Biology subjects

O'Sullivan, L.

Publications and source records attributed to O'Sullivan, L..

4 recordsLinked to original sources

bioRxiv2026

Pharmacologic DPP-4 inhibition promotes CD8⁺ T cell metabolic fitness to enhance anti-tumor activity

Metabolic dysfunction is a hallmark of CD8+ T cell exhaustion in the tumor microenvironment. Thus, there is growing interest in developing strategies that enhance anti-tumor functions of CD8+ T cells via metabolic reprogramming. Here, we identify dipeptidyl peptidase 4 (DPP-4) as a previously unknown regulator of CD8+ T cell function and metabolism. We discovered that DPP-4 is upregulated in exhausted CD8+ T cells. Pharmacological inhibition of DPP-4 with the FDA-approved anti-diabetic drug sitagliptin transcriptionally and metabolically reprogrammed CD8+ T cells, increasing spare mitochondrial respiratory capacity, proliferation, cytotoxic mediator production, and antigen-specific cancer cell killing capability. The functional effects of sitagliptin were dependent on upregulation of glutamate decarboxylase 1 (GAD1), an enzyme that feeds glutamate into the tricarboxylic acid (TCA) cycle, highlighting a new role for GAD1 in CD8+ T cell respiration and proliferation. We found that systemic inhibition of DPP-4 in preclinical mouse glioblastoma (GBM) models prolongs survival in a CD8+ T cell-dependent manner, and retrospective clinical cohort analysis revealed better outcomes in GBM patients using DPP-4 inhibitors. Importantly, preconditioning of Chimeric Antigen Receptor (CAR) T-cells with DPP-4 inhibition enhanced their cytotoxicity, persistence, and therapeutic efficacy in pediatric GBM. Together, our findings provide mechanistic and biological rationale for repurposing readily accessible DPP-4 inhibitors to enhance anti-tumor CD8+ T cell responses.

immunology↗

bioRxiv2025

Whole genome sequencing of pre-treatment and post-treatment locally advanced rectal cancer using long and short read technologies

We performed Illumina short-read and nanopore (ONT) whole genome sequencing (WGS) on samples obtained from a 37-year-old patient with locally advanced rectal cancer who did not respond to neoadjuvant chemoradiotherapy (nCRT). Pre-treatment and post-nCRT tumour biopsy, adjacent normal tissue, and matched pre-treatment blood samples were sequenced to identify somatic alterations. We used DNA methylation from ONT WGS to detect changes in the tumour epigenomes compared to adjacent normal tissue. We employed established pipelines for the identification of somatic alterations to assess the concordance of SNV, short indel, copy number and structural variation from the short-read and long-read tumour genome data. Overall, 69.4% and 30.1% SNVs were concordant between technologies in the pre- and post-treatment tumours, respectively. A multinomial logistic regression was performed to further understand discordant SNV calls, highlighting tumour purity, presence in a repetitive region, strand bias, and germline variant allele frequency as factors contributing to discordance. Indel concordance was poor (26.8% and 9.2% in the pre- and post-treatment tumour, respectively). Copy number alteration profiles were highly similar while minimal concordance was reported for structural variants (2.4% and 0.3% for pre- and post-treatment tumours, respectively). Finally, we used the ONT data to detect DNA modifications (5-methylcytosine and 5-hydroxymethylcytosine) between tumour and matched adjacent normal tissue. Based on genome-wide average CpG modification rates, global hypomethylation was observed in tumours compared to adjacent normal tissues. Biologically relevant epigenomic changes related to epithelial-mesenchymal transition were detected in the post-treatment tumour, as well as potential radiation-induced changes in the post-treatment adjacent normal tissue.

genomics↗

bioRxiv2024

Early Intervention with Low-Dose Sclerostin Antibody Therapy can Reduce Osteocyte-mediated Secondary Mineralization after initial bone loss in Ovariectomised Rats

