Prediction and validation of gene regulatory elements active in human development

Embryonic development relies on well-tuned expression of thousands of genes across developing tissues and organs. Gene regulatory regions such as enhancers control these gene expression patterns, and properly functioning regulatory regions are vital for healthy development. To better characterize genes and regulatory regions that are important in embryonic development, we developed a new approach to identify developmental enhancers and a database of genes with known developmental functions, validated our predictions in transgenic mouse and zebrafish enhancer assays, and applied these tools to several interesting questions in embryonic development.While many large-scale studies have investigated the location and function of enhancers in specific developmental tissues and timepoints, a general predictor of developmental enhancers was lacking. To leverage the massive amount of available data and fill this void, we developed EnhancerFinder, a computational tool that integrates thousands of genetic and epigenetic datasets to predict tissue-specific developmental enhancers. With this tool we predicted over 80,000 developmental enhancers, plus tissue specificity for thousands of these predicted enhancers. We surveyed the enhancer landscape across the whole genome and found that predicted enhancers tend to cluster around developmental genes and that genes near tissue-specific enhancers are expressed in relevant tissues. We tested 12 developmental enhancers in transgenic mouse and zebrafish enhancer assays and found that 10 candidate enhancers validated with consistent expression patterns in at least one of the animal models. One cluster of these validated enhancers near developmental transcription factor FOXC1 pointed us towards a specific developmental brain structure known to be involved in cerebral malformations. We further investigated these candidate enhancers and developed a model for a possible non-coding genetic cause of the brain development disorder Dandy-Walker malformations.We developed an improved framework for predicting enhancers, cataloged thousands of genes with developmental functions, predicted tens of thousands of novel developmental enhancers in the human genome that validate well in animal models, and showed applications of these tools in several interesting questions in developmental biology. We hope other researchers will be able to use these tools to further their own investigations in gene regulation during embryonic development

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins.

T-cell genome engineering holds great promise for cell-based therapies for cancer, HIV, primary immune deficiencies, and autoimmune diseases, but genetic manipulation of human T cells has been challenging. Improved tools are needed to efficiently "knock out" genes and "knock in" targeted genome modifications to modulate T-cell function and correct disease-associated mutations. CRISPR/Cas9 technology is facilitating genome engineering in many cell types, but in human T cells its efficiency has been limited and it has not yet proven useful for targeted nucleotide replacements. Here we report efficient genome engineering in human CD4(+) T cells using Cas9:single-guide RNA ribonucleoproteins (Cas9 RNPs). Cas9 RNPs allowed ablation of CXCR4, a coreceptor for HIV entry. Cas9 RNP electroporation caused up to ∼40% of cells to lose high-level cell-surface expression of CXCR4, and edited cells could be enriched by sorting based on low CXCR4 expression. Importantly, Cas9 RNPs paired with homology-directed repair template oligonucleotides generated a high frequency of targeted genome modifications in primary T cells. Targeted nucleotide replacement was achieved in CXCR4 and PD-1 (PDCD1), a regulator of T-cell exhaustion that is a validated target for tumor immunotherapy. Deep sequencing of a target site confirmed that Cas9 RNPs generated knock-in genome modifications with up to ∼20% efficiency, which accounted for up to approximately one-third of total editing events. These results establish Cas9 RNP technology for diverse experimental and therapeutic genome engineering applications in primary human T cells

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins.

T-cell genome engineering holds great promise for cell-based therapies for cancer, HIV, primary immune deficiencies, and autoimmune diseases, but genetic manipulation of human T cells has been challenging. Improved tools are needed to efficiently "knock out" genes and "knock in" targeted genome modifications to modulate T-cell function and correct disease-associated mutations. CRISPR/Cas9 technology is facilitating genome engineering in many cell types, but in human T cells its efficiency has been limited and it has not yet proven useful for targeted nucleotide replacements. Here we report efficient genome engineering in human CD4(+) T cells using Cas9:single-guide RNA ribonucleoproteins (Cas9 RNPs). Cas9 RNPs allowed ablation of CXCR4, a coreceptor for HIV entry. Cas9 RNP electroporation caused up to ∼40% of cells to lose high-level cell-surface expression of CXCR4, and edited cells could be enriched by sorting based on low CXCR4 expression. Importantly, Cas9 RNPs paired with homology-directed repair template oligonucleotides generated a high frequency of targeted genome modifications in primary T cells. Targeted nucleotide replacement was achieved in CXCR4 and PD-1 (PDCD1), a regulator of T-cell exhaustion that is a validated target for tumor immunotherapy. Deep sequencing of a target site confirmed that Cas9 RNPs generated knock-in genome modifications with up to ∼20% efficiency, which accounted for up to approximately one-third of total editing events. These results establish Cas9 RNP technology for diverse experimental and therapeutic genome engineering applications in primary human T cells

