146 Publications

Axisymmetric membranes with edges under external force: buckling, minimal surfaces, and tethers

L. Jia, Steven Pei, Robert A. Pelcovits, Thomas R. Powers

We use theory and numerical computation to determine the shape of an axisymmetric fluid membrane with a resistance to bending and constant area. The membrane connects two rings in the classic geometry that produces a catenoidal shape in a soap film. In our problem, we find infinitely many branches of solutions for the shape and external force as functions of the separation of the rings, analogous to the infinite family of eigenmodes for the Euler buckling of a slender rod. Special attention is paid to the catenoid, which emerges as the shape of maximal allowable separation when the area is less than a critical area equal to the planar area enclosed by the two rings. A perturbation theory argument directly relates the tension of catenoidal membranes to the stability of catenoidal soap films in this regime. When the membrane area is larger than the critical area, we find additional cylindrical tether solutions to the shape equations at large ring separation, and that arbitrarily large ring separations are possible. These results apply for the case of vanishing Gaussian curvature modulus; when the Gaussian curvature modulus is nonzero and the area is below the critical area, the force and the membrane tension diverge as the ring separation approaches its maximum value. We also examine the stability of our shapes and analytically show that catenoidal membranes have markedly different stability properties than their soap film counterparts.

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June 2, 2021

Single nucleus multi-omics regulatory atlas of the murine pituitary

F Ruf-Zamojski, Z. Zhang, M Zamojski, O. Troyanskaya, S Sealfon, et al.

To provide a multi-omics resource and investigate transcriptional regulatory mechanisms, we profile the transcriptome, chromatin accessibility, and methylation status of over 70,000 single nuclei (sn) from adult mouse pituitaries. Paired snRNAseq and snATACseq datasets from individual animals highlight a continuum between developmental epigenetically-encoded cell types and transcriptionally-determined transient cell states. Co-accessibility analysis-based identification of a putative Fshb cis-regulatory domain that overlaps the fertility-linked rs11031006 human polymorphism, followed by experimental validation illustrate the use of this resource for hypothesis generation. We also identify transcriptional and chromatin accessibility programs distinguishing each major cell type. Regulons, which are co-regulated gene sets sharing binding sites for a common transcription factor driver, recapitulate cell type clustering. We identify both cell type-specific and sex-specific regulons that are highly correlated with promoter accessibility, but not with methylation state, supporting the centrality of chromatin accessibility in shaping cell-defining transcriptional programs. The sn multi-omics atlas is accessible at snpituitaryatlas.princeton.edu.

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SynNotch-CAR T cells overcome challenges of specificity, heterogeneity, and persistence in treating glioblastoma

J. Choe, P. Watchmaker, M. Simic , O. Troyanskaya, et al.

Two major hurdles in chimeric antigen receptor (CAR) T cell therapy for solid tumors are ensuring specificity to tumor cells without affecting healthy cells and avoiding tumor escape due to antigen loss. To address these challenges, Hyrenius-Wittsten et al. and Choe et al. developed synthetic notch (synNotch)–CAR T cells targeting solid tumor antigens and used them to treat mouse models of mesothelioma, ovarian cancer, and glioblastoma. In both studies, the authors demonstrated that synNotch-CAR T cells were better at controlling tumors than traditional CAR T cells and did not result in toxicity or damage to healthy tissue. These results suggest that synNotch-CAR T cells may be an effective treatment strategy for solid tumors.

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Tissue-specific enhancer functional networks for associating distal regulatory regions to disease

X. Chen, J. Zhou, R. Zhang, A. Wong, C. Park, C. Theesfeld, O. Troyanskaya

Systematic study of tissue-specific function of enhancers and their disease associations is a major challenge. We present an integrative machine-learning framework, FENRIR, that integrates thousands of disparate epigenetic and functional genomics datasets to infer tissue-specific functional relationships between enhancers for 140 diverse human tissues and cell types, providing a regulatory-region-centric approach to systematically identify disease-associated enhancers. We demonstrated its power to accurately prioritize enhancers associated with 25 complex diseases. In a case study on autism, FENRIR-prioritized enhancers showed a significant proband-specific de novo mutation enrichment in a large, sibling-controlled cohort, indicating pathogenic signal. We experimentally validated transcriptional regulatory activities of eight enhancers, including enhancers not previously reported with autism, and demonstrated their differential regulatory potential between proband and sibling alleles. Thus, FENRIR is an accurate and effective framework for the study of tissue-specific enhancers and their role in disease. FENRIR can be accessed at fenrir.flatironinstitute.org/.

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Modeling transcriptional regulation of model species with deep learning

E. Cofer, A. Wong, O. Troyanskaya, et al.

To enable large-scale analyses of regulatory logic in model species, we developed DeepArk, a set of deep learning models of the cis-regulatory codes of four widely-studied species: Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, and Mus musculus DeepArk accurately predicts the presence of thousands of different context-specific regulatory features, including chromatin states, histone marks, and transcription factors. In vivo studies show that DeepArk can predict the regulatory impact of any genomic variant (including rare or not previously observed), and enables the regulatory annotation of understudied model species.

