Biology subjects

Huang, J. Y.

Publications and source records attributed to Huang, J. Y..

8 recordsLinked to original sources

bioRxiv2026

Natural variation in transplacental transfer efficiency exposes distinct transcriptional network architectures of PFAS effects on birth weight and gestational age

Per- and polyfluoroalkyl substances (PFAS) are environmental contaminants that produce heterogeneous effects on perinatal outcomes despite chemical similarity. Natural variation in transplacental transfer efficiency (TPTE, the degree to which compounds cross the placental barrier) presents a mechanistic lens for understanding this heterogeneity, but whether TPTE systematically shapes the transcriptional pathways linking exposure to outcomes has not been tested. Using isoform-resolved placental transcriptomics from n = 124 term deliveries with eight PFAS measured in maternal and cord blood, validated against patient-derived placental explants (n = 18) using a tissue-specific long-read transcriptome assembly, we show that PFAS influence perinatal outcomes primarily through co-expression network hubs rather than differentially expressed features, indicating that network position, not fold-change magnitude, determines mediator importance. Leveraging TPTE as a natural experiment, we find that direct fetal exposure recruits increasingly numerous and tightly coordinated transcriptional mediators for both birth weight and gestational age, but the two outcomes diverge in network architecture: network centrality and maternal-fetal compartmentalization scale with TPTE exclusively for birth weight, while gestational age shows no such topological reorganization. These outcome-specific patterns are detectable only at the transcript level, as gene-level aggregation masks systematic TPTE-network relationships. This framework distinguishes which perinatal outcomes are mechanistically vulnerable to fetal exposure dose, with implications for risk assessment and therapeutic target identification for environmental contaminants.

developmental biology↗

bioRxiv2025

Long-read transcriptome assembly reveals vast isoform diversity in the placenta associated with metabolic and endocrine function

The placenta is critical for fetal development and mediates the effects of pregnancy complications on offspring metabolic health, yet it is often poorly characterized in genomic studies. Existing transcriptomic analyses rely on adult tissue-based references, which overlook developmentally important isoform diversity. We used largest-in-class long-read RNA-seq (N=72) to create a comprehensive placental transcriptome reference, identifying 37,661 high-confidence isoforms (14,985 novel) across 12,302 genes (2,759 novel). Contrary to characterizations of the placenta as a "transcriptomic void," we found transcriptional breadth and complexity comparable to adult tissues, with extraordinary splicing diversity in genes controlling obesity, lactogen production and growth, including 108 distinct CSH1 (placental lactogen) isoforms. This improved reference offers two advantages: First, it reduced inferential uncertainty in isoform quantification by 30% and increased the yield of high-confidence transcripts. Applying this reference to short-read RNA-seq datasets (N=344) of gestational diabetes mellitus (GDM), we found that placental transcription mediated 36% of GDM effects on birth weight, with novel CSH1 isoforms identified as key mediators. We further uncovered ancestry-specific effects, with distinct CSH1 isoforms mediating larger effects in European (24.4%) than Asian (13.4%) populations. Our results establish that utilizing long-read-based, tissue-specific transcriptomic annotations is critical, enabling isoform-resolved analyses that provide greater sensitivity than conventional gene-level approaches for understanding placental function and context-specific variation across diverse biobanks.

genomics↗

bioRxiv2024

Live-cell transcriptomics with engineered virus-like particles

The transcriptional state of a cell provides a multi-parameter representation of gene expression programs that reflect its identity and phenotype. However, current transcriptomic profiling technologies result in destruction of the biological sample, preventing direct analysis of transcriptional dynamics in the same living cells over time. Here, we developed a synthetic RNA export system called cellular self-reporting to address this fundamental technological limitation. We repurposed the murine leukemia virus retroviral protein Gag to enable diverse types of immortalized and primary mammalian cells to package cellular RNA molecules in virus-like particles (VLPs) for export into the extracellular environment. We applied self-reporting to interrogate the transcriptome-wide dynamics that occur during neuronal differentiation from induced pluripotent stem cells and detected gene expression profiles from individual live cells. Leveraging this genetically encodable approach, we expanded the capabilities of self-reporting through molecular engineering of VLP components. Pseudotyping VLPs with epitope-tagged envelope proteins enabled multiplexed selective live-cell readout of transcriptional states from heterogeneous co-cultures. Furthermore, structure-guided protein engineering of Gag fusions with human RNA binding domains improved the mRNA representation in self-reporting readouts and enabled the directed export of libraries of synthetic barcode transcripts. Taken together, this work establishes self-reporting as a facile and broadly enabling technology for live-cell, transcriptome-scale profiling of dynamic processes across diverse cell types and biological applications.

