About

Our work employs a variety of techniques ranging from oligo chip synthesis and library-based screening to iPS cell differentiation and live-cell imaging. We utilize a variety of model systems ranging from yeast to human cell culture to assure that the technologies we generate are applicable to a broad swath of the scientific community. Our research group strives to push the boundaries of genetic engineering and synthetic biology by developing methods with which to manipulate eukaryotic genomes and probe biological phenomena in high-throughput. We apply these tools ourselves or through collaboration with a particular focus towards understanding neurobiology and infectious disease.

Research topics

• Biochemistry
• Biology
• Virology
• Medicine
• Genetics
• Computational biology
• Chemistry

Selected publications

• Pharmacy HIV pre-exposure prophylaxis/post-exposure prophylaxis furnishing: The benefits of collaborating with peer navigators

  Journal of the American Pharmacists Association · 2025-11-01 · 1 citations

  articleOpen access

  BACKGROUND: California Senate Bill 159 (2019) enables pharmacists to furnish oral human immunodeficiency virus pre-exposure prophylaxis (PrEP) and post-exposure prophylaxis (PEP) without a clinician's prescription; however, its implementation has been limited by barriers including time and space constraints. Noting these barriers, a peer navigator-led pharmacy PrEP/PEP program was created within a Southern California Federally Qualified Health Center (FQHC). OBJECTIVE: The program aimed to enable pharmacist PrEP/PEP furnishing through collaboration with navigators and increase the FQHC's number of PrEP patients by 25% in 2 years. METHODS: In 2021, a multidisciplinary team developed a program that involved navigators meeting with patients, conducting eligibility assessments, and providing human immunodeficiency virus testing to facilitate pharmacists' PrEP/PEP furnishing. From 2021 to 2023, the team implemented the program at 11 FQHC pharmacies by providing SB-159-required online trainings followed by in-person simulation trainings, allowing pharmacists to practice the workflow with navigators. This study evaluates the program using components of the RE-AIM framework, assessing the program's reach (number/type of encounters and demographics of program users) and efficacy (percentage of encounters that led to follow-up PrEP/PEP clinic visits) in its first 2 years. RESULTS: The pharmacy program had 238 total encounters within its first 2 years; 161 (67.6%) were for PrEP and 77 (32.4%) were for PEP. Of the 216 unique program users, 166 (76.9%) were documented as having Hispanic/Latinx ethnicity, and 145 (67.1%) were documented as LGBTQ+. Encounters led to 195 (81.9%) follow-up appointments scheduled, of which 156 (80.0%) were attended. The FQHC's number of enrolled PrEP patients increased from 239 in January 2022 to 339 in December 2023 (41.8%). CONCLUSION: This pharmacy program successfully increased PrEP/PEP access by creating a collaborative workflow led by peer navigators. Navigators are key to facilitating PrEP/PEP furnishing by aiding pharmacists in completing requirements and offering individuals a nonjudgmental peer encounter to obtain PrEP/PEP.

  PublisherOA PDFDOI

• Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut

  Nature Biotechnology · 2025-11-17 · 1 citations

  articleOpen access
  PublisherOA PDFDOI

• Multiplex neurodegeneration proteotoxicity platform reveals DNAJB6 promotes non-toxic FUS condensate gelation and inhibits neurotoxicity

  Nature Communications · 2025-11-21 · 2 citations

  articleOpen accessSenior author

  Neurodegenerative disorders (NDDs) are a family of diseases that remain poorly treated despite their growing global health burden. To gain insight into the mechanisms and modulators of neurodegeneration, we developed a yeast-based multiplex genetic screening platform. Using this platform, 32 NDD-associated proteins are probed against a library of 132 molecular chaperones from both yeast and humans, and an unbiased set of ~900 human proteins. We identify both broadly active and specific modifiers of our various cellular models. To illustrate the translatability of this platform, we extensively characterize a potent hit from our screens, the human chaperone DNAJB6. We show that DNAJB6 modifies the toxicity and solubility of multiple amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD)-linked RNA-binding proteins (RBPs). Biophysical examination of DNAJB6 demonstrated that it co-phase separates with, and alters the behavior of FUS containing condensates by locking them into a loose gel-like state which prevents their fibrilization. Domain mapping and a deep mutational scan of DNAJB6 revealed key residues required for its activity and identified variants with enhanced activity. Finally, we show that overexpression of DNAJB6 prevents motor neuron loss and the associated microglia activation in a mouse model of FUS-ALS.

