The adaptive immune response critically hinges on the functionality of T cell receptors, governed by complex molecular mechanisms, including ubiquitination. In this study, we delved into the role of in T cell immunity, focusing on T cell-B cell conjugate formation and T cell activation. Using a CRISPR-Cas9 screening approach targeting deubiquitinases genes in Jurkat T cells, we identified BAP1 as a key positive regulator of T cell-B cell conjugate formation. Subsequent investigations into BAP1 knockout cells revealed impaired T cell activation, evidenced by decreased MAPK and NF-kB signaling pathways and reduced CD69 expression upon T cell receptor stimulation. Flow cytometry and qPCR analyses demonstrated that BAP1 deficiency leads to decreased surface expression of T cell receptor complex components and reduced mRNA levels of the co-stimulatory molecule CD28. Notably, the observed phenotypes associated with BAP1 knockout are specific to T cells and fully dependent on BAP1 catalytic activity. In-depth RNA-seq and mass spectrometry analyses further revealed that BAP1 deficiency induces broad mRNA and protein expression changes. Overall, our findings elucidate the vital role of BAP1 in T cell biology, especially in T cell-B cell conjugate formation and T cell activation, offering new insights and directions for future research in immune regulation.

• Klíčová slova
• BAP1, CRISPR-Cas9 screening, T cell activation, T cell receptor (TCR), T cell-B cell conjugates,
• MeSH
• aktivace lymfocytů * imunologie   MeSH
• B-lymfocyty * imunologie   metabolismus   MeSH
• Jurkat buňky MeSH
• lidé MeSH
• nádorové supresorové proteiny * metabolismus   genetika   MeSH
• receptory antigenů T-buněk * metabolismus   MeSH
• signální transdukce MeSH
• T-lymfocyty * imunologie   metabolismus   MeSH
• thiolesterasa ubikvitinu * genetika   metabolismus   nedostatek   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• BAP1 protein, human MeSH Prohlížeč
• nádorové supresorové proteiny * MeSH
• receptory antigenů T-buněk * MeSH
• thiolesterasa ubikvitinu * MeSH

AIMS: This retrospective non-randomised study aims to identify new and rare fusion partners with USP6 in the setting of nodular fasciitis. It has been proven, that nodular fasciitis can harbour different variants of USP6 fusions, which can be used in routine diagnostics and even determine the biological behaviour of the process. METHODS: A total of 19 cases of nodular fasciitis examined between 2011 and 2022 at Motol University Hospital in Prague were included into this study. Next to the histopathological evaluation, all cases were assessed using immunohistochemistry, RT-PCR and Anchored multiplex RNA methods. Patient's main demographic characteristics and corresponding clinical data were also analysed. RESULTS: This study presents one novel (KIF1A) and five rare examples (TMP4, SPARC, EIF5A, MIR22HG, COL1A2) of fusion partners with USP6 among 19 cases of nodular fasciitis. CONCLUSION: Identification of USP6 fusion partners in nodular fasciitis helps to understand the biology of such lesions. Moreover, it can be useful in routine histopathological practice of soft-tissues diagnostics, especially in preventing possible misdiagnosis of malignancy.

• Klíčová slova
• Pathology Department, Hospital, Pathology, Molecular, Soft Tissue Neoplasms,
• MeSH
• fasciitida * genetika   patologie   MeSH
• genová přestavba * MeSH
• imunohistochemie MeSH
• kineziny genetika   MeSH
• lidé MeSH
• retrospektivní studie MeSH
• thiolesterasa ubikvitinu * genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• kineziny MeSH
• thiolesterasa ubikvitinu * MeSH
• USP6 protein, human MeSH Prohlížeč

Low-grade serous carcinoma (LGSC) may develop from serous borderline tumor (SBT) tissue, where the micropapillary type (mSBT) presents the highest risk for progression. The sensitivity of LGSC to standard chemotherapy is limited, so alternative therapeutic approaches, including targeted treatment, are needed. However, knowledge about the molecular landscape of LGSC and mSBT is limited. A sample set of 137 pathologically well-defined cases (LGSC, 97; mSBT, 40) was analyzed using capture DNA next-generation sequencing (727 genes) and RNA next-generation sequencing (147 genes) to show the landscape of somatic mutations, gene fusions, expression pattern, and prognostic and predictive relevance. Class 4/5 mutations in the main driver genes (KRAS, BRAF, NRAS, ERBB2, USP9X) were detected in 48% (14/29) of mSBT cases and 63% (47/75) of LGSC cases. The USP9X mutation was detected in only 17% of LGSC cases. RNA next-generation sequencing revealed gene fusions in 6 of 64 LGSC cases (9%) and 2 of 33 mSBT cases (9%), and a heterogeneous expression profile across LGSC and mSBT. No molecular characteristics were associated with greater survival. The somatic genomic and transcriptomic profiles of 35 mSBT and 85 LGSC cases are compared for the first time. Candidate oncogenic gene fusions involving BRAF, FGFR2, or NF1 as a fusion partner were identified. Molecular testing of LGSC may be used in clinical practice to reveal therapeutically significant targets.

