Biology subjects

Patel, N.

Publications and source records attributed to Patel, N..

At least 91 records · Page 5Linked to original sources

bioRxiv2020

Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate

Vaccine efforts against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the current COVID-19 pandemic are focused on SARS-CoV-2 spike glycoprotein, the primary target for neutralizing antibodies. Here, we performed cryo-EM and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax based on a full-length spike protein formulated in polysorbate 80 (PS 80) detergent. Our studies reveal a stable prefusion conformation of the spike immunogen with slight differences in the S1 subunit compared to published spike ectodomain structures. Interestingly, we also observed novel interactions between the spike trimers allowing formation of higher order spike complexes. This study confirms the structural integrity of the full-length spike protein immunogen and provides a basis for interpreting immune responses to this multivalent nanoparticle immunogen.

immunology↗

bioRxiv2020

SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 elicits immunogenicity in baboons and protection in mice

The COVID-19 pandemic continues to spread throughout the world with an urgent need for a safe and protective vaccine to effectuate herd immunity to control the spread of SARS-CoV-2. Here, we report the development of a SARS-CoV-2 subunit vaccine (NVX-CoV2373) produced from the full-length spike (S) protein, stabilized in the prefusion conformation. Purified NVX-CoV2373 S form 27.2nm nanoparticles that are thermostable and bind with high affinity to the human angiotensin-converting enzyme 2 (hACE2) receptor. In mice and baboons, low-dose NVX-CoV2373 with saponin-based Matrix-M adjuvant elicits high titer anti-S IgG that is associated with blockade of hACE2 receptor binding, virus neutralization, and protection against SARS-CoV-2 challenge in mice with no evidence of vaccine-associated enhanced respiratory disease (VAERD). NVX-CoV2373 vaccine also elicits multifunctional CD4+ and CD8+ T cells, CD4+ T follicular helper T cells (Tfh), and the generation of antigen-specific germinal center (GC) B cells in the spleen. These results support the ongoing phase 1/2 clinical evaluation of the safety and immunogenicity of NVX-CoV2327 with Matrix-M (NCT04368988).

microbiology↗

bioRxiv2020

Primary platinum resistance and immune exclusion in ovarian carcinomas with high expression of the homologous recombination mediator RAD51

BackgroundHomologous recombination deficiency (HRD) in ovarian cancer confers increased sensitivity to Poly-ADP-Ribose-Polymerase (PARP) inhibitors and platinum. The homologous recombination (HR) mediator RAD51, however, is commonly overexpressed, potentially driving unregulated HR. Due to non-quantitative measurements and heterogeneous cohorts, the clinical relevance of RAD51 expression in ovarian cancer is unclear. MethodsFluorescent immunohistochemistry and multispectral imaging were used to quantitate RAD51 expression, in relation to other markers, in independent cohorts of ovarian carcinomas from British Columbia Cancer (BCC n=284) and the phase III SCOTROC4 trial (n=268). Independent cohorts (TCGA n=566, GSE9891 n=267, GSE26712 n=185 and GSE3149 n=146) were used for mRNA expression and immune infiltration analyses. ResultsRAD51-High tumours had shorter progression-free and overall survival compared to RAD51-Low cases in both BCC and SCOTROC4. The negative prognostic significance of high RAD51 was primarily evident in cases classified "HRD negative" by the Myriad genomic scar assay. Unexpectedly, overexpression of RAD51 in ovarian cancer cell lines did not affect sensitivity to platinum or PARP inhibitors, but modified the expression of immune-regulatory genes. Accordingly, tumours with high RAD51 mRNA showed consistent changes in immunomodulatory transcripts across four independent ovarian cancer cohorts. In-situ multiplexed imaging confirmed that high RAD51 tumours correlated with tumour exclusion of cytotoxic-T-cells, possibly explaining their poor outcomes after chemotherapy. ConclusionsHigh RAD51 expression, in conjunction with a HRD score <42, identifies a subgroup of EOC cases with platinum resistance and an immune excluded tumour microenvironment. Tumours with high RAD51 may require alternate or additional adjuvant therapeutic strategies to overcome immune exclusion. Statement of Translational RelevanceHomologous recombination deficiency (HRD) in ovarian cancer confers increased sensitivity to Poly-ADP-Ribose-Polymerase (PARP) inhibitors and platinum. Currently, methods to identify patients who do poorly on first-line platinum based chemotherapy in ovarian cancer represent an unmet clinical need. In this report we show that RAD51 expression can identify patients with primary platinum resistance in two large cohorts, including a unique phase-III trial of carboplatin as adjuvant monotherapy. The clinical relevance of a positive genomic scar HRD score, a biomarker for assessing HRD status, in predicting benefit to PARP inhibitors has been established following recent phase 3 trials in first line and 2nd line maintenance treatment of ovarian cancer. Our findings suggest that HRD negative ovarian tumours may be further stratified by RAD51 expression status in the context of platinum sensitivity, and may serve to guide future trials of HRD targeted agents.

