers in the putatively toxic size range, revealed shapes that agree well with previous estimates by cryo-EM with the added advantage that nanopore-based analysis occurs rapidly, in solution, and has the potential to become a widely accessible technique.

biophysics↗

bioRxiv2022

Beyond BRCA: Discovery of novel causes and consequences of homologous recombination deficiencies

Since the discovery of BRCA1 and BRCA2 mutations as cancer risk factors, we have gained substantial insight into their role in maintaining genomic stability through homologous recombination (HR) DNA repair. However, upon pan-cancer analysis of tumors from The Cancer Genome Atlas (TCGA), we found that mutations in BRCA1/2 and other classical HR genes only identified 10-20% of tumors that display genomic evidence of HR deficiency (HRD), suggesting that the cause of the vast majority of HR defects in tumors is unknown. As HRD both predisposes individuals to cancer development and leads to therapeutic vulnerabilities, it is critical to define the spectrum of genetic events that drive HRD. Here, we employed a network-based approach leveraging the abundance of molecular characterization data from TCGA to identify novel drivers of HRD. We discovered that over half of putative genes driving HRD originated outside of canonical DNA damage response genes, with a particular enrichment for RNA binding protein (RBP)-encoding genes. These novel drivers of HRD were cross-validated using an independent ICGC cohort, and were enriched in GWAS loci associated with cancer risk. Experimental approaches validated over 90% of our predictions in a panel of 50 genes tested by siRNA and 31 additional engineered mutations identified from TCGA patient tumors. Moreover, genetic suppression of identified RBPs or pharmacological inhibition of RBPs induced PARP inhibition. Further mechanistic studies indicate that some RBPs are recruited to sites of DNA damage to facilitate repair, whereas others control the expression of canonical HR genes. Overall, this study greatly expands the repertoire of known drivers of HRD and their contributions to DNA damage repair, which has implications for not only future mechanistic studies, but also for genetic screening and therapy stratification. HIGHLIGHTSO_LIThe majority of HR deficiencies detected cannot be directly attributed to aberrations in canonical HR genes. C_LIO_LIIntegrated network analysis identifies RNA binding proteins (RBPs) as a novel driver of HR deficiency in patient tumors. C_LIO_LIRBP dysfunction can produce HR deficiencies through both dysregulation of canonical HR genes and action at sites of DNA damage. C_LI

systems biology↗

bioRxiv2022

Site-specific C-terminal fluorescent labeling of Tau protein

Formation of Tau protein aggregates in neurons is a pathological hallmark of several neurodegenerative diseases, including Alzheimers disease. Fluorescently-labeled Tau protein is therefore useful to study the aggregation of these pathological proteins and to identify potential therapeutic targets. Conventionally, cysteine residues are used for labeling Tau proteins, however, the full-length Tau isoform contains two cysteine residues in the microtubule-binding region, which are implicated in Tau aggregation by forming intermolecular disulfide bonds. In order to prevent the fluorescent label from disturbing the microtubule binding region, we developed a strategy to fluorescently label Tau at its C-terminus while leaving cysteine residues unperturbed. We took advantage of a Sortase A-mediated transpeptidation approach to bind a short peptide (GGGH6-Alexa647) with a His-tag and a covalently attached Alexa 647 fluorophore to the C-terminus of Tau. This reaction relies on the presence of a Sortase recognition motif (LPXTG), which we attached to the C-terminus of recombinantly expressed Tau. We determined the possible effects of the resulting C-terminal modification on the secondary structure of Tau protein, its aggregation kinetics, and fibril morphology compared to the unlabeled native Tau protein in vitro. The results showed no significant differences between the native and C-terminally labeled Tau monomer with regard to aggregation kinetics, secondary structure, and morphology.

biophysics↗

bioRxiv2022

DNAJC13 influences responses of the extended reward system to conditioned stimuli: a genome-wide association study