• MeSH
• azosloučeniny * MeSH
• genomika MeSH
• lidé MeSH
• mutace MeSH
• nádory vaječníků * diagnóza   genetika   MeSH
• protoonkogenní proteiny B-Raf genetika   MeSH
• RNA MeSH
• serózní cystadenokarcinom * diagnóza   genetika   MeSH
• stanovení celkové genové exprese MeSH
• stupeň nádoru MeSH
• thiolesterasa ubikvitinu genetika   MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• azosloučeniny * MeSH
• Martius scarlet blue trichrome MeSH Prohlížeč
• protoonkogenní proteiny B-Raf MeSH
• RNA MeSH
• thiolesterasa ubikvitinu MeSH
• USP9X protein, human MeSH Prohlížeč

Clear cell mesothelioma is uncommon and shows predominance of clear cells with resemblance to clear cell carcinomas. Clinicopathologic and molecular descriptions of clear cell mesothelioma remained limited. In this study, we identified an index patient with clear cell mesothelioma, confirmed by immunohistochemical and ultrastructural studies. Targeted next-generation sequencing revealed the presence of an inactivating VHL mutation. We then systematically searched for VHL-mutant mesotheliomas in a comprehensive genomic profiling database of 1532 mesotheliomas. Collectively, we identified a cohort of four VHL-mutant clear cell mesotheliomas, including three peritoneal and one pleural tumors from three females and one male, with age range of 47-68 (median 63) years. Histologically, each tumor showed a microcystic to tubulopapillary architecture with prominent clear cells. By next-generation DNA sequencing, each of the four clear cell mesotheliomas harbored inactivating VHL mutations, while lacking other alterations typical of mesotheliomas such as BAP1, NF2, SETD2, CDKN2A, CDKN2B, TP53, and PTEN. By using low-pass whole genome sequencing on the index case and targeted next-generation sequencing on the remaining three cases, we identified extensive loss of heterozygosity throughout the genome but consistently sparing chromosomes 5, 7, and 20, characteristic of genomic near-haploidization. In summary, clear cell mesotheliomas were characterized by inactivating VHL mutations and genomic near-haploidization and appeared to represent a distinct clinicopathologic and molecular category of mesotheliomas. Our findings implicate VHL in the pathogenesis of a subset of mesotheliomas, particularly those with clear cell morphology.

• Klíčová slova
• VHL, clear cell, genetics, genomic near haploidization, mesothelioma, near haploid,
• MeSH
• chromozomální aberace MeSH
• genomika MeSH
• haploidie MeSH
• lidé středního věku MeSH
• lidé MeSH
• maligní mezoteliom * MeSH
• mezoteliom * genetika   MeSH
• mutace MeSH
• nádorový supresorový protein VHL genetika   MeSH
• nádory plic * genetika   MeSH
• senioři MeSH
• thiolesterasa ubikvitinu genetika   MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• systematický přehled MeSH
• Názvy látek
• nádorový supresorový protein VHL MeSH
• thiolesterasa ubikvitinu MeSH
• VHL protein, human MeSH Prohlížeč

INTRODUCTION: Ubiquitination is an important protein modification that regulates various essential cellular processes, including the functions of innate immune cells. Deubiquitinases are enzymes responsible for removing ubiquitin modification from substrates, and the regulation of deubiquitinases in macrophages during infection with Salmonella Typhimurium and Yersinia enterocolitica remains unknown. METHODS: To identify deubiquitinases regulated in human macrophages during bacterial infection, an activity-based proteomics screen was conducted. The effects of pharmacological inhibition of the identified deubiquitinase, USP8, were examined, including its impact on bacterial survival within macrophages and its role in autophagy regulation during Salmonella infection. RESULTS: Several deubiquiitnases were differentially regulated in infected macrophages. One of the deubiquitinases identified was USP8, which was downregulated upon Salmonella infection. Inhibition of USP8 was associated with a decrease in bacterial survival within macrophages, and it was found to play a distinct role in regulating autophagy during Salmonella infection. The inhibition of USP8 led to the downregulation of the p62 autophagy adaptor. DISCUSSION: The findings of this study suggest a novel role of USP8 in regulating autophagy flux, which restricts intracellular bacteria, particularly during Salmonella infection.

