Scholars@Duke
Charles Gersbach

Charles Gersbach

John W. Strohbehn Distinguished Professor of Biomedical Engineering
Biomedical Engineering
Charles.gersbach@duke.edu
Box 90281, 136 Hudson Hall, Durham, NC 27708
2123 CIEMAS, Durham, NC 27708

Scholarly Works - Journal articles

Molecular and cellular engineering: Epigenetic engineering

Journal article Current Opinion in Biomedical Engineering · September 1, 2026 Full text Cite

Transcription factor collaboration enables precise T cell state engineering.

Journal article bioRxiv · April 22, 2026 Transcription factors (TFs) collaborate to regulate gene expression programs that define cell fate. In CD8+ T cells, this coordinated regulation underlies exhaustion, a dysfunctional state that constrains immunity in chronic infection and cancer. Here, we ... Full text Link to item Cite

Enhancer hubs govern chromatin topology and Th17 cell identity.

Journal article bioRxiv · April 8, 2026 A wealth of noncoding regulatory elements has been described across mammalian cell types, yet determining their functional role remains a challenge. Regulatory control of gene expression is critical during active processes such as the adaptive immune respo ... Full text Link to item Cite

Monitoring biological effects of somatic cell genome editing.

Journal article Nature reviews. Genetics · April 2026 CRISPR-based genome editing therapeutics are entering the clinic, offering transformative potential but also presenting potential risks. Preclinical-to-clinical toolkits are needed to assess the safety and efficacy of these new therapies and accelerate pro ... Full text Cite

Reprogramming of neuronal genome function and phenotype by astrocytes.

Journal article bioRxiv · March 7, 2026 Heterotypic cell-cell interactions are critical to governing cellular physiology, disease progression, and responses to the environment and pharmacologic interventions. For example, neurons and astrocytes engage in intricate interactions that are essential ... Full text Link to item Cite

dHyperCas12a enables multiplexed CRISPRi screens.

Journal article Nat Commun · February 12, 2026 Interactions between genes or cis-regulatory elements (CREs) underlie many biological processes. High-throughput CRISPR screens have allowed researchers to assess the impact of activation or repression of gene and regulatory elements on many phenotypes. Ho ... Full text Link to item Cite

Mismatch tolerance of a gRNA for CRISPR-based gene activation confers broad activity critical for cell reprogramming.

Journal article bioRxiv · February 3, 2026 CRISPR activation and interference systems (CRISPRa/i) are widely used for programmable transcriptional control. Although these technologies are capable of highly specific single-gene activity, some applications of transcriptional network reprogramming req ... Full text Link to item Cite

The IGVF catalog-from genetic variation to function.

Journal article Nucleic Acids Res · January 6, 2026 Genomic variation between individuals is essential for understanding how differences in the genome sequence affect molecular and cellular processes. The Impact of Genomic Variation on Function (IGVF) Consortium aims to uncover the relationships among genom ... Full text Link to item Cite

Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness.

Journal article Science · December 11, 2025 Epigenetic control of gene expression and cellular phenotype is influenced by changes in the local microenvironment, yet how mechanical cues precisely influence epigenetic state to regulate transcription remains largely unmapped. In this study, we combined ... Full text Link to item Cite

SMARCA2 is an essential and potent cofactor for a specific subset of the glucocorticoid response in A549 cells.

Journal article bioRxiv · November 14, 2025 Glucocorticoids are a widely used, potent class of anti-inflammatory drugs that modulate the expression of hundreds of genes across the genome. Although the glucocorticoid response is primarily carried out by the glucocorticoid receptor (NR3C1, a.k.a. GR), ... Full text Link to item Cite

Circuit-specific gene editing for precision modulation of neuronal activity with CRISPR-rabies virus.

Journal article bioRxiv · November 7, 2025 CRISPR gene editing has revolutionized our ability to study and manipulate specific genes, enabling novel insights into gene function and potential therapies for brain disorders. Recent advances in cell-type-specific regulatory elements and viral delivery ... Full text Link to item Cite

A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress.

Journal article Genome Res · November 3, 2025 A hallmark of heart disease is gene dysregulation and reactivation of fetal gene programs. Reactivation of these fetal programs has compensatory effects during heart failure, depending on the type and stage of the underlying cardiomyopathy. Thousands of pu ... Full text Link to item Cite

Comprehensive profiling of transcription factors for reprogramming human astrocytes to neuronal cells through endogenous CRISPR-based gene activation.

Journal article bioRxiv · October 12, 2025 Neuronal loss is a hallmark of neurodegeneration and brain injury. Direct reprogramming of astrocytes into neurons has emerged as a promising approach to restore lost neurons. Comprehensive mapping and characterization of candidate astrocyte-to-neuron repr ... Full text Link to item Cite

RELB Reprograms Exhausted Tumor-Infiltrating Lymphocytes for Improved Adoptive Cell Therapy.

Journal article bioRxiv · October 12, 2025 Tumor-infiltrating lymphocytes (TILs) are a promising autologous cell therapy to treat solid tumors. TILs are manufactured by expanding and reinfusing tumor-reactive T cells from tumor biopsies. Efficacy of TIL therapies has been limited by the heterogenei ... Full text Link to item Cite

A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress.

Journal article bioRxiv · July 20, 2025 A hallmark of heart disease is gene dysregulation and reactivation of fetal gene programs. Reactivation of these fetal programs has compensatory effects during heart failure, depending on the type and stage of the underlying cardiomyopathy. Thousands of pu ... Full text Link to item Cite

HyperCas12a enables multiplexed CRISPRi screens.

Journal article bioRxiv · July 8, 2025 Interactions between multiple genes or cis-regulatory elements (CREs) underlie a wide range of biological processes in both health and disease. High-throughput screens using dCas9 fused to epigenome editing domains have allowed researchers to assess the im ... Full text Link to item Cite

Gene regulation technologies for gene and cell therapy.

Journal article Molecular therapy : the journal of the American Society of Gene Therapy · May 2025 Gene therapy stands at the forefront of medical innovation, offering unique potential to treat the underlying causes of genetic disorders and broadly enable regenerative medicine. However, unregulated production of therapeutic genes can lead to decreased c ... Full text Cite

Synthetic biomolecular condensates enhance translation from a target mRNA in living cells.

Journal article Nat Chem · March 2025 Biomolecular condensates composed of proteins and RNA are one approach by which cells regulate post-transcriptional gene expression. Their formation typically involves the phase separation of intrinsically disordered proteins with a target mRNA, sequesteri ... Full text Link to item Cite

Characterization of diverse Cas9 orthologs for genome and epigenome editing.

Journal article Proceedings of the National Academy of Sciences of the United States of America · March 2025 CRISPR-Cas9 systems have revolutionized biotechnology, creating diverse new opportunities for biomedical research and therapeutic genome and epigenome editing. Despite the abundance of bacterial CRISPR-Cas9 systems, relatively few are effective in human ce ... Full text Cite

Characterization and bioinformatic filtering of ambient gRNAs in single-cell CRISPR screens using CLEANSER.