Reward system dysfunction is implicated in the pathogenesis of major psychiatric disorders. We conducted a genome-wide association study (GWAS) to identify genes that influence activation strength of brain regions within the extended reward system in humans. A large homogeneous sample of 214 participants was genotyped and underwent functional magnetic resonance imaging (fMRI). All subjects performed the desire-reason dilemma (DRD) paradigm allowing systematic investigation of systems-level mechanisms of reward processing in humans. As a main finding, we identified the single nucleotide variant rs113408797 in the DnaJ Heat Shock Protein Family Member C13 gene (DNAJC13, alias RME-8), that strongly influenced the activation of the ventral tegmental area (VTA; p = 2.50E-07) and the nucleus accumbens (NAcc; p = 5.31E-05) in response to conditioned reward stimuli. Moreover, haplotype analysis assessing the information across the entire DNAJC13 locus demonstrated an impact of a five-marker haplotype on VTA activation (p = 3.21E-07), which further corroborates a link between this gene and reward processing. The present findings provide first direct empirical evidence that genetic variation of DNAJC13 influences neural responses within the extended reward system to conditioned stimuli. Further studies are required to investigate the role of this gene in the pathogenesis and pathophysiology of neuropsychiatric disorders.

genomics↗

bioRxiv2021

Role of RALBP1 in Oxidative Stress and Mitochondrial Dysfunction in Alzheimer's Disease

The purpose of our study is to understand the role of the Ralbp1 gene in oxidative stress (OS), mitochondrial dysfunction and cognition in Alzheimers disease (AD) pathogenesis. The Ralbp1 gene encodes the 76 kDa protein Rlip (aka RLIP76). Previous studies have revealed its role in OS-related cancer. However, Rlip is transcriptionally regulated by EP300, a CREB-binding protein that is important for synaptic plasticity in the brain. Rlip functions as a stress-responsive/protective transporter of glutathione conjugates (GS-E) and xenobiotic toxins. OS causes rapid cellular accumulation of Rlip and its translocation from a tubulin-bound complex to the plasma membrane, mitochondria and nucleus. Therefore, Rlip may play an important role in maintaining cognitive function in the face of OS-related injury. This study is aimed to determine whether Rlip deficiency in mice is associated with AD-like cognitive and mitochondrial dysfunction. Brain tissue obtained from cohorts of wildtype and Rlip+/- mice were analyzed for OS markers, expression of genes that regulate mitochondrial fission/fusion, and synaptic integrity. We also examined mitochondrial ultrastructure in mouse brains obtained from these mice and further analyzed the impact of Rlip deficiency on gene networks of AD, aging, inhibition of stress-activated gene expression, mitochondrial function, and CREB signaling. Our studies revealed a significant increase in the levels of OS markers and alterations in the expression of genes and proteins involved in mitochondrial biogenesis, dynamics and synapses in brain tissues of these mice. Furthermore, we compared the cognitive function of wildtype and Rlip+/- mice. Behavioral, basic motor and sensory function tests in Rlip+/- mice revealed cognitive decline, similar to AD. Gene network analysis indicated dysregulation of stress-activated gene expression, mitochondrial function, and CREB signaling genes in the Rlip+/- mouse liver. Our results suggest that the Rlip deficiency-associated increase in OS and mitochondrial dysfunction could contribute to the development of OS-related AD processes. Therefore, the restoration of Rlip activity and endogenous cytoprotective mechanisms by pharmacological interventions is a novel approach to protect against AD.

neuroscience↗

bioRxiv2021

Macrophage-derived cholesterol contributes to therapeutic resistance in prostate cancer

