Biology subjects

Yuan, J. S.

Publications and source records attributed to Yuan, J. S..

3 recordsLinked to original sources

bioRxiv2025

Activated Notch1 Redirects CD4-Fated CD4+ CD8+ Precursors to the CD8 Lineage During Thymocyte Selection Without Causing T Cell Leukemia

Positive selection of CD4/CD8 double-positive (DP) thymocytes generates helper and cytotoxic T lineages whose CD4 or CD8 co-receptor expression matches their {beta} T cell receptor (TCR{beta}) specificity MHCII or MHCI, respectively. Notch1 signaling is critical for early T cell development and was suggested to regulate CD4/CD8 lineage determination during DP thymocyte selection. However, early studies expressing activated Notch1 in pre-DP progenitors did not resolve this question. Here we showed that CD4-Cre-mediated activation of canonical Rbpj-dependent Notch1 signalling potently skews DP selection to the CD8 lineage. We used a tamoxifen-inducible "time-stamp" model coupled with phenotypic staging to show that that activated Notch1 decreases generation of Gata3+ CD4+CD8lo selection intermediates during the earliest stages of DP selection, thereby preventing ThPOK induction and emergence of CD4 lineage cells. Finally, activated Notch1 efficiently re-directed DP thymocytes expressing MHCII-specific TCR{beta} into the CD8 lineage. These studies show that activated Notch1 acts early during DP selection to skew selection of CD4-fated, MHCII-specific DP precursors to the CD8 lineage.

immunology↗

bioRxiv2023

Functional microRNA-Targeting Drug Discovery by Graph-Based Deep Learning

MicroRNAs are recognized as key drivers in many cancers, but targeting them with small molecules remains a challenge. We present RiboStrike, a deep learning framework that identifies small molecules against specific microRNAs. To demonstrate its capabilities, we applied it to microRNA-21 (miR-21), a known driver of breast cancer. To ensure the selected molecules only targeted miR-21 and not other microRNAs, we also performed a counter-screen against DICER, an enzyme involved in microRNA biogenesis. Additionally, we used auxiliary models to evaluate toxicity and select the best candidates. Using datasets from various sources, we screened a pool of nine million molecules and identified eight, three of which showed anti-miR-21 activity in both reporter assays and RNA sequencing experiments. One of these was also tested in mouse models of breast cancer, resulting in a significant reduction of lung metastases. These results demonstrate RiboStrikes ability to effectively screen for microRNA-targeting compounds in cancer.

cancer biology↗

bioRxiv2019

Chlamydomonas sp. UWO241 exhibits high cyclic electron flow and rewired metabolism under high salinity

The Antarctic green alga Chlamydomonas sp. UWO241 (UWO241) was isolated from the deep photic zone of a permanently Antarctic ice-covered lake. Adaptation to permanent low temperatures, hypersalinity, and extreme shade has resulted in survival strategies in this halotolerant psychrophile. One of the most striking phenotypes of UWO241 is an altered photosystem I (PSI) organization and constitutive PSI cyclic electron flow (CEF). To date, little attention has been paid to CEF during long-term stress acclimation and the consequences of sustained CEF in UWO241 are not known. In this study, we combined photobiology, proteomics, and metabolomics to understand the underlying role of sustained CEF in high salinity stress acclimation. High salt-grown UWO241 exhibited increased thylakoid proton motive flux and an increased capacity for NPQ. A Bestrophin-like Cl- channel was identified in the whole cell proteomes and transcriptome of UWO241 which likely supports ion homeostasis during high transthylakoid pH. Under high salt, a significant proportion of the upregulated enzymes were associated with the Calvin Benson Bassham Cycle (CBB), secondary metabolite biosynthesis, and protein translation. Two key enzymes of the Shikimate pathway, DAHP synthase and chorismate synthase, were also upregulated, as well as indole-3-glycerol phosphate synthase, an enzyme involved in biosynthesis of L-tryptophan and indole acetic acid. In addition, several compatible solutes (glycerol, proline and sucrose) accumulated to high levels in high salt-grown UWO241 cultures. We suggest that UWO241 maintains constitutively high CEF with associated PSI-cytb6f supercomplex to support robust growth and strong photosynthetic capacity under a constant growth regime of low temperatures and high salinity.

plant biology↗