• Klíčová slova
• Salmonella, USP8, autophagy, chemical proteomics, deubiquitinases, deubiquitinating enzymes,
• MeSH
• autofagie MeSH
• deubikvitinasy metabolismus   MeSH
• endopeptidasy genetika   MeSH
• endozomální třídící komplexy pro transport genetika   MeSH
• lidé MeSH
• Salmonella typhimurium metabolismus   MeSH
• salmonelóza * MeSH
• thiolesterasa ubikvitinu genetika   metabolismus   MeSH
• ubikvitinace MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• deubikvitinasy MeSH
• endopeptidasy MeSH
• endozomální třídící komplexy pro transport MeSH
• thiolesterasa ubikvitinu MeSH
• USP8 protein, human MeSH Prohlížeč

BAP1-inactivated melanocytic tumors represent a subset of epithelioid melanocytic neoplasms resulting from biallelic inactivation of the BAP1 gene and by a driver mutation that activate the MAP kinase pathway, most commonly BRAFV600E. They occur sporadically or, less common, in the setting of BAP1 tumor predisposition syndrome caused by a BAP1 germline mutation that predisposes to several malignancies including cutaneous and uveal melanoma. To date, only few cases of BAP1-inactivated melanomas have been reported. We present a case of a 35-year-old woman presented with a melanocytic lesion microscopically composed of 3 distinct melanocytic populations, suggesting a stepwise progression model to melanoma from a conventional nevus through a melanocytoma stage. This progression was also supported from a molecular viewpoint given BRAFV600E, BAP1, and TERT-p hot spot mutations detected by targeted mutational analysis. Four atypical melanocytic lesions were removed from the patient's back, and the same A BAP1 c.856A>T, p.(Lys286Ter) mutation was detected on either tumoral or normal tissue samples. To the best of our knowledge, this is the first case of BAP1-inactivated melanoma with a documented TERT-p hot spot mutation manifesting as the first presentation of BAP1 tumor predisposition syndrome.

• MeSH
• dědičné nádorové syndromy * patologie   MeSH
• dospělí MeSH
• epiteloidní a vřetenobuněčný névus * patologie   MeSH
• lidé MeSH
• melanocyty patologie   MeSH
• melanom * patologie   MeSH
• mutace MeSH
• nádorové supresorové proteiny genetika   metabolismus   MeSH
• nádory kůže * patologie   MeSH
• thiolesterasa ubikvitinu genetika   MeSH
• zárodečné mutace MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• kazuistiky MeSH
• přehledy MeSH
• Názvy látek
• BAP1 protein, human MeSH Prohlížeč
• nádorové supresorové proteiny MeSH
• thiolesterasa ubikvitinu MeSH

BAP1-inactivated melanocytic tumor (BIMT) is a group of melanocytic neoplasms with epithelioid cell morphology molecularly characterized by the loss of function of BAP1, a tumor suppressor gene located on chromosome 3p21, and a mutually exclusive mitogenic driver mutation, more commonly BRAF. BIMTs can occur as a sporadic lesion or, less commonly, in the setting of an autosomal dominant cancer susceptibility syndrome caused by a BAP1 germline inactivating mutation. Owing to the frequent identification of remnants of a conventional nevus, BIMTs are currently classified within the group of combined melanocytic nevi. "Pure" lesions can also be observed. We studied 50 BIMTs from 36 patients. Most lesions were composed of epithelioid melanocytes of varying size and shapes, resulting extreme cytomorphological heterogeneity. Several distinctive morphological variants of multinucleated/giant cells were identified. Some hitherto underrecognized microscopic features, especially regarding nuclear characteristics included nuclear blebbing, nuclear budding, micronuclei, shadow nuclei, peculiar cytoplasmic projections (ant-bear cells) often containing micronuclei and cell-in-cell structures (entosis). In addition, there were mixed nests of conventional and BAP1-inactivated melanocytes and squeezed remnants of the original nevus. Of the 26 lesions studied, 24 yielded a BRAF mutation, while in the remaining two cases there was a RAF1 fusion. BAP1 biallelic and singe allele mutations were found in 4/22 and 16/24 neoplasms, respectively. In five patients, there was a BAP1 germline mutation. Six novel, previously unreported BAP1 mutations have been identified. BAP1 heterozygous loss was detected in 11/22 lesions. Fluorescence in situ hybridization for copy number changes revealed a related amplification of both RREB1 and MYC genes in one tumor, whereas the remaining 20 lesions studied were negative; no TERT-p mutation was found in 14 studied neoplasms. Tetraploidy was identified in 5/21 BIMTs. Of the 21 patients with available follow-up, only one child had a locoregional lymph node metastasis. Our results support a progression of BIMTs from a conventional BRAF mutated in which the original nevus is gradually replaced by epithelioid BAP1-inactivated melanocytes. Some features suggest more complex underlying pathophysiological events that need to be elucidated.

