Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease often associated with underlying inflammatory bowel disease (IBD). This study investigates how PSC predisposes individuals to altered inflammatory immune responses compared with IBD alone. A case-control study was conducted with a cohort of 75 patients, including 16 with PSC (14 with concomitant IBD), 39 with IBD alone, and 20 controls. Serum bile acid profile, proteomic analysis, and immune-related gene expression in the colon tissue were examined. Colonic tissue from PSC patients exhibited up-regulation of immune regulation and inflammatory signaling mRNA markers, including LGR5, IL-8, CCL2, COX2, TWIST1, and SNAIL. Additionally, PSC patients displayed a distinct proinflammatory serum proteomic signature and moderate elevation of some bile acids, such as glycochenodeoxycholic acid (GCDCA). Co-incubation of human-derived monocytes with GCDCA partially replicated the inflammatory profile observed in PSC. These findings suggest that circulating bile acids modulate the peripheral immune system proinflammatory response, contributing to the unique PSC phenotype.

• Klíčová slova
• GCDCA, IBD, PSC, bile acids, immune response,
• MeSH
• dospělí MeSH
• idiopatické střevní záněty * imunologie   komplikace   krev   genetika   MeSH
• kolon metabolismus   imunologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• monocyty imunologie   metabolismus   MeSH
• proteomika metody   MeSH
• sklerozující cholangitida * imunologie   krev   komplikace   genetika   MeSH
• studie případů a kontrol MeSH
• žlučové kyseliny a soli * krev   imunologie   MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• žlučové kyseliny a soli * MeSH

Anaplastic Large Cell Lymphoma (ALCL) is an aggressive T-cell lymphoma affecting children and young adults. About 30% of patients develop therapy resistance therefore new precision medicine drugs are highly warranted. Multiple rounds of structure-activity optimization of Caffeic Acid Phenethyl Ester have resulted in CM14. CM14 causes upregulation of genes involved in oxidative stress response and downregulation of DNA replication genes leading to G2/M arrest and subsequent apoptosis induction. In accordance with this, an unbiased proteomics approach, confocal microscopy and molecular modeling showed that TUBGCP2, member of the centrosomal γ-TuRC complex, is a direct interaction partner of CM14. CM14 overcomes ALK inhibitor resistance in ALCL and is also active in T-cell Acute Lymphoblastic Leukemia and Acute Myeloid Leukemia. Interestingly, CM14 also induced cell death in docetaxel-resistant prostate cancer cells thus suggesting an unexpected role in solid cancers. Thus, we synthesized and thoroughly characterized a novel TUBGCP2 targeting drug that is active in ALCL but has also potential for other malignancies.

• MeSH
• apoptóza účinky léků   MeSH
• centrozom * účinky léků   metabolismus   MeSH
• chemorezistence účinky léků   MeSH
• fenethylalkohol * farmakologie   analogy a deriváty   chemie   MeSH
• kyseliny kávové * farmakologie   chemie   MeSH
• lidé MeSH
• nádorové buněčné linie MeSH
• protinádorové látky * farmakologie   chemie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• caffeic acid phenethyl ester MeSH Prohlížeč
• fenethylalkohol * MeSH
• kyseliny kávové * MeSH
• protinádorové látky * MeSH

Faithful meiotic segregation requires pairwise alignment of the homologous chromosomes and their synaptonemal complex (SC) mediated stabilization. Here, we investigate factors that promote and coordinate these events during C. elegans meiosis. We identify BRA-2 (BMP Receptor Associated family member 2) as an interactor of HIM-17, previously shown to promote double-strand break formation. We found that loss of bra-2 impairs synapsis elongation without affecting homolog recognition, chromosome movement or SC maintenance. Epistasis analyses reveal previously unrecognized activities for HIM-17 in regulating homolog pairing and SC assembly in a partially overlapping manner with BRA-2. We show that removing bra-2 or him-17 restores nuclear clustering, recruitment of PLK-2 at the nuclear periphery, and abrogation of ectopic synapsis in htp-1 mutants, suggesting intact CHK-2-mediated signaling and presence of a barrier that prevents SC polymerization in the absence of homology. Our findings shed light on the regulatory mechanisms ensuring faithful pairing and synapsis.

