Hua Huang

Bio: Hua Huang is an academic researcher from University of Pennsylvania. The author has contributed to research in topics: Medicine & Biology. The author has an hindex of 3, co-authored 5 publications receiving 22 citations. Previous affiliations of Hua Huang include Children's Hospital of Philadelphia.

Brain charts for the human lifespan

Abstract: Over the past 25 years, neuroimaging has become a ubiquitous tool in basic research and clinical studies of the human brain. However, no reference standards currently exist to quantify individual differences in neuroimaging metrics over the lifespan, in contrast to growth charts for anthropometric traits such as height and weight. Here, we built an interactive resource (www.brainchart.io) to benchmark individual differences in brain morphology, measured from any current or future magnetic resonance imaging (MRI) study, against normative age-related trends. With the goal of basing these reference charts on the largest and most inclusive dataset available, we aggregated 123,984 MRI scans from 101,457 participants in over 100 studies - from 115 days post-conception through 100 postnatal years. Cerebrum tissue volumes and other global or regional MRI metrics were quantified by centile scores, relative to non-linear trajectories, demonstrating concurrent validity with non-MRI brain growth milestones, high stability over longitudinal assessments, and robustness to differences between studies. Brain charts identified previously unreported neurodevelopmental milestones, and centile scores had increased heritability compared to non-centiled MRI phenotypes. Crucially, for clinical purposes, centile scores provided a standardised and interpretable measure of deviation that revealed new patterns of neuroanatomical differences across neurological and psychiatric disorders. In sum, brain charts for the human lifespan are an essential first step towards robust, standardised quantification of deviation from age-related trends in multiple commonly-used neuroimaging phenotypes. Our global collaborative study provides such an anchorpoint for neuroimaging research and will facilitate implementation of quantitative standards in clinical studies.

High-content CRISPR screening

Abstract: CRISPR screens are a powerful source of biological discovery, enabling the unbiased interrogation of gene function in a wide range of applications and species. In pooled CRISPR screens, various genetically encoded perturbations are introduced into pools of cells. The targeted cells proliferate under a biological challenge such as cell competition, drug treatment or viral infection. Subsequently, the perturbation-induced effects are evaluated by sequencing-based counting of the guide RNAs that specify each perturbation. The typical results of such screens are ranked lists of genes that confer sensitivity or resistance to the biological challenge of interest. Contributing to the broad utility of CRISPR screens, adaptations of the core CRISPR technology make it possible to activate, silence or otherwise manipulate the target genes. Moreover, high-content read-outs such as single-cell RNA sequencing and spatial imaging help characterize screened cells with unprecedented detail. Dedicated software tools facilitate bioinformatic analysis and enhance reproducibility. CRISPR screening has unravelled various molecular mechanisms in basic biology, medical genetics, cancer research, immunology, infectious diseases, microbiology and other fields. This Primer describes the basic and advanced concepts of CRISPR screening and its application as a flexible and reliable method for biological discovery, biomedical research and drug development — with a special emphasis on high-content methods that make it possible to obtain detailed biological insights directly as part of the screen. CRISPR screening is a high-throughput approach for identifying genes, pathways and mechanisms involved in a given phenotype or biological process. High-content read-outs of these screens, such as imaging and single-cell sequencing techniques, have further broadened its applicability. This Primer by Bock et al. describes the main concepts of CRISPR screening and gives examples of its application as a method for biological discovery, with a focus on the use of high-content read-outs.

A genome-scale screen for synthetic drivers of T cell proliferation

Abstract: The engineering of autologous patient T cells for adoptive cell therapies has revolutionized the treatment of several types of cancer1. However, further improvements are needed to increase response and cure rates. CRISPR-based loss-of-function screens have been limited to negative regulators of T cell functions2–4 and raise safety concerns owing to the permanent modification of the genome. Here we identify positive regulators of T cell functions through overexpression of around 12,000 barcoded human open reading frames (ORFs). The top-ranked genes increased the proliferation and activation of primary human CD4+ and CD8+ T cells and their secretion of key cytokines such as interleukin-2 and interferon-γ. In addition, we developed the single-cell genomics method OverCITE-seq for high-throughput quantification of the transcriptome and surface antigens in ORF-engineered T cells. The top-ranked ORF—lymphotoxin-β receptor (LTBR)—is typically expressed in myeloid cells but absent in lymphocytes. When overexpressed in T cells, LTBR induced profound transcriptional and epigenomic remodelling, leading to increased T cell effector functions and resistance to exhaustion in chronic stimulation settings through constitutive activation of the canonical NF-κB pathway. LTBR and other highly ranked genes improved the antigen-specific responses of chimeric antigen receptor T cells and γδ T cells, highlighting their potential for future cancer-agnostic therapies5. Our results provide several strategies for improving next-generation T cell therapies by the induction of synthetic cell programmes. A genome-scale gain-of-function screen using overexpression of nearly 12,000 open reading frames (ORFs) identifies positive regulators of human T cell function and suggests that ORF-based screens could be applied clinically to improve T cell therapies.

A genome-scale screen for synthetic drivers of T cell proliferation

Abstract: The engineering of autologous patient T cells for adoptive cell therapies has revolutionized the treatment of several types of cancer1. However, further improvements are needed to increase response and cure rates. CRISPR-based loss-of-function screens have been limited to negative regulators of T cell functions2–4 and raise safety concerns owing to the permanent modification of the genome. Here we identify positive regulators of T cell functions through overexpression of around 12,000 barcoded human open reading frames (ORFs). The top-ranked genes increased the proliferation and activation of primary human CD4+ and CD8+ T cells and their secretion of key cytokines such as interleukin-2 and interferon-γ. In addition, we developed the single-cell genomics method OverCITE-seq for high-throughput quantification of the transcriptome and surface antigens in ORF-engineered T cells. The top-ranked ORF—lymphotoxin-β receptor (LTBR)—is typically expressed in myeloid cells but absent in lymphocytes. When overexpressed in T cells, LTBR induced profound transcriptional and epigenomic remodelling, leading to increased T cell effector functions and resistance to exhaustion in chronic stimulation settings through constitutive activation of the canonical NF-κB pathway. LTBR and other highly ranked genes improved the antigen-specific responses of chimeric antigen receptor T cells and γδ T cells, highlighting their potential for future cancer-agnostic therapies5. Our results provide several strategies for improving next-generation T cell therapies by the induction of synthetic cell programmes. A genome-scale gain-of-function screen using overexpression of nearly 12,000 open reading frames (ORFs) identifies positive regulators of human T cell function and suggests that ORF-based screens could be applied clinically to improve T cell therapies.