cancer biology↗

bioRxiv2020

Induction of pancreatic neoplasia in the KRAS/TP53 Oncopig: preliminary report

IntroductionFive year survival of pancreatic cancer (PC) remains low. Current murine models may not adequately mimic human PC and can be too small for medical device development. A large animal PC model could address these issues. We induced and characterized pancreatic tumors in Oncopigs (transgenic swine with a somatic floxed cassette containing KRASG12D and TP53R167H). MethodsOncopigs underwent injection of adenovirus expressing Cre recombinase (AdCre) +/- interleukin 8 (IL-8) into one of the main pancreatic ducts (induction procedure). Subjects were necropsied after [≤]10 week, followed by histological analysis, cytokine expression analysis, exome sequencing and transcriptome analysis of resultant tumors. ResultsFourteen Oncopigs underwent the induction procedure; ten (71%) had gross tumor within three weeks, one of these subjects expired suddenly and the other 9 required premature euthanasia secondary to lack of oral intake. At necropsy all of ten of these subjects had gastric outlet obstruction secondary to pancreatic tumor and phlegmon. Two Oncopigs underwent a control injection (no AdCre) and four WT littermates of the Oncopigs underwent AdCre injection without notable effect. Exome and transcriptome analysis of the porcine pancreatic tumors revealed similarity with the molecular signatures and pathways of human PC. ConclusionOncopigs with ductal injection of AdCre developed pancreatic tumor in a short period of time with molecular characteristics similar to human PC. While further optimization and validation of this porcine PC model would be beneficial, it is anticipated that this model will be useful for focused research and development of diagnostic and therapeutic technologies for PC.

cancer biology↗

bioRxiv2020

A target enrichment probe set for resolving the flagellate plant tree of life

Premise of the studyNew sequencing technologies enable the possibility of generating large-scale molecular datasets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate plants, comprising hornworts, liverworts, mosses, lycophytes, ferns, and gymnosperms. Methods and ResultsWe leveraged existing transcriptome and genome sequence data to design a set of 56,989 probes for target enrichment sequencing of 451 nuclear exons and non-coding flanking regions across flagellate plant lineages. We describe the performance of target enrichment using the probe set across flagellate plants and demonstrate the potential of the data to resolve relationships among both ancient and closely related taxa. ConclusionsA target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate plants.

evolutionary biology↗

bioRxiv2020

Transparency in butterflies and moths: structural diversity, optical properties and ecological relevance

