Biology subjects

Baker, I. M.

Publications and source records attributed to Baker, I. M..

4 recordsLinked to original sources

bioRxiv2026

Impact of Aging, Sex, and Species on the mRNA Expression of Matrix Metalloproteinases Following Ischemic Stroke

Matrix metalloproteinase (MMP) expression and function are highly context dependent, varying across physiological and pathological conditions. We previously documented the expression profiles of select MMPs in the ischemic brains of young male rodents. However, aging is a major risk factor for stroke in humans and is associated with vasculature alterations, increased oxidative stress, and elevated inflammation. In addition, sex differences have been reported in stroke incidence and severity. Despite this, the effects of age, sex, and species on brain MMP gene expression after cerebral ischemia/reperfusion (I/R) has not been systematically examined. Therefore, we investigated how age, sex, and species influence the mRNA expression of all known MMPs (22 total) in the brain following cerebral I/R. Moderate-to-severe neurological deficits were induced by transient middle cerebral artery occlusion (MCAO) followed by reperfusion in young and aged male and female C57BL/6 mice and in young male Sprague-Dawley rats. Brain tissue from the ipsilateral (ischemic) hemisphere was collected on post-MCAO day 1, and MMP mRNA levels were quantified by real-time PCR and expressed as fold change relative to the sham control group. Across species, MMP-3, MMP-8, MMP-12, MMP-13, MMP-19, MMP-20, and MMP-27 were upregulated in both rats and mice. Species-specific increases were also observed: MMP-1, MMP-7, MMP-9, MMP-14, MMP-21, and MMP-25 were upregulated only in rats, whereas MMP-10 was upregulated only in mice. The most strongly upregulated MMPs were MMP-12 in rats and MMP-3, MMP-10, and MMP-12 in mice. By contrast, MMP-15 and MMP-17 were downregulated in both species, whereas MMP-23 and MMP-24 were downregulated only in rats and mice, respectively. Within mice, MMP-3, MMP-10, MMP-12, MMP-19, MMP-20, and MMP-21 increased in both sexes and age groups, except for MMP-19 in aged males and MMP-21 in young males. MMP-14 increased only in females (young and aged), whereas MMP-27 increased only in males (young and aged). Notably, MMP-3, MMP-10, and MMP-12 were the three most highly upregulated MMPs in both male and female mice regardless of age. Overall MMP mRNA expression levels were higher in aged male mice and lower in aged female mice relative to sex-matched young mice. Among all MMPs examined, MMP-12 showed the most marked upregulation across species and, within mice, across age groups and sexes. Collectively, these findings demonstrate that brain MMP gene expression after cerebral I/R is modulated by age, sex, and species, underscoring the importance of incorporating these biological variables when targeting MMPs individually or in combination in preclinical rodent stroke models.

neuroscience↗

bioRxiv2025

B7-H3 upregulation in ischemic stroke: friend or foe?

B7-H3 (CD276) is an immune checkpoint co-signaling molecule expressed on immune and non-immune cells. It is best known for suppressing T-cell responses but can also promote inflammation depending on the microenvironment. In neuroinflammatory models such as experimental autoimmune encephalomyelitis, B7H3 expression increases concomitantly with the inflammatory response, and its inhibition is associated with reduced disease progression. Although its role in ischemic stroke remains unclear, we hypothesized that cerebral ischemia/reperfusion (I/R) would upregulate B7-H3 expression in the ischemic brain and that increased B7-H3 expression would positively correlate with pro-inflammatory cytokine expression. Young and aged male and female rodents, including normotensive and spontaneously hypertensive rats to model comorbid hypertension, underwent transient middle cerebral artery occlusion (MCAO) followed by reperfusion. Brain tissue was collected on post-ischemic days 1, 3, 5, or 7. B7-H3 mRNA was analyzed by real-time PCR, whereas protein expression was assessed by Western blotting and immunohistochemistry at selected time points. B7-H3 expression was significantly upregulated in the ischemic brain across sexes, age groups, and species. The extent of B7-H3 degradation in the ischemic brain was influenced by species, sex, age, and time after cerebral I/R. Upregulation of B7-H3 was observed at both the mRNA and protein levels, and increased expression was localized primarily to the somatosensory cortex and caudate putamen in the ipsilateral hemisphere, the main regions affected in this MCAO model. Elevated B7-H3 expression in the ischemic brain positively correlated with the pro-inflammatory mediator TNF. The temporal profile of B7-H3 expression observed in rats paralleled the early inflammatory phase associated with secondary tissue damage following ischemic stroke. These findings identify B7-H3 as an ischemia-induced immune checkpoint molecule in the brain that may modulate post-stroke immune responses and support further investigation into its beneficial versus detrimental roles in neuroinflammation, as well as its potential as a therapeutic target following cerebral I/R.

neuroscience↗

bioRxiv2025

Rapid degradation of 6 class I HDAC complexes reveals minimal functional overlap between complexes

The class 1 HDACs 1, 2 and 3 form seven families of distinct large multiprotein complexes that regulate gene expression via deacetylation of lysines in histone tails. The degree of redundancy and functional overlap between complexes and their primary gene targets, remains unknown. We used CRISPR/Cas9 to independently tag HDAC complexes with FKBP12F36V in HCT116 cells enabling rapid (<1 hr), PROTAC-mediated, degradation. RNA sequencing at 6 h reveals that together, the 4 major complexes (CoREST, NuRD, NCoR/SMRT and SIN3A) perturbed >50% of expressed genes. More than 60% of these are specific to an individual complex. Of genes regulated by more than one complex, approaching 50% are reciprocally regulated such that HDAC complexes act as antagonistic regulators. Homer analysis strongly suggests that the complexes are reliant on different transcription factors. This is the first study to identify the primary targets of individual HDAC complexes and directly compare the effects of rapid degradation on gene regulation in the same biological system.

molecular biology↗

bioRxiv2024

Rapid degradation of Histone Deacetylase 1 (HDAC1) reveals essential roles in both gene repression and active transcription

Histone Deacetylase 1 (HDAC1) removes acetyl groups from lysine residues on the core histones, a critical step in the regulation of chromatin accessibility. Despite histone deacetylation being an apparently repressive activity, suppression of HDACs causes both up- and down-regulation of gene expression. Here we exploited the degradation tag (dTAG) system to rapidly degrade HDAC1 in embryonic stem cells (ESCs) lacking its paralog, HDAC2. Unlike HDAC inhibitors that lack isoform specificity, the dTAG system allowed specific degradation and removal of HDAC1 in <1 hour (100x faster than genetic knockouts). This rapid degradation caused increased histone acetylation in as little as 2 hours, with H2BK5 and H2BK11 being the most sensitive. The majority of differentially expressed genes following 2 hours of HDAC1 degradation were upregulated (275 genes up vs 15 down) with increased proportions of downregulated genes observed at 6 (1,153 up vs 443 down) and 24 hours (1,146 up vs 967 down) respectively. Upregulated genes showed increased H2BK5ac and H3K27ac around their transcriptional start site (TSS). In contrast, decreased acetylation of super-enhancers (SEs) was linked to the most strongly downregulated genes. These findings suggest a paradoxical role for HDAC1 in the maintenance of histone acetylation levels at critical enhancer regions required for the pluripotency-associated gene network.

molecular biology↗