Biology subjects

Marie, S. K. N.

Publications and source records attributed to Marie, S. K. N..

8 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↗

bioRxiv2025

Fractal and Machine Learning analyses of MALDI-TOF Mass Spectrometry data in glioblastoma

Data pre-processing is a critical step in the analysis of MALDI-TOF MS spectra for machine learning applications, typically involving steps such as spectra trimming, baseline correction, smoothing, transformation, and peak picking or spectral binning. While traditional approaches focus on protein/peptide peaks as features, this study explores a novel method of feature extraction by treating MALDI-TOF spectra as time-series data. This study investigates the use of computational fractal-based analysis to assess the complexity of MALDI-TOF spectra. Fractal analysis, previously successful in glioblastoma diagnosis using MRI, was applied here to proteomics data for the first time. By treating each MALDI spectrum as a time series and calculating its fractal dimension using various algorithms, machine learning models were trained to differentiate between glioblastoma patients and healthy controls. We demonstrate that fractals are sufficient to obtain accurate models for glioblastoma diagnosis, despite still underperforming when compared to the traditional feature extraction method. We also show that fractals can be used as support features to increase model performance. This work highlights the potential and limitations of fractal analysis in proteomics, offering a new perspective for disease diagnosis and broadening the applicability of time-series data analysis in mass spectrometry.

bioinformatics↗

bioRxiv2025

Identification of astrocytomas through serum protein fingerprint using MALDI-TOF MS and machine learning

Gliomas account for most brain malignancies, with astrocytomas being the most common subtype. Among these, glioblastoma (GBM) stands out as the most aggressive form, exhibiting a median survival time of just 15 months despite intensive therapy. Current diagnostic practices rely on magnetic resonance imaging (MRI) and histopathological analysis, which often necessitate invasive surgical sampling. This underscores the need for minimally invasive diagnostic tools capable of characterizing glioma progression and guiding treatment strategies. Advances in glioma classification have integrated histological and molecular markers, notably IDH1 mutations, which are prognostically significant, particularly in low-grade gliomas and in the previously defined "secondary GBM" (IDH-mutant astrocytoma grade 4). This study aimed to explore the potential of serum proteomics as a non-invasive diagnostic tool using MALDI-TOF mass spectrometry (MS) combined with machine learning techniques. We analyzed serum samples from 269 patients, employing machine learning models to differentiate between healthy individuals and astrocytoma patients. The MALDI-TOF MS approach achieved a balanced accuracy of 94.5% in distinguishing GBM patients from healthy controls. However, it showed limited efficacy in classifying tumor grades or determining IDH1 mutational status. Further investigation using bottom-up proteomics by GeLC-MS/MS identified potential biomarkers, such as transthyretin, previously associated with high-grade gliomas. These findings highlight the promise of MALDI-TOF MS in identifying serum-based biomarkers for astrocytoma diagnosis. While the results are promising, further validation in independent cohorts is essential to assess the clinical utility of these biomarkers for non-invasive glioma diagnostics and patient monitoring.

systems 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

ST8Sia2 polysialyltransferase protects against infection by Trypanosoma cruzi

Glycosylation is one of the most structurally and functionally diverse co- and post-translational modifications in a cell. Addition and removal of glycans, especially to proteins and lipids, characterize this process which have important implications in several biological processes. In mammals, the repeated enzymatic addition of a sialic acid unit to underlying sialic acids (Sia) by polysialyltransferases, including ST8Sia2, leads to the formation of a sugar polymer called polysialic acid (polySia). The functional relevance of polySia has been extensively demonstrated in the nervous system. However, the role of polysialylation in infection is still poorly explored. Previous reports have shown that Trypanosoma cruzi (T. cruzi), a flagellated parasite that causes Chagas disease (CD), changes host sialylation of glycoproteins. To understand the role of host polySia during T. cruzi infection, we used a combination of in silico and experimental tools. We observed that T. cruzi reduces both the expression of the ST8Sia2 and the polysialylation of target substrates. We also found that chemical and genetic inhibition of host ST8Sia2 increased the parasite load in mammalian cells. These findings suggest a novel approach to interfere with parasite infections through modulation of host polysialylation. AUTHOR SUMMARYGlycosylation is a co- and/or post-translational modification regulated by the addition and removal of glycans. This process shapes the cellular glycome, which in turn, holds significant implications in various biological processes. Trypanosoma cruzi (T. cruzi), the etiological agent of Chagas disease, a globally concerning neglected tropical disease affecting 6 to 8 million individuals worldwide, exerts a profound influence on host glycoprotein sialylation. Remarkably, T. cruzi is incapable of synthesizing sialic acid (Sia) and relies on acquiring it from host glycoconjugates. In mammals, the formation of polysialic acid (polySia) is mediated by polysialyltransferases, such as ST8Sia2. The functional relevance of polySia has been extensively documented in the nervous system. Nevertheless, its role within the context of infectious processes remains largely unexplored. Herein, we demonstrate that in T. cruzi-infected host cells, the expression of the ST8Sia2 enzyme is downregulated, resulting in diminished levels of polysialylation. Furthermore, a reduction in the levels of NCAM1 and SCN5A was observed, which can be attributed to the decreased host polysialylation. Moreover, enzymatic removal of polySia, along with chemical inhibition and genetic silencing of ST8Sia2, led to a marked increase in the number of intracellular parasites. We posit that ST8Sia2 inhibition favors T. cruzi infection, thereby elucidating novel avenues for understanding the mechanisms associated with Chagas disease pathogenesis, prominently featuring the pivotal role of host polysialylation.