Journal article Cell Genom · February 12, 2025 Single-cell RNA sequencing CRISPR (perturb-seq) screens enable high-throughput investigation of the genome, allowing for characterization of thousands of genomic perturbations on gene expression. Ambient gRNAs, which are contaminating gRNAs, are a major so ... Full text Link to item Cite

Activation of the imprinted Prader-Willi syndrome locus by CRISPR-based epigenome editing

Journal article Cell Genomics · February 12, 2025 Epigenome editing with DNA-targeting technologies such as CRISPR-dCas9 can be used to dissect gene regulatory mechanisms and potentially treat associated disorders. For example, Prader-Willi syndrome (PWS) results from loss of paternally expressed imprinte ... Full text Cite

Respiratory pathology in the mdx/utrn -/- mouse: A murine model for Duchenne Muscular Dystrophy (DMD).

Journal article PLoS One · 2025 Duchenne muscular dystrophy (DMD) is an X-linked devastating disease caused by a lack of dystrophin which results in progressive muscle weakness. As muscle weakness progresses, respiratory insufficiency and hypoventilation result in significant morbidity a ... Full text Link to item Cite

Engineered Cas9 variants bypass Keap1-mediated degradation in human cells and enhance epigenome editing efficiency.

Journal article Nucleic acids research · October 2024 As a potent and convenient genome-editing tool, Cas9 has been widely used in biomedical research and evaluated in treating human diseases. Numerous engineered variants of Cas9, dCas9 and other related prokaryotic endonucleases have been identified. However ... Full text Cite

Characterization and bioinformatic filtering of ambient gRNAs in single-cell CRISPR screens using CLEANSER.

Journal article bioRxiv · September 4, 2024 Recent technological developments in single-cell RNA-seq CRISPR screens enable high-throughput investigation of the genome. Through transduction of a gRNA library to a cell population followed by transcriptomic profiling by scRNA-seq, it is possible to cha ... Full text Link to item Cite

Deciphering the impact of genomic variation on function.

Journal article Nature · September 2024 Our genomes influence nearly every aspect of human biology-from molecular and cellular functions to phenotypes in health and disease. Studying the differences in DNA sequence between individuals (genomic variation) could reveal previously unknown mechanism ... Full text Open Access Link to item Cite

Proximity analysis of native proteomes reveals phenotypic modifiers in a mouse model of autism and related neurodevelopmental conditions.

Journal article Nat Commun · August 9, 2024 One of the main drivers of autism spectrum disorder is risk alleles within hundreds of genes, which may interact within shared but unknown protein complexes. Here we develop a scalable genome-editing-mediated approach to target 14 high-confidence autism ri ... Full text Link to item Cite

Respiratory characterization of a humanized Duchenne muscular dystrophy mouse model.

Journal article Respir Physiol Neurobiol · August 2024 Duchenne muscular dystrophy (DMD) is the most common X-linked disease. DMD is caused by a lack of dystrophin, a critical structural protein in striated muscle. Dystrophin deficiency leads to inflammation, fibrosis, and muscle atrophy. Boys with DMD have pr ... Full text Link to item Cite

Epigenome editing technologies for discovery and medicine.

Journal article Nature biotechnology · August 2024 Epigenome editing has rapidly evolved in recent years, with diverse applications that include elucidating gene regulation mechanisms, annotating coding and noncoding genome functions and programming cell state and lineage specification. Importantly, given ... Full text Cite

Machine learning methods for predicting guide RNA effects in CRISPR epigenome editing experiments.

Journal article bioRxiv · April 19, 2024 CRISPR epigenomic editing technologies enable functional interrogation of non-coding elements. However, current computational methods for guide RNA (gRNA) design do not effectively predict the power potential, molecular and cellular impact to optimize for ... Full text Link to item Cite

Multicenter integrated analysis of noncoding CRISPRi screens.

Journal article Nat Methods · April 2024 The ENCODE Consortium's efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms. The E ... Full text Link to item Cite

A humanized mouse model for adeno-associated viral gene therapy.

Journal article Nat Commun · March 4, 2024 Clinical translation of AAV-mediated gene therapy requires preclinical development across different experimental models, often confounded by variable transduction efficiency. Here, we describe a human liver chimeric transgene-free Il2rg-/-/Rag2-/-/Fah-/-/A ... Full text Link to item Cite

AAV-based CRISPR-Cas9 genome editing: Challenges and engineering opportunities

Journal article Current Opinion in Biomedical Engineering · March 1, 2024 Recent innovations in the field of gene therapy have paved the way for advances towards developing genome editing medicines. Despite these steps forward, challenges with viral delivery of genome editing tools persist. Efforts currently underway include dev ... Full text Cite

Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness.

Journal article bioRxiv · January 10, 2024 Epigenetic control of cellular transcription and phenotype is influenced by changes in the cellular microenvironment, yet how mechanical cues from these microenvironments precisely influence epigenetic state to regulate transcription remains largely unmapp ... Full text Link to item Cite

PCSK9 activation promotes early atherosclerosis in a vascular microphysiological system.

Journal article APL bioengineering · December 2023 Atherosclerosis is a primary precursor of cardiovascular disease (CVD), the leading cause of death worldwide. While proprotein convertase subtilisin/kexin 9 (PCSK9) contributes to CVD by degrading low-density lipoprotein receptors (LDLR) and altering lipid ... Full text Cite

Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens.

Journal article Nat Genet · December 2023 Clinical response to adoptive T cell therapies is associated with the transcriptional and epigenetic state of the cell product. Thus, discovery of regulators of T cell gene networks and their corresponding phenotypes has potential to improve T cell therapi ... Full text Link to item Cite

Nonviral In Vivo Delivery of CRISPR-Cas9 Using Protein-Agnostic, High-Loading Porous Silicon and Polymer Nanoparticles.

Journal article ACS nano · September 2023 The complexity of CRISPR machinery is a challenge to its application for nonviral in vivo therapeutic gene editing. Here, we demonstrate that proteins, regardless of size or charge, efficiently load into porous silicon nanoparticles (PSiNPs). Optimi ... Full text Cite

Orthogonal CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function.

Journal article bioRxiv · May 1, 2023 The clinical response to adoptive T cell therapies is strongly associated with transcriptional and epigenetic state. Thus, technologies to discover regulators of T cell gene networks and their corresponding phenotypes have great potential to improve the ef ... Full text Link to item Cite

An enhancer-based gene-therapy strategy for spatiotemporal control of cargoes during tissue repair.

Journal article Cell stem cell · January 2023 The efficacy and safety of gene-therapy strategies for indications like tissue damage hinge on precision; yet, current methods afford little spatial or temporal control of payload delivery. Here, we find that tissue-regeneration enhancer elements (TREEs) i ... Full text Cite

Cross-species evolution of a highly potent AAV variant for therapeutic gene transfer and genome editing.

Journal article Nat Commun · October 10, 2022 Recombinant adeno-associated viral (AAV) vectors are a promising gene delivery platform, but ongoing clinical trials continue to highlight a relatively narrow therapeutic window. Effective clinical translation is confounded, at least in part, by difference ... Full text Link to item Cite

Robust, Durable Gene Activation In Vivo via mRNA-Encoded Activators.