• MeSH
• dítě MeSH
• epiteloidní a vřetenobuněčný névus * genetika   MeSH
• hybridizace in situ fluorescenční MeSH
• lidé MeSH
• nádorové supresorové proteiny genetika   MeSH
• nádory kůže * genetika   patologie   MeSH
• névus * MeSH
• pigmentový névus * genetika   patologie   MeSH
• protoonkogenní proteiny B-Raf genetika   MeSH
• thiolesterasa ubikvitinu genetika   MeSH
• Check Tag
• dítě MeSH
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• BAP1 protein, human MeSH Prohlížeč
• nádorové supresorové proteiny MeSH
• protoonkogenní proteiny B-Raf MeSH
• thiolesterasa ubikvitinu MeSH

Nuclear deubiquitinase BAP1 (BRCA1-associated protein 1) is a core component of multiprotein complexes that promote transcription by reversing the ubiquitination of histone 2A (H2A). BAP1 is a tumor suppressor whose germline loss-of-function variants predispose to cancer. To our knowledge, there are very rare examples of different germline variants in the same gene causing either a neurodevelopmental disorder (NDD) or a tumor predisposition syndrome. Here, we report a series of 11 de novo germline heterozygous missense BAP1 variants associated with a rare syndromic NDD. Functional analysis showed that most of the variants cannot rescue the consequences of BAP1 inactivation, suggesting a loss-of-function mechanism. In T cells isolated from two affected children, H2A deubiquitination was impaired. In matching peripheral blood mononuclear cells, histone H3 K27 acetylation ChIP-seq indicated that these BAP1 variants induced genome-wide chromatin state alterations, with enrichment for regulatory regions surrounding genes of the ubiquitin-proteasome system (UPS). Altogether, these results define a clinical syndrome caused by rare germline missense BAP1 variants that alter chromatin remodeling through abnormal histone ubiquitination and lead to transcriptional dysregulation of developmental genes.

• Klíčová slova
• BAP1, BRCA1, UPS, cancer, chromatin remodeling, deubiquitination, histone 2A, intellectual disability, neurodevelopment, tumor, ubiquitin, ubiquitin-proteasome system,
• MeSH
• chromatin chemie   imunologie   MeSH
• dítě MeSH
• faktor C1 hostitelské buňky genetika   imunologie   MeSH
• heterozygot MeSH
• histony genetika   imunologie   MeSH
• kojenec MeSH
• lidé MeSH
• missense mutace * MeSH
• mladiství MeSH
• mutace ztráty funkce * MeSH
• nádorové supresorové proteiny nedostatek   genetika   imunologie   MeSH
• neurovývojové poruchy genetika   imunologie   patologie   MeSH
• předškolní dítě MeSH
• proteasomový endopeptidasový komplex genetika   imunologie   MeSH
• protein BRCA1 genetika   imunologie   MeSH
• regulace genové exprese MeSH
• restrukturace chromatinu genetika   imunologie   MeSH
• rodina MeSH
• T-lymfocyty imunologie   patologie   MeSH
• thiolesterasa ubikvitinu nedostatek   genetika   imunologie   MeSH
• ubikvitin genetika   imunologie   MeSH
• ubikvitinace MeSH
• ubikvitinligasy genetika   imunologie   MeSH
• zárodečné mutace * MeSH
• Check Tag
• dítě MeSH
• kojenec MeSH
• lidé MeSH
• mladiství MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• BAP1 protein, human MeSH Prohlížeč
• BARD1 protein, human MeSH Prohlížeč
• BRCA1 protein, human MeSH Prohlížeč
• chromatin MeSH
• faktor C1 hostitelské buňky MeSH
• HCFC1 protein, human MeSH Prohlížeč
• histony MeSH
• nádorové supresorové proteiny MeSH
• proteasomový endopeptidasový komplex MeSH
• protein BRCA1 MeSH
• thiolesterasa ubikvitinu MeSH
• ubikvitin MeSH
• ubikvitinligasy MeSH

