PAM-flexible genome editing with an engineered chimeric Cas9
Pranam Chatterjee and team enhance the versatility of CRISPR-based genome editing by addressing the limitations imposed by the requirement of specific protospacer adjacent motifs (PAMs) for Cas endonucleases. They combined previously engineered variants to develop a hybrid Cas9 enzyme called SpRYc, which can edit a broad range of PAM sequences and offer significant potential for genome editing applications and therapeutic uses.
Spinal cord repair is modulated by the neurogenic factor Hb-egf under direction of a regeneration-associated enhancer
Ken Poss, Aravind Asokan, and team used molecular genetic, biomaterials, and profiling approaches in zebrafish to show a new role for Hb-egfa as a neurogenic factor necessary for innate spinal cord regeneration. Their results suggest strategies to improve spinal cord repair in mammals.
Atrx deletion impairs CGAS/STING signaling and increases sarcoma response to radiation and oncolytic herpesvirus
ATRX is one of the most frequently altered genes in solid tumors, and mutation is especially frequent in soft tissue sarcomas. David Kirsch and team developed a primary mouse model of soft tissue sarcoma and showed that Atrx-deleted tumors were more sensitive to radiation therapy and to oncolytic herpesvirus. Translating their results to patients with TRX mutant cancers could enable genomically-guided cancer therapeutic approaches that improve patient outcomes.
Genetic and epigenetic signatures associated with plasma oxytocin levels in children and adolescents with autism spectrum disorder
Simon Gregory and team investigated the genetic, epigenetic, and transcriptomic variation associated with plasma levels of oxytocin in biospecimens from 175 participants from the Study of Oxytocin in Autism and Reciprocal Social Behaviors (SOARS-B) trial, and provide the most comprehensive genetic and epigenetic analysis of the peripheral oxytocin system to date.
An Enhancer-Based Gene Therapy Strategy for Spatiotemporal Control of Cargoes During Tissue Repair
Ken Poss, Nenad Bursac, Charlie Gersbach, Aravind Asokan and team discovered that tissue-regeneration enhancer elements (TREEs) isolated from zebrafish can direct targeted, injury-associated gene expression from viral DNA vectors delivered systemically in small and large adult mammalian species.
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Cross-species evolution of a highly potent AAV variant for therapeutic gene transfer and genome editing
Aravind Asokan, Charlie Gersbach and team have begun to tackle the challenges of recombinant AAV vectors in clinical translation by corroborating the notion that iterative evolution in multiple animal models can yield potent AAV variants with cross-species compatibility that can potentially enable better predictive preclinical modeling and help improve the therapeutic window of AAV gene therapies in humans.
Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis
Eda Yilidrim and team investigated the functional and mechanistic roles of Xist in hematopoietic stem cell and progenitor cells (HSPCs) and the role of Xist in regulating X-linked gene expression during X chromosome inactivation (XCI) maintenance. Their findings on the role of Xist in regulation of expression of XCI escape and subjective genes will provide insights for treatment strategies of X-linked diseases.
Enhancer selection dictates gene expression responses in remote organs during tissue regeneration
Ken Poss, Greg Crawford and colleagues explored long-range tissue interactions during regeneration by assessing the brain transcriptomes of zebrafish subjected to severe cardiac injury. Their findings suggest a concept in whole-animal management of tissue regeneration in which injury-responsive enhancer elements expand the range and functions of key regulatory genes.
Human distal lung maps and lineage hierarchies reveal a bipotent progenitor
Purushothama Rao Tata, along with Simon Gregory and team, identified molecularly distinct terminal and respiratory bronchioles (TRBs) cell types that have not been previously characterized. Their findings revise human lung cell maps and lineage trajectories and implicate an epithelial transitional state in primate lung regeneration and disease.
Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity
Greg Crawford, Purushothama Rao Tata, and Tim Reddy were part of a team that identified two orthogonal processes in Kras-mutant distal airway club cells. Mutant KRAS is one of the most frequent drivers of epithelial cancers, and they found that oncogenic Kras activity in epithelia of several organs, including lung, skin, and intestine all follow a similar trajectory. Their study implicates a conserved pathway to target Kras-driven tumors.
Engineered bacterial voltage-gated sodium channel platform for cardiac gene therapy
Nenad Bursac and colleagues have demonstrated a gene therapy that helps heart muscle cells electrically activate in live mice. The first demonstration of its kind, the approach features engineered bacterial genes that code for sodium ion channels and could lead to therapies to treat a wide variety of electrical heart diseases and disorders.
Focused goodness of fit tests for gene set analyses
Andrew Allen and team developed a flexible gene set-based signal detection framwork based on tail-focused goodness of fit statistics. The team provides guidance on statistics to choose , and they apply these methods to a whole exome sequencing of amyotrophic sclerosis.
Hif-1a suppresses ROS-induced proliferation of cardiac fibroblasts following myocardial infarction
Nenad Bursac and colleagues report that a progenitor-like subpopulation of cardiac fibroblasts (CFs) resides in a hypoxic niche, expresses Hif-1a, and exhibits a distinct metabolic profile. They investigated the function of HIF-1α in CFs in homeostasis and after myocardial infarction using conditional gene targeting and single-cell genomics.
The membrane associated accessory protein is an adeno-associated viral egress factor
Aravind Asokan and team provide structural and functional insights into the recently identified membrane-associated accessory protein (MAAP), which is encoded from a different, alternative open reading frames (ORF) within the adeno-associated virus (AAV) cap gene.
Cnksr2 loss in mice leads to increased neural activity and behavioral phenotypes of Epilepsy-Aphasia Syndrome
Scott Soderling and team developed a genetic mouse model for epilepsy-aphasia syndromes (EAS) - a spectrum of childhood epileptic, cognitive and language disorders - and show how these mice exhibit electrophysiological and behavioral phenotypes similar to those of patients, providing an important new model for future studies of EAS.
DMD gene editing restores full-length dystrophin
Charlie Gersbach, Aravind Asokan, Bill Majoros and team used an AAV-based homology-independent targeted integration (HITI) approach to correct full-length dystrophin expression in a humanized mouse model of Duchenne muscular dystrophy.
Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF-PU.1-DPP4 Axis
Xiling Shen, David Hsu, Greg Crawford, Charlie Gersbach, Perushothama Rao Tata and team investigate chromatin remodeling in metastatic cells in the liver and present a potential strategy to target that chromatic remodeling in metastatic cancer and the promise of repurposing drugs to treat metastasis.
Transgenic mice for in vivo epigenome editing with CRISPR-based systems
Aravind Asokan, Maria Ciofani, Ken Poss, Tim Reddy, Anne West and Charlie Gersbach collaborated to develop two conditional transgenic mouse lines for epigenome editing. They demonstrated the flexibility, versatility and robustness of these mouse lines through a variety of experiments. The mice are publicly available through The Jackson Laboratory.
Action potential-coupled Rho GTPase signaling drives presynaptic plasticity
Scott Soderling and team applied BioID to presynaptic terminals in vivo to discover a new mechanism of presynaptic plasticity. Their results provide a new proteomic framework from which to view the cellular biology of presynaptic physiology.
Receptor switching in newly evolved adeno-associated viruses
Aravind Asokan and team demonstrate that distinct epitopes on the surface of adeno-associated viruses can be evolved by infectious cycling to recognize different cell surface carbohydrates and glycoprotein receptors and solve the 3D structure of one such newly evolved AAV capsid, which provides a roadmap for designing viruses with improved attributes for gene therapy applications.
Living fabrication of functional semi-interpenetrating polymeric materials
Xiling Shen was part of a team that created a new approach to fabricate semi-interpenetrating polymer networks (IPN) that is living, functional and biocompatible. This is the first time bacterially-fabricated living materials have been used in a setting with direct clinical relelvance: to protect the gut microbiota against unintended perturbations by antibiotics.