Journal article ACS nano · April 2022 Programmable control of gene expression via nuclease-null Cas9 fusion proteins has enabled the engineering of cellular behaviors. Here, both transcriptional and epigenetic gene activation via synthetic mRNA and lipid nanoparticle delivery was demonstrated ... Full text Cite

Full-length dystrophin restoration via targeted exon integration by AAV-CRISPR in a humanized mouse model of Duchenne muscular dystrophy.

Journal article Mol Ther · November 3, 2021 Targeted gene-editing strategies have emerged as promising therapeutic approaches for the permanent treatment of inherited genetic diseases. However, precise gene correction and insertion approaches using homology-directed repair are still limited by low e ... Full text Link to item Cite

Cas9-specific immune responses compromise local and systemic AAV CRISPR therapy in multiple dystrophic canine models.

Journal article Nature communications · November 2021 Adeno-associated virus (AAV)-mediated CRISPR-Cas9 editing holds promise to treat many diseases. The immune response to bacterial-derived Cas9 has been speculated as a hurdle for AAV-CRISPR therapy. However, immunological consequences of AAV-mediated Cas9 e ... Full text Cite

Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF-PU.1-DPP4 Axis.

Journal article Adv Sci (Weinh) · October 2021 Colorectal cancer (CRC) metastasizes mainly to the liver, which accounts for the majority of CRC-related deaths. Here it is shown that metastatic cells undergo specific chromatin remodeling in the liver. Hepatic growth factor (HGF) induces phosphorylation ... Full text Open Access Link to item Cite

Transgenic mice for in vivo epigenome editing with CRISPR-based systems.

Journal article Nat Methods · August 2021 CRISPR-Cas9 technologies have dramatically increased the ease of targeting DNA sequences in the genomes of living systems. The fusion of chromatin-modifying domains to nuclease-deactivated Cas9 (dCas9) has enabled targeted epigenome editing in both culture ... Full text Link to item Cite

AP-1 subunits converge promiscuously at enhancers to potentiate transcription.

Journal article Genome Res · April 2021 The AP-1 transcription factor (TF) dimer contributes to many biological processes and environmental responses. AP-1 can be composed of many interchangeable subunits. Unambiguously determining the binding locations of these subunits in the human genome is c ... Full text Link to item Cite

The NIH Somatic Cell Genome Editing program.

Journal article Nature · April 2021 The move from reading to writing the human genome offers new opportunities to improve human health. The United States National Institutes of Health (NIH) Somatic Cell Genome Editing (SCGE) Consortium aims to accelerate the development of safer and more-eff ... Full text Link to item Cite

CRISPR Clocks: The Times They Are a-Changin'.

Journal article The CRISPR journal · April 2021 Full text Cite

Branched-chain α-ketoacids are preferentially reaminated and activate protein synthesis in the heart.

Journal article Nat Commun · March 15, 2021 Branched-chain amino acids (BCAA) and their cognate α-ketoacids (BCKA) are elevated in an array of cardiometabolic diseases. Here we demonstrate that the major metabolic fate of uniformly-13C-labeled α-ketoisovalerate ([U-13C]KIV) in the heart is reaminati ... Full text Link to item Cite

In Vivo Gene Editing of Muscle Stem Cells with Adeno-Associated Viral Vectors in a Mouse Model of Duchenne Muscular Dystrophy.

Journal article Mol Ther Methods Clin Dev · December 11, 2020 Delivery of therapeutic transgenes with adeno-associated viral (AAV) vectors for treatment of myopathies has yielded encouraging results in animal models and early clinical studies. Although certain AAV serotypes efficiently target muscle fibers, transduct ... Full text Link to item Cite

Master Regulators and Cofactors of Human Neuronal Cell Fate Specification Identified by CRISPR Gene Activation Screens.

Journal article Cell Rep · December 1, 2020 Technologies to reprogram cell-type specification have revolutionized the fields of regenerative medicine and disease modeling. Currently, the selection of fate-determining factors for cell reprogramming applications is typically a laborious and low-throug ... Full text Link to item Cite

The once and future gene therapy.

Journal article Nature communications · November 2020 Full text Cite

Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems.

Journal article Nucleic acids research · September 2020 Genomic enhancer elements regulate gene expression programs important for neuronal fate and function and are implicated in brain disease states. Enhancers undergo bidirectional transcription to generate non-coding enhancer RNAs (eRNAs). However, eRNA funct ... Full text Cite

Redirecting Vesicular Transport to Improve Nonviral Delivery of Molecular Cargo.

Journal article Adv Biosyst · August 2020 Cell engineering relies heavily on viral vectors for the delivery of molecular cargo into cells due to their superior efficiency compared to nonviral ones. However, viruses are immunogenic and expensive to manufacture, and have limited delivery capacity. N ... Full text Link to item Cite

Unwinding the Role of FACT in Cas9-based Genome Editing.

Journal article Molecular cell · August 2020 In a recent issue of Molecular Cell, Wang et al. (2020) employ unbiased proteomics approaches and live-cell imaging to reveal a key role for the histone chaperone complex FACT (SPT16 and SSRP1) in governing Cas9 turnover at the DNA target site during genom ... Full text Cite

Immunity to Cas9 as an Obstacle to Persistent Genome Editing.

Journal article Molecular therapy : the journal of the American Society of Gene Therapy · June 2020 Full text Cite

Myogenic Progenitor Cell Lineage Specification by CRISPR/Cas9-Based Transcriptional Activators.

Journal article Stem cell reports · May 2020 Engineered CRISPR/Cas9-based transcriptional activators can potently and specifically activate endogenous fate-determining genes to direct differentiation of pluripotent stem cells. Here, we demonstrate that endogenous activation of the PAX7 transcription ... Full text Cite

Prospective isolation of chondroprogenitors from human iPSCs based on cell surface markers identified using a CRISPR-Cas9-generated reporter.

Journal article Stem cell research & therapy · February 2020 BackgroundArticular cartilage shows little or no capacity for intrinsic repair, generating a critical need of regenerative therapies for joint injuries and diseases such as osteoarthritis. Human-induced pluripotent stem cells (hiPSCs) offer a prom ... Full text Cite

Genome-wide CRISPR Screen to Identify Genes that Suppress Transformation in the Presence of Endogenous KrasG12D.

Journal article Sci Rep · November 20, 2019 Cooperating gene mutations are typically required to transform normal cells enabling growth in soft agar or in immunodeficient mice. For example, mutations in Kras and transformation-related protein 53 (Trp53) are known to transform a variety of mesenchyma ... Full text Open Access Link to item Cite

An anionic, endosome-escaping polymer to potentiate intracellular delivery of cationic peptides, biomacromolecules, and nanoparticles.

Journal article Nature communications · November 2019 Peptides and biologics provide unique opportunities to modulate intracellular targets not druggable by conventional small molecules. Most peptides and biologics are fused with cationic uptake moieties or formulated into nanoparticles to facilitate delivery ... Full text Cite

AAV9 Edits Muscle Stem Cells in Normal and Dystrophic Adult Mice.