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April 19, 2021

ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach

X. Chen, A. Neuwald, L. Hilakivi-Clarke, R. Clarke, J. Xuan

ChIP-seq combines chromatin immunoprecipitation assays with sequencing and identifies genome-wide binding sites for DNA binding proteins. While many binding sites have strong ChIP-seq ‘peak’ observations and are well captured, there are still regions bound by proteins weakly, with a relatively low ChIP-seq signal enrichment. These weak binding sites, especially those at promoters and enhancers, are functionally important because they also regulate nearby gene expression. Yet, it remains a challenge to accurately identify weak binding sites in ChIP-seq data due to the ambiguity in differentiating these weak binding sites from the amplified background DNAs.

ChIP-BIT2 (http://sourceforge.net/projects/chipbitc/) is a software package for ChIP-seq peak detection. ChIP-BIT2 employs a mixture model integrating protein and control ChIP-seq data and predicts strong or weak protein binding sites at promoters, enhancers, or other genomic locations. For binding sites at gene promoters, ChIP-BIT2 simultaneously predicts their target genes. ChIP-BIT2 has been validated on benchmark regions and tested using large-scale ENCODE ChIP-seq data, demonstrating its high accuracy and wide applicability.

ChIP-BIT2 is an efficient ChIP-seq peak caller. It provides a better lens to examine weak binding sites and can refine or extend the existing binding site collection, providing additional regulatory regions for decoding the mechanism of gene expression regulation.

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April 15, 2021

An automated framework for efficiently designing deep convolutional neural networks in genomics

Convolutional neural networks (CNNs) have become a standard for analysis of biological sequences. Tuning of network architectures is essential for a CNN’s performance, yet it requires substantial knowledge of machine learning and commitment of time and effort. This process thus imposes a major barrier to broad and effective application of modern deep learning in genomics. Here we present Automated Modelling for Biological Evidence-based Research (AMBER), a fully automated framework to efficiently design and apply CNNs for genomic sequences. AMBER designs optimal models for user-specified biological questions through the state-of-the-art neural architecture search (NAS). We applied AMBER to the task of modelling genomic regulatory features and demonstrated that the predictions of the AMBER-designed model are significantly more accurate than the equivalent baseline non-NAS models and match or even exceed published expert-designed models. Interpretation of AMBER architecture search revealed its design principles of utilizing the full space of computational operations for accurately modelling genomic sequences. Furthermore, we illustrated the use of AMBER to accurately discover functional genomic variants in allele-specific binding and disease heritability enrichment. AMBER provides an efficient automated method for designing accurate deep learning models in genomics.

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AMBIENT: Accelerated Convolutional Neural Network Architecture Search for Regulatory Genomics

Convolutional neural networks (CNN) have become a standard approach for modeling genomic sequences. CNNs can be effectively built by Neural Architecture Search (NAS) by trading computing power for accurate neural architectures. Yet, the consumption of immense computing power is a major practical, financial, and environmental issue for deep learning. Here, we present a novel NAS framework,
AMBIENT, that generates highly accurate CNN architectures for biological sequences of diverse functions, while substantially reducing the computing cost of conventional NAS.

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February 27, 2021

mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge

M. Meyer, Y. Wang, D. Edwards, G. Smith, A. Rubenstein, P. Ramanathan, C. Mire, C. Pietzch, X. Chen, Y. Ge, W. Cheng, C. Henry, A. Woods, L. Ma, G. Stewart-Jones, K. Bock, M. Minai, B. Nagata, S. Periasamy, P. Shi, B. Graham, I. Moore, I. Ramos, O. Troyanskaya, E. Zaslavsky, A. Carfi, S. Sealfon, A. Bukreyev

The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.

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January 25, 2021

Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk

C. Park, J. Zhou, A. Wong, K. Chen, C. Theesfeld, R. Darnell , O. Troyanskaya

Despite the strong genetic basis of psychiatric disorders, the underlying molecular mechanisms are largely unmapped. RNA-binding proteins (RBPs) are responsible for most post-transcriptional regulation, from splicing to translation to localization. RBPs thus act as key gatekeepers of cellular homeostasis, especially in the brain. However, quantifying the pathogenic contribution of noncoding variants impacting RBP target sites is challenging. Here, we leverage a deep learning approach that can accurately predict the RBP target site dysregulation effects of mutations and discover that RBP dysregulation is a principal contributor to psychiatric disorder risk. RBP dysregulation explains a substantial amount of heritability not captured by large-scale molecular quantitative trait loci studies and has a stronger impact than common coding region variants. We share the genome-wide profiles of RBP dysregulation, which we use to identify DDHD2 as a candidate schizophrenia risk gene. This resource provides a new analytical framework to connect the full range of RNA regulation to complex disease.

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Nature Genetics, 53(2): 166-173
January 18, 2021
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