bioengineering↗

bioRxiv2022

Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC

The ability to differentiate stem cells into human cell types is essential to define basic mechanisms and therapeutics, especially for cell types not routinely accessible by biopsies. But while engineered expression of transcription factors (TFs) identified through TF screens has been found to rapidly and efficiently produce some cell types, generation of other cell types that require complex combinations of TFs has been elusive. Here we develop an iterative, pooled single-cell TF screening method that improves the identification of effective TF combinations using the generation of human microglia-like cells as a testbed: Two iterations identified a combination of SPI1, CEBPA, FLI1, MEF2C, CEBPB, and IRF8 as sufficient to differentiate human iPSC into microglia-like cells in 4 days. Characterization of TF-induced microglia demonstrated molecular and functional similarity to primary microglia. We explore the use of single-cell atlas reference datasets to confirm identified TFs and how combining single-cell TF perturbation and gene expression data can enable the construction of causal gene regulatory networks. We describe what will be needed to fashion these methods into a generalized integrated pipeline, further ideas for enhancement, and possible applications.

bioengineering↗

bioRxiv2022

CRISPR-Mediated Generation and Characterization of a Gaa Homozygous c.1935C>A (p.D645E) Pompe Disease Knock-in Mouse Model Recapitulates Human Infantile Onset-Pompe Disease

Pompe disease (PD) is an autosomal recessive disorder caused by deficient lysosomal acid -glucosidase (GAA), leading to reduced degradation and subsequent accumulation of intra-lysosomal glycogen in tissues, especially skeletal and oftentimes cardiac muscle. The c.1935C>A (p.Asp645Glu) variant is the most frequent GAA pathogenic mutation in people of Taiwanese and Southern Chinese ethnicity, causing infantile-onset PD (IOPD), which presents neonatally with severe hypertrophic cardiomyopathy, profound muscle hypotonia, and respiratory failure leading to premature death if untreated. To further investigate the pathogenic mechanism and facilitate development of therapies pertaining to this variant, we applied CRISPR-Cas9 homology-directed repair (HDR) using a novel dual sgRNA approach flanking the target site to generate a GaaEm1935C>A knock-in mouse model as well as a myoblast cell line carrying the Gaa c.1935C>A mutation. Herein we describe the molecular, biochemical, physiological, histological, and behavioral characterization of 3-month-old homozygous GaaEm1935C>A mice. Homozygous GaaEm1935C>A knock-in mice exhibited normal Gaa mRNA expression levels relative to wild-type mice, but GAA enzymatic activity was almost completely abolished, leading to a substantial increase in tissue glycogen storage, and significant concomitant impairment of autophagy. Echocardiography of 3-month-old knock-in mice revealed significant cardiac hypertrophy. The mice also demonstrated skeletal muscle weakness but, paradoxically, not early mortality. Longitudinal studies of this model, including assessment of its immune response to exogenously supplied GAA enzyme, are currently underway. In summary, the GaaEm1935C>A knock-in mouse model recapitulates the molecular, biochemical, histopathologic, and phenotypic aspects of human IOPD caused by the GAA c.1935C>A pathogenic variant. It is an ideal model to assess innovative therapies to treat IOPD, including personalized therapeutic strategies that correct pathogenic variants, restore GAA activity and produce functional phenotypes.

genetics↗

bioRxiv2021

Hot water extract of Arthrospira maxima (AHWE) has broad-spectrum antiviral activity against RNA virus including coronavirus SARS-CoV2, and the antivirus spray application

The emergence and re-emergence of RNA virus outbreaks highlight the urgent need for the development of broad-spectrum antiviral agents. Arthrospira maxima has be used as a food source for a long time, and the protein or polysaccharide fractions were evidenced to have antiviral activity, therefore we examined the antiviral efficacy of hot water extract from Arthrospira maxima (AHWE), on Enterovirus 71 (EV71), Influenza virus, Herpes simplex virus (HSV), Respiratory syncytial virus (RSV), Ebola virus, and Coronavirus for antiviral spray application. In this study, we demonstrated that the AHWE shown 90 to 100% inhibition rate on the plaque formation of EV71, HSV-1, HSV-2, influenza virus, RSV, 229E and SARS-COV2 at virus attachment stage, and the long-lasting protection study also found while the AHWE was pre-exposed to the open air for more than 4 hours in plaque reduction assay. In addition, AHWE also had inhibitory effect on Ebola virus replication at 500 ug/ml. Finally, AHWE also shown no toxicity and skin sensitivity that imply it could be safe for future clinical use if approved by FDA. In conclusion, this study suggests that AHWE could be developed as a potential broad-spectrum antivirus spray product and therapeutic agent.