Tumor-associated macrophages are key immune cells associated with cancer progression. Here we sought to determine the role of macrophages in castration-resistant prostate cancer (CRPC) using a syngeneic model that reflected the mutational landscape of the disease. A transcriptomic analysis of CRPC tumors following macrophage depletion revealed lower molecular signatures for steroid and bile acid synthesis, indicating potential perturbation of cholesterol metabolism. Since cholesterol is the precursor of the five major classes of steroid hormones, we reasoned that macrophages were regulating androgen biosynthesis within the prostate tumor microenvironment. Indeed, macrophage depletion reduced the levels of androgens within prostate tumors and restricted androgen receptor (AR) nuclear localization in vitro and in vivo. Macrophages were cholesterol rich and had the ability to transfer cholesterol to tumor cells in vitro, and AR nuclear translocation was inhibited by activation of Liver X Receptor (LXR)-{beta}, the master regulator of cholesterol homeostasis. Finally, combining macrophage depletion with androgen deprivation therapy increased survival, supporting the therapeutic potential of targeting macrophages in CRPC.

cancer biology↗

bioRxiv2020

Real-time biomedical knowledge synthesis of the exponentially growing world wide web using unsupervised neural networks

Decoding disease mechanisms for addressing unmet clinical need demands the rapid assimilation of the exponentially growing biomedical knowledge. These are either inherently unstructured and non-conducive to current computing paradigms or siloed into structured databases requiring specialized bioinformatics. Despite the recent renaissance in unsupervised neural networks for deciphering unstructured natural languages and the availability of numerous bioinformatics resources, a holistic platform for real-time synthesis of the scientific literature and seamless triangulation with deep omic insights and real-world evidence has not been advanced. Here, we introduce the nferX platform that makes the highly unstructured biomedical knowledge computable and supports the seamless visual triangulation with statistical inference from diverse structured databases. The nferX platform will accelerate and amplify the research potential of subject-matter experts as well as non-experts across the life science ecosystem (https://academia.nferx.com/).

bioinformatics↗

bioRxiv2019

Commercial gene expression tests for prostate cancer prognosis provide paradoxical estimates of race-specific risk

BackgroundCommercial gene expression signatures of prostate cancer (PCa) prognosis were developed and validated in cohorts of predominantly European American men (EAM). Limited research exists on the value of such signatures in African American men (AAM), who have poor PCa outcomes. We explored differences in gene expression between EAM and AAM for three commercially available panels recommended by the National Comprehensive Cancer Network for PCa prognosis. Materials and Methods: 232 EAM and 95 AAM patients provided radical prostatectomy specimens. Gene expression was quantified using Nanostring for 60 genes spanning the Oncotype DX Prostate, Prolaris, and Decipher panels. A continuous expression-based risk score was approximated for each. Differential expression, intrapanel co-expression and risk by race were assessed.\n\nResults and limitationsClinical and pathologic features were similar between AAM and EAM. Differential expression by race was observed for 48% of genes measured, though the magnitudes of expression differences were small. Coexpression patterns were more strongly preserved by race group for Oncotype DX and Decipher versus Prolaris (integrative correlations of 0.87, 0.73, and 0.62, respectively). Poorer prognosis was estimated in EAM versus AAM for Oncotype DX (p < 0.001), whereas no difference in prognosis was predicted between AAM and EAM using Prolaris or Decipher (p > 0.05). Replication of our findings directly on the commercial panels with long-term follow-up is warranted.\n\nConclusionsDue to observed racial differences across three commercial gene expression panels for PCa prognosis, caution is warranted when applying these panels in clinical decision-making in AAM.