Journal article Molecular therapy : the journal of the American Society of Gene Therapy · September 2019 CRISPR editing of muscle stem cells (MuSCs) with adeno-associated virus serotype-9 (AAV9) holds promise for sustained gene repair therapy for muscular dystrophies. However, conflicting evidence exists on whether AAV9 transduces MuSCs. To rigorously address ... Full text Cite

Jumping at the chance for precise DNA integration.

Journal article Nature biotechnology · September 2019 Full text Cite

The next generation of CRISPR-Cas technologies and applications.

Journal article Nature reviews. Molecular cell biology · August 2019 The prokaryote-derived CRISPR-Cas genome editing systems have transformed our ability to manipulate, detect, image and annotate specific DNA and RNA sequences in living cells of diverse species. The ease of use and robustness of this technology have revolu ... Full text Cite

Increasing the specificity of CRISPR systems with engineered RNA secondary structures.

Journal article Nature biotechnology · June 2019 CRISPR (clustered regularly interspaced short palindromic repeat) systems have been broadly adopted for basic science, biotechnology, and gene and cell therapy. In some cases, these bacterial nucleases have demonstrated off-target activity. This creates a ... Full text Cite

Long-term evaluation of AAV-CRISPR genome editing for Duchenne muscular dystrophy.

Journal article Nat Med · March 2019 Duchenne muscular dystrophy (DMD) is a monogenic disorder and a candidate for therapeutic genome editing. There have been several recent reports of genome editing in preclinical models of Duchenne muscular dystrophy1-6, however, the long-term persistence a ... Full text Link to item Cite

Enhancer Histone Acetylation Modulates Transcriptional Bursting Dynamics of Neuronal Activity-Inducible Genes.

Journal article Cell Rep · January 29, 2019 Neuronal activity-inducible gene transcription correlates with rapid and transient increases in histone acetylation at promoters and enhancers of activity-regulated genes. Exactly how histone acetylation modulates transcription of these genes has remained ... Full text Link to item Cite

Step-Wise Chondrogenesis of Human Induced Pluripotent Stem Cells and Purification Via a Reporter Allele Generated by CRISPR-Cas9 Genome Editing.

Journal article Stem cells (Dayton, Ohio) · January 2019 The differentiation of human induced pluripotent stem cells (hiPSCs) to prescribed cell fates enables the engineering of patient-specific tissue types, such as hyaline cartilage, for applications in regenerative medicine, disease modeling, and drug screeni ... Full text Cite

AAV CRISPR editing rescues cardiac and muscle function for 18 months in dystrophic mice.

Journal article JCI insight · December 2018 Adeno-associated virus-mediated (AAV-mediated) CRISPR editing is a revolutionary approach for treating inherited diseases. Sustained, often life-long mutation correction is required for treating these diseases. Unfortunately, this has never been demonstrat ... Full text Cite

Genetic Engineering of Mesenchymal Stem Cells for Differential Matrix Deposition on 3D Woven Scaffolds.

Journal article Tissue engineering. Part A · October 2018 Tissue engineering approaches for the repair of osteochondral defects using biomaterial scaffolds and stem cells have remained challenging due to the inherent complexities of inducing cartilage-like matrix and bone-like matrix within the same local environ ... Full text Cite

Synthetic transcription factors for cell fate reprogramming.

Journal article Current opinion in genetics & development · October 2018 The ability to reprogram cell lineage specification through the activity of master regulatory transcription factors has transformed disease modeling, drug screening, and cell therapy for regenerative medicine. Recent advances in the engineering of syntheti ... Full text Cite

Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding.

Journal article Genome Res · September 2018 Glucocorticoids are potent steroid hormones that regulate immunity and metabolism by activating the transcription factor (TF) activity of glucocorticoid receptor (GR). Previous models have proposed that DNA binding motifs and sites of chromatin accessibili ... Full text Link to item Cite

Gene delivery and biomedical engineering

Journal article Current Opinion in Biomedical Engineering · September 1, 2018 Full text Cite

Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids.

Journal article Cell Syst · August 22, 2018 The glucocorticoid receptor (GR) is a hormone-inducible transcription factor involved in metabolic and anti-inflammatory gene expression responses. To investigate what controls interactions between GR binding sites and their target genes, we used in situ H ... Full text Link to item Cite

CRISPR-based methods for high-throughput annotation of regulatory DNA.

Journal article Current opinion in biotechnology · August 2018 Developments in CRISPR/Cas9-based technologies provide a new paradigm in functional screening of the genome. Conventional screening methods have focused on high-throughput perturbations of the protein-coding genome with technologies such as RNAi. However, ... Full text Cite

From CRISPR scissors to virus sensors.

Journal article Nature · May 2018 Full text Cite

RNA-guided transcriptional silencing in vivo with S. aureus CRISPR-Cas9 repressors.

Journal article Nature communications · April 2018 CRISPR-Cas9 transcriptional repressors have emerged as robust tools for disrupting gene regulation in vitro but have not yet been adapted for systemic delivery in adult animal models. Here we describe a Staphylococcus aureus Cas9-based repressor (dSaCas9 Full text Cite

Pulling the genome in opposite directions to dissect gene networks.

Journal article Genome biology · March 2018 Orthogonal CRISPR-Cas systems have been integrated into combinatorial screens to decipher complex genetic relationships in two recent studies. ... Full text Cite

Boosting, Not Breaking: CRISPR Activators Treat Disease Models.

Journal article Molecular therapy : the journal of the American Society of Gene Therapy · February 2018 Full text Cite

Gene therapies for hemophilia hit the mark in clinical trials.

Journal article Nature medicine · February 2018 Full text Cite

Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing.

Journal article Methods Mol Biol · 2018 Genomic regulatory elements that control gene expression play an important role in many traits and diseases. Identifying the regulatory elements associated with each gene or phenotype and understanding the function of that element remain a significant chal ... Full text Link to item Cite

Editorial Overview: Synthetic biology and biomedical engineering

Journal article Current Opinion in Biomedical Engineering · December 1, 2017 Full text Cite

Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies.

Journal article Nucleic Acids Res · November 16, 2017 Our current understanding of cellular transdifferentiation systems is limited. It is oftentimes unknown, at a genome-wide scale, how much transdifferentiated cells differ quantitatively from both the starting cells and the target cells. Focusing on transdi ... Full text Link to item Cite

An Engineered Optogenetic Switch for Spatiotemporal Control of Gene Expression, Cell Differentiation, and Tissue Morphogenesis.

Journal article ACS synthetic biology · November 2017 The precise spatial and temporal control of gene expression, cell differentiation, and tissue morphogenesis has widespread application in regenerative medicine and the study of tissue development. In this work, we applied optogenetics to control cell diffe ... Full text Cite

Genome engineering: a new approach to gene therapy for neuromuscular disorders.

Journal article Nature reviews. Neurology · November 2017 For many neuromuscular disorders, including Duchenne muscular dystrophy, spinal muscular atrophy and myotonic dystrophy, the genetic causes are well known. Gene therapy holds promise for the treatment of these monogenic neuromuscular diseases, and many suc ... Full text Cite

Bidirectional approaches for optogenetic regulation of gene expression in mammalian cells using Arabidopsis cryptochrome 2.