BRCA1-associated protein (BAP1)-inactivated melanocytic tumor (BIMT) is a group of epithelioid melanocytic neoplasms characterized by the loss of function of BAP1, a tumor suppressor gene located on chromosome 3p21. They occur sporadically or in the setting of an autosomal-dominant cancer susceptibility syndrome that predisposes to the development of different internal malignancies. Most of these cutaneous lesions are associated with a BRAF-mutated melanocytic nevus and therefore are included in the group of combined nevi in the last WHO classification of skin tumors. Apart from a BRAF mutation, an NRAS mutation has been reported in rare cases, whereas in some lesions no driver mutation has been detected. Here, we report 2 cases of BIMTs with a BAP1 mutation and a RAF1 fusion. Both lesions proved to be BRAF and NRAS wild type and were associated with a conventional melanocytic nevus with dysplastic junctional features. We suggest that RAF1 fusions can represent an underlying driver genetic event in these cases. Our study extends the morphological and molecular spectrum in BIMTs.

• MeSH
• dítě MeSH
• dospělí MeSH
• fenotyp MeSH
• fúze genů * MeSH
• genetická predispozice k nemoci MeSH
• GTP-fosfohydrolasy genetika   MeSH
• imunohistochemie MeSH
• lidé MeSH
• membránové proteiny genetika   MeSH
• mutační analýza DNA MeSH
• nádorové biomarkery analýza   genetika   MeSH
• nádorové supresorové proteiny genetika   MeSH
• nádory kůže chemie   genetika   patologie   chirurgie   MeSH
• pigmentový névus chemie   genetika   patologie   chirurgie   MeSH
• protoonkogenní proteiny B-Raf genetika   MeSH
• protoonkogenní proteiny c-raf genetika   MeSH
• thiolesterasa ubikvitinu genetika   MeSH
• umlčování genů * MeSH
• Check Tag
• dítě MeSH
• dospělí MeSH
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• kazuistiky MeSH
• Názvy látek
• BAP1 protein, human MeSH Prohlížeč
• BRAF protein, human MeSH Prohlížeč
• GTP-fosfohydrolasy MeSH
• membránové proteiny MeSH
• nádorové biomarkery MeSH
• nádorové supresorové proteiny MeSH
• NRAS protein, human MeSH Prohlížeč
• protoonkogenní proteiny B-Raf MeSH
• protoonkogenní proteiny c-raf MeSH
• Raf1 protein, human MeSH Prohlížeč
• thiolesterasa ubikvitinu MeSH

Nodular fasciitis (NF) is a benign self-limiting soft tissue lesion that has long been considered a reactive process. Recently, however, the USP6 gene rearrangement has been discovered, and the neoplastic nature of this tumor was suggested. Since then, many fusion partners of the USP6 gene have been reported, with the MYH9 gene as the most common. In this article, we describe a case of NF with a novel EIF5A-USP6 gene fusion associated with unusual pathological features. A 41-year-old healthy woman with a painful, rapidly growing subcutaneous mass on the left forearm with a size of 0.8 cm is presented. A soft tissue fragment measuring 1 cm was surgically excised. Owing to positive surgical margins, re-excision was performed, yielding another 2-cm fragment. The lesion was extensively histologically investigated. Immunohistochemical and molecular-genetic analysis, namely fluorescence in situ hybridization, next-generation sequencing, and reverse transcriptase-polymerase chain reaction, were also performed. Histology revealed a dermally located, mitotically active myofibroblastic proliferation with myxoid areas that ulcerated the overlying epidermis. One atypical mitotic figure was also found. The lesion showed positive immunohistochemical staining with smooth muscle actin, whereas S100 protein and CD34 stains were negative. Using fluorescence in situ hybridization, the USP6 gene rearrangement was detected and subsequent analysis using the Archer fusionPlex Sarcoma kit revealed a novel EIF5A-USP6 gene fusion. In the appropriate clinicopathological context, the detection of USP6 gene rearrangement is extremely useful when diagnosing NF, significantly reducing the risk of misdiagnosis and inappropriate overtreatment.

• MeSH
• dospělí MeSH
• eukaryotický translační iniciační faktor 5A MeSH
• fasciitida genetika   patologie   MeSH
• iniciační faktory genetika   MeSH
• lidé MeSH
• onkogenní fúze MeSH
• proteiny vázající RNA genetika   MeSH
• thiolesterasa ubikvitinu genetika   MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• kazuistiky MeSH
• přehledy MeSH
• Názvy látek
• iniciační faktory MeSH
• proteiny vázající RNA MeSH
• thiolesterasa ubikvitinu MeSH
• USP6 protein, human MeSH Prohlížeč