Biology subjects

Chao, G.

Publications and source records attributed to Chao, G..

8 recordsLinked to original sources

bioRxiv2026

Mutant Isocitrate Dehydrogenase 1 Alters Extracellular Vesicle Secretion and Cargo Composition in Cellular Models

Somatic mutations in isocitrate dehydrogenase 1 (IDH1) define major subtypes of adult diffuse gliomas and occur across a broad spectrum of cancers. These mutations ablate the conventional turnover of isocitrate to alpha-ketoglutarate and confer the neomorphic production of D-2-hydroxyglutarate (D2HG), which drives epigenetic remodeling. Growing evidence suggests this neomorphic activity may also affect how tumor cells communicate; small extracellular vesicles (sEVs) are elevated in gliomas, though how mutant IDH1 shapes sEV production and cargo remains poorly understood. Using glioblastoma and chondrosarcoma cell models, we show expression of mutant IDH1 correlates with a trend of increased sEV secretion, and that D2HG is packaged into sEVs that are taken up by cells. Cell-permeable D2HG treatment dose-dependently increased sEV release from IDH1 wild type cells. Untargeted proteomics showed that mutant IDH1 expression remodeled sEV cargo in a cell type-specific fashion, with mutant chondrosarcoma sEVs enriched in one-carbon metabolism enzymes, and mutant glioma sEVs in lysosomal luminal proteins and endoplasmic reticulum (ER) chaperones. Mutant IDH1 glioma cell transcriptomics suggested expanded ER folding capacity and reduced ribosomal pathways, and sEVs from these cells decreased nascent protein synthesis in IDH1 wild type recipient cells. Together, this suggests sEVs can serve as carriers of mutant IDH1 phenotypes.

cancer biology↗

bioRxiv2025

Simulating a for-loop in the human genome: Design and evaluation of recombinase genetic programs that count to three.

Pluripotent cells specialize into numerous cell types by receiving external signals, making fate decisions, and executing differentiation functions - a paradigm similar to computer algorithms. While advances in biosensor design have enabled cells to respond to diverse stimuli, the ability to maintain a synthetic memory of the cells experiences that then informs its behaviors remains elusive. Here, we developed a system for cellular memory-driven behaviors by simulating a "for-loop" that counts to three using recombinase STepwise gene Expression Programs (STEPs). STEPs were genomically integrated into human cells, genotyped through targeted nanopore sequencing, and evaluated for function through changes in fluorescent reporter expression. While all STEPs were capable of heritable memory and sequential gene expression, the STEP design using tyrosine recombinases for successive excisions (TRex) significantly outperformed the others tested. We then used live cell imaging to track TRex cells as they incremented from count zero to three and observed the successive emergence of four cell states from an initially homogeneous population. The STEPs framework provides biological memory and conditional expression capabilities that, coupled with input mechanisms such as biosensors, can start to approach a programming language for biology.

synthetic biology↗

bioRxiv2024

Mining for microbial metabolites associated with disease progression in an age-dependent model of experimental autoimmune encephalomyelitis

Age is a risk factor for the neurological decline and physical disability that characterize progressive multiple sclerosis (MS). The intestinal microbiota and the bioactive compounds it produces can influence aging, immunity, and the central nervous system (CNS). Here, we use an experimental autoimmune encephalomyelitis (EAE) model that mimics features of progressive MS in aged, but not young, mice to address the intersection of age and the microbiota on EAE outcomes. Although the microbiota of SJL/J mice aged under controlled laboratory conditions does not promote an aged non-remitting EAE phenotype, young mice harboring heterochronic human fecal microbiota transplants (hFMT) developed a range of EAE phenotypes. Metabolomic profiling of mice colonized with an aged hFMT that promoted non-remitting EAE indicated a severe reduction in circulating levels of the microbiota-derived tryptophan metabolite indole 3-propionic acid (IPA). IPA-supplementation enforced remission in mice colonized with the non-remitting hFMT, demonstrating the utility of this in vivo pipeline for discovering metabolites associated with progressive MS-like disease. SummaryThe microbiota is a critical determinant of disease susceptibility in mouse models of MS. Here, Pu & Fettig et al. demonstrate that disease outcomes (remitting or non-remitting) are microbiota-responsive, and describe an in vivo pipeline that can be mined for microbial metabolites with therapeutic potential for progressive MS.

