Biology subjects

Pastar, I.

Publications and source records attributed to Pastar, I..

4 recordsLinked to original sources

bioRxiv2025

Multi-omics identification of activated T cells and spatial PD-1/PD-L1 signaling as biomarkers of diabetic foot ulcer healing

Diabetic foot ulcers (DFUs) are a common and debilitating complication of diabetes, and amputations from non-healing ulcers carry high morbidity and mortality. A critical need exists for biomarkers that can identify healing potential early and guide targeted interventions. To address this, we applied an integrated multi-omics approach across four patient cohorts comprising 51 DFUs (29 Healing, 22 Non-healing). Bulk RNA-sequencing revealed marked activation of Th1 and Th2 pathways (activation z-score +4.8, p = 3.8x10-{superscript 1}), and immune cell deconvolution predicted higher proportions of T cell populations in Healers. Spatial proteomics in a second cohort identified elevated CD3 T cell density and selective enrichment of PD-1 and PD-L1 expression in vascular niches of the papillary dermis in Healers (p < 0.001). Flow cytometry in a third cohort further demonstrated higher proportions of CD3PD-1 and CD3PD-L1 T cells in Healers compared with Non-healers. Single-cell RNA-sequencing from a fourth cohort showed upregulation of PD-1 and PD-L1 within CD4 T cells from Healers. Complementary immunofluorescence and serological profiling confirmed that both PD-1 and PD-L1 are elevated in tissue and circulating serum of healing DFUs, supporting their potential use as systemic biomarkers. Taken together, vascular-enriched PD-1/PD-L1 signaling and T cell activation were observed in association with healing DFUs, supporting PD-1/PD-L1 as candidate biomarkers in both tissue and blood with potential translational relevance for predicting DFU outcomes and informing precision therapies.

immunology↗

bioRxiv2025

A human ex vivo model of radiation-induced skin injury reveals p53-driven DNA damage signaling and recapitulates a TGFβ fibrotic response

Radiation-induced skin injury is a poorly understood complication affecting cancer patients who undergo radiotherapy, with no current therapies able to prevent or halt its progression to debilitating radiation-induced skin fibrosis (RISF). Addressing the need for clinically relevant human models, this study developed and characterized a human ex vivo skin model that recapitulates the temporal molecular processes of cutaneous radiation injury, as demonstrated through bulk RNA-sequencing and tissue validation studies. Human skin explants subjected to ionizing radiation demonstrated rapid induction of DNA double-strand breaks, followed by a robust, p53-driven transcriptional program involving genes related to cell cycle arrest, apoptosis, and senescence. Over time, the irradiated skin exhibited increasing activation of pro-fibrotic pathways, notably epithelial-mesenchymal transition and TGF{beta}1-mediated signaling. This resulted in upregulation of classic fibrosis markers such as COL1A1, FN1, and increased collagen thickness. Importantly, regulators of the p53 axis, MDM2 and miR-34a, was observed, implicating these factors as potential therapeutic targets to modulate the balance between repair of radiation injury and pathologic fibrosis. Transcriptome analysis of irradiated and non-irradiated breast skin from post-mastectomy patients showed notable concordance of p53 and pro-fibrotic gene signatures comparable to the ex vivo model, underscoring its translational relevance. This work provides a platform for identifying early biomarkers and testing therapeutic strategies to prevent or mitigate cutaneous radiation toxicities, including RISF, beginning with elucidating the dynamic interplay between the p53-mediated DNA damage response and the onset of fibrosis following radiation. Ultimately, this work aims to improve long-term skin health and quality of life for cancer patients. One Sentence SummaryHuman ex vivo skin recapitulates a clinically relevant p53-mediated DNA damage and pro-fibrotic response to radiation.

genomics↗

bioRxiv2022

Urine-derived exosomes from individuals with IPF carry pro-fibrotic cargo.

BackgroundMicroRNAs (miRNA) and other components contained in extracellular vesicles may reflect the presence of a disease. Lung tissue, sputum and sera of individuals with idiopathic pulmonary fibrosis (IPF) show alterations in miRNA expression. We designed this study to test whether urine and/or tissue derived exosomal miRNAs from individuals with IPF carry cargo that can promote fibrosis. MethodsExosomes were isolated from urine (U-IPFexo), lung tissue myofibroblasts (MF-IPFexo), serum from individuals with IPF (n=16) and age/sex-matched controls without lung disease (n=10). We analyzed microRNA expression of isolated exosomes and their in vivo bio-distribution. We investigated the effect on ex vivo skin wound healing and in in vivo mouse lung models. ResultsU-IPFexo or MF-IPFexo expressed miR let-7d, miR-29a-5p, miR 181b-3p and miR-199a-3p consistent with previous reports of miRNA expression obtained from lung tissue/sera from patients with IPF. In vivo bio-distribution experiments detected bioluminescent exosomes in the lung of normal C57Bl6 mice within 5 minutes after intravenous infusion, followed by distribution to other organs irrespective of exosome source. Exosomes labeled with gold nanoparticles and imaged by transmission electron microscopy were visualized in alveolar epithelial type I and type II cells. Treatment of human and mouse lung punches obtained from control, non-fibrotic lungs with either U-IPFexo or MF-IPFexo produced a fibrotic phenotype. A fibrotic phenotype was also induced in a human ex vivo skin model and in in vivo lung models. ConclusionsOur results provide evidence of a systemic feature of IPF whereby exosomes contain pro-fibrotic miRNAs when obtained from a fibrotic source and interfere with response to tissue injury as measured in skin and lung models. FundingThis work was supported in part by Lester and Sue Smith Foundation and The Samrick Family Foundation and NIH grants R21 AG060338 (SE and MKG), U01 DK119085 (IP, RS, MTC).

cell biology↗

bioRxiv2021

Genome-wide, integrative analysis of microRNA-mediated gene regulation in human wounds reveals cooperating microRNAs as therapeutic targets

MicroRNAs (miR) are important posttranscriptional regulators and exhibit a high potential to be utilized in diagnosis and therapy. However, our insufficient knowledge of the miR-mediated gene regulation in human skin wound healing severely hinders the identification of clinically relevant miRs. Here, we performed paired small RNA and long RNA sequencing in human tissue samples, including matched skin and acute wounds collected at each healing stage and chronic non-healing venous ulcers (VU). With integrative small and long RNA-omics analysis, we developed a compendium (https://www.xulandenlab.com/humanwounds-mirna-mrna), which will be an open, comprehensive resource to broadly aid wound healing research. With this first clinical, wound-centric resource of miRs and mRNAs, we identified 17 pathologically relevant miRs that exhibited abnormal VU expression and displayed their targets enriched explicitly in the VU gene signature. Intermeshing regulatory networks controlled by these miRs revealed their high cooperativity in contributing to chronic wound pathology characterized by persistent inflammation and proliferative phase initiation failure. Furthermore, we demonstrated that miR-34a, miR-424, and miR-516, upregulated in VU, cooperatively suppressed keratinocyte growth while promoting inflammatory response. Collectively, our study opens the possibility of developing innovative wound treatment that targets pathologically relevant cooperating miRs to attain higher therapeutic efficacy and specificity.

systems biology↗