  PublisherOA PDFDOI

• High throughput identification of genetic regulators of microglial inflammatory processes in Alzheimer's disease

  Journal of Neuroinflammation · 2025-12-03 · 2 citations

  articleOpen access

  Greater than a hundred genetic risk factors for Alzheimer’s disease (AD) have been identified by genome-wide association studies (GWAS), many of which are primarily expressed in microglia. However, the pathogenic role for most of them remains unclear. We sought to assess at scale how AD GWAS hits influence human microglial inflammatory responses. Thus, we conducted CRISPR inhibition (CRISPRi) screens of 119 AD GWAS hits in hiPSC-derived microglia (iMGLs), with reactive oxygen species (ROS) produced in response to the viral mimic poly(I:C) as a readout. Top hits that either decreased or increased ROS in response to poly(I:C) when knocked down were then interrogated in CROP-seq experiments, where CRISPRi was combined with single cell RNA-sequencing (scRNA-seq). These analyses identified 9 unique microglial clusters, including a poly(I:C)-driven inflammatory cluster (2). Emerging evidence supports a pathogenic role of viral infections in AD and our scRNA-seq showed significant overlap with AD-relevant microglial clusters. Knockdown (KD) of two hit genes, MS4A6A and EED, which lead to high levels of ROS in the presence of poly(I:C), increased the proportion of inflammatory cluster 2 cells and led to functionally related changes in gene expression. In addition, KD of MS4A6A reduced the proportion of iMGLs in the disease-associated microglia (DAM) cluster under all conditions, suggesting that MS4A6A may modulate the DAM response. In contrast, KD of hit genes, INPP5D or RABEP1 which led to low levels of ROS in the presence of poly(I:C), did not significantly affect the proportion of cells in inflammatory cluster 2 but rather shaped the inflammatory response. This included upregulation of a poly(I:C)-independent HLA inflammatory cluster (6) by INPP5D KD under all conditions. Despite INPP5D or RABEP1 being involved in disparate biological processes, their perturbation led to similar changes in gene expression, which included changes in genes related to metabolism such as oxidative phosphorylation, suggesting a shared conversion point by which AD GWAS hits affect cell state. Overall, our data begin to elucidate the functional roles played by various AD GWAS hits, including how they regulate and shape inflammatory responses such as those observed in AD.

  PublisherDOI

• Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening

  Nature Communications · 2025-01-02 · 8 citations

  articleOpen access

  Variants of SARS-CoV-2 have continued to emerge across the world and cause hundreds of deaths each week. Due to the limited efficacy of vaccines against SARS-CoV-2 and resistance to current therapies, additional anti-viral therapeutics with pan-coronavirus activity are of high interest. Here, we screen 2.8 billion compounds from a DNA-encoded chemical library and identify small molecules that are non-covalent inhibitors targeting the conserved 3CL protease of SARS-CoV-2 and other coronaviruses. We perform structure-based optimization, leading to the creation of a series of potent, non-covalent SARS-CoV-2 3CL protease inhibitors, for coronavirus infections. To characterize their binding mechanism to the 3CL protease, we determine 16 co-crystal structures and find that optimized inhibitors specifically interact with both protomers of the native homodimer of 3CL protease. Since 3CL protease is catalytically competent only in the dimeric state, these data provide insight into the design of drug-like inhibitors targeting the native homodimer state. With a binding mode different from the covalent 3CL inhibitor nirmatrelvir, the protease inhibitor in the COVID drug Paxlovid, these compounds may overcome resistance reported for nirmatrelvir and complement its clinical utility. Due to the limited efficacy of vaccines against SARS-CoV-2 and resistance to current therapies additional anti-viral therapeutics with pan-coronavirus activity are of high interest. Here, the authors screened 2.8 billion compounds from a DNA-encoded chemical library and identified small molecules that are non-covalent inhibitors targeting the conserved 3CL protease of SARS-CoV-2 and other coronaviruses.

