A field guide to the proteomics of post-translational modifications in DNA repair

Cryogenic mouse tissue homogenization as an alternative to fresh-frozen biopsy use for genomics, transcriptomics, proteomics and metabolomics

The classical approach of using adjacent pieces of fresh-frozen tissue for various omics analysis from the same sample possesses a risk of biological mismatch between arising from intrinsic tissue heterogeneity. We propose an alternative approach of tissue cryogenic pulverization and lyophilization before distribution for omics studies for a more reliable analysis. Here, we compare individual omics layer readouts from fresh-frozen adjacent tissue pieces and homogenized powder in mouse brain, kidney, and liver. Genomics, transcriptomics, proteomics, and metabolomics analyses showed comparable RNA integrity, DNA methylation, and coverage of transcripts, proteins, and metabolites across both methods. Moreover, the homogenized-lyophilized powder usage led to reduced heterogeneity between biological replicates. We conclude that the cryogenically pulverized-lyophilized tissue approach not only maintains a critical molecular feature coverage and quality but also provides a homogenous basis for various omics analysis enhancing reproducibility, sample transport, storage and enabling multi omics base on one and the same tissue aliquot.

Skin Fibroblasts from Individuals Self-Diagnosed as Electrosensitive Reveal Two Distinct Subsets with Delayed Nucleoshuttling of the ATM Protein in Common

Electromagnetic hyper-sensitivity (EHS) and its causal link with radio-frequencies raise a major question of public health. In the frame of the clinical study DEMETER, 26 adult volunteers self-diagnosed as EHS-positive agreed to reply to a self-assessment questionnaire and to provide a skin biopsy sampling to establish a primary fibroblast cell line. The questionnaire and the biological data revealed, independently, 2 subsets of donors associated each with a low background, highly responsive (LBHR) and a high background, lowly responsive (HBLR) phenotype. A couple of subsets based on questionnaire data and based on the yield of spontaneous DNA double-strand breaks were found to be composed of the same donors at 64% identity. After exposure to X-rays, and application of anti-γH2AX, pATM, and MRE11 immunofluorescence, all the DEMETER fibroblasts (26/26) elicited a delayed radiation-induced ATM nucleoshuttling (RIANS). The use of RIANS biomarkers showed that the 2 phenotypes described above corresponded to DEMETER donors with a high risk of cancer (LBHR) or high risk of accelerated aging (HBLR). By exposing DEMETER cells to H2O2 followed by an antioxidative agent, we confirmed that EHS may be related to the management of DNA strand breaks. A preliminary molecular model of EHS inspired by the RIANS model was proposed.

N4-acetylcytidine and other RNA modifications in epitranscriptome: insight into DNA repair and cancer development

N4-acetylcytidine (ac4C) is a post-transcriptional RNA modification that plays a crucial role in the epitranscriptome, influencing gene expression and cellular function. This modification occurs at the cytosine base, where an acetyl group is installed to the nitrogen at the 4th position (N4). This co-transcription modification affects RNA stability, RNA structure, and translation efficiency. Recent studies have uncovered a potential link between RNA modifications and DNA repair mechanisms, suggesting that ac4C-modified or methylated RNAs may interact with factors involved in DNA repair pathways; thus, influencing the cellular response to DNA damage. Dysregulation of modified RNAs, including ac4C RNA, has been implicated in cancer development, where aberrant levels of these RNAs may contribute to oncogenic transformation by altering genome stability and the expression of key genes regulating cell proliferation, cell cycle progression, and apoptosis. Understanding the dynamics of modified RNAs offers promising insights into the role of epitranscriptome in DNA repair processes and cancer treatment.

The main sources of molecular organization in the cell. Atlas of self-organized and self-regulated dynamic biostructures

One of the most important goals of contemporary biology is to understand the principles of the molecular order underlying the complex dynamic architecture of cells. Here, we present an overview of the main driving forces involved in the cellular molecular complexity and in the emergent functional dynamic structures, spanning from the most basic molecular organization levels to the complex emergent integrative systemic behaviors. First, we address the molecular information processing which is essential in many complex fundamental mechanisms such as the epigenetic memory, alternative splicing, regulation of transcriptional system, and the adequate self-regulatory adaptation to the extracellular environment. Next, we approach the biochemical self-organization, which is central to understand the emergency of metabolic rhythms, circadian oscillations, and spatial traveling waves. Such a complex behavior is also fundamental to understand the temporal compartmentalization of the cellular metabolism and the dynamic regulation of many physiological activities. Numerous examples of biochemical self-organization are considered here, which show that practically all the main physiological processes in the cell exhibit this type of dynamic molecular organization. Finally, we focus on the biochemical self-assembly which, at a primary level of organization, is a basic but important mechanism for the order in the cell allowing biomolecules in a disorganized state to form complex aggregates necessary for a plethora of essential structures and physiological functions. In total, more than 500 references have been compiled in this review. Due to these main sources of order, systemic functional structures emerge in the cell, driving the metabolic functionality towards the biological complexity.