Characterization of liver GSD IX γ2 pathophysiology in a novel Phkg2−/− mouse model
Aravind Asokan was part of a team that made the first mouse model that can recapitulate the liver-specific pathology of patients with Liver Glycogen Storage Disease IX.
Three-dimensional tissue-engineered human skeletal muscle model of Pompe disease
Nenad Bursac and team developed a 3-D model of infantile-onset Pompe disease that demonstrates the signature pathological features of the disease.
The NIH Somatic Cell Genome Editing program
Charlie Gersbach, Nenad Bursac and Aravind Asokan are part of the NIH Somatic Cell Gene Editing Consortium. In this publication, the team lays our their plans to develop and benchmark approaches to induce and measure genome modifications, and define downstream functional consequences of genome editing within human cells.
In vivo proximity labeling identifies cardiomyocyte protein networks during zebrafish heart regeneration
Ken Poss and team used a transgenic BioID2 strategy to capture cell-specific proteome changes in cardiomyocytes during heart regeneration in adult zebrafish.
Correcting signal biases and detecting regulatory elements in STARR-seq data
Bill Majoros, Andrew Allen, Tim Reddy and team developed a statistical model that corrects technical biases in STARR-seq data and improves detection of regulatory elements.
AP-1 subunits converge promiscuously at enhancers to potentiate transcription
Charlie Gersbach, Tim Reddy and team definitively established the genome-wide binding patterns of five AP-1 subunits using CRISPR to introduce a common antibody tag on each subunit.
Mutational processes in cancer preferentially affect binding of particular transcription factors
Raluca Gordan collaborated with Duke-NUS to develop the "Signature-QBiC" model that integrates signature profiles of mutational processes with the QBiC estimates of changes in binding affinity to investigate the effect of mutational signatures on the binding of 582 human transcription factors.
Adeno-Associated Virus-Mediated Gene Therapy in the Mashlool, Atp1a3 Mashl/+, Mouse Model of Alternating Hemiplegia of Childhood
Boris Kantor and Aravid Asokan were part of a team that investigated the effects of delivering an extra copy of the normal gene in a mouse model carrying the most common mutation that causes Alternating Hemiplegia of Childhood (AHC) in humans. AHC is a devastating autosomal dominant that can cause evere hemiplegia and dystonia spells, ataxia, debilitating disabilities, and premature death.
Exercise mimetics and JAK inhibition attenuate IFN-γ–induced wasting in engineered human skeletal muscle
Nenad Bursac and team demonstrated that human muscle has an innate ability to ward off the damaging effects of chronic inflammation when exercised. The discovery was made possible through the use of lab-grown, engineered human muscle.
Causal network inference from gene transcriptional time-series response to glucocorticoids
Tim Reddy and team developed a new method, BETS, that infers causal gene networks from gene expression time series. BETS runs quickly because it is parallelized, allowing even data sets with thousands of genes to be analyzed.
Induced organoids derived from patients with ulcerative colitis recapitulate colitic reactivity
Xiling Shen was part of a team that provided evidence linking recent advances in stem cell biology with intestinal development to reprogram colonic fibroblasts isolated from ulcerative colitis patients to induced pluripotent stem cells, followed by directed differentiation to induced human ulcerative colitis organoids. This patient-derived organoid model will generate new insights into the underlying pathogenesis of ulcerative colitis while offering opportunities to tailor interventions to the individual patient.
Control of osteoblast regeneration by a train of Erk activity waves
Ken Poss and team applied transgenic tools, live imaging, quantitative analysis and mathematical modelling to investigate how signalling dynamics regulate bone regeneration in adult zebrafish. They discovered a signaling protein molecules called Erks that cause cells to divide also tell them when to stop dividing. This discovery could have future implications for regenerative therapy in humans.