epidemiology↗

bioRxiv2019

RICOPILI: Rapid Imputation for COnsortias PIpeLIne

MotivationGenome-wide association study (GWAS) analyses, at sufficient sample sizes and power, have successfully revealed biological insights for several complex traits. RICOPILI, an open sourced Perl-based pipeline was developed to address the challenges of rapidly processing large scale multi-cohort GWAS studies including quality control, imputation and downstream analyses. The pipeline is computationally efficient with portability to a wide range of high-performance computing (HPC) environments.\n\nSummaryRICOPILI was created as the Psychiatric Genomics Consortium (PGC) pipeline for GWAS and has been adopted by other users. The pipeline features i) technical and genomic quality control in case-control and trio cohorts ii) genome-wide phasing and imputation iv) association analysis v) meta-analysis vi) polygenic risk scoring and vii) replication analysis. Notably, a major differentiator from other GWAS pipelines, RICOPILI leverages on automated parallelization and cluster job management approaches for rapid production of imputed genome-wide data. A comprehensive meta-analysis of simulated GWAS data has been incorporated demonstrating each step of the pipeline. This includes all of the associated visualization plots, to allow ease of data interpretation and manuscript preparation. Simulated GWAS datasets are also packaged with the pipeline for user training tutorials and developer work.\n\nAvailability and ImplementationRICOPILI has a flexible architecture to allow for ongoing development and incorporation of newer available algorithms and is adaptable to various HPC environments (QSUB, BSUB, SLURM and others). Specific links for genomic resources are either directly provided in this paper or via tutorials and external links. The central location hosting scripts and tutorials is found at this URL: https://sites.google.com/a/broadinstitute.org/RICOPILI/home\n\nContactsripke@broadinstitute.org\n\nSupplementary informationSupplementary data are available.

genetics↗

bioRxiv2018

Quantitative mass spectrometry to interrogate proteomic heterogeneity in metastatic lung adenocarcinoma and validate a novel somatic mutation CDK12-G879V

Lung cancer is the leading cause of cancer death both in men and women. Tumor heterogeneity is an impediment to targeted treatment of all cancers, including lung cancer. Here, we sought to characterize changes in tumor proteome and phosphoproteome by longitudinal, prospective collection of tumor tissue of an exceptional responder lung adenocarcinoma patient who survived with metastatic lung adenocarcinoma for more than seven years with HER2-directed therapy in combination with chemotherapy. We employed \"Super-SILAC\" and TMT labeling strategies to quantify the proteome and phosphoproteome of a lung metastatic site and ten different metastatic progressive lymph nodes collected across a span of seven years, including five lymph nodes procured at autopsy. We identified specific signaling networks enriched in lung compared to the lymph node metastatic sites. We correlated the changes in protein abundance with changes in copy number alteration (CNA) and transcript expression. To further interrogate the mass spectrometry data, patient-specific database was built incorporating all the somatic variants identified by whole genome sequencing (WGS) of genomic DNA from the lung, one lymph node metastatic site and blood. An extensive validation pipeline was built for confirmation of variant peptides. We validated 360 spectra corresponding to 55 germline and 6 somatic variant peptides. Targeted MRM assays demonstrated expression of two novel variant somatic peptides, CDK12-G879V and FASN-R1439Q, with expression in lung and lymph node metastatic sites, respectively. CDK12 G879V mutation likely results in a nonfunctional CDK12 kinase and chemotherapy susceptibility in lung metastatic sites. Knockdown of CDK12 in lung adenocarcinoma cells results in increased chemotherapy sensitivity, explaining the complete resolution of the lung metastatic sites in this patient.

cancer biology↗

bioRxiv2017

GWAS meta-analysis (N=279,930) identifies new genes and functional links to intelligence

Intelligence is highly heritable1 and a major determinant of human health and well-being2. Recent genome-wide meta-analyses have identified 24 genomic loci linked to intelligence3-7, but much about its genetic underpinnings remains to be discovered. Here, we present the largest genetic association study of intelligence to date (N=279,930), identifying 206 genomic loci (191 novel) and implicating 1,041 genes (963 novel) via positional mapping, expression quantitative trait locus (eQTL) mapping, chromatin interaction mapping, and gene-based association analysis. We find enrichment of genetic effects in conserved and coding regions and identify 89 nonsynonymous exonic variants. Associated genes are strongly expressed in the brain and specifically in striatal medium spiny neurons and cortical and hippocampal pyramidal neurons. Gene-set analyses implicate pathways related to neurogenesis, neuron differentiation and synaptic structure. We confirm previous strong genetic correlations with several neuropsychiatric disorders, and Mendelian Randomization results suggest protective effects of intelligence for Alzheimers dementia and ADHD, and bidirectional causation with strong pleiotropy for schizophrenia. These results are a major step forward in understanding the neurobiology of intelligence as well as genetically associated neuropsychiatric traits.

genetics↗