A Mass Spectrometry-Based Proteomics Workflow for Concurrent Profiling of Protein Thiol Oxidation and Phosphorylation

Multiple types of protein posttranslational modifications (PTMs) play vital roles in the regulation of normal cellular functions and pathogenesis. Two of the most relevant and well-studied PTMs are protein thiol oxidation (redox) and phosphorylation. Both processes involve the reversible addition of a chemical group to a specific amino acid residue, altering the protein activity, stability, or interaction with other molecules. Environmental stressors are known to trigger rapid and dynamic regulation of both thiol oxidation and phosphorylation, and these PTMs on key proteins serve as molecular switches in response to external stimuli. Studies have also shown interplay between phosphorylation and redox modifications, as one PTM type can alter the conformation of a protein, thus exposing or masking the sites for another type of PTM. Such crosstalk represents a complex regulatory mechanism that fine-tunes cellular signaling pathways such as those involved in DNA damage responses (DDR). Despite significant advances in our ability to analyze the redox proteome and phosphoproteome individually, a method that allows the detection of both PTM types from the same sample is still lacking. Herein, we describe a method for simultaneous analysis of protein thiol oxidation and phosphorylation in the same sample. This integrated workflow consists of cell lysis, acetone precipitation, tryptic digestion and isobaric labeling, and subsequent enrichment of thiol-containing peptides utilizing resin-assisted capture (RAC) and phosphopeptides using immobilized metal affinity chromatography (IMAC), respectively. The immediate alkylation of samples and other measures incorporated throughout the protocol prevents artificial oxidation of nascent free thiols and preservation of phosphorylation sites to ensure accurate identification and quantification.

A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics

Recent advancements in mass spectrometry (MS) have revolutionized quantitative proteomics, with multiplex isotope labeling emerging as a key strategy for enhancing accuracy, precision, and throughput. This tutorial review offers a comprehensive overview of multiplex isotope labeling techniques, including precursor-based, mass defect-based, reporter ion-based, and hybrid labeling methods. It details their fundamental principles, advantages, and inherent limitations along with strategies to mitigate the limitation of ratio-distortion. This review will also cover the applications and latest progress in these labeling techniques across various domains, including cancer biomarker discovery, neuroproteomics, post-translational modification analysis, cross-linking MS, and single-cell proteomics. This Review aims to provide guidance for researchers on selecting appropriate methods for their specific goals while also highlighting the potential future directions in this rapidly evolving field.

Discovery of a Hidden Proinflammatory Signaling Proteome Using a Large-Scale, Targeted Antibody Microarray Platform

Dynamic post-translational processes regulate protein expression in eukaryotic cells. However, the processes are difficult to assess on a proteomic scale because protein levels actually reflect the sum of individual biosynthesis and degradation rates. These rates are presently hidden from the conventional proteomic technologies. We present here a novel and dynamic, antibody microarray-based time-resolved approach to simultaneously measure not only the total protein changes but also the rates of biosynthesis of low abundance proteins in the proteome of lung epithelial cells. In this chapter, we describe the feasibility of this technique by investigating the complete proteomic kinetics of 507 low abundance proteins in cultured cystic fibrosis (CF) lung epithelial cells using ³⁵[S] methionine or ³²[P] and the consequences of repair by gene therapy with [wildtype] CFTR. This novel antibody microarray-based technology identifies relevant, hidden proteins whose regulation by the CF genotype would never have been detected by simple measurements of total proteomic masses.

Integrative proteomics and phosphoproteomics profiling on osteogenic differentiation of periodontal ligament stem cell

This study aims to elucidate the phosphorylated profile of periodontal ligament stem cells (PDLSCs) osteogenic differentiation, which contributes to the promotion of periodontium regeneration. PDLSCs cultured in the osteogenic induction medium for 14 days were analyzed by proteomics and phosphoproteomics. Potential functions of phosphorylated differentially expressed proteins (DEPs) were annotated and enriched based on Gene Ontology (GO). Furtherly, overlapped DEPs were identified and conducted protein-protein interaction (PPI) network united with the top 20 up/downregulated phosphorylated DEPs. Hub phosphorylated DEPs were analyzed by Cytoscape, and the protein kinase phosphorylation network was predicted by iGPS. Proteomics identified 87 upregulated and 227 downregulated DEPs. Phosphoproteomics identified 460 upregulated and 393 downregulated phosphorylated DEPs, and they were primarily enriched in mitochondrial function and ion-channel related terms. Furthermore, 63 overlapped DEPs were recognized for more accurate predictions. Among the top 10 hub phosphorylated DEPs, only Integrin alpha-5 (ITGA5) expressed upregulated phosphorylation, and half of them belonged to extracellular matrix (ECM) proteins. In addition, numerous kinases corresponding to four interactive hub phosphorylated DEPs were predicted, including Collagen alpha-2(I) (COL1A2), Syndecan-1 (SDC1), Fibrillin-1 (FBN1), and ITGA5. Our findings established a basis for further elucidation of the phosphorylation of PDLSCs osteogenic differentiation, and COL1A2/SDC1/ITGA5/FBN1 phosphorylated network may dominate this process.