In water, transparency seems an ideal concealment strategy, as testified by the variety of transparent aquatic organisms. By contrast, transparency is nearly absent on land, with the exception of insect wings, and knowledge is scarce about its functions and evolution, with fragmentary studies and no comparative perspective. Lepidoptera (butterflies and moths) represent an outstanding group to investigate transparency on land, as species typically harbour opaque wings covered with coloured scales, a key multifunctional innovation. Yet, many Lepidoptera species have evolved partially or fully transparent wings. At the interface between physics and biology, the present study investigates transparency in 123 Lepidopteran species (from 31 families) for its structural basis, optical properties and biological relevance in relation to thermoregulation and vision. Our results establish that transparency has likely evolved multiple times independently. Efficiency at transmitting light is largely determined by clearwing microstructure (scale shape, insertion, colouration, dimensions and density) and macrostructure (clearwing area, species size or wing area). Microstructural traits - density, dimensions - are tightly linked in their evolution, with different constraints according to scale shape, insertion, and colouration. Transparency appears highly relevant for vision, especially for camouflage, with size-dependent and activity-rhythm dependent variations. Links between transparency and latitude are consistent with an ecological relevance of transparency in thermoregulation, and not so for protection against UV radiation. Altogether, our results shed new light on the physical and ecological processes driving the evolution of transparency on land and underline that transparency is a more complex than previously thought colouration strategy.

evolutionary biology↗

bioRxiv2020

Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta)

BackgroundMosses compose one of the three lineages that form the sister group to extant vascular plants. Having emerged from an early split in the diversification of embryophytes, mosses may offer complementary insights into the evolution of traits following the transition to and colonization of land. Here, we report the draft nuclear genome of Fontinalis antipyretica (Fontinalaceae, Hypnales), a charismatic aquatic moss widespread in temperate regions of the Northern Hemisphere. We sequenced and de novo assembled its genome using the 10 x genomics method. The genome comprises 486.3 Mb, with a scaffold N50 of 38.8 kb. The assembly captured 89.4% of the 303 genes in the BUSCO eukaryote dataset. The newly generated F. antipyretica genome is the third genome of mosses, and the second genome for a seedless aquatic plant.

genomics↗

bioRxiv2020

A survey of rare epigenetic variation in 23,116 human genomes identifies disease-relevant epivariations and novel CGG expansions

There is growing recognition that epivariations, most often recognized as promoter hypermethylation events that lead to gene silencing, are associated with a number of human diseases. However, little information exists on the prevalence and distribution of rare epigenetic variation in the human population. In order to address this, we performed a survey of methylation profiles from 23,116 individuals using the Illumina 450k array. Using a robust outlier approach, we identified 4,452 unique autosomal epivariations, including potentially inactivating promoter methylation events at 384 genes linked to human disease. For example, we observed promoter hypermethylation of BRCA1 and LDLR at population frequencies of ~1 in 3,000 and ~1 in 6,000 respectively, suggesting that epivariations may underlie a fraction of human disease which would be missed by purely sequence-based approaches. Using expression data, we confirmed that many epivariations are associated with outlier gene expression. Analysis of SNV data and monozygous twin pairs suggests that approximately two thirds of epivariations segregate in the population secondary to underlying sequence mutations, while one third are likely sproradic events that occur post-zygotically. We identified 25 loci where rare hypermethylation coincided with the presence of an unstable CGG tandem repeat, and validated the presence of novel CGG expansions at several of these, identifying the molecular defect underlying most of the known folate-sensitive fragile sites in the genome. Our study provides a catalog of rare epigenetic changes in the human genome, gives insight into the underlying origins and consequences of epivariations, and identifies many novel hypermethylated CGG repeat expansions.

genomics↗

bioRxiv2020

Whole Genome De Novo Variant Identification with FreeBayes and Neural Network Approaches