microbiology↗

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↗

bioRxiv2022

β-catenin programs a tissue-specific epigenetic vulnerability in aggressive adrenocortical carcinoma

Adrenocortical carcinoma (ACC) is a rare cancer in which tissue-specific differentiation is paradoxically associated with dismal outcomes. The differentiated ACC subtype CIMP-high is prevalent, incurable, and routinely fatal. CIMP-high ACC possess abnormal DNA methylation and frequent {beta}-catenin activating mutations. Here, we demonstrate that ACC differentiation is maintained by a balance between nuclear, tissue-specific {beta}-catenin-containing complexes and the epigenome. On chromatin, {beta}-catenin binds master adrenal transcription factor SF1 and hijacks the adrenocortical super-enhancer landscape to maintain differentiation. Off chromatin, {beta}-catenin binds histone methyltransferase EZH2, which is redistributed by the CIMP-high DNA methylation signature. SF1/{beta}-catenin and EZH2/{beta}-catenin complexes exist in normal adrenals and are selected for through all phases of ACC evolution. Pharmacologic EZH2 inhibition in CIMP-high ACC favors EZH2/{beta}-catenin assembly and purges SF1/{beta}-catenin from chromatin, erasing differentiation and restraining cancer growth in vitro and in vivo. Our studies illustrate how tissue-specific programs shape oncogene selection, surreptitiously encoding targetable therapeutic vulnerabilities.

cancer biology↗

bioRxiv2021

Protein arginylation is regulated during SARS-CoV-2 infection

In 2019, the world witnessed the onset of an unprecedented pandemic. In September 2021, the infection by SARS-CoV-2 had already been responsible for the death of more than 4 million people worldwide. Recently, we and other groups discovered that SARS-CoV-2 infection induces ER-stress and activation of unfolded protein response (UPR) pathway. The degradation of misfolded/unfolded proteins is an essential element of proteostasis and occurs mainly in lysosomes or proteasomes. The N-terminal arginylation of proteins is characterized as an inducer of ubiquitination and proteasomal degradation by the N-end rule pathway. Here we present, for the first time, data on the role of arginylation during SARS-CoV-2 infection. We studied the modulation of protein arginylation in Vero CCL-81 and Calu-3 cells infected after 2h, 6h, 12h, 24h, and 48h. A reanalysis of in vivo and in vitro public omics data combined with immunoblotting was performed to measure the levels of ATE1 and arginylated proteins. This regulation is seen specifically during infections by coronaviruses. We demonstrate that during SARS-CoV-2 infection there is an increase in the expression of the ATE1 enzyme associated with regulated levels of specific arginylated proteins. On the other hand, infected macrophages showed no ATE1 regulation. An important finding revealed that modulation of the N-end rule pathway differs between different types of infected cells. We also confirmed the potential of tannic acid to reduce viral load, and furthermore, to modulate ATE1 levels during infection. In addition, the arginylation inhibitor merbromin (MER) is also capable of both reducing viral load and reducing ATE1 levels. Taken together, these data show the importance of arginylation during the progression of SARS-CoV-2 infection and open the door for future studies that may unravel the role of ATE1 and its inhibitors in pathogen infection.

cell biology↗