Journal article Nucleic acids research · November 2017 Optogenetic tools allow regulation of cellular processes with light, which can be delivered with spatiotemporal resolution. In previous work, we used cryptochrome 2 (CRY2) and CIB1, Arabidopsis proteins that interact upon light illumination, to regulate tr ... Full text Cite

Genome Engineering for Personalized Arthritis Therapeutics.

Journal article Trends in molecular medicine · October 2017 Arthritis represents a family of complex joint pathologies responsible for the majority of musculoskeletal conditions. Nearly all diseases within this family, including osteoarthritis, rheumatoid arthritis, and juvenile idiopathic arthritis, are chronic co ... Full text Cite

* CRISPR-Based Epigenome Editing of Cytokine Receptors for the Promotion of Cell Survival and Tissue Deposition in Inflammatory Environments.

Journal article Tissue engineering. Part A · August 2017 Musculoskeletal diseases have been associated with inflammatory cytokine action, particularly action by TNF-α and IL-1β. These inflammatory cytokines promote apoptosis and senescence of cells in diseased tissue and extracellular matrix breakdown. Stem cell ... Full text Cite

Generation and comparison of CRISPR-Cas9 and Cre-mediated genetically engineered mouse models of sarcoma.

Journal article Nat Commun · July 10, 2017 Genetically engineered mouse models that employ site-specific recombinase technology are important tools for cancer research but can be costly and time-consuming. The CRISPR-Cas9 system has been adapted to generate autochthonous tumours in mice, but how th ... Full text Link to item Cite

CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.

Journal article Nat Biotechnol · June 2017 Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative ... Full text Link to item Cite

Mammalian Synthetic Biology: Engineering Biological Systems.

Journal article Annual review of biomedical engineering · June 2017 The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and reg ... Full text Cite

CRISPR/Cas9 Editing of Murine Induced Pluripotent Stem Cells for Engineering Inflammation-Resistant Tissues.

Journal article Arthritis & rheumatology (Hoboken, N.J.) · May 2017 ObjectiveProinflammatory cytokines such as interleukin-1 (IL-1) are found in elevated levels in diseased or injured tissues and promote rapid tissue degradation while preventing stem cell differentiation. This study was undertaken to engineer infl ... Full text Cite

Genome Engineering of Stem Cells for Autonomously Regulated, Closed-Loop Delivery of Biologic Drugs.

Journal article Stem cell reports · May 2017 Chronic inflammatory diseases such as arthritis are characterized by dysregulated responses to pro-inflammatory cytokines such as interleukin-1 (IL-1) and tumor necrosis factor α (TNF-α). Pharmacologic anti-cytokine therapies are often effective at diminis ... Full text Cite

Expanding the CRISPR Toolbox: Targeting RNA with Cas13b.

Journal article Molecular cell · February 2017 In this issue of Molecular Cell, Smargon et al. (2017) unearth Cas13b from type VI-B CRISPR-Cas immune systems and characterize its RNA-guided, RNA-targeting activity, including regulation by the novel co-factors Csx27 and Csx28, as well as non-specific co ... Full text Cite

Loss-of-function genetic tools for animal models: cross-species and cross-platform differences.

Journal article Nature reviews. Genetics · January 2017 Our understanding of the genetic mechanisms that underlie biological processes has relied extensively on loss-of-function (LOF) analyses. LOF methods target DNA, RNA or protein to reduce or to ablate gene function. By analysing the phenotypes that are caus ... Full text Cite

Genetic engineering: Chemical control for CRISPR editing.

Journal article Nature chemical biology · January 2017 Full text Cite

Differential effects of toll-like receptor stimulation on mRNA-driven myogenic conversion of human and mouse fibroblasts.

Journal article Biochem Biophys Res Commun · September 23, 2016 Transfection with in vitro transcribed mRNAs is a safe and effective tool to convert somatic cells to any cell type of interest. One caveat of mRNA transfection is that mRNAs are recognized by multiple RNA-sensing toll like receptors (TLRs). These TLRs can ... Full text Link to item Cite

Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells.

Journal article Cell Stem Cell · September 1, 2016 Featured Publication Overexpression of exogenous fate-specifying transcription factors can directly reprogram differentiated somatic cells to target cell types. Here, we show that similar reprogramming can also be achieved through the direct activation of endogenous genes usin ... Full text Link to item Cite

Gene therapies that restore dystrophin expression for the treatment of Duchenne muscular dystrophy.

Journal article Human genetics · September 2016 Duchenne muscular dystrophy is one of the most common inherited genetic diseases and is caused by mutations to the DMD gene that encodes the dystrophin protein. Recent advances in genome editing and gene therapy offer hope for the development of potential ... Full text Cite

Anatomically shaped tissue-engineered cartilage with tunable and inducible anticytokine delivery for biological joint resurfacing.

Journal article Proceedings of the National Academy of Sciences of the United States of America · August 2016 Biological resurfacing of entire articular surfaces represents an important but challenging strategy for treatment of cartilage degeneration that occurs in osteoarthritis. Not only does this approach require anatomically sized and functional engineered car ... Full text Cite

N-cadherin is Key to Expression of the Nucleus Pulposus Cell Phenotype under Selective Substrate Culture Conditions.

Journal article Scientific reports · June 2016 Nucleus pulposus (NP) cells of the intervertebral disc are essential for synthesizing extracellular matrix that contributes to disc health and mechanical function. NP cells have a unique morphology and molecular expression pattern derived from their notoch ... Full text Cite

Engineering Delivery Vehicles for Genome Editing.

Journal article Annual review of chemical and biomolecular engineering · June 2016 The field of genome engineering has created new possibilities for gene therapy, including improved animal models of disease, engineered cell therapies, and in vivo gene repair. The most significant challenge for the clinical translation of genome engineeri ... Full text Cite

In Vivo Zinc Finger Nuclease-mediated Targeted Integration of a Glucose-6-phosphatase Transgene Promotes Survival in Mice With Glycogen Storage Disease Type IA.

Journal article Mol Ther · April 2016 Glycogen storage disease type Ia (GSD Ia) is caused by glucose-6-phosphatase (G6Pase) deficiency in association with severe, life-threatening hypoglycemia that necessitates lifelong dietary therapy. Here we show that use of a zinc-finger nuclease (ZFN) tar ... Full text Link to item Cite

Genome-editing Technologies for Gene and Cell Therapy.

Journal article Molecular therapy : the journal of the American Society of Gene Therapy · March 2016 Featured Publication Gene therapy has historically been defined as the addition of new genes to human cells. However, the recent advent of genome-editing technologies has enabled a new paradigm in which the sequence of the human genome can be precisely manipulated to achieve a ... Full text Cite

Cas9 loosens its grip on off-target sites.

Journal article Nature biotechnology · March 2016 Full text Cite

Editing the epigenome: technologies for programmable transcription and epigenetic modulation.

Journal article Nature methods · February 2016 Featured Publication Gene regulation is a complex and tightly controlled process that defines cell identity, health and disease, and response to pharmacologic and environmental signals. Recently developed DNA-targeting platforms, including zinc finger proteins, transcription a ... Full text Cite

In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy.