MotivationDe novo variant (DNV) calling typically relies on heuristic filters intrinsic to specific platforms and variant calling algorithms. FreeBayes and neural network approaches have overcome this limitation for variant calling, and we implemented a similar approach for DNV identification. ResultsWe developed a DNV calling framework that uses Genome Analysis Toolkit (GATK), FreeBayes and a neural network trained on Integrative Genomics Viewer pile-up plots (IGV-bot). We identified DNVs in 2,390 WGS trios and benchmarked results against heuristics based on GATK parameters. Results were validated in silico and with Sanger sequencing, with the latter showing true positive rates of 98.4% and 97.3% for SNVs and indels, respectively. Taken together we describe a scalable framework for DNV identification based on both FreeBayes and neural network methods. AvailabilitySource code and documentation are available at https://github.com/ShenLab/igv-classifier and https://github.com/frichter/dnv_pipeline under the MIT license. Contactys2411@cumc.columbia.edu

genomics↗

bioRxiv2019

Regulation of heterotopic ossification through local inflammatory monocytes in a mouse model of aberrant wound healing

Heterotopic ossification (HO) is an aberrant regenerative process with ectopic bone induction in response to musculoskeletal trauma, in which mesenchymal stem cells (MSC) differentiate into osteochondrogenic cells instead of myocytes or tenocytes. Despite frequent cases of hospitalized musculoskeletal trauma, the inflammatory responses and cell population dynamics that regulate subsequent wound healing and tissue regeneration are still unclear. Here we examine, using a mouse model of trauma-induced HO, the local microenvironment of the initial post-injury inflammatory response. Single cell transcriptome analyses identify distinct monocyte/macrophage populations at the injury site, with their dynamic changes over time elucidated using trajectory analyses. Mechanistically, transforming growth factor beta-1 (TGF{beta}1)-producing monocytes/macrophages are associated with HO and aberrant chondrogenic progenitor cell differentiation, while CD47-activating peptides that reduce systemic TGF{beta} levels help ameliorate HO. Our data thus implicate CD47 activation as a novel therapeutic approach for modulating monocyte/macrophage phenotypes, MSC differentiation and HO formation during wound healing.

immunology↗

bioRxiv2019

A New Role for Telomerase in Promoting Meiotic Homolog Pairing Fidelity

We report a role for telomerase, beyond its known function of telomeric DNA end extension, in maintaining normal chromosome dynamics during meiosis in Saccharomyces cerevisiae. When telomerase at telomeres was reduced by various genetic means, increased frequencies of crossover and noncrossover recombination events occurred. To investigate the mechanism of this increased meiotic recombination, we examined the kinetics of meiosis events, and tracked the movement of chromosomes in live cells during meiotic prophase. Cytoskeletal forces acting on telomeres during meiosis have been shown to promote active chromosome motion needed to pair homologous chromosomes. Here we show that changes in telomerase interaction with telomeres using a tlc1-11 mutant result in altered meiotic motion. Specifically, reduction in telomerase at telomeres leads to a decreased frequency of high velocity chromosome pulls. In the tlc1-11 mutant, we see earlier synapsis and increased genome-wide recombination for the majority of the cells and lower gamete viability. Notably, homologous pairing is not delayed unlike other telomere binding mutants. Although synapsis initiates earlier, the overall timing of synapsis remains the same, except for a subset of cells that do not exit meiosis I. Together, these results suggest that the strong pulling component of the active chromosome motion promotes homolog pairing fidelity, likely by pulling apart improperly associated regions. Our combined observations are consistent with a model in which telomerase-mediated telomeric anchoring to the nuclear envelope helps engage and properly transmit cytoskeletal forces to chromosomes. Thus, telomerase contributes to efficient chromosome movements leading to normal gamete viability.

cell biology↗

bioRxiv2019

Do available protein 3D structures reflect human genetic and functional diversity?