immunology↗

bioRxiv2024

Catalytically distinct IDH1 mutants tune phenotype severity in tumor models

Mutations in isocitrate dehydrogenase 1 (IDH1) impart a neomorphic reaction that produces D-2-hydroxyglutarate (D2HG), which can inhibit DNA demethylases to drive tumorigenesis. Mutations affect residue R132 and display distinct catalytic profiles for D2HG production. We show that catalytic efficiency of D2HG production is greater in IDH1 R132Q than R132H mutants, and expression of R132Q in cellular and xenograft models leads to higher D2HG concentrations in cells, tumors, and sera compared to R132H. Though expression of IDH1 R132Q leads to hypermethylation in DNA damage pathways, DNA hypomethylation is more notable when compared to R132H expression. Transcriptome analysis shows increased expression of many pro-tumor pathways upon expression of IDH1 R132Q versus R132H, including transcripts of EGFR and PI3K signaling pathways. Thus, IDH1 mutants appear to modulate D2HG levels via altered catalysis, resulting in distinct epigenetic and transcriptomic consequences where higher D2HG levels appear to be associated with more aggressive tumors.

genomics↗

bioRxiv2023

Immunogenicity of COVID-19 vaccines and their effect on the HIV reservoir in older people with HIV

Older individuals and people with HIV (PWH) were prioritized for COVID-19 vaccination, yet comprehensive studies of the immunogenicity of these vaccines and their effects on HIV reservoirs are not available. We followed 68 PWH aged 55 and older and 23 age-matched HIV-negative individuals for 48 weeks from the first vaccine dose, after the total of three doses. All PWH were on antiretroviral therapy (cART) and had different immune status, including immune responders (IR), immune non-responders (INR), and PWH with low-level viremia (LLV). We measured total and neutralizing Ab responses to SARS-CoV-2 spike and RBD in sera, total anti-spike Abs in saliva, frequency of anti-RBD/NTD B cells, changes in frequency of anti-spike, HIV gag/nef-specific T cells, and HIV reservoirs in peripheral CD4+ T cells. The resulting datasets were used to create a mathematical model for within-host immunization. Various regimens of BNT162b2, mRNA-1273, and ChAdOx1 vaccines elicited equally strong anti-spike IgG responses in PWH and HIV- participants in serum and saliva at all timepoints. These responses had similar kinetics in both cohorts and peaked at 4 weeks post-booster (third dose), while half-lives of plasma IgG also dramatically increased post-booster in both groups. Salivary spike IgA responses were low, especially in INRs. PWH had diminished live virus neutralizing titers after two vaccine doses which were rescued after a booster. Anti-spike T cell immunity was enhanced in IRs even in comparison to HIV- participants, suggesting Th1 imprinting from HIV, while in INRs it was the lowest. Increased frequency of viral blips in PWH were seen post-vaccination, but vaccines did not affect the size of the intact HIV reservoir in CD4+ T cells in most PWH, except in LLVs. Thus, older PWH require three doses of COVID-19 vaccine to maximize neutralizing responses against SARS-CoV-2, although vaccines may increase HIV reservoirs in PWH with persistent viremia.

immunology↗

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

helixCAM: A Platform for Programmable Cellular Assembly in Bacteria and Human Cells

Interactions between cells are indispensable for creating structure and signaling. The ability to direct precise cell-cell interactions would be powerful for engineering tissues, understanding signaling pathways, and directing immune cell targeting. In humans, intercellular interactions are mediated by cell adhesion molecules (CAMs). However, CAMs are natively expressed by many cells and have cross-reactivity, making them unsuitable for programming specific interactions. Here, we showcase "helixCAM," a platform for engineering novel CAMs by presenting coiled-coil peptides on the cell surface. helixCAMs were able to create specific cell-cell interactions and direct patterned aggregate formation in bacteria and human cells. We built rationally designed helixCAM libraries and discovered novel high-performance helixCAM pairs. High-affinity helixCAMs were then used for multicellular engineering applications, such as spherical layering, adherent cell targeting, and surface patterning. The helixCAMs are an expandable platform for directing complex multicellular assemblies, and we foresee its utility in tissue engineering, immunology, and developmental biology.

synthetic biology↗

bioRxiv2019

Genetic design automation for autonomous formation of multicellular shapes from a single cell progenitor

AO_SCPLOWBSTRACTC_SCPLOWMulti-cellular organisms originate from a single cell, ultimately giving rise to mature organisms of heterogeneous cell type composition in complex structures. Recent work in the areas of stem cell biology and tissue engineering have laid major groundwork in the ability to convert certain types of cells into other types, but there has been limited progress in the ability to control the morphology of cellular masses as they grow. Contemporary approaches to this problem have included the use of artificial scaffolds, 3D bioprinting, and complex media formulations, however, there are no existing approaches to controlling this process purely through genetics and from a single-cell starting point. Here we describe a computer-aided design approach for designing recombinase-based genetic circuits for controlling the formation of multi-cellular masses into arbitrary shapes in human cells.

synthetic biology↗