Biology subjects

Oba-Shinjo, S. M.

Publications and source records attributed to Oba-Shinjo, S. M..

3 recordsLinked to original sources

bioRxiv2025

Transcriptomic and functional profiling reveal autophagy inhibition and persistent bioenergetic collapse following parallel photodamage to lysosomes and mitochondria

Photodynamic therapy (PDT) using 1,9-dimethyl methylene blue (DMMB) induces coordinated mitochondrial and lysosomal damage and results in strong cellular death induction. However, the underlying transcriptional regulation in response to DMMB remains elusive. We compared the transcriptome response of photoactivated DMMB (paDMMB) to the gene signature triggered by autophagy-modulating agents: rapamycin (an autophagy activator) and bafilomycin A1 (a lysosomal acidification inhibitor). Transcriptome analysis revealed a pronounced transcriptomic response to paDMMB, with 884 differentially expressed genes (DEGs), compared to 291 for bafilomycin and 154 for rapamycin. paDMMB treatment upregulated genes associated with autophagy, mitochondrial stress responses, and proteostasis, while downregulating genes involved in miRNA processing and lipid catabolism. Rapamycin treatment downregulated amino acid biosynthesis pathways, while upregulating processes associated with nutrient starvation. Conversely, bafilomycin treatment upregulated genes related to lipid metabolism, while suppressing cytoskeletal programs. Transcriptomic comparisons revealed a striking overlap (95%) between paDMMB and bafilomycin signatures. Among the several biological processes affected by paDMMB, mitochondrial-related processes were strongly enriched. To determine whether the acute transcriptome changes caused by paDMMB led to persistent functional effects, we stimulated cells with DMMB and assessed mitochondrial respiration after a recovery period. paDMMB reduced basal respiration, ATP production, proton leak, and maximal respiration. These effects were not further altered by bafilomycin co-treatment but were markedly exacerbated by rapamycin. Collectively, we show that paDMMB leads to a transcriptome rewiring, closely resembling autophagy inhibition with a sustained mitochondrial dysfunction. These findings provide a valuable resource to understand the interplay between DMMB-induced lysosomal stress, transcriptional regulation, and PDT.

cell biology↗

bioRxiv2024

Stage-specific phenotypic and transcriptional alterations in keratinocytes exposed to acute and chronic blue light

Despite evidence that visible light (VL) has similar effects on human skin as those of UVA, VL is often viewed as harmless. High SPF sunscreen prevents erythema but can lead to overexposure to UVA and VL, with unknown consequences. To explore the impact of chronic blue light exposure, we irradiated (50 J/cm{superscript 2}, {lambda}= 408 nm, three times a week) human immortalized keratinocytes under acute (3 irradiations), intermediate (14 irradiations), and chronic (42 irradiations) blue-light exposure, monitoring phenotypic and gene expression changes. Chronically exposed keratinocytes exhibit increased nuclei area, chromatin alterations, higher proliferation, and apoptosis resistance, mirroring the consequences of chronic UVA exposure. While acute exposure upregulated keratinization and downregulated tissue repair and apoptosis genes, chronically exposed cells had upregulated genes involved with energy metabolism and oxidative phosphorylation and downregulated genes were enriched for immune and inflammatory responses. Specific transcriptional factors were identified in the acute and chronic stages, some of them had been associated with UVB exposure. We identified some changes in chronically irradiated keratinocytes similar to the malignant transformation, emphasizing the need for further research on the long-term impacts of blue light exposure on human skin.

cell biology↗

bioRxiv2023

ATE1 activates ER-stress and UPR pathways in glioblastoma

Post-translational modifications (PTM) have been recognized as a relevant regulation of key processes in cancer pathophysiology, such as cell migration, adhesion, and proliferation. N-terminal protein arginylation is an emerging PTM involved in tumor progression; however, the mechanisms by which this modification influences these events are poorly understood and vary according to cancer type. Glioblastoma (GBM) is an aggressive intra-axial brain tumor associated with poor prognosis, low survival, and high recurrence rate. We performed a study combining in silico, in vitro, and patients samples analysis to understand the impact of N-terminal protein arginylation in GBM, including overexpression and silencing of ATE1 in GBM-U87MG cell line with RNASeq analysis, immunofluorescence, and validation of the identified targets at the protein level by immunoblotting. The arginylation pattern differed in GBM compared with non-neoplastic brain tissues, and upregulation of ATE1 was associated with increased tumor cell proliferation. We identified a strong activation of the unfolded protein response (UPR) pathway associated with increased ATE1 level, inducing autophagy and not apoptosis. Protein arginylation in GBM proved to be an important mechanism for tumor growth, with the recycling of cell substrates by autophagy, providing fitness for tumor cells. The expressions of the main markers of UPR and autophagy pathways were validated in human GBM samples, reinforcing the role of ATE1 in the most aggressive brain tumor.

cancer biology↗