Genomic databases are substantially biased towards European ancestry populations, and this bias contributes to health disparities. Here, we quantify how well 66,971 experimentally characterized human protein 3D structures represent the diversity of protein sequences observed across the 1000 Genomes Project. More than 85% of available structures do not match a sequence observed in at least one individual, and on average structures match the sequence of 74% of individuals. Nearly 23% of human structures do not match any observed sequences; however, after masking engineered/known mutations, this decreases to ~4%. African ancestry sequences are modestly, but significantly, less likely to be represented by structures (73.5% vs. 74.0%). These differences are mainly driven by the greater genetic diversity of African populations. We identify thousands of variants unrepresented in available structures that influence protein structure and function. Thus, the use of a single structure as representative of \"the wild type\" protein will often bias results against many individuals. The diversity of protein sequence and structure must be considered to enable accurate, reproducible, and generalizable conclusions from structural analyses.

genetics↗

bioRxiv2019

Optimal policy for multi-alternative decisions

Every-day decisions frequently require choosing among multiple alternatives. Yet, the optimal policy for such decisions is unknown. Here we derive the normative policy for general multi-alternative decisions. This strategy requires evidence accumulation to nonlinear, time-dependent bounds, that trigger choices. A geometric symmetry in those boundaries allows the optimal strategy to be implemented by a simple neural circuit involving a normalization with fixed decision bounds and an urgency signal. The model captures several key features of the response of decision-making neurons as well as the increase in reaction time as a function of the number of alternatives, known as Hicks law. In addition, we show that, in the presence of divisive normalization and internal variability, our model can account for several so called irrational behaviors such as the similarity effect as well as the violation of both the independent irrelevant alternative principle and the regularity principle.

neuroscience↗

bioRxiv2018

GLU: A tool for analysing continuously measured glucose in epidemiology

MotivationContinuous glucose monitors (CGM) record interstitial glucose continuously, producing a sequence of measurements for each participant (e.g. the average glucose every 5 minutes over several days, both day and night). To analyze these data, researchers tend to derive summary variables such as the Area Under the Curve (AUC), to then use in subsequent analyses. To date, a lack of consistency and transparency of precise definitions used for these summary variables has hindered interpretation, replication and comparison of results across studies. We present GLU, an open-source software package for deriving a consistent set of summary variables from CGM data.\n\nGeneral featuresGLU performs quality control of each CGM sample (e.g. addressing missing data), derives a diverse set of summary variables (e.g. AUC, and proportion of time spent in hypo-, normo- and hyper-glycaemic levels) covering six broad domains, and outputs these (with quality control information) to the user.\n\nImplementationGLU is implemented in R.\n\nAVAILABILITYGLU is available on GitHub at [https://github.com/MRCIEU/GLU]. Git tag v0.1 corresponds to the version presented here.

epidemiology↗

bioRxiv2018

Slow delivery immunization enhances HIV neutralizing antibody and germinal center responses via modulation of immunodominance

The observation that humans can produce broadly neutralizing antibodies (bnAbs) against HIV-1 has generated enthusiasm about the potential for a bnAb vaccine against HIV-1. Conventional immunization strategies will likely be insufficient for the development of a bnAb HIV vaccine and vaccines to other difficult pathogens, due to the significant immunological hurdles posed, including B cell immunodominance and germinal center (GC) quantity and quality. Using longitudinal lymph node fine needle aspirates, we found that two independent methods of slow delivery immunization of rhesus macaques (RM) resulted in larger GCs, more robust and sustained GC Tfh cell responses, and GC B cells with improved Env-binding, which correlated with the development of ~20 to 30-fold higher titers of tier 2 HIV-1 nAbs. Using a new RM genomic immunoglobulin loci reference sequence, we identified differential IgV gene usage between slow delivery immunized and conventional bolus immunized animals. The most immunodominant IgV gene used by conventionally immunized animals was associated with many GC B cell lineages. Ab mapping of those GC B cell specificities demonstrated targeting of an immunodominant non-neutralizing trimer base epitope, while that response was muted in slow delivery immunized animals. Thus, alternative immunization strategies appear to enhance nAb development by altering GCs and modulating immunodominance of non-neutralizing epitopes.

immunology↗

bioRxiv2018

SREBP1 drives KRT80-dependent cytoskeletal changes and invasive behavior in endocrine resistant ERα breast cancer

