Biology subjects

Hyde, E.

Publications and source records attributed to Hyde, E..

6 recordsLinked to original sources

bioRxiv2026

Beyond the Catalytic Serine: Selective Protease Engagement with Covalent Macrocyclic Activity-based Probes

Activity-based probes (ABPs) are widely used to profile serine protease activity - enzymes central to diverse physiological and pathological processes - but most rely on covalent modification of the conserved catalytic serine residue, often resulting in poor selectivity across related proteases. Here, we introduce covalent macrocyclic activity-based probes (cmABPs) that selectively target non-catalytic residues within serine protease active sites. By combining phage display with systematic electrophile scanning, we identify macrocyclic scaffolds that position sulfur(VI) fluoride (SuFEx) electrophiles to covalently engage alternative nucleophiles such as lysine and tyrosine. Applied to plasma kallikrein, this approach yielded a macrocyclic scaffold that was converted into covalent probes via fluorosulfate scanning. Remarkably, small changes in electrophile structure produced large, tuneable differences in covalent kinetics, with benzenesulfonyl fluoride derivative 23 achieving rapid and complete protein modification. Biochemical and mass spectrometry analyses confirmed selective modification of an active-site lysine by 23, along with robust performance in complex biological samples. Extension to urokinase plasminogen activator further demonstrates the generality of this strategy. More broadly, this work establishes electrophile scanning within macrocyclic scaffolds as a general approach for tuning covalent reactivity and provides a blueprint for designing selective probes that move beyond catalytic-residue targeting.

biochemistry↗

bioRxiv2026

IL-2- and IL-4-dependent signaling play separate and sequential roles in the differentiation of GATA3-hi TH2 cells in vivo

Naive CD4+ T cells differentiation into T-helper type 2 (TH2) cells requires Interleukin 2 (IL-2) and IL-4-dependent signaling as well as presentation of allergens by dendritic cells (DCs). The role of IL-2 and IL-4 in TH2 differentiation has been mostly studied in vitro, however, these models do not account for the heterogeneity of TH responses and bypass the DC-derived signals that are necessary in vivo. We used cytokine-blocking antibodies and IL-4RKO/IL-4RWT mixed bone marrow chimeras to show that IL-4 signaling was not required for initial upregulation of GATA3 by CD4+ T cells after intradermal immunization, but was necessary for later TH2 cell expansion and further GATA3 upregulation. Single-cell transcriptomics and computational analyses confirmed that IL-4 signaling was not necessary for TH2 identity but promoted TH2 proliferation and expression of a pathogenic signature. Early IL-2 blockade prevented GATA3 upregulation without affecting TH2 proliferation or the differentiation of TH1 and TFH subsets after immunization. Adoptive transfer experiments showed that reduced competition for IL-4 in vivo drove extensive T cell proliferation and preferential expansion of the GATA3hi population. Overall, our results suggest temporally and functionally distinct roles of IL-2 and IL-4 during TH2 differentiation: IL-2 is necessary for GATA3 upregulation, while IL-4 drives subsequent TH2 proliferation and licensing to effector activity. Therefore, IL-2 and IL-4 act in a co-ordinated manner to respectively promote TH2 differentiation, expansion, and effector commitment in the LN.

immunology↗

bioRxiv2025

PTEN-loss confers dependence on the guanylate synthesis enzyme IMPDH in T-cell acute lymphoblastic leukemia

Loss of the tumor suppressor PTEN is common in T-cell acute lymphoblastic leukemia (T-ALL), and is associated with poor prognosis. PTEN-loss drives robust activation of AKT/mTORC1 signaling to promote leukemic cell growth. We find that PTEN-loss in T-ALL confers dependence on the guanylate nucleotide synthesis enzyme inosine 5-monophosphate dehydrogenase (IMPDH) for cell growth and viability. This metabolic vulnerability is dependent on sustained mTORC1 signaling and can be exploited using clinically approved IMPDH inhibitors to selectively kill PTEN-deficient T-ALL cells, and extend survival in genetic and xenograft T-ALL models in mice. Mechanistically, IMPDH inhibitors cause early DNA replication stress, followed by DNA damage. In contrast to treatment with mTORC1 inhibitors, these events culminate in robust and selective cell death in PTEN-deficient T-ALL cells. These findings reveal a targetable metabolic vulnerability in T-ALL, which could provide rationale for repurposing clinically approved IMPDH inhibitors. Statement of SignificanceWe find that the IMPDH inhibitors mycophenolic acid and mizoribine, which are currently used as well-tolerated immunosuppressants, exert anti-leukemic activity in an aggressive molecular subset of T-ALL cells that are associated with poor prognosis. The use of clinically approved compounds to exploit this vulnerability could lead to rapid drug repurposing.