  PublisherOA PDFDOI

• Development of a Cervical Cancer Screening Program in Rural Guatemala

  Global Health Science and Practice · 2025-08-14

  articleOpen access

  <h3>ABSTRACT</h3> <h3>Background:</h3> In San Lucas Tolimán (SLT), Guatemala, a rural municipality with a large Indigenous population, women seeking cervical cancer screening face many barriers. We describe the process from design to implementation of a culturally appropriate and accessible cervical cancer screening and treatment pilot program for women aged 30–49 years. <h3>Methods:</h3> After conducting a community needs assessment, we trained community health workers (CHWs) on basic cervical cancer pathophysiology and human papillomavirus (HPV) self-swab kit use. CHWs provided educational seminars and enrolled interested, eligible women in a mobile health application. Women collected samples at home and returned completed kits to CHWs, who sent the kits to a partner lab. Women who were positive for HPV received follow-up care at the local hospital, where physicians had received training in visual inspection with acetic acid (VIA) with same-day cryotherapy or thermocoagulation. Women with advanced lesions received access to care from gynecologists free of cost. <h3>Results:</h3> Between February and November 2023, of the 230 women eligible to participate in the program, 132 completed HPV self-swabs and received results, and 34 received positive HPV tests (25.76% prevalence). Sixty-seven women had VIA exams as their first screening. Women who received VIA exams had an overall positivity rate of 24.47% (23/94). Twenty-three women received treatment: cryotherapy (n=8), thermocoagulation (n=7), or loop electrosurgical excision procedure (n=8). SLT had higher HPV-positivity rates than nearby Escuintla (21.6%; <i>P</i>=.29) and significantly higher than Santiago Atitlán (17.4% HPV+; <i>P</i>=.02). <h3>Conclusion:</h3> Our screening program found significantly higher HPV-positivity rates in SLT than in previous Guatemalan studies. Our research reinforces that adequately treating cervical cancer in Guatemala requires accompaniment during care and economic support to make care affordable or free. Based on our pilot program, organizations worldwide can further invest in culturally sensitive cervical cancer screening and treatment.

  PublisherOA PDFDOI

• CRISPR activation to repair electrocardiogram abnormalities caused by a FLNC truncating variant in mice

  European Heart Journal · 2025-08-23 · 6 citations

  articleOpen access

  BackgroundTruncating variants in the Filamin C gene (FLNCtv) are a frequent cause of genetic dilated cardiomyopathy (DCM) and non-dilated left ventricular cardiomyopathy (NDLVC), both characterized by arrhythmic complications and increased risk of sudden cardiac death. MethodsWe generated a mouse model with a constitutive heterozygous deletion of FLNC exon 15 (FLNC-Ex15del/wt), mimicking a pathogenic human variant.We assessed cardiac expression of FLNC by qRT-PCR and western blot and evaluated electrical function via electrocardiography (ECG), including flecainide challenge.We designed a cardiacspecific, all-in-one AAV-CRISPRa system encoding a dead Cas9 linked to the transcription activation domain of VP64 (dSaCas9-VP64) under the cTnT promoter and sgRNAs previously optimised in HL-1 cardiomyocytes.The final construct was packaged in a myotropic AAVMYO capsid and systemically administered to FLNC mutant mice.Five weeks post-injection, qRT-PCR and ECGs and expression analyses were carried out to determine restoration of FLNC expression and rescue of ECG abnormalities. ResultsFLNC-Ex15del/wt mice exhibited no overt systolic dysfunction but showed significant ECG abnormalities, including prolonged QRS duration and reduced amplitude.Flecainide induced ventricular arrhythmias in ~40% of mutant mice, further exacerbating ECG changes.Mutant hearts showed reduced FLNC mRNA and protein levels, consistent with haploinsufficiency.Transfection studies in HL-1 cells identified a highly effective sgRNA and scaffold combination, achieving up to 1.8-fold upregulation of endogenous FLNC expression.Systemic AAV delivery of the CRISPRa construct to mutant mice at 32 weeks restored FLNC mRNA to wild-type levels.Post-treatment ECGs showed increased QRS amplitude, and flecainide-induced arrhythmias were completely prevented in treated animals. ConclusionsOur heterozygous FLNCtv model partially recapitulates the electrical abnormalities observed in FLNCtv carriers with DCM/NDLVC, offering valuable insight into disease pathogenesis.Most importantly, this study provides the first in vivo demonstration that CRISPRa-AAV-mediated gene activation can effectively treat an inherited cardiomyopathy driven by haploinsufficiency.We show that even after disease onset, electrical dysfunction can be reversed through this targeted therapeutic approach.Our findings open new avenues for broader applications of CRISPRa-AAV platforms in addressing cardiac disorders rooted in insufficient gene dosage.

