Expert Review of Proteomics最新文献

Introduction: Induced pluripotent stem (iPS) cell technology has transformed biomedical research. New opportunities now exist to create new organoids, microtissues, and body-on-a-chip systems for basic biology investigations and clinical translations.

Areas covered: We discuss the utility of proteomics for attaining an unbiased view into protein expression changes during iPS cell differentiation, cell maturation, and tissue generation. The ability to discover cell-type specific protein markers during the differentiation and maturation of iPS-derived cells has led to new strategies to improve cell production yield and fidelity. In parallel, proteomic characterization of iPS-derived organoids is helping to realize the goal of bridging in vitro and in vivo systems.

Expert opinions: We discuss some current challenges of proteomics in iPS cell research and future directions, including the integration of proteomic and transcriptomic data for systems-level analysis.

Introduction: Male infertility is a major public health concern globally. Proteomics has revolutionized our comprehension of male fertility by identifying potential infertility biomarkers and reproductive defects. Studies comparing sperm proteome with other male reproductive tissues have the potential to refine fertility diagnostics and guide infertility treatment development.

Areas covered: This review encapsulates literature using proteomic approaches to progress male reproductive biology. Our search methodology included systematic searches of databases such as PubMed, Scopus, and Web of Science for articles up to 2023. Keywords used included 'male fertility proteomics,' 'spermatozoa proteome,' 'testis proteomics,' 'epididymal proteomics,' and 'non-hormonal male contraception.' Inclusion criteria were robust experimental design, significant contributions to male fertility, and novel use of proteomic technologies.

Expert opinion: Expert analysis shows a shift from traditional research to an integrative approach that clarifies male reproductive health's molecular intricacies. A gap exists between proteomic discoveries and clinical application. The expert opinions consolidated here not only navigate the current findings but also chart the future proteomic applications for scientific and clinical breakthroughs. We underscore the need for continued investment in proteomic research - both in the technological and collaborative arenas - to further unravel the secrets of male fertility, which will be central to resolving fertility issues in the coming era.

Introduction: Development of new methods is essential to make great leaps in science, opening up new avenues for research, but the process behind method development is seldom described.

Areas covered: Over the last twenty years we have been developing several new methods, such as in situ PLA, proxHCR, and MolBoolean, using oligonucleotide-conjugated antibodies to visualize protein-protein interactions. Herein, we describe the rationale behind the oligonucleotide systems of these methods. The main objective of this paper is to provide researchers with a description on how we thought when we designed those methods. We also describe in detail how the methods work and how one should interpret results.

Expert opinion: Understanding how the methods work is important in selecting an appropriate method for your experiments. We also hope that this paper may be an inspiration for young researchers to enter the field of method development. Seeing a problem is a motivation to develop a solution.

Introduction: The analysis of doping control samples is preferably performed by mass spectrometry, because obtained results meet the highest analytical standards and ensure an impressive degree of reliability. The advancement in mass spectrometry and all its associated technologies thus allow for continuous improvements in doping control analysis.

Areas covered: Modern mass spectrometric systems have reached a status of increased sensitivity, robustness, and specificity within the last decade. The improved sensitivity in particular has, on the other hand, also led to the detection of drug residues that were attributable to scenarios where the prohibited substances were not administered consciously but rather by the unconscious ingestion of or exposure to contaminated products. These scenarios and their doubtless clarification represent a great challenge. Here, too, modern MS systems and their applications can provide good insights in the interpretation of dose-related metabolism of prohibited substances. In addition to the development of new instruments itself, software-assisted analysis of the sometimes highly complex data is playing an increasingly important role and facilitating the work of doping control laboratories.

Expert opinion: The sensitive analysis and evaluation of a higher number of samples in a shorter time is made possible by the ongoing developments in mass spectrometry.

Introduction: Around 20% of individuals diagnosed with acute pancreatitis (AP) may develop severe acute pancreatitis (SAP), possibly resulting in a mortality rate ranging from 15% to 35%. There is an urgent need to thoroughly understand the molecular phenotypes of SAP resulting from diverse etiologies. The field of translational research on AP has seen the use of several innovative proteomic methodologies via the ongoing improvement of isolation, tagging, and quantification methods.

Areas covered: This paper provides a comprehensive overview of differentially abundant proteins (DAPs) identified in AP by searching the PubMed/MEDLINE database (2003-2023) and adds significantly to the current theoretical framework.

Expert opinion: DAPs for potentially diagnosing AP based on proteomic identification need to be confirmed by multi-center studies that include larger samples. The discovery of DAPs in various organs at different AP stages via proteomic technologies is essential better to understand the pathophysiology of AP-related multiple organ dysfunction syndrome. Regarding the translational research of AP, novel approaches like single-cell proteomics and imaging using mass spectrometry may be used as soon as they become available.

Introduction: Due to the segmented functions and complexity of the human brain, the characterization of molecular profiles within specific areas such as brain structures and biofluids is essential to unveil the molecular basis for structure specialization as well as the molecular imbalance associated with neurodegenerative and psychiatric diseases.

Areas covered: Much of our knowledge about brain functionality derives from neurophysiological, anatomical, and transcriptomic approaches. More recently, laser capture and imaging proteomics, technological and computational developments in LC-MS/MS, as well as antibody/aptamer-based platforms have allowed the generation of novel cellular, spatial, and posttranslational dimensions as well as innovative facets in biomarker validation and druggable target identification.

Expert opinion: Proteomics is a powerful toolbox to functionally characterize, quantify, and localize the extensive protein catalog of the human brain across physiological and pathological states. Brain function depends on multi-dimensional protein homeostasis, and its elucidation will help us to characterize biological pathways that are essential to properly maintain cognitive functions. In addition, comprehensive human brain pathological proteomes may be the basis in computational drug-repositioning methods as a strategy for unveiling potential new therapies in neurodegenerative and psychiatric disorders.

Introduction: Every year about 800,000 complete suicide events occur. The identification of biologic markers to identify subjects at risk would be helpful in targeting specific support treatments.

Area covered: A narrative review defines the meta-analytic level of current evidence about the biologic markers of suicide behavior (SB). The meta-analytic evidence gathered so far indicates that the hypothesis-driven research largely failed to identify the biologic markers of suicide. The most consistent and replicated result was reported for: 1) 5-HTR2A T102C, associated with SB in patients with schizophrenia (OR = 1.73 (1.11-2.69)) and 2) BDNF Val66Met (rs6265), with the Met-Val + Val-Val carriers found to be at risk for suicide in the Caucasian population (OR: 1.96 (1.58-2.43)), while Val-Val vs. Val-Met + Met carriers found to be at risk for suicide in the Asian populations (OR: 1.36 (1.04-1.78)). GWAS-based meta-analyses indicate some positive replicated findings regarding the DRD2, Neuroligin gene, estrogen-related genes, and genes involved in gene expression.

Expert opinion: Most consistent results were obtained when analyzing sub-samples of patients. Some promising results come from the implementation of the polygenic risk score. There is no current consensus about an implementable biomarker for SB.