Biology subjects

Tran, R.

Publications and source records attributed to Tran, R..

5 recordsLinked to original sources

bioRxiv2026

Machine learning-guided olivetolic acid cyclase engineering enables tailored cannabinoid biosynthesis in yeast

Cannabinoids comprise a diverse class of bioactive natural products with important therapeutic potential, but efficient microbial production remains limited by pathway bottlenecks and challenges in engineering key biosynthetic enzymes. Here, we develop a machine learning-guided approach to engineer olivetolic acid cyclase (OAC), a critical control point in cannabinoid biosynthesis that governs both pathway flux and product selectivity. We first generated sequence-function data from 152 CsOAC variants spanning homolog screening, recombination, and mutagenesis libraries. Using these measurements, we trained multi-task models to predict pathway-level production of olivetolic acid (OA), divarinic acid (DVA), and competing byproducts, together with a variational autoencoder that captured evolutionary constraints across the broader enzyme family. Across three rounds of iterative design and testing, this approach identified CsOAC variants that substantially increased production and selectivity of both OA and DVA. When introduced into engineered Yarrowia lipolytica strains, these variants enabled production of tetrahydrocannabinolic acid (THCA) and the minor cannabinoid tetrahydrocannabivarinic acid (THCVA) at titers exceeding previous yeast systems. Analysis of top-performing variants revealed mutations influencing substrate selectivity and catalytic performance, providing insight into the determinants of CsOAC function. More broadly, this work demonstrates how machine learning-guided enzyme engineering can improve pathway performance and expand access to major and minor cannabinoids through microbial biosynthesis.

bioengineering↗

bioRxiv2024

Multi-Niche Human Bone Marrow On-A-Chip for Studying the Interactions of Adoptive CAR-T Cell Therapies with Multiple Myeloma

Multiple myeloma (MM), a cancer of bone marrow plasma cells, is the second-most common hematological malignancy. However, despite immunotherapies like chimeric antigen receptor (CAR)-T cells, relapse is nearly universal. The bone marrow (BM) microenvironment influences how MM cells survive, proliferate, and resist treatment. Yet, it is unclear which BM niches give rise to MM pathophysiology. Here, we present a 3D microvascularized culture system, which models the endosteal and perivascular bone marrow niches, allowing us to study MM-stroma interactions in the BM niche and model responses to therapeutic CAR-T cells. We demonstrated the prolonged survival of cell line-based and patient-derived multiple myeloma cells within our in vitro system and successfully flowed in donor-matched CAR-T cells. We then measured T cell survival, differentiation, and cytotoxicity against MM cells using a variety of analysis techniques. Our MM-on-a-chip system could elucidate the role of the BM microenvironment in MM survival and therapeutic evasion and inform the rational design of next-generation therapeutics. TEASERA multiple myeloma model can study why the disease is still challenging to treat despite options that work well in other cancers.

cancer biology↗

bioRxiv2021

Identifying The "Core" Transcriptome of SARS-CoV-2 Infected Cells

In 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first emerged, causing the COVID-19 pandemic. Consequently, ongoing research has focused on better understanding the mechanisms underlying the symptoms of this disease. Although COVID-19 symptoms span a range of organ systems, the specific changes in gene regulation that lead to the variety of symptoms are still unclear. In our study, we used publicly available transcriptome data from previous studies on SARS-CoV-2 to identify commonly regulated genes across cardiomyocytes, human bronchial epithelial cells, alveolar type II cells, lung adenocarcinoma, human embryonic kidney cells, and patient samples. Additionally, using this common "core" transcriptome, we could identify the genes that were specifically and uniquely regulated in bronchial epithelial cells, embryonic kidney cells, or cardiomyocytes. For example, we found that genes related to cell metabolism were uniquely upregulated in kidney cells, providing us with the first mechanistic clue about specifically how kidney cells may be affected by SARS-CoV-2. Overall, our results uncover connections between the differential gene regulation in various cell types in response to the SARS-CoV-2 infection and help identify targets of potential therapeutics.

bioinformatics↗

bioRxiv2021

Adaptation in outbred sexual yeast is repeatable, polygenic, and favors rare haplotypes

We describe the results of a 200 generation Evolve and Resequence (E&R) study initiated from an outbred dipliod recombined synthetic base population derived from 18 genetically diverse founders. Replicate populations were maintained at large effective population sizes (>105 individuals), exposed to several different chemical challenges over 12 weeks of evolution, and whole-genome resequenced. Weekly forced outcrossing implies a per gene per cell-division recombination rate higher than that achieved in Drosophila E&R studies. In 55 sexual populations we observe large fitness gains and highly repeatable patterns of genome-wide haplotype change within each chemical challenge. There was little evidence for pervasive pleiotropy, as evidenced by patterns of haplotype change between drug treatments. Within treatment adaptation appears highly polygenic with almost the entire genome showing significant consistent haplotype change. Finally, adaptation was almost always associated with only one of the 18 founder alleles, suggesting selection primarily acts on rare variants private to a founder or haplotype blocks harboring multiple mutations. This observation contradicts the notion that adaptation is often due to subtle frequency shifts at intermediate frequency variants.

evolutionary biology↗

bioRxiv2021

Stress decreases serotonin tone in the nucleus accumbens to promote aversion and potentiate cocaine preference via decreased stimulation of 5-HT1B receptors

Stress-induced release of dynorphins (Dyn) activates kappa opioid receptors (KOR) in monoaminergic neurons to produce dysphoria and potentiate drug reward; however, the circuit mechanisms responsible for this effect are not known. We found that conditional deletion of KOR from Slc6a4 (SERT)-expressing neurons blocked stress-induced potentiation of cocaine conditioned place preference (CPP). Within the dorsal raphe nucleus (DRN), two overlapping populations of KOR-expressing neurons: Slc17a8 (VGluT3) and SERT, were distinguished functionally and anatomically. Optogenetic inhibition of these SERT+ neurons potentiated subsequent cocaine CPP, whereas optical inhibition of the VGluT3+ neurons blocked subsequent cocaine CPP. SERT+/VGluT3- expressing neurons were concentrated in the lateral aspect of the DRN. SERT projections from the DRN were observed in the medial nucleus accumbens (mNAc), but VGluT3 projections were not. Optical inhibition of SERT+ neurons produced place aversion, whereas optical stimulation of SERT+ terminals in the mNAc attenuated stress-induced increases in forced swim immobility and subsequent cocaine CPP. KOR neurons projecting to mNAc were confined to the lateral aspect of the DRN, and the principal source of dynorphinergic (Pdyn) afferents in the mNAc was from local neurons. Excision of Pdyn from the mNAc blocked stress-potentiation of cocaine CPP. Prior studies suggested that stress-induced dynorphin release within the mNAc activates KOR to potentiate cocaine preference by a reduction in 5-HT tone. Consistent with this hypothesis, a transient pharmacological blockade of mNAc 5-HT1B receptors potentiated subsequent cocaine CPP. 5-HT1B is known to be expressed on 5-HT terminals in NAc, and 5-HT1B transcript was also detected in Pdyn+, Adora2a+ and ChAT+ (markers for direct pathway, indirect pathway, and cholinergic interneurons, respectively). Following stress exposure, 5-HT1B transcript was selectively elevated in Pdyn+ cells of the mNAc. These findings suggest that Dyn/KOR regulates serotonin activation of 5HT1B receptors within the mNAc and dynamically controls stress response, affect, and drug reward.

neuroscience↗