  PublisherOA PDFDOI

• High throughput identification of genetic regulators of microglial inflammatory processes in Alzheimer’s disease

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-11 · 1 citations

  preprintOpen access

  Abstract Genome-wide association studies (GWAS) have identified over a hundred genetic risk factors for Alzheimer’s disease (AD), many of which are predominantly expressed in microglia. However, the pathogenic role for most of them remains unclear. To systematically investigate how AD GWAS variants influence human microglial inflammatory responses, we conducted CRISPR inhibition (CRISPRi) screens targeting 119 AD GWAS hits in hiPSC-derived microglia (iMGLs) and used the production of reactive oxygen species (ROS) in response to the viral mimic poly(I:C) as a functional readout. Top hits whose knockdown either increased or decreased ROS levels in response to poly(I:C) were further analyzed using CROP-seq to integrate CRISPRi with single-cell RNA sequencing (scRNA-seq). This analysis identified 9 unique microglial clusters, including a poly(I:C)-driven inflammatory cluster 2. Emerging evidence supports a pathogenic role of viral infections in AD and cross comparison of our scRNA-seq data with iMGLs xenotransplanted into an AD mouse model shows significant overlap between our clusters and AD-relevant microglial clusters. Knockdown of MS4A6A and EED , which resulted in elevated ROS production in the presence of poly(I:C), increased the proportion of cluster 2 cells and induced functionally related changes in gene expression. In addition, KD of MS4A6 led to a reduction in the proportion of iMGLs in the DAM (disease associated microglia) cluster under all conditions, suggesting that this gene may modulate the DAM response. In contrast, KD of INPP5D or RAPEP1 which lead to low levels of ROS in the presence of poly(I:C), did not significantly affect the proportion of cells in cluster 2 but rather shaped the inflammatory response. This included the upregulation of an HLA-associated inflammatory cluster (cluster 6) by INPP5D knockdown under all conditions, independent of poly(I:C) stimulation. Importantly, KD of INPP5D or RAPEP1 had many shared differentially expressed genes (DEGs) under both vehicle and poly(I:C) treated conditions. Overall, our findings demonstrate that despite the diverse biological functions of AD GWAS variants, they converge functionally to regulate human microglial states and shape inflammatory responses relevant to AD pathology.

  PublisherOA PDFDOI

• Combinatorial protein engineering identifies potent CRISPR activators with reduced toxicity

  Nature Communications · 2025-11-20

  articleOpen accessSenior author

  Current protein engineering methods are inadequate to explore the combinatorial potential offered by nature's vast repertoire of protein domains-limiting our ability to create optimal synthetic tools. To overcome this barrier, we develop an approach to create and test thousands of chimeric proteins and employ it to probe an expansive combinatorial landscape of over 15,000 multi-domain CRISPR activators. Our findings indicate that many activators produce substantial cellular toxicity, often unrelated to their capacity to regulate gene expression. We also explore the biochemical features of activation domains and determine how their combinatorial interactions shape activator behavior. Finally, we identify two potent CRISPR activators, MHV and MMH, and demonstrate their enhanced activity across diverse targets and cell types compared to the gold-standard MCP activator, synergistic activation mediator (SAM).

  PublisherOA PDFDOI

• A multiplex method for rapidly identifying viral protease inhibitors

  Molecular Systems Biology · 2025-01-06 · 2 citations

  articleOpen accessSenior author

  With current treatments addressing only a fraction of pathogens and new viral threats constantly evolving, there is a critical need to expand our existing therapeutic arsenal. To speed the rate of discovery and better prepare against future threats, we establish a high-throughput platform capable of screening compounds against 40 diverse viral proteases simultaneously. This multiplex approach is enabled by using cellular biosensors of viral protease activity combined with DNA-barcoding technology, as well as several design innovations that increase assay sensitivity and correct for plate-to-plate variation. Among >100,000 compound-target interactions explored within our initial screen, a series of broad-acting inhibitors against coronavirus proteases were uncovered and validated through orthogonal assays. A medicinal chemistry campaign was performed to improve one of the inhibitor's potency while maintaining its broad activity. This work highlights the power of multiplex screening to efficiently explore chemical space at a fraction of the time and costs of previous approaches.

  PublisherOA PDFDOI

Frequent coauthors

• George M. Church

  Harvard–MIT Division of Health Sciences and Technology

  62 shared

• James J. Collins

  Massachusetts Institute of Technology

  47 shared

• Sho Iketani

  Aaron Diamond AIDS Research Center

  25 shared

• Xiaoge Guo

  Xinxiang Medical University

  24 shared

• Rebecca S. Shapiro

  University of Guelph

  24 shared

• David D. Ho

  Columbia University

  22 shared

• F. Brad Johnson

  19 shared

• Mingqiang Li

  Shanghai Stomatological Hospital

  18 shared