Jérôme Zoidakis
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View article: A proteomics resource investigating fibrosis: proof-of-concept for identifying novel drug candidates
A proteomics resource investigating fibrosis: proof-of-concept for identifying novel drug candidates Open
View article: Easy Proteomics Sample Preparation: Technical Repeatability and Workflow Optimization Across 8 Biological Matrices in a New Core Facility Setting
Easy Proteomics Sample Preparation: Technical Repeatability and Workflow Optimization Across 8 Biological Matrices in a New Core Facility Setting Open
Bottom‐up proteomics relies on efficient and repeatable sample preparation for accurate protein identification and precise quantification. This study evaluates the performance of adapted SPEED (Sample Preparation by Easy Extraction and Dig…
View article: Computational Drug Repurposing Across the Multiple Myeloma Spectrum: From MGUS to MM
Computational Drug Repurposing Across the Multiple Myeloma Spectrum: From MGUS to MM Open
Background/Objectives: Multiple myeloma (MM) is a challenging, B cell malignancy characterised by the uncontrolled proliferation of plasma cells within the bone marrow. Despite significant advances in treatment options nowadays, MM remains…
View article: A Naturally Occurring Urinary Collagen Type I Alpha 1-Derived Peptide Inhibits Collagen Type I-Induced Endothelial Cell Migration at Physiological Concentrations
A Naturally Occurring Urinary Collagen Type I Alpha 1-Derived Peptide Inhibits Collagen Type I-Induced Endothelial Cell Migration at Physiological Concentrations Open
Collagen type I (COL(I)) is a key component of the extracellular matrix (ECM) and is involved in cell signaling and migration through cell receptors. Collagen degradation produces bioactive peptides (matrikines), which influence cellular p…
View article: Proteomic Analysis of Bone Marrow CD138+ Cells to Identify Proteins Associated With the Response of Multiple Myeloma Patients to Commonly Used Therapeutic Regimens
Proteomic Analysis of Bone Marrow CD138+ Cells to Identify Proteins Associated With the Response of Multiple Myeloma Patients to Commonly Used Therapeutic Regimens Open
Multiple myeloma (MM) remains incurable; gaps in our understanding of MM molecular pathogenesis and drugs’ resistance mechanisms are involved in the failure of therapies. This study aims to identify proteins significantly impacting MM pati…
View article: Profiling Neoadjuvant Therapy Response in Rectal Cancer Using Publicly Available Transcriptomic RNA-seq Datasets
Profiling Neoadjuvant Therapy Response in Rectal Cancer Using Publicly Available Transcriptomic RNA-seq Datasets Open
Neoadjuvant chemoradiotherapy followed by total mesorectal excision is standard for locally advanced rectal cancer, but response varies and current markers are insufficient. This study integrates public bulk RNAseq data to identify predict…
View article: Simple, fast, and reliable analysis of label-free proteomics data with the Proteomics Eye (ProtE)
Simple, fast, and reliable analysis of label-free proteomics data with the Proteomics Eye (ProtE) Open
View article: A naturally occurring urinary collagen type I alpha 1-derived peptide inhibits collagen type I-induced endothelial cell migration at physiological concentrations
A naturally occurring urinary collagen type I alpha 1-derived peptide inhibits collagen type I-induced endothelial cell migration at physiological concentrations Open
Collagen type I (COL(I)) is a key component of the extracellular matrix (ECM) and is involved in cell signalling and migration through cell receptors. Collagen degradation produces bioactive peptides (matrikines), which influence cellular …
View article: A proteomics resource investigating fibrosis: proof-of-concept for identifying novel drug candidates
A proteomics resource investigating fibrosis: proof-of-concept for identifying novel drug candidates Open
View article: Unraveling proteotoxic and oxidative stress - Driven adaptations in multiple myeloma
Unraveling proteotoxic and oxidative stress - Driven adaptations in multiple myeloma Open
View article: The privilege of a new core facility: Optimising technical repeatability and workflow efficiency in proteomics across diverse biological matrices
The privilege of a new core facility: Optimising technical repeatability and workflow efficiency in proteomics across diverse biological matrices Open
View article: Proteome Profiling of Cucurbita pepo Phyllosphere After Infection by Podosphaera xanthii and Application of Reynoutria sachalinensis Extract