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins

T-cell genome engineering holds great promise for cell-based therapies for cancer, HIV, primary immune deficiencies, and autoimmune diseases, but genetic manipulation of human T cells has been challenging. Improved tools are needed to efficiently “knock out” genes and “knock in” targeted genome modifications to modulate T-cell function and correct disease-associated mutations. CRISPR/Cas9 technology is facilitating genome engineering in many cell types, but in human T cells its efficiency has been limited and it has not yet proven useful for targeted nucleotide replacements. Here we report efficient genome engineering in human CD4(+) T cells using Cas9:single-guide RNA ribonucleoproteins (Cas9 RNPs). Cas9 RNPs allowed ablation of CXCR4, a coreceptor for HIV entry. Cas9 RNP electroporation caused up to ∼40% of cells to lose high-level cell-surface expression of CXCR4, and edited cells could be enriched by sorting based on low CXCR4 expression. Importantly, Cas9 RNPs paired with homology-directed repair template oligonucleotides generated a high frequency of targeted genome modifications in primary T cells. Targeted nucleotide replacement was achieved in CXCR4 and PD-1 (PDCD1), a regulator of T-cell exhaustion that is a validated target for tumor immunotherapy. Deep sequencing of a target site confirmed that Cas9 RNPs generated knock-in genome modifications with up to ∼20% efficiency, which accounted for up to approximately one-third of total editing events. These results establish Cas9 RNP technology for diverse experimental and therapeutic genome engineering applications in primary human T cells

Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment

The past two decades have brought many important advances in our understanding of the hereditary susceptibility to cancer. Numerous studies have provided convincing evidence that identification of germline mutations associated with hereditary cancer syndromes can lead to reductions in morbidity and mortality through targeted risk management options. Additionally, advances in gene sequencing technology now permit the development of multigene hereditary cancer testing panels. Here, we describe the 2016 revision of the Counsyl Inherited Cancer Screen for detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy number variants (CNVs) in 36 genes associated with an elevated risk for breast, ovarian, colorectal, gastric, endometrial, pancreatic, thyroid, prostate, melanoma, and neuroendocrine cancers. To determine test accuracy and reproducibility, we performed a rigorous analytical validation across 341 samples, including 118 cell lines and 223 patient samples. The screen achieved 100% test sensitivity across different mutation types, with high specificity and 100% concordance with conventional Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). We also demonstrated the screen’s high intra-run and inter-run reproducibility and robust performance on blood and saliva specimens. Furthermore, we showed that pathogenic Alu element insertions can be accurately detected by our test. Overall, the validation in our clinical laboratory demonstrated the analytical performance required for collecting and reporting genetic information related to risk of developing hereditary cancers

Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment

<p>Sanger and MLPA datasets for the article "Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment" (http://dx.doi.org/10.1101/088252).</p

A tissue checkpoint regulates type 2 immunity

Group 2 innate lymphoid cells (ILC2s) and CD4(+) T helper type 2 (Th2) cells are defined by their similar effector cytokines, which together mediate the features of allergic immunity. Here, we show that tissue ILC2s and Th2 cells differentiate independently but share overlapping effector function programs mediated by exposure to the tissue-derived cytokines interleukin (IL)-25, IL-33, and thymic stromal lymphopoietin (TSLP). Loss of these three tissue signals does not affect lymph node priming but abrogates terminal differentiation of effector Th2 cells and adaptive lung inflammation in a T cell-intrinsic manner. Our findings suggest how diverse perturbations activate type 2 immunity, uncovering a shared local tissue-elicited checkpoint that can be exploited to control both innate and adaptive allergic inflammation