Biology subjects

Clark, Z.

Publications and source records attributed to Clark, Z..

5 recordsLinked to original sources

bioRxiv2026

Metformin Redirects Autophagy from Bulk Turnover to Mitochondrial Clearance

Metformin is the most widely prescribed antidiabetic drug and an active candidate for repurposing in oncology. How it engages autophagy - a pathway central to both its metabolic and its anti-tumor effects - has remained unresolved, with reports of induction, suppression, and no effect. Here we show that metformin reroutes rather than induces or inhibits autophagy in human cancer cells: at therapeutic concentrations, it suppresses bulk cytosolic turnover by selectively blocking WIPI2-mediated phagophore tethering, while the ULK1 initiation complex relocates toward mitochondria and engages selective mitochondrial clearance. We trace this redirection to mitochondrial complex I inhibition, registered as a shift in the NAD+/NADH ratio before any change in the adenylate pool, and to a non-canonical reprogramming of the ULK1 complex that operates independently of mTORC1 and of the proposed PEN2-lysosomal route. AMPK is engaged in a subunit-specific manner that restrains ATG13 at initiation and enables WIPI2 displacement at maturation. The ULK1 complex is therefore the node at which metformin sets autophagic substrate selection, with direct implications for combination therapy in diabetes and cancer.

cell biology↗

bioRxiv2025

Non-Contrast microCT Analysis of Obese Adipose in Response to Cold-Exposure Reveals Sex-Specific Alterations

In 2020, it was reported that obesity in the United States had increased by 12% from 1999 to 2018. While exercise and diet are optimal lifestyle modifications to curb obesity, drug-based therapeutics focus on glucagon-like peptide (GLP) modifiers. Alternatively, current research suggests that a specialized type of adipose, called thermogenic adipose, may help protect against obesity. Active thermogenic adipose can metabolize free fatty acids (FFAs) and carbohydrates to carry out non-shivering thermogenesis (NST), potentially providing a method for reducing excess energy stores. While brown adipose tissue (BAT) provides the primary thermogenic response, we hypothesized that exposing diet-induced obese (DIO) mice to colder temperatures would also diminish white adipose tissue (WAT) depots and suppress their inflammatory signature. To measure adipose response to cold in vivo, we applied a non-contrast microCT ({micro}CT) imaging analysis. Male and female mice were housed at thermoneutrality (TN) and fed a Western-style diet (WD) ad lib until they became obese. Once they reached this stage, the mice were subjected to a thermalshift (TS) and exposed to either room temperature (RT) of 22{degrees}C or a colder temperature of 18{degrees}C. The adipose response was then assessed in post-exposure tissues by histological analysis, proteomics, and molecular characterization to correlate phenotypic changes with our {micro}CT findings. Results from this analysis revealed a sex-specific response to cold exposure: thermogenic adipose was predominantly formed in the interscapular BAT (iBAT) of male mice, while female mice showed formation in their perigonadal WAT (pgWAT) and iBAT when exposed to 18{degrees}C. Furthermore, male mice exhibited a decline in serum glucose levels when subjected to 18{degrees}C, which was increased in TS female mice. Serum-free fatty acids (FFAs) were unaffected by either sex across different environmental conditions. Importantly, using a mass-spectrometry-based approach, we detected a reduction in pro-inflammatory cytokines in the conditioned media (CM) of pgWAT and iBAT from TS male mice compared to TN DIO male mice. Overall, our studies demonstrated a new {micro}CT-based analytical method to detect changes in obese adipose tissue and highlighted unique sex-specific responses to environmental exposure. Our findings suggest that thermogenic adipose may offer a promising avenue for combating obesity and reducing its pathologic characteristics.

cell biology↗

bioRxiv2024

Analysis of FAIMS for the Study of Affinity-Purified Protein Complexes Using the Orbitrap Ascend Tribrid Mass Spectrometer

In this study, we analyzed the combination of affinity purification mass spectrometry (AP-MS) with high-field asymmetric waveform ion mobility spectrometry (FAIMS), integrated between nanoLC-MS and an Orbitrap Ascend Tribrid Mass Spectrometer. Our primary objective was to evaluate the application of the FAIMS interface for detecting affinity purified SAP25 protein complexes with enhanced sensitivity and robustness. As a result, we observed that nanoLC-FAIMS-MS (with FAIMS) significantly improved the sensitivity and detection limits at the protein level, peptide level and significantly reduced chemical contaminants compared to nanoLC-MS alone without FAIMS (No FAIMS). This FAIMS configuration resulted in 42% and 92% increases for the total proteins and unique proteins, respectively, and 44% and 88% increases for total peptides and unique peptides compared to the No FAIMS configuration. Our in-depth comparison of FAIMS and No FAIMS shows that FAIMS outperforms by significantly reducing the missing value by <15% in datasets and plays a significant role in filtering chemical contaminants. Our findings highlight the potential of FAIMS with Orbitrap Ascend Tribrid Mass Spectrometer to enhance the depth of AP-MS analysis. The data were deposited with the MASSIVE repository with the identifier MSV000096548.

systems biology↗

bioRxiv2023

Running to remember: The effects of exercise on perineuronal nets, microglia, and hippocampal angiogenesis in female and male mice

Exercise is accepted as a positive health behaviour; however, the mechanisms of exercise on neuroprotection and cognitive health are not completely understood. The purpose of this study was to explore the neurobiological benefits of chronic treadmill exercise in female and male mice through its role in microglial content and morphology, cerebral vascularization, and perineuronal net (PNN) expression. We further examined how these neurobiological changes relate to spatial memory outcomes. Adult mice were assigned to a sedentary or treadmill exercise group for eight weeks. During the final week, all mice were trained on a spatial memory task (Barnes maze) and brains were collected for immunohistochemistry. Exercised mice made fewer errors than sedentary mice during the first two days of training and probe trial. Females, regardless of exercise training, made fewer errors during Barnes maze training and demonstrated a greater frequency of spatial strategy use compared to males. Exercised mice, regardless of sex, had fewer PNNs in the dentate gyrus of the hippocampus compared to sedentary controls. The number of PNNs in the dorsal dentate gyrus was positively correlated with total errors during training. During the probe, greater errors correlated with more PNNs among the exercised group only. Microglia count and cerebral vascularization were not affected by exercise, although proportions of microglia type (ameboid, stout/thick, and thick/thin) were regulated by exercise in the ventral dentate gyrus. We conclude that exercise decreases PNNs in the dentate gyrus in both sexes and this may be related to better spatial learning and memory.

neuroscience↗

bioRxiv2022

An endogenous Rtn4/Nogo-interacting micropeptide that modulates synaptic plasticity with age.

Micropeptides, encoded from small open reading frames of 300 nucleotides or less, are hidden throughout mammalian genomes, though few functional studies of micropeptides in the brain are published. Here, we describe a micropeptide known as the Plasticity -Associated Neural Transcript Short (Pants), located in the 22q11.2 region of the human genome, the microdeletion of which conveys a high risk for schizophrenia. Our data show that Pants is upregulated in early adulthood in the mossy fiber circuit of the hippocampus, where it exerts a powerful negative effect on long-term potentiation (LTP). Further, we find that Pants is secreted from neurons, where it associates with synapses but is rapidly degraded with stimulation. Pants dynamically interacts with Rtn4/Nogo-A, a well-studied regulator of adult plasticity. Pants interaction with Nogo-A augments its influence over postsynaptic AMPA receptor clustering, thus gating plasticity at adult synapses. This work shows that neural micropeptides can act as architectural modules that increase the functional diversity of the known proteome.

neuroscience↗