• MeSH
• Caenorhabditis elegans * genetika   metabolismus   cytologie   MeSH
• meióza * genetika   fyziologie   MeSH
• mutace MeSH
• párování chromozomů * genetika   MeSH
• proteiny buněčného cyklu * metabolismus   genetika   MeSH
• proteiny Caenorhabditis elegans * metabolismus   genetika   MeSH
• synaptonemální komplex metabolismus   genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• Htp-1 protein, C elegans MeSH Prohlížeč
• proteiny buněčného cyklu * MeSH
• proteiny Caenorhabditis elegans * MeSH

Microbore columns with a 1.0 mm inner diameter (i.d.) have gained popularity in microflow liquid chromatography-mass spectrometry (LC-MS) workflows for exploratory proteomics applications due to their high throughput, robustness, and reproducibility. However, obtaining highly efficient separation using these columns remains unachievable, primarily due to significant radial flow heterogeneity caused by uneven particle packing density across the column cross-section. In this study, we evaluated the integration of a 1.5 mm i.d. column, which offers greater packing uniformity and reduced radial flow dispersion, into a microflow LC-MS setup for bottom-up proteomics analysis. The performance of the 1.5 mm i.d. column was compared with that of the 1.0 mm i.d. column using protein samples of varying complexity. The results demonstrate that 1.5 mm i.d. columns provide superior chromatographic separation and better compatibility with conventional-flow LC systems, yielding higher reproducibility and comparable protein and peptide identifications to the 1.0 mm i.d. columns at higher sample amounts. These findings suggest that 1.5 mm i.d. columns could be a suitable alternative to 1.0 mm i.d. columns for microflow LC-MS/MS proteomic analysis, particularly in laboratories with only conventional-flow LC systems.

• Publikační typ
• časopisecké články MeSH

Cyclic electron transport around photosystem I (PSI) is essential for the protection of the photosynthetic apparatus in plants under diverse light conditions. This process is primarily mediated by Proton Gradient Regulation 5 protein/Proton Gradient Regulation 5-like photosynthetic phenotype 1 protein (PGR5/PGRL1) and NADH dehydrogenase-like complex (NDH). In angiosperms, NDH interacts with two PSI complexes through distinct monomeric antennae, LHCA5 and LHCA6, which is crucial for its higher stability under variable light conditions. This interaction represents an advanced evolutionary stage and offers limited insight into the origin of the PSI-NDH supercomplex in evolutionarily older organisms. In contrast, the moss Physcomitrium patens (Pp), which retains the lhca5 gene but lacks the lhca6, offers a glimpse into an earlier evolutionary stage of the PSI-NDH supercomplex. Here we present structural evidence of the Pp PSI-NDH supercomplex formation by single particle electron microscopy, demonstrating the unique ability of Pp to bind a single PSI in two different configurations. One configuration closely resembles the angiosperm model, whereas the other exhibits a novel PSI orientation, rotated clockwise. This structural flexibility in Pp is presumably enabled by the variable incorporation of LHCA5 within PSI and is indicative of an early evolutionary adaptation that allowed for greater diversity at the PSI-NDH interface. Our findings suggest that this variability was reduced as the structural complexity of the NDH complex increased in vascular plants, primarily angiosperms. This study not only clarifies the evolutionary development of PSI-NDH supercomplexes but also highlights the dynamic nature of the adaptive mechanisms of plant photosynthesis.