Proteome Profiling of Cucurbita pepo Phyllosphere After Infection by Podosphaera xanthii and Application of Reynoutria sachalinensis Extract Open
Podosphaera xanthii is the main causal agent of powdery mildew (PM) disease for Cucurbita pepo. Disease control is attained principally by applications of chemical fungicides, along with parallel use of tolerant crop varieties and alternat…
View article: Tear Proteomics in Children and Adolescents with Type 1 Diabetes: A Promising Approach to Biomarker Identification of Diabetes Pathogenesis and Complications
Tear Proteomics in Children and Adolescents with Type 1 Diabetes: A Promising Approach to Biomarker Identification of Diabetes Pathogenesis and Complications Open
The aim of the current study was to investigate the tear proteome in children and adolescents with type 1 diabetes (T1D) compared to healthy controls, and to identify differences in the tear proteome of children with T1D depending on diffe…
View article: Investigation of the human-gut-kidney axis by fecal proteomics, highlights molecular mechanisms affected in CKD
Investigation of the human-gut-kidney axis by fecal proteomics, highlights molecular mechanisms affected in CKD Open
Collectively, this exploratory fecal proteomic analysis highlighted changes in human and bacterial proteins reflecting inflammation and reduced saccharolytic fermentation in CKD4/CKD1, plausibly affecting the butyrate synthesis pathways in…
View article: #1165 Targeted-release budesonide can preserve the glomerular filtration rate in patients diagnosed with IgA nephropathy after 3 months of administration.
#1165 Targeted-release budesonide can preserve the glomerular filtration rate in patients diagnosed with IgA nephropathy after 3 months of administration. Open
Background and Aims The four-hit hypothesis constitutes the main immunological sequence of the IgA nephropathy (IgAN) pathogenesis. However, the activation of intestinal-renal axis is considered the initial step during IgA nephropathy (IgA…
View article: Complement Cascade Proteins Correlate with Fibrosis and Inflammation in Early-Stage Type 1 Diabetic Kidney Disease in the Ins2Akita Mouse Model
Complement Cascade Proteins Correlate with Fibrosis and Inflammation in Early-Stage Type 1 Diabetic Kidney Disease in the Ins2Akita Mouse Model Open
Diabetic kidney disease (DKD) is characterized by histological changes including fibrosis and inflammation. Evidence supports that DKD is mediated by the innate immune system and more specifically by the complement system. Using Ins2Akita …
View article: Methylenetetrahydrofolate reductase polymorphic variants C677T and A1298C in rectal cancer in Slavic population: significance for cancer risk and response to chemoradiotherapy
Methylenetetrahydrofolate reductase polymorphic variants C677T and A1298C in rectal cancer in Slavic population: significance for cancer risk and response to chemoradiotherapy Open
Background: Methylenetetrahydrofolate reductase (MTHFR) single nucleotide polymorphisms (SNPs) have been suggested as risk, prognostic, and predictive factors for colorectal cancer in various populations, but have not been validated so far…
View article: Performance and Dimensionality of Pretreatment MRI Radiomics in Rectal Carcinoma Chemoradiotherapy Prediction
Performance and Dimensionality of Pretreatment MRI Radiomics in Rectal Carcinoma Chemoradiotherapy Prediction Open
(1) Background: This study aimed to develop a machine learning model based on radiomics of pretreatment magnetic resonance imaging (MRI) 3D T2W contrast sequence scans combined with clinical parameters (CP) to predict neoadjuvant chemoradi…
View article: Dysregulation of transcripts SMAD4-209 and SMAD4-213 and their respective promoters in colon cancer cell lines
Dysregulation of transcripts SMAD4-209 and SMAD4-213 and their respective promoters in colon cancer cell lines Open
Background: The pervasive role of alternative promoters in context-specific isoform expression and the importance of promoter choice over its level of transcriptional activity have been recently implied based on pan-cancer in sil…
View article: A Peripheral Blood Signature of Increased Th1 and Myeloid Cells Combined with Serum Inflammatory Mediators Is Associated with Response to Abatacept in Rheumatoid Arthritis Patients
A Peripheral Blood Signature of Increased Th1 and Myeloid Cells Combined with Serum Inflammatory Mediators Is Associated with Response to Abatacept in Rheumatoid Arthritis Patients Open