Approximately 30% of women diagnosed with ER breast cancer relapse with metastatic disease following adjuvant treatment with endocrine therapies1,2. The connection between acquisition of drug resistance and invasive potential is poorly understood. In this study, we demonstrate that the type II keratin topological associating domain (TAD)3 undergoes epigenetic reprogramming in cells that develop resistance to aromatase inhibitors (AI), leading to keratin 80 (KRT80) upregulation. In agreement, an increased number of KRT80-positive cells are observed at relapse in vivo while KRT80 expression associates with poor outcome using several clinical endpoints. KRT80 expression is driven by de novo enhancer activation by sterol regulatory element-binding protein 14 (SREBP1). KRT80 upregulation directly promotes cytoskeletal rearrangements at the leading edge, increased focal adhesion maturation and cellular stiffening, which collectively promote cancer cell invasion. Shear-wave elasticity imaging of prospective patients shows that KRT80 levels correlate with stiffer tumors in vivo. Collectively, our data uncover an unpredicted and potentially targetable direct link between epigenetic and cytoskeletal reprogramming promoting cell invasion in response to chronic AI treatment.

cancer biology↗

bioRxiv2018

Identification of rare de novo epigenetic variations in congenital disorders

Certain human traits such as neurodevelopmental disorders (NDs) and congenital anomalies (CAs) are believed to be primarily genetic in origin. With recent dramatic advances in genomic technologies, genome-wide surveys of cohorts of patients with ND/CAs for point mutations and structural variations have greatly advanced our understanding of their genetic etiologies1,2. However, even after whole genome sequencing (WGS), a substantial fraction of such disorders remain unexplained3. In contrast, the possibility that constitutive epigenetic variations (epivariations) might underlie such traits has not been well explored. We hypothesized that some cases of ND/CA are caused by aberrations of DNA methylation that lead to a dysregulation of normal genome function. By comparing DNA methylation profiles from 489 individuals with ND/CAs against 1,534 population controls, we identified epivariations as a frequent occurrence in the human genome. De novo epivariations were significantly enriched in cases when compared to controls. RNAseq data from population studies showed that epivariations often have an impact on gene expression comparable to loss-of-function mutations. Additionally, we detected and replicated an enrichment of rare sequence mutations overlapping CTCF binding sites close to epivariations. Thus, some epivariations occur secondary to cis-linked mutations in regulatory regions, providing a rationale for interpreting non-coding genetic variation. We propose that epivariations likely represent the causative genomic defect in 5-10% of patients with unexplained ND/CAs. This constitutes a yield comparable to CNV microarrays, and as such has significant diagnostic relevance.

genomics↗

bioRxiv2017

Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors

Multiple tools have been developed to identify copy number variants (CNVs) from whole exome (WES) and whole genome sequencing (WGS) data. Current tools such as XHMM for WES and CNVnator for WGS identify CNVs based on changes in read depth. For WGS, other methods to identify CNVs include utilizing discordant read pairs and split reads and genome-wide local assembly with tools such as Lumpy and SvABA, respectively. Here, we introduce a new method to identify deletion CNVs from WES and WGS trio data based on the clustering of Mendelian errors (MEs). Using our Mendelian Error Method (MEM), we identified 127 deletions (inherited and de novo) in 2,601 WES trios from the Pediatric Cardiac Genomics Consortium, with a validation rate of 88% by digital droplet PCR. MEM identified additional de novo deletions compared to XHMM, and also identified sample switches, DNA contamination, a significant enrichment of 15q11.2 deletions compared to controls and eight cases of uniparental disomy. We applied MEM to WGS data from the Genome In A Bottle Ashkenazi trio and identified deletions with 97% specificity. MEM provides a robust, computationally inexpensive method for identifying deletions, and an orthogonal approach for verifying deletions called by other tools.

genetics↗