cancer biology↗

bioRxiv2025

How low temperatures affect long-tailed bat (Chalinolobus tuberculatus) and lesser short-tailed bat (Mystacina tuberculata) activity, central North Island, New Zealand

Bat activity generally increases with temperature, so bat surveys are considered more effective in summer. Less is known about survey effectiveness at low temperatures and whether activity ceases under certain thresholds. Literature provides piecemeal information on winter activity of threatened New Zealand lesser short-tailed bats (Mystacina tuberculata) and long-tailed bats (Chalinolobus tuberculatus), no data exist on lower temperature thresholds below which activity is halted in some regions. We recorded bat echolocation calls over seven nights in winter 2021 to determine whether a lower temperature threshold exists where both species are inactive in the Pikiariki Ecological Area, Pureora Forest Park, central North Island, Aotearoa New Zealand. Long-tailed bat detection rates greatly reduced at <5 {degrees}C, ceasing at <2.6 {degrees}C; at edge sites, long-tailed bats had higher activity rates at higher temperatures, but this pattern did not hold in the forest interior. Lesser short-tailed bats were detected at all sampled temperatures, (1 {degrees}C-10 {degrees}C), 56% of detections occurred at the forest edge; no lower temperature threshold beyond which activity ceased was found. While winter surveys may detect bats, rates are likely lower than in warmer months. Lesser short-tailed bat surveys could be worthwhile in winter due to their broader activity range, depending on the surveys objectives, but should be conducted over extended periods, and any conclusions about the presence or absence of bats made cautiously. Further research is needed to refine lower temperature thresholds and improve winter survey effectiveness.

zoology↗

bioRxiv2023

The Dietary Supplement Taurine Suppresses Ovarian Cancer Growth

Taurine, a non-proteogenic amino acid, and commonly used nutritional supplement can protect various tissues from degeneration associated with the action of the DNA-damaging chemotherapeutic agent cisplatin. Whether and how taurine protects human ovarian cancer (OC) cells from DNA damage caused by cisplatin is not well understood. We have found that OC ascites-derived cells contained significantly more intracellular taurine than cell cultures modeling OC. In culture, elevation of intracellular taurine concentration to OC ascites-cells-associated levels suppressed proliferation of various OC cell lines and patient-derived organoids, reduced glycolysis, and induced cell protection from cisplatin. Taurine cell protection was associated with decreased DNA damage in response to cisplatin. A combination of RNA sequencing, reverse phase protein arrays, live-cell microscopy, flow cytometry, and biochemical validation experiments provided evidence for taurine-mediated induction of mutant- or wild-type p53 binding to DNA, and activation of p53 effectors involved in negative regulation of the cell cycle (p21), and glycolysis (TIGAR). Paradoxically, taurines suppression of cell proliferation was associated with activation of pro-mitogenic signal transduction including ERK, mTOR, and increased mRNA expression of major DNA damage sensing molecules such as DNAPK, ATM and ATR. While inhibition of ERK or p53 did not interfere with taurines ability to protect cells from cisplatin, suppression of mTOR with Torin2, a clinically relevant inhibitor that also targets DNAPK and ATM/ATR, broke taurines cell protection. Our studies implicate that elevation of intracellular taurine could suppress cell growth, metabolism, and activate cell protective mechanisms involving mTOR and DNA damage sensing signal transduction.

cancer biology↗

bioRxiv2021

Placental uptake and metabolism as determinants of pregnancy vitamin D status

Pregnancy 25-hydroxyvitamin D (25(OH)D) concentrations are associated with maternal and fetal health outcomes. Using physiological human placental perfusion and villous explants, we investigate the role of the placenta in regulating the relationships between maternal 25(OH)D and fetal physiology. We demonstrate active placental uptake of 25(OH)D3 by endocytosis, placental metabolism of 25(OH)D3 into 24,25-dihydroxyvitamin D3 and active 1,25-dihydroxyvitamin D [1,25(OH)2D3], with subsequent release of these metabolites into both the maternal and fetal circulations. Active placental transport of 25(OH)D3 and synthesis of 1,25(OH)2D3 demonstrate that fetal supply is dependent on placental function rather than simply the availability of maternal 25(OH)D3. We demonstrate that 25(OH)D3 exposure induces rapid effects on the placental transcriptome and proteome. These map to multiple pathways central to placental function and thereby fetal development, independent of vitamin D transfer. Our data suggest that the underlying epigenetic landscape helps dictate the transcriptional response to vitamin D treatment. This is the first quantitative study demonstrating vitamin D transfer and metabolism by the human placenta, with widespread effects on the placenta itself. These data demonstrate a complex interplay between vitamin D and the placenta and will inform future interventions using vitamin D to support fetal development and maternal adaptations to pregnancy.

physiology↗