Neutralizing sclerostin antibodies (Scl-Ab) mitigate bone loss and promote bone formation to address fracture risk in postmenopausal osteoporosis. Clinically, this treatment is administered monthly for women at high risk of fragility fractures, who are often years into menopause. Preclinical studies have demonstrated that dampening of bone formation occurs with continuous dosing at supraphysiological doses. Osteoporotic bone loss occurs rapidly during early menopause, followed by longer-term changes in bone mineralization and osteocyte activity. Whether earlier administration of lower-exposure Scl-Ab can mitigate bone loss and osteocyte-driven secondary mineralisation is unknown. The objective of this study was to evaluate the effects of early intermittent low-dose Scl-Abon: (1) osteoclastogenesis and bone resorption, (2) perilacunar remodelling, (3) secondary mineralization, and (4) osteocyte mechanosensitivity. Female retired breeder Wistar rats underwent bilateral ovariectomy and received monthly low-dose Scl-Ab injections (2 mg/kg/month) from 3 to 14 weeks post-OVX, while a control group remained untreated. Early intermittent low-dose Scl-Ab treatment increased bone formation and reduced osteoclastogenesis and catabolic gene expression ((Sost, Ctsk, Mmp9) compared to untreated rats. Treatment also decreased the percentage of empty lacunae and the number of MMP14+ osteocytes, accompanied by lower perilacunar mineral density and smaller lacunar size, indicating improved osteocyte survival and reduced perilacunar remodelling. Conversely, expression of osteocyte-mediated mineralization genes (DMP1, PHEX, OPN, ALP) and mechanotransduction-related genes (Vcl, integrins 5, V, {beta}1, CX43, Axin2, IFT88, Adcy6, Pkd1, Cav1) were reduced. Together, these findings suggest that early intermittent low-dose Scl-Ab therapy promotes surface bone formation while attenuating osteocyte-mediated secondary mineralization after initial bone loss. Mini AbstractEarly intermittent low-dose sclerostin antibody treatment reduced osteoclastogenesis, bone resorption, and perilacunar remodelling, while promoting bone formation, decreasing osteocyte apoptosis, and downregulating genes associated with secondary mineralization and mechanosensitivity in ovariectomized rats. These findings suggest early intervention with Scl-Ab enhances bone formation and limits osteocyte apoptosis and subsequent secondary mineralization.

molecular biology↗

bioRxiv2021

Amino acid availability determines plant immune homeostasis in the rhizosphere microbiome

Microbes possess conserved microbe-associated molecular patterns (MAMPs) such as flagellin that are recognized by plant receptors to induce immunity. Despite containing the same MAMPs as pathogens, commensals thrive in the plant rhizosphere microbiome indicating they must suppress or evade host immunity. The beneficial bacteria Pseudomonas capeferrum WCS358 can suppress Arabidopsis root immunity via acidification by secreting gluconic acid. While gluconic acid is sufficient to suppress immunity, we found that it is not necessary in a second beneficial strain Pseudomonas simiae WCS417, which produces more gluconic acid than WCS358. To uncover mechanisms that contribute to the suppression of Arabidopsis immunity, we performed a forward genetic screen in EMS-mutagenized P. simiae WCS417 using a flagellin-inducible CYP71A12pro:GUS reporter as an Arabidopsis immune readout. We identified a mutant that cannot suppress flagellin-elicited CYP71A12pro:GUS expression or acidify the rhizosphere. Next generation sequencing revealed a mutation in the catabolic site of an ornithine carbamoyltransferase argF, which is required for arginine biosynthesis. The mutant could be complemented by expression of argF from a plasmid, and a {Delta}argF mutant could not suppress immunity. Fungal pathogens can use alkalization through production of ammonia and glutamate, the arginine biosynthetic precursors, to promote their own growth and virulence. Therefore, we hypothesized that the biosynthesis of specific amino acids may be necessary to reduce levels of ammonia and glutamate to prevent rhizosphere alkalization and bacterial overgrowth. Genetically blocking arginine, glutamine, or proline biosynthesis, or by adding corresponding exogenous amino acids, resulted in rhizosphere alkalization. Interestingly, exogenous amino acids caused bacterial overgrowth in a gluconic acid-deficient mutants. Our findings show that bacterial amino acid biosynthesis contributes to acidification by preventing accumulation of glutamate precursors and the resulting alkalization. Collectively this work shows that by regulating nutrient availability, plants have the potential to regulate their immune homeostasis in the rhizosphere microbiome.

microbiology↗