Journal article Science · January 22, 2016 Featured Publication Duchenne muscular dystrophy (DMD) is a devastating disease affecting about 1 out of 5000 male births and caused by mutations in the dystrophin gene. Genome editing has the potential to restore expression of a modified dystrophin gene from the native locus ... Full text Link to item Cite

Design, Assembly, and Characterization of TALE-Based Transcriptional Activators and Repressors.

Journal article Methods in molecular biology (Clifton, N.J.) · January 2016 Transcription activator-like effectors (TALEs) are modular DNA-binding proteins that can be fused to a variety of effector domains to regulate the epigenome. Nucleotide recognition by TALE monomers follows a simple cipher, making this a powerful and versat ... Full text Cite

The Development of TALE Nucleases for Biotechnology.

Journal article Methods in molecular biology (Clifton, N.J.) · January 2016 The development of a facile genome engineering technology based on transcription activator-like effector nucleases (TALENs) has led to significant advances in diverse areas of science and medicine. In this review, we provide a broad overview of the develop ... Full text Cite

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements.

Journal article Nat Methods · December 2015 Featured Publication Epigenome editing with the CRISPR (clustered, regularly interspaced, short palindromic repeats)-Cas9 platform is a promising technology for modulating gene expression to direct cell phenotype and to dissect the causal epigenetic mechanisms of gene regulati ... Full text Link to item Cite

Genome editing: the end of the beginning.

Journal article Genome biology · December 2015 Full text Cite

Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage.

Journal article Nucleic acids research · October 2015 CRISPR-associated endonuclease Cas9 cuts DNA at variable target sites designated by a Cas9-bound RNA molecule. Cas9's ability to be directed by single 'guide RNA' molecules to target nearly any sequence has been recently exploited for a number of emerging ... Full text Cite

Enabling functional genomics with genome engineering.

Journal article Genome research · October 2015 Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunitie ... Full text Cite

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.

Journal article Genome Res · August 2015 Genome engineering technologies based on the CRISPR/Cas9 and TALE systems are enabling new approaches in science and biotechnology. However, the specificity of these tools in complex genomes and the role of chromatin structure in determining DNA binding ar ... Full text Link to item Cite

Enhanced MyoD-induced transdifferentiation to a myogenic lineage by fusion to a potent transactivation domain.

Journal article ACS Synth Biol · June 19, 2015 Genetic reprogramming holds great potential for disease modeling, drug screening, and regenerative medicine. Genetic reprogramming of mammalian cells is typically achieved by forced expression of natural transcription factors that control master gene netwo ... Full text Link to item Cite

Single-molecule analysis of myocyte differentiation reveals bimodal lineage commitment.

Journal article Integrative biology : quantitative biosciences from nano to macro · June 2015 Cell differentiation is the foundation for tissue development and regeneration, disease modeling, and cell-based therapies. Although the differentiation of cell populations has been extensively studied in many systems, much less is known about the distribu ... Full text Cite

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers.

Journal article Nat Biotechnol · May 2015 Featured Publication Technologies that enable targeted manipulation of epigenetic marks could be used to precisely control cell phenotype or interrogate the relationship between the epigenome and transcriptional control. Here we describe a programmable, CRISPR-Cas9-based acety ... Full text Link to item Cite

Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.

Journal article Nat Neurosci · May 2015 To identify chromatin mechanisms of neuronal differentiation, we characterized chromatin accessibility and gene expression in cerebellar granule neurons (CGNs) of the developing mouse. We used DNase-seq to map accessibility of cis-regulatory elements and R ... Full text Link to item Cite

Knockdown of the cell cycle inhibitor p21 enhances cartilage formation by induced pluripotent stem cells.

Journal article Tissue engineering. Part A · April 2015 The limited regenerative capacity of articular cartilage contributes to progressive joint dysfunction associated with cartilage injury or osteoarthritis. Cartilage tissue engineering seeks to provide a biological substitute for repairing damaged or disease ... Full text Cite

Correction of dystrophin expression in cells from Duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases

Journal article Molecular Therapy · March 5, 2015 Duchenne muscular dystrophy (DMD) is caused by genetic mutations that result in the absence of dystrophin protein expression. Oligonucleotide-induced exon skipping can restore the dystrophin reading frame and protein production. However, this requires cont ... Full text Cite

Correction of dystrophin expression in cells from Duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases.

Journal article Mol Ther · March 2015 Duchenne muscular dystrophy (DMD) is caused by genetic mutations that result in the absence of dystrophin protein expression. Oligonucleotide-induced exon skipping can restore the dystrophin reading frame and protein production. However, this requires cont ... Full text Link to item Cite

A light-inducible CRISPR-Cas9 system for control of endogenous gene activation.

Journal article Nature chemical biology · March 2015 Featured Publication Optogenetic systems enable precise spatial and temporal control of cell behavior. We engineered a light-activated CRISPR-Cas9 effector (LACE) system that induces transcription of endogenous genes in the presence of blue light. This was accomplished by fusi ... Full text Cite

Multiplex CRISPR/Cas9-based genome editing for correction of dystrophin mutations that cause Duchenne muscular dystrophy.

Journal article Nat Commun · February 18, 2015 Featured Publication The CRISPR/Cas9 genome-editing platform is a promising technology to correct the genetic basis of hereditary diseases. The versatility, efficiency and multiplexing capabilities of the CRISPR/Cas9 system enable a variety of otherwise challenging gene correc ... Full text Link to item Cite

A light-inducible CRISPR-Cas9 system for control of endogenous gene activation

Journal article Nature Chemical Biology · January 1, 2015 Optogenetic systems enable precise spatial and temporal control of cell behavior. We engineered a light-activated CRISPR-Cas9 effector (LACE) system that induces transcription of endogenous genes in the presence of blue light. This was accomplished by fusi ... Full text Cite

Vector modifications to eliminate transposase expression following piggyBac-mediated transgenesis.

Journal article Scientific reports · December 2014 Transgene insertion plays an important role in gene therapy and in biological studies. Transposon-based systems that integrate transgenes by transposase-catalyzed "cut-and-paste" mechanism have emerged as an attractive system for transgenesis. Hyperactive ... Full text Cite

A CRISPR/Cas9-based system for reprogramming cell lineage specification.

Journal article Stem cell reports · December 2014 Gene activation by the CRISPR/Cas9 system has the potential to enable new approaches to science and medicine, but the technology must be enhanced to robustly control cell behavior. We show that the fusion of two transactivation domains to Cas9 dramatically ... Full text Cite

Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector.

Journal article Nucleic acids research · October 2014 Engineered DNA-binding proteins that manipulate the human genome and transcriptome have enabled rapid advances in biomedical research. In particular, the RNA-guided CRISPR/Cas9 system has recently been engineered to create site-specific double-strand break ... Full text Cite

Genome engineering: the next genomic revolution.

Journal article Nature methods · October 2014 Full text Cite

Special issue on engineered DNA-binding proteins.

Journal article ACS synthetic biology · October 2014 Full text Cite

Engineering synthetic TALE and CRISPR/Cas9 transcription factors for regulating gene expression.

