Advances in immunology, Journal Year: 2023, Volume and Issue: unknown, P. 1 - 36
Published: Jan. 1, 2023
Language: Английский
Journal of Proteome Research, Journal Year: 2024, Volume and Issue: 23(2), P. 532 - 549
Published: Jan. 17, 2024
Since 2010, the Human Proteome Project (HPP), flagship initiative of Organization (HUPO), has pursued two goals: (1) to credibly identify protein parts list and (2) make proteomics an integral part multiomics studies human health disease. The HPP relies on international collaboration, data sharing, standardized reanalysis MS sets by PeptideAtlas MassIVE-KB using Guidelines for quality assurance, integration curation non-MS neXtProt, plus extensive use antibody profiling carried out Protein Atlas. According neXtProt release 2023-04-18, expression now been detected (PE1) 18,397 19,778 predicted proteins coded in genome (93%). Of these PE1 proteins, 17,453 were with mass spectrometry (MS) accordance 944 a variety methods. number PE2, PE3, PE4 missing stands at 1381. Achieving unambiguous identification 93% encoded from across all chromosomes represents remarkable experimental progress list. Meanwhile, there are several categories that have proved resistant detection regardless protein-based methods used. Additionally some PE1–4 probably should be reclassified PE5, specifically 21 LINC entries ∼30 HERV entries; being addressed present year. Applying wide array biological clinical ensures other omics platforms as reported Biology Disease-driven teams pathology resource pillars. Current positioned transition its Grand Challenge focused determining primary function(s) every itself networks pathways within context
Language: Английский
Citations
15
Deleted Journal, Journal Year: 2024, Volume and Issue: 6(6)
Published: May 31, 2024
Abstract Microfluidic devices have become a vastly popular technology, particularly because of the advantages they offer over their traditional counterparts. They such wide range uses and can make complex tasks quite efficient. One area research or work that has benefited greatly from use microfluidics is biosensing, where microfluidic chips are integrated into biosensor setups. There growing numbers applications in this as researchers look for efficient ways to tackle disease diagnostics drug discovery, which critical era recurring pandemics. In work, authors review integration with biosensors, well food security, molecular biology, cell diagnostics, at some most recent these areas. The covers including cellular life science research, agro-food processing, immunological veterinarian diagnostics. Microfluidics field combines fundamental laws physics chemistry solve miniaturization problems involving fluids nanoscale microscale, such, also examine mathematical concepts biosensing. relatively new technologies great potential terms applications.
Language: Английский
Citations
9
Cell Reports Methods, Journal Year: 2023, Volume and Issue: 3(6), P. 100511 - 100511
Published: June 1, 2023
The identification of tumor-specific antigens (TSAs) is critical for developing effective cancer immunotherapies. Mass spectrometry (MS)-based immunopeptidomics has emerged as a powerful tool identifying TSAs physical molecules. However, current platforms face challenges in measuring low-abundance precise, sensitive, and reproducible manner from small needle-tissue biopsies (<1 mg). Inspired by recent advances single-cell proteomics, microfluidics technology offers promising solution to these limitations providing improved isolation human leukocyte antigen (HLA)-associated peptides with higher sensitivity. In this context, we highlight the sample preparation rationale immunopeptidomics. Additionally, provide an overview microfluidic methods, including microchip pillar arrays, valved-based systems, droplet microfluidics, digital discuss latest research on their application MS-based proteomics.
Language: Английский
Citations
18
Human Vaccines & Immunotherapeutics, Journal Year: 2024, Volume and Issue: 20(1)
Published: Feb. 12, 2024
Efficacy of cancer immunotherapies relies on correct recognition tumor antigens by lymphocytes, eliciting thus functional responses capable eliminating cells. Therefore, important efforts have been carried out in antigen identification, with the aim understanding mechanisms response to immunotherapy and design safer more efficient strategies. In addition classical tumor-associated identified during last decades, implementation next-generation sequencing methodologies is enabling identification neoantigens (neoAgs) arising from mutations, leading development new neoAg-directed therapies. Moreover, there are numerous non-classical originated other sources methodologies. Here, we review relevance neoAgs different results obtained applying neoAg-based addition, types best approaches for their described. This will help increase spectrum targetable molecules useful immunotherapies.
Language: Английский
Citations
5
Engineering, Journal Year: 2024, Volume and Issue: unknown
Published: Sept. 1, 2024
Language: Английский
Citations
4
npj Systems Biology and Applications, Journal Year: 2025, Volume and Issue: 11(1)
Published: Jan. 17, 2025
T cells mediate pathogenesis of several autoimmune disorders by recognizing self-epitopes presented on Major Histocompatibility Complex (MHC) or Human Leukocyte Antigen (HLA) complex. The majority autoantigens to in various are not known, which has impeded autoantigen identification. Recent advances immunopeptidomics have started unravel the repertoire antigenic epitopes MHC. In diseases, led identification novel and enhanced our understanding mechanisms behind autoimmunity. Especially, provided key evidence explain genetic risk posed HLA alleles. this review, we shed light how can be leveraged discover potential autoantigens. We highlight application Type 1 Diabetes (T1D), Systemic Lupus Erythematosus (SLE), Rheumatoid Arthritis (RA). Finally, practical considerations implementing successfully technical challenges that need addressed. Overall, review will provide an important context for using
Language: Английский
Citations
0
Molecular & Cellular Proteomics, Journal Year: 2025, Volume and Issue: unknown, P. 100913 - 100913
Published: Jan. 1, 2025
Language: Английский
Citations
0
Frontiers in Immunology, Journal Year: 2025, Volume and Issue: 16
Published: Jan. 29, 2025
The immunopeptidome, a diverse set of peptides presented by Major Histocompatibility Complex (MHC) molecules, is critical component immune recognition and response. This review article delves into the mechanisms peptide presentation MHC particularly emphasizing roles ncRNA-derived extracellular vesicles (EVs) in shaping immunopeptidome landscape. We explore established emerging insights molecule interactions with peptides, including dynamics loading, transport, influence cellular genetic variations. highlights novel research on non-coding RNA (ncRNA)-derived which challenge conventional views antigen processing role EVs transporting these thereby modulating responses at remote body sites. not only challenges but also opens up new avenues for understanding responses. Furthermore, we discuss implications developing therapeutic strategies, cancer immunotherapy. By conducting comprehensive analysis current literature advanced methodologies immunopeptidomics, this aims to deepen complex interplay between system, offering perspectives potential diagnostic applications. Additionally, provide mechanism enhanced surface highlight pathway their systemic distribution, potentially altering surveillance landscapes.
Language: Английский
Citations
0
Nature Methods, Journal Year: 2025, Volume and Issue: unknown
Published: March 3, 2025
Abstract RNA velocity exploits the temporal information contained in spliced and unspliced counts to infer transcriptional dynamics. Existing models often rely on coarse biophysical simplifications or numerical approximations solve underlying ordinary differential equations (ODEs), which can compromise accuracy challenging settings, such as complex weak transcription rate changes across cellular trajectories. Here we present cell2fate, a formulation of based linearization ODE, allows solving biophysically more accurate model fully Bayesian fashion. As result, cell2fate decomposes solutions into modules, providing connection between statistical dimensionality reduction. We comprehensively benchmark real-world demonstrating enhanced interpretability power reconstruct dynamics dynamical signals rare mature cell types. Finally, apply developing human brain, where spatially map modules onto tissue architecture, connecting spatial organization tissues with transcription.
Language: Английский
Citations
0
Discover Chemistry., Journal Year: 2025, Volume and Issue: 2(1)
Published: March 22, 2025
Language: Английский
Citations
0