microbiology↗

bioRxiv2019

CRISPR-Cas9 generated Pompe knock-in murine model exhibits early-onset cardiomyopathy and impaired skeletal muscle function

Infantile-onset Pompe Disease (IOPD), caused by mutations in lysosomal acid alpha-glucosidase (Gaa), manifests rapidly progressive fatal cardiac and skeletal myopathy incompletely attenuated by synthetic GAA intravenous infusions. The currently available murine model does not fully simulate human IOPD, displaying skeletal myopathy with late-onset hypertrophic cardiomyopathy. Bearing a Cre-LoxP induced exonic disruption of the murine Gaa gene, this model is also not amenable to genome-editing based therapeutic approaches. We report the early onset of severe hypertrophic cardiomyopathy in a novel murine IOPD model generated utilizing CRISPR-Cas9 homology-directed recombination to harbor the orthologous Gaa mutation c.1826dupA (p.Y609*), which causes human IOPD. We demonstrate the dual sgRNA approach with a single-stranded oligonucleotide donor is highly specific for the Gaac.1826 locus without genomic off-target effects or rearrangements. Cardiac and skeletal muscle were deficient in Gaa mRNA and enzymatic activity and accumulated high levels of glycogen. The mice demonstrated skeletal muscle weakness but did not experience early mortality. Altogether, these results demonstrate that the CRISPR-Cas9 generated Gaac.1826dupA murine model recapitulates hypertrophic cardiomyopathy and skeletal muscle weakness of human IOPD, indicating its utility for evaluation of novel therapeutics.

molecular biology↗

bioRxiv2019

Bacteriophage to Combat Biofilms in Hospital Drains

BackgroundAccording to the World Health Organization, nearly 15% of all hospitalized patients worldwide acquire nosocomial infections. A particular area of concern for bacterial build up in hospitals is sink drains. The moist, microbiologically active environment of drains promotes the formation of biofilms that are difficult to target with standard chemical disinfectants. Bacteriophages, however, show potential to be used as disinfecting agents in hospital drains. Not only do bacteriophages increase in titer as they infect, spreading to hard-to-reach surfaces, phages have been shown to degrade the extracellular matrix of biofilms and gain access to underlying bacteria. This research explores the potential of bacteriophages to eradicate biofilms in an environment modeling a sink drain by comparing the efficacy, range, and durability of bacteriophage to a chemical disinfectant.\n\nMethodsE. coli biofilms were grown in M9 minimal media placed in sink P-traps assigned one of three treatments: chemical disinfectant, bacteriophage, or deionized water (control). Biofilms were quantified at five time points -- 1, 12, 24, 36, and 48 hours -- using the crystal violet assay.\n\nResultsBoth chemical disinfectant and bacteriophage significantly decreased the optical densities of biofilms (p < 0.001***). P-traps treated with bacteriophages showed more uniform destruction of biofilm across P-trap compared to chemical disinfectant (p < 0.01**). A trend may suggest that over time bacteriophage became more effective at reducing biofilm than chemical disinfectant.\n\nConclusionThis work highlights the potential of bacteriophage as an alternative to conventional chemical disinfectants for biofilm control in settings such as hospital drains.\n\nImportanceNosocomial infections prolong hospital stay, costing the U.S. healthcare system $5-10 billion annually. An increasing number of reports demonstrate that sink drains -- reservoirs for multidrug resistant bacteria -- may be a source of hospital-related outbreaks. Recent studies have elucidated the mechanism of dispersal of bacteria from contaminated sinks to patients, but limited data are available identifying disinfecting methods for hospital drains. Not only did this study demonstrate that bacteriophages could reduce biofilms on sink drains just as effectively as a commercial disinfectant, it showed that phages tended to spread more thoroughly across P-traps and may work for longer. With hand-washing an imperative activity for disease prevention, hospital sinks should remain clean. This work explores an alternative disinfecting method for hospital sink drains.

microbiology↗