Journal article Methods (San Diego, Calif.) · September 2014 Engineered DNA-binding proteins that can be targeted to specific sites in the genome to manipulate gene expression have enabled many advances in biomedical research. This includes generating tools to study fundamental aspects of gene regulation and the dev ... Full text Cite

Synthetic zinc finger proteins: the advent of targeted gene regulation and genome modification technologies.

Journal article Accounts of chemical research · August 2014 The understanding of gene regulation and the structure and function of the human genome increased dramatically at the end of the 20th century. Yet the technologies for manipulating the genome have been slower to develop. For instance, the field of gene the ... Full text Cite

Activating human genes with zinc finger proteins, transcription activator-like effectors and CRISPR/Cas9 for gene therapy and regenerative medicine.

Journal article Expert opinion on therapeutic targets · August 2014 New technologies have recently been developed to control the expression of human genes in their native genomic context by engineering synthetic transcription factors that can be targeted to any DNA sequence. The ability to precisely regulate any gene as it ... Full text Cite

Tissue-engineered cartilage with inducible and tunable immunomodulatory properties.

Journal article Biomaterials · July 2014 The pathogenesis of osteoarthritis is mediated in part by inflammatory cytokines including interleukin-1 (IL-1), which promote degradation of articular cartilage and prevent human mesenchymal stem cell (MSC) chondrogenesis. In this study, we combined gene ... Full text Cite

CRISPR technology for gene therapy.

Journal article Nature medicine · May 2014 Full text Cite

Scaffold-mediated lentiviral transduction for functional tissue engineering of cartilage.

Journal article Proceedings of the National Academy of Sciences of the United States of America · March 2014 The ability to develop tissue constructs with matrix composition and biomechanical properties that promote rapid tissue repair or regeneration remains an enduring challenge in musculoskeletal engineering. Current approaches require extensive cell manipulat ... Full text Cite

Comparing genome editing technologies

Journal article Genetic Engineering and Biotechnology News · March 1, 2014 Full text Cite

Light-inducible gene regulation with engineered zinc finger proteins.

Journal article Methods in molecular biology (Clifton, N.J.) · January 2014 The coupling of light-inducible protein-protein interactions with gene regulation systems has enabled the control of gene expression with light. In particular, heterodimer protein pairs from plants can be used to engineer a gene regulation system in mammal ... Full text Cite

RNA-guided gene activation by CRISPR-Cas9-based transcription factors.

Journal article Nat Methods · October 2013 Featured Publication Technologies for engineering synthetic transcription factors have enabled many advances in medical and scientific research. In contrast to existing methods based on engineering of DNA-binding proteins, we created a Cas9-based transactivator that is targete ... Full text Link to item Cite

Reading frame correction by targeted genome editing restores dystrophin expression in cells from Duchenne muscular dystrophy patients.

Journal article Molecular therapy : the journal of the American Society of Gene Therapy · September 2013 Genome editing with engineered nucleases has recently emerged as an approach to correct genetic mutations by enhancing homologous recombination with a DNA repair template. However, many genetic diseases, such as Duchenne muscular dystrophy (DMD), can be tr ... Full text Cite

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering.

Journal article Trends in biotechnology · July 2013 Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) comprise a powerful class of tools that are redefining the boundaries of biological research. These chimeric nucleases are composed of programmable, sequence-specific ... Full text Cite

How vinculin regulates force transmission.

Journal article Proceedings of the National Academy of Sciences of the United States of America · June 2013 Focal adhesions mediate force transfer between ECM-integrin complexes and the cytoskeleton. Although vinculin has been implicated in force transmission, few direct measurements have been made, and there is little mechanistic insight. Using vinculin-null ce ... Full text Cite

The role of single-cell analyses in understanding cell lineage commitment.

Journal article Biotechnology journal · April 2013 The study of cell lineage commitment is critical for improving our understanding of tissue development and regeneration, and for realizing stem cell-based therapies and engineered tissue replacements. Recently, the discovery of an unanticipated degree of v ... Full text Cite

Highly active zinc-finger nucleases by extended modular assembly.

Journal article Genome research · March 2013 Zinc-finger nucleases (ZFNs) are important tools for genome engineering. Despite intense interest by many academic groups, the lack of robust noncommercial methods has hindered their widespread use. The modular assembly (MA) of ZFNs from publicly available ... Full text Cite

Synergistic and tunable human gene activation by combinations of synthetic transcription factors.

Journal article Nat Methods · March 2013 Mammalian genes are regulated by the cooperative and synergistic actions of many transcription factors. In this study we recapitulate this complex regulation in human cells by targeting endogenous gene promoters, including regions of closed chromatin upstr ... Full text Link to item Cite

Translating the genomics revolution: the need for an international gene therapy consortium for monogenic diseases.

Journal article Molecular therapy : the journal of the American Society of Gene Therapy · February 2013 Full text Cite

Reading frame correction by targeted genome editing restores dystrophin expression in cells from duchenne muscular dystrophy patients

Journal article Molecular Therapy · 2013 Genome editing with engineered nucleases has recently emerged as an approach to correct genetic mutations by enhancing homologous recombination with a DNA repair template. However, many genetic diseases, such as Duchenne muscular dystrophy (DMD), can be tr ... Full text Cite

Gene Delivery into Cells and Tissues

Journal article · January 1, 2013 There are significant engineering challenges in translating the remarkable medical implications of gene and nucleic acid delivery from cell and animal models into the clinic. Off-target effects and inefficient delivery to the proper intracellular compartme ... Full text Cite

Targeted plasmid integration into the Human Genome by engineered recombinases

Journal article Topics in Current Genetics · January 1, 2013 The targeted integration of transgenes into cellular genomes is central to numerous applications in biotechnology, basic science, and medicine. In recent years, a variety of advances have improved upon conventional methods for site-specific transgene integ ... Full text Cite

RNA-guided gene activation by CRISPR-Cas9-based transcription factors

Journal article Nature Methods · 2013 Technologies for engineering synthetic transcription factors have enabled many advances in medical and scientific research. In contrast to existing methods based on engineering of DNA-binding proteins, we created a Cas9-based transactivator that is targete ... Full text Cite

Photoregulated gene expression in human cells with light-inducible engineered transcription factors

Journal article ASME 2012 Summer Bioengineering Conference Sbc 2012 · December 1, 2012 Full text Cite

Light-inducible spatiotemporal control of gene activation by customizable zinc finger transcription factors.

Journal article Journal of the American Chemical Society · October 2012 Advanced gene regulatory systems are necessary for scientific research, synthetic biology, and gene-based medicine. An ideal system would allow facile spatiotemporal manipulation of gene expression within a cell population that is tunable, reversible, repe ... Full text Cite

Advances in targeted genome editing.

Journal article Current opinion in chemical biology · August 2012 New technologies have recently emerged that enable targeted editing of genomes in diverse systems. This includes precise manipulation of gene sequences in their natural chromosomal context and addition of transgenes to specific genomic loci. This progress ... Full text Cite

Engineered Proteins for Controlling Gene Expression

Journal article · December 1, 2011 This chapter describes the potential uses of natural transcriptional regulators, enhancement of these regulators through molecular engineering, and the engineering of entirely synthetic transcription factors for targeted gene regulation. HIF-1 is a heterod ... Full text Cite

Engineered bioactive molecules

Journal article · October 1, 2011 The field of biamaterials is undergoing a paradigm change. Foundational work in this area focused on inert materials that induced a minimal biological response. However, it is now clear that this approach to biomaterial design neglects the tremendous oppor ... Cite

Targeted plasmid integration into the human genome by an engineered zinc-finger recombinase.