• Klíčová slova
• LHCA5, PSI‐NDH supercomplex, Physcomitrium patens, cyclic electron transport, single particle analysis, transmission electron microscopy,
• MeSH
• fotosyntéza MeSH
• fotosystém I (proteinový komplex) * metabolismus   genetika   MeSH
• mechy * genetika   metabolismus   MeSH
• NADH-dehydrogenasa metabolismus   genetika   MeSH
• rostlinné proteiny * metabolismus   genetika   MeSH
• světlosběrné proteinové komplexy metabolismus   genetika   chemie   MeSH
• transport elektronů MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• fotosystém I (proteinový komplex) * MeSH
• NADH-dehydrogenasa MeSH
• rostlinné proteiny * MeSH
• světlosběrné proteinové komplexy MeSH

Actomyosin contractility represents an ancient feature of eukaryotic cells participating in many developmental and homeostasis events, including tissue morphogenesis, muscle contraction and cell migration, with dysregulation implicated in various pathological conditions, such as cancer. At the molecular level, actomyosin comprises actin bundles and myosin motor proteins that are sensitive to posttranslational modifications like phosphorylation. While the molecular components of actomyosin are well understood, the coordination of contractility by extracellular and intracellular signals, particularly from cellular signalling pathways, remains incompletely elucidated. This study focuses on WNT/planar cell polarity (PCP) signalling, previously associated with actomyosin contractility during vertebrate neurulation. Our investigation reveals that the main cytoplasmic PCP proteins, Prickle and Dishevelled, interact with key actomyosin components such as myosin light chain 9 (MLC9), leading to its phosphorylation and localized activation. Using proteomics and microscopy approaches, we demonstrate that both PCP proteins actively control actomyosin contractility through Rap1 small GTPases in relevant in vitro and in vivo models. These findings unveil a novel mechanism of how PCP signalling regulates actomyosin contractility through MLC9 and Rap1 that is relevant to vertebrate neurulation.

• Klíčová slova
• MDCK cells, Xenopus embryos, actomyosin contractility, neurulation, planar cell polarity, vertebrates,
• MeSH
• aktomyosin * metabolismus   MeSH
• fosforylace MeSH
• lehké řetězce myosinu metabolismus   MeSH
• lidé MeSH
• myši MeSH
• neurulace * MeSH
• obratlovci metabolismus   MeSH
• polarita buněk * MeSH
• protein dishevelled metabolismus   genetika   MeSH
• signální transdukce MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• aktomyosin * MeSH
• lehké řetězce myosinu MeSH
• protein dishevelled MeSH

Polyglutamylation is a reversible posttranslational modification that is catalyzed by enzymes of the tubulin tyrosine ligase-like (TTLL) family. Here, we found that TTLL11 generates a previously unknown type of polyglutamylation that is initiated by the addition of a glutamate residue to the free C-terminal carboxyl group of a substrate protein. TTLL11 efficiently polyglutamylates the Wnt signaling protein Dishevelled 3 (DVL3), thereby changing the interactome of DVL3. Polyglutamylation increases the capacity of DVL3 to get phosphorylated, to undergo phase separation, and to act in the noncanonical Wnt pathway. Both carboxy-terminal polyglutamylation and the resulting reduction in phase separation capacity of DVL3 can be reverted by the deglutamylating enzyme CCP6, demonstrating a causal relationship between TTLL11-mediated polyglutamylation and phase separation. Thus, C-terminal polyglutamylation represents a new type of posttranslational modification, broadening the range of proteins that can be modified by polyglutamylation and providing the first evidence that polyglutamylation can modulate protein phase separation.

• Klíčová slova
• Dishevelled 3, Noncanonical Wnt Signaling, Polyglutamylation, Protein Condensates, TTLL11,
• MeSH
• fosforylace MeSH
• HEK293 buňky MeSH
• kyselina polyglutamová metabolismus   analogy a deriváty   MeSH
• lidé MeSH
• peptidsynthasy * metabolismus   genetika   MeSH
• posttranslační úpravy proteinů * MeSH
• protein dishevelled * metabolismus   genetika   MeSH
• separace fází MeSH
• signální dráha Wnt MeSH
• signální transdukce MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DVL3 protein, human MeSH Prohlížeč
• kyselina polyglutamová MeSH
• peptidsynthasy * MeSH
• protein dishevelled * MeSH
• tubulin polyglutamylase MeSH Prohlížeč

