Artificial intelligence and neoantigens: paving the path for precision cancer immunotherapy

Cancer immunotherapy has witnessed rapid advancement in recent years, with a particular focus on neoantigens as promising targets for personalized treatments. The convergence of immunogenomics, bioinformatics, and artificial intelligence (AI) has propelled the development of innovative neoantigen discovery tools and pipelines. These tools have revolutionized our ability to identify tumor-specific antigens, providing the foundation for precision cancer immunotherapy. AI-driven algorithms can process extensive amounts of data, identify patterns, and make predictions that were once challenging to achieve. However, the integration of AI comes with its own set of challenges, leaving space for further research. With particular focus on the computational approaches, in this article we have explored the current landscape of neoantigen prediction, the fundamental concepts behind, the challenges and their potential solutions providing a comprehensive overview of this rapidly evolving field

The SMN Tudor SIM-like domain is key to SmD1 and coilin interactions and to Cajal body biogenesis

Cajal bodies (CBs) are nuclear organelles involved in the maturation of spliceosomal small nuclear ribonucleoproteins (snRNPs). They concentrate coilin, snRNPs and the survival motor neuron protein (SMN). Dysfunction of CB assembly occurs in spinal muscular atrophy (SMA). Here, we demonstrate that SMN is a SUMO1 target that has a small ubiquitin-related modifier (SUMO)-interacting motif (SIM)-like motif in the Tudor domain. The expression of SIM-like mutant constructs abolishes the interaction of SMN with the spliceosomal SmD1 (also known as SNRPD1), severely decreases SMN-coilin interaction and prevents CB assembly. Accordingly, the SMN SIM-like-mediated interactions are important for CB biogenesis and their dysfunction can be involved in SMA pathophysiology

The International Virus Bioinformatics Meeting 2023

The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24–26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting

Dual role of CD9 protein in mast cell activation

Mast cells are well known effector cells in immune system. They have been implicated in such important processes as host defense against bacteria, toxins or parasites. However, in some cases they can develop improper reaction against harmless environmental antigens and thus causing allergies. It is therefore essential to understand signaling events that lead to activation of these cells in order to develop new treatment strategies. Newly prepared rat monoclonal antibody of IgG1 subtype raised against murine mast cells was characterized and found suitable for flow cytometry, immunoblotting and immunoprecipitation. Employing of optimized procedure for immunopurification in combination with mass spectrometry led to identification of its target cluster of differentiation (CD)9 protein. CD9 is a member of large protein family called tetraspanins. Functional studies showed that binding of this antibody to mast cells induced degranulation and early activation events such as increased tyrosine phosphorylation and enhanced levels of free cytoplasmic calcium. Interestingly, subsequent activation of these cells via antigen-mediated aggregation of the high-affinity IgE receptor (FcεRI) led to decreased degranulation, calcium response and tyrosine phosphorylation of several substrates. Importantly, anti-CD9 antibody did..

STIM1 and its role in cellular signaling

Dep. of Physiology and Develop. Biology (obsolete)Katedra fyziol. živočichů a vývoj. biol. (zrušena)Faculty of SciencePřírodovědecká fakult

STIM1 and its role in cellular signaling

Dep. of Physiology and Develop. Biology (obsolete)Katedra fyziol. živočichů a vývoj. biol. (zrušena)Faculty of SciencePřírodovědecká fakult

Coilin: The first 25 years

This find is registered at Portable Antiquities of the Netherlands with number PAN-0000092