Journal article Nucleic acids research · September 2011 The development of new methods for gene addition to mammalian genomes is necessary to overcome the limitations of conventional genetic engineering strategies. Although a variety of DNA-modifying enzymes have been used to directly catalyze the integration o ... Full text Cite

Structure-guided reprogramming of serine recombinase DNA sequence specificity

Journal article Proceedings of the National Academy of Sciences of the United States of America · January 11, 2011 Routine manipulation of cellular genomes is contingent upon the development of proteins and enzymes with programmable DNA sequence specificity. Here we describe the structure-guided reprogramming of the DNA sequence specificity of the invertase Gin from ba ... Full text Cite

Structure-guided reprogramming of serine recombinase DNA sequence specificity.

Journal article Proceedings of the National Academy of Sciences of the United States of America · January 2011 Routine manipulation of cellular genomes is contingent upon the development of proteins and enzymes with programmable DNA sequence specificity. Here we describe the structure-guided reprogramming of the DNA sequence specificity of the invertase Gin from ba ... Full text Cite

Directed evolution of recombinase specificity by split gene reassembly.

Journal article Nucleic acids research · July 2010 The engineering of new enzymes that efficiently and specifically modify DNA sequences is necessary for the development of enhanced gene therapies and genetic studies. To address this need, we developed a robust strategy for evolving site-specific recombina ... Full text Cite

Synthesis of programmable integrases.

Journal article Proceedings of the National Academy of Sciences of the United States of America · March 2009 Accurate modification of the 3 billion-base-pair human genome requires tools with exceptional sequence specificity. Here, we describe a general strategy for the design of enzymes that target a single site within the genome. We generated chimeric zinc finge ... Full text Cite

Identification of novel Runx2 targets in osteoblasts: cell type-specific BMP-dependent regulation of Tram2.

Journal article Journal of cellular biochemistry · December 2007 Runx2 is an osteoblast master transcription factor and a target for bone morphogenetic protein (BMP) signaling, but our knowledge of events downstream of Runx2 is limited. In this study, we used ChIP Display to discover seven novel genomic regions occupied ... Full text Cite

Biomaterial-mediated retroviral gene transfer using self-assembled monolayers.

Journal article Biomaterials · December 2007 Biomaterial-mediated gene delivery has recently emerged as a promising alternative to conventional gene transfer technologies that focus on direct delivery of viral vectors or DNA-polymer/matrix complexes. However, biomaterial-based strategies have primari ... Full text Cite

In vitro and in vivo osteoblastic differentiation of BMP-2- and Runx2-engineered skeletal myoblasts.

Journal article Journal of cellular biochemistry · April 2007 Genetic engineering with osteogenic factors is a promising approach for cell-based therapeutics and orthopedic regeneration. However, the relative efficacy of different strategies for inducing osteoblastic differentiation remains unclear and is further com ... Full text Cite

Genetic engineering for skeletal regenerative medicine.

Journal article Annual review of biomedical engineering · January 2007 The clinical challenges of skeletal regenerative medicine have motivated significant advances in cellular and tissue engineering in recent years. In particular, advances in molecular biology have provided the tools necessary for the design of gene-based st ... Full text Cite

Virus-based gene therapy strategies for bone regeneration.

Journal article Biomaterials · January 2007 Gene therapy has emerged as a promising strategy for the repair and regeneration of damaged musculoskeletal tissues. Application of this paradigm to bone healing has shown enhanced efficacy in preclinical animal studies compared to conventional bone grafti ... Full text Cite

Inducible regulation of Runx2-stimulated osteogenesis.

Journal article Gene therapy · June 2006 Ex vivo gene therapy is a promising approach to orthopedic regenerative medicine. These strategies typically focus on the constitutive overexpression of osteogenic factors to induce osteoblastic differentiation and matrix mineralization. However, the unreg ... Full text Cite

Glucocorticoid-induced osteogenesis is negatively regulated by Runx2/Cbfa1 serine phosphorylation.

Journal article Journal of cell science · February 2006 Glucocorticoid hormones have complex stimulatory and inhibitory effects on skeletal metabolism. Endogenous glucocorticoid signaling is required for normal bone formation in vivo, and synthetic glucocorticoids, such as dexamethasone, promote osteoblastic di ... Full text Cite

Runx2-genetically engineered cells for bone tissue engineering

Journal article Proceedings of the 2005 Summer Bioengineering Conference · December 1, 2005 Cite

Myoblast proliferation and differentiation on fibronectin-coated self assembled monolayers presenting different surface chemistries.

Journal article Biomaterials · August 2005 Biomaterial surface properties modulate protein adsorption and cell adhesion to elicit diverse cellular responses in biomedical and biotechnological applications. We used alkanethiol self-assembled monolayers presenting well-defined chemistries (OH, CH(3), ... Full text Cite

Soluble markers for the assessment of biological activity with PTK787/ZK 222584 (PTK/ZK), a vascular endothelial growth factor receptor (VEGFR) tyrosine kinase inhibitor in patients with advanced colorectal cancer from two phase I trials.

Journal article Annals of oncology : official journal of the European Society for Medical Oncology · April 2005 BackgroundPlasma and serum biomarkers of angiogenesis and activated endothelial cells were evaluated to assess biological activity of PTK787/ZK 222584 (PTK/ZK), a novel oral angiogenesis inhibitor targeting all known vascular endothelial growth fa ... Full text Cite

Runx2-stimulated transdifferentiation of primary skeletal myoblasts into an osteoblastic mineralizing phenotype for bone tissue engineering

Journal article Transactions 7th World Biomaterials Congress · December 1, 2004 The Runx2-stimulated transdifferentiation in skeletal primary myoblasts into an osteoblastic phenotype for bone tissue engineering, was investigated. The primary myoblasts were isolated from Balb/c mice and cultured in growth media. The microscopy and immu ... Cite

Runx2/Cbfa1 stimulates transdifferentiation of primary skeletal myoblasts into a mineralizing osteoblastic phenotype.

Journal article Experimental cell research · November 2004 Runx2, a transcriptional activator downstream of bone morphogenetic protein (BMP) signaling, is essential to osteoblastic differentiation and bone formation and maintenance. BMPs activate complex signaling networks, utilizing numerous signaling molecules a ... Full text Cite

Runx2/Cbfa1-genetically engineered skeletal myoblasts mineralize collagen scaffolds in vitro.

Journal article Biotechnology and bioengineering · November 2004 Genetic engineering of progenitor and stem cells is an attractive approach to address cell sourcing limitations associated with tissue engineering applications. Bone tissue engineering represents a promising strategy to repair large bone defects, but has b ... Full text Cite

Addressing cell-sourcing limitations with gene therapy.

Journal article IEEE engineering in medicine and biology magazine : the quarterly magazine of the Engineering in Medicine & Biology Society · September 2003 Full text Cite