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer, and deeper proteome coverage is needed for its molecular characterization. We present comprehensive library of targeted mass spectrometry assays specific for TNBC and demonstrate its applicability. Proteins were extracted from 105 TNBC tissues and digested. Aliquots were pooled, fractionated using hydrophilic chromatography and analyzed by LC-MS/MS in data-dependent acquisition (DDA) parallel accumulation-serial fragmentation (PASEF) mode on timsTOF Pro LC-MS system. 16 individual lysates were analyzed in data-independent acquisition (DIA)-PASEF mode. Hybrid library was generated in Spectronaut software and covers 244,464 precursors, 168,006 peptides and 11,564 protein groups (FDR = 1%). Application of our library for pilot quantitative analysis of 16 tissues increased identification numbers in Spectronaut 18.5 and DIA-NN 1.8.1 software compared to library-free setting, with Spectronaut achieving the best results represented by 190,310 precursors, 140,566 peptides, and 10,463 protein groups. In conclusion, we introduce assay library that offers the deepest coverage of TNBC proteome to date. The TNBC library is available via PRIDE repository (PXD047793).

• MeSH
• chromatografie kapalinová MeSH
• lidé MeSH
• proteom MeSH
• proteomika metody   MeSH
• software MeSH
• tandemová hmotnostní spektrometrie * MeSH
• triple-negativní karcinom prsu * genetika   MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• dataset MeSH
• Názvy látek
• proteom MeSH

NF-κB pathway is involved in inflammation; however, recent data shows its role also in cancer development and progression, including metastasis. To understand the role of NF-κB interactome dynamics in cancer, we study the complexity of breast cancer interactome in luminal A breast cancer model and its rearrangement associated with NF-κB modulation. Liquid chromatography-mass spectrometry measurement of 160 size-exclusion chromatography fractions identifies 5460 protein groups. Seven thousand five hundred sixty eight interactions among these proteins have been reconstructed by PrInCE algorithm, of which 2564 have been validated in independent datasets. NF-κB modulation leads to rearrangement of protein complexes involved in NF-κB signaling and immune response, cell cycle regulation, and DNA replication. Central NF-κB transcription regulator RELA co-elutes with interactors of NF-κB activator PRMT5, and these complexes are confirmed by AlphaPulldown prediction. A complementary immunoprecipitation experiment recapitulates RELA interactions with other NF-κB factors, associating NF-κB inhibition with lower binding of NF-κB activators to RELA. This study describes a network of pro-tumorigenic protein interactions and their rearrangement upon NF-κB inhibition with potential therapeutic implications in tumors with high NF-κB activity.

• Klíčová slova
• AlphaPullDown, NF-κB, RELA, breast cancer, interaction, protein complexes, protein correlation profiling, proteomics,
• MeSH
• karcinogeneze metabolismus   MeSH
• lidé MeSH
• mapování interakce mezi proteiny MeSH
• mapy interakcí proteinů * MeSH
• nádorové buněčné linie MeSH
• nádory prsu * metabolismus   patologie   MeSH
• NF-kappa B * metabolismus   MeSH
• proteinarginin-N-methyltransferasy metabolismus   MeSH
• signální transdukce MeSH
• transkripční faktor RelA * metabolismus   MeSH
• vazba proteinů MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• NF-kappa B * MeSH
• proteinarginin-N-methyltransferasy MeSH
• RELA protein, human MeSH Prohlížeč
• transkripční faktor RelA * MeSH

The current repertoire of methods available for studying RNA-protein interactions in plants is somewhat limited. Employing an RNA-centric approach, particularly with less abundant RNAs, presents various challenges. Many of the existing methods were initially designed for different model systems, with their application in plants receiving limited attention thus far. The Comprehensive Identification of RNA-Binding Proteins by Mass Spectrometry (ChIRP-MS) technique, initially developed for mammalian cells, has been adapted in this study for application in Arabidopsis thaliana. The procedures have been meticulously modified and optimized for telomerase RNA, a notable example of a low-abundance RNA recently identified. Following these optimization steps, ChIRP-MS can serve as an effective screening method for identifying candidate proteins interacting with any target RNA of interest.

• Klíčová slova
• Arabidopsis thaliana, ChIRP-MS, RNA, RNA-centric methods, RNA-protein interactions, telomerase, telomerase RNA,
• Publikační typ
• časopisecké články MeSH