Biology subjects

Dao, K.

Publications and source records attributed to Dao, K..

6 recordsLinked to original sources

bioRxiv2025

Rapid Liquid Chromatography-Mass Spectrometry (rLC-MS) for Deep Metabolomics Analysis of Population Scale Studies

Mass spectrometry (MS)-based metabolomics is a key technology for the interrogation of exogenous and endogenous small molecule mediators that influence human health and disease. To date, however, low throughput of MS systems have largely precluded large-scale metabolomics studies of human populations, limiting power to discover physiological roles of metabolites. Here, we introduce a fully automated rapid liquid chromatography-mass spectrometry (rLC-MS) system coupled to an AI-enabled computational pipeline that enables high-throughput, reproducible, non-targeted metabolite measurements across tens of thousands of samples. This system captures thousands of polar, amphipathic and nonpolar (lipid) metabolites in a human plasma sample in 53 seconds of analytical time, enabling analysis of greater than 1,000 samples per day per instrument. To demonstrate the discovery power of the rLC-MS platform, a subset of samples from Sapients DynamiQ biorepository - comprised of 62,039 total plasma samples collected longitudinally from 11,045 individuals - were selected for deep analysis by rLC-MS to capture a rich, dynamic landscape of chemical variation that reflects both physiological processes and environmental influences. 26,042 plasma samples with matched real-world data (RWD) were chosen for the study, representing 6,935 individuals with diverse demographic backgrounds and disease profiles. Unbiased exploratory analysis revealed human metabotypes that correlate with heterogenous disease phenotypes, including key sub-populations of cardiometabolic and other human diseases. Moreover, a metabolic aging clock machine learning model trained on healthy individuals in this dataset accurately predicted accelerated aging in various chronic diseases, with dynamic reversal of metabolic aging following definitive therapy. These data demonstrate that the rLC-MS platform enables prediction of clinically relevant physiological states from plasma metabolomics at scale in human populations.

biochemistry↗

bioRxiv2024

U-rich elements drive pervasive cryptic splicing in 3' UTR massively parallel reporter assays

Non-coding RNA sequences play essential roles in orchestrating gene expression. However, the sequence codes and mechanisms underpinning post-transcriptional regulation remain incompletely understood. Here, we revisit the finding from a prior massively parallel reporter assay (MPRA) that AU-rich (U-rich) elements in 3 untranslated regions (3 UTRs) can drive upregulation or downregulation of mRNA expression depending on 3 UTR context. We unexpectedly discover that this variable regulation arises from widespread cryptic splicing, predominately from an unannotated splice donor in the coding sequence of GFP to diverse acceptor sites in reporter 3 UTRs. Splicing is activated by U-rich sequences, which function as potent position-dependent regulators of 5 and 3 splice site choice and overall splicing efficiency. Splicing has diverse impacts on reporter expression, causing both increases and decreases in reporter expression via multiple mechanisms. We further provide evidence that cryptic splicing impacts between 10 to 50% of measurements made by other published 3 UTR MPRAs. Overall, our work emphasizes U-rich sequences as principal drivers of splicing and provides strategies to minimize cryptic splicing artifacts in reporter assays.

biochemistry↗

bioRxiv2022

Establishment and Characterization of Novel Canine Organoids with Organ-Specific Physiological Similarity

Organoids are 3-dimensional (3D) stem cell-derived cell culture lines that offer a variety of technical advantages compared to traditional 2-dimensional (2D) cell cultures. Although murine models have proved useful in biomedical research, rodent models often fail to adequately mimic human physiology and disease progression, resulting in poor preclinical prediction of therapeutic drug efficacy and toxicity. With the advent of organoid technology, many of these challenges can be overcome. Previously, the use of canine organoids in drug testing and disease modeling was limited to organoids originating from the intestine, liver, kidney, lung, and urinary bladder. Here, we report the cultivation, maintenance, and molecular characterization of two novel adult-stem cell-derived canine organoid cell lines, including the endometrium and pancreas, in addition to previously reported bladder, lung, and liver organoids from two genetically related canines. Five tissues and organoid lines from each donor were characterized using bulk RNA-seq, allowing for a unique, multi-organ comparison between these two individuals and identification of specific cell types such as glandular epithelial cells in endometrial organoids.

genetics↗

bioRxiv2022

Riboflavin Depletion Promotes Longevity and Metabolic Hormesis in Caenorhabditis elegans

Riboflavin is an essential cofactor in many enzymatic processes and in the production of flavin adenine dinucleotide (FAD). Here we report that the partial depletion of riboflavin through knockdown of the C. elegans riboflavin transporter 1 (rft-1) promotes metabolic health by reducing intracellular flavin concentrations. Knockdown of rft-1 significantly increases lifespan in a manner dependent on FOXO/daf-16, AMP-activated protein kinase (AMPK)/aak-2, the mitochondrial unfolded protein response, and mTOR complex 2 (mTORC2). Riboflavin depletion promotes altered energetic and redox states and increases adiposity, independent of lifespan genetic dependencies. Riboflavin depleted animals also exhibit activation of caloric restriction reporters without a reduction in TORC1 signaling. Our findings indicate that riboflavin depletion activates an integrated, hormetic response that promotes lifespan and healthspan in C. elegans.

genetics↗

bioRxiv2021

Ether Lipid Biosynthesis Promotes Lifespan Extension and Enables Diverse Prolongevity Paradigms

Biguanides, including the worlds most commonly prescribed drug for type 2 diabetes, metformin, not only lower blood sugar, but also promote longevity in preclinical models. Epidemiologic studies in humans parallel these findings, indicating favorable effects of metformin on longevity and on reducing the incidence and morbidity associated with aging-related diseases. In spite of this promise, the full spectrum of molecular effectors responsible for these health benefits remains elusive. Through unbiased screening in C. elegans, we uncovered a role for genes necessary for ether lipid biosynthesis in the favorable effects of biguanides. We demonstrate that biguanides prompt lifespan extension by stimulating ether lipid biogenesis. Loss of the ether lipid biosynthetic machinery also mitigates lifespan extension attributable to dietary restriction, target of rapamycin (TOR) inhibition, and mitochondrial electron transport chain inhibition. A possible mechanistic explanation for this finding is that ether lipids are required for activation of longevity-promoting, metabolic stress defenses downstream of the conserved transcription factor Nrf2/skn-1. In alignment with these findings, overexpression of a single, key, ether lipid biosynthetic enzyme, fard-1/FAR1, is sufficient to promote lifespan extension. These findings illuminate the ether lipid biosynthetic machinery as a novel therapeutic target to promote healthy aging.

genetics↗

bioRxiv2021

CULTURE AND MAINTENANCE OF URINE-DERIVED, 3-DIMENSIONAL CANINE TRANSITIONAL CELL CARCINOMA ORGANOIDS

Bladder cancer is the ninth most common malignancy in the world. Transitional cell carcinoma (TCC), also referred to as urothelial carcinoma (UC) is the most common form of bladder cancer, occurring in 90% of cases. In this study, we explore urine-derived, 3-dimensional, canine TCC organoids as a possible model to study bladder TCC ex vivo. After establishing the cell lines, we subjected the 3D cells to RNA in situ hybridization (RNA-ISH) and cell viability assays. Overall, 3D cell culture from urine samples of TCC diagnosed canines expressed RNA biomarkers in a similar manner to parent tumors via RNA-ISH and showed more sensitivity to cisplatin treatment when compared to 2D human TCC cells. With further experimentation, canine TCC organoids could become an ideal model to study TCC ex vivo.

cancer biology↗