Abatacept (CTLA4-Ig)—a monoclonal antibody which restricts T cell activation—is an effective treatment for rheumatoid arthritis (RA). Nevertheless, only 50% of RA patients attain clinical responses, while predictors of response are rather …
View article: Ferroptosis-protective membrane domains in quiescence
Ferroptosis-protective membrane domains in quiescence Open
View article: 3′-tRF-CysGCA overexpression in HEK-293 cells alters the global expression profile and modulates cellular processes and pathways
3′-tRF-CysGCA overexpression in HEK-293 cells alters the global expression profile and modulates cellular processes and pathways Open
View article: Identification of Immune-Based Biomarkers Associated With Response to Abatacept (CTLA4-Ig) in Rheumatoid Arthritis Patients
Identification of Immune-Based Biomarkers Associated With Response to Abatacept (CTLA4-Ig) in Rheumatoid Arthritis Patients Open
Abatacept (CTLA4-Ig) – a monoclonal antibody which restricts T cell activation – is an effective treatment for rheumatoid arthritis (RA). Herein, we aimed to investigate for biomarkers of response to abatacept. We performed a d…
View article: Data-Independent Acquisition Mass Spectrometry Analysis of FFPE Rectal Cancer Samples Offers In-Depth Proteomics Characterization of the Response to Neoadjuvant Chemoradiotherapy
Data-Independent Acquisition Mass Spectrometry Analysis of FFPE Rectal Cancer Samples Offers In-Depth Proteomics Characterization of the Response to Neoadjuvant Chemoradiotherapy Open
Locally advanced rectal cancer (LARC) presents a challenge in identifying molecular markers linked to the response to neoadjuvant chemoradiotherapy (nCRT). This study aimed to utilize a sensitive proteomic method, data-independent mass spe…
View article: Performance and Dimensionality of Pretreatment MRI Radiomics in Rectal Carcinoma Chemoradiotherapy Prediction
Performance and Dimensionality of Pretreatment MRI Radiomics in Rectal Carcinoma Chemoradiotherapy Prediction Open
This study aimed to establish a predictive model for neoadjuvant chemoradiotherapy (nCRT) response in patients with locally advanced rectal carcinoma (LARC) using clinicopathological (CP) features along with radiomics from pretreatment Mag…
View article: Methylenetetrahydrofolate reductase polymorphic variants in rectal cancer: significance for cancer risk and response to chemoradiotherapy
Methylenetetrahydrofolate reductase polymorphic variants in rectal cancer: significance for cancer risk and response to chemoradiotherapy Open
Background Methylenetetrahydrofolate reductase (MTHFR) small nucleotide polymorphisms (SNPs) have been suggested as risk, prognostic, and predictive factors for colorectal cancer in various populations, but have not been validated so far. …
View article: Exploring novel genetic and hematological predictors of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer
Exploring novel genetic and hematological predictors of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer Open
Introduction: The standard treatment for locally advanced rectal cancer (LARC) is neoadjuvant chemoradiotherapy (nCRT). To select patients who would benefit the most from nCRT, there is a need for predictive biomarkers. The aim of this stu…
View article: Tissue proteomics repositories for data reanalysis
Tissue proteomics repositories for data reanalysis Open
We are approaching the third decade since the establishment of the very first proteomics repositories back in the mid‐'00s. New experimental approaches and technologies continuously enrich the field while producing vast amounts of mass spe…
View article: Exploring novel inflammation-related genetic and hematological predictors of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer
Exploring novel inflammation-related genetic and hematological predictors of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer Open
Background The standard initial treatment for locally advanced rectal cancer (LARC) is neoadjuvant chemoradiotherapy (nCRT). In order to select patients who would benefit the most from nCRT, there is a strong need for predictive biomarkers…
View article: Reviewing the Regulators of COL1A1
Reviewing the Regulators of COL1A1 Open
The collagen family contains 28 proteins, predominantly expressed in the extracellular matrix (ECM) and characterized by a triple-helix structure. Collagens undergo several maturation steps, including post-translational modifications (PTMs…