Single-cell RNA sequencing (scRNA-seq) methods are widely used in life sciences, including immunology. Typical scRNA-seq analysis pipelines quantify the abundance of particular transcripts without accounting for alternative splicing. However, a well-established pan-leukocyte surface marker, CD45, encoded by the PTPRC gene, presents alternatively spliced variants that define different immune cell subsets. Information about some of the splicing patterns in particular cells in the scRNA-seq data can be obtained using isotype-specific DNA oligo-tagged anti-CD45 antibodies. However, this requires generation of an additional sequencing DNA library. Here, we present IDEIS, an easy-to-use software for CD45 isoform quantification that uses single-cell transcriptomic data as the input. We showed that IDEIS accurately identifies canonical human CD45 isoforms in datasets generated by 10× Genomics 5' sequencing assays. Moreover, we used IDEIS to determine the specificity of the Ptprc splicing pattern in mouse leukocyte subsets.

• MeSH
• alternativní sestřih MeSH
• analýza jednotlivých buněk metody   MeSH
• antigeny CD45 * genetika   metabolismus   MeSH
• leukocyty metabolismus   imunologie   MeSH
• lidé MeSH
• myši MeSH
• protein - isoformy genetika   MeSH
• sekvenční analýza RNA metody   MeSH
• software * MeSH
• stanovení celkové genové exprese metody   MeSH
• transkriptom MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Advances in single-cell level analytical techniques, especially cytometric approaches, have led to profound innovation in biomedical research, particularly in the field of clinical immunology. This has resulted in an expansion of high-dimensional data, posing great challenges for comprehensive and unbiased analysis. Conventional manual analysis is thus becoming untenable to handle these challenges. Furthermore, most newly developed computational methods lack flexibility and interoperability, hampering their accessibility and usability. Here, we adapted Seurat, an R package originally developed for single-cell RNA sequencing (scRNA-seq) analysis, for high-dimensional flow cytometric data analysis. Based on a 20-marker antibody panel and analyses of T-cell profiles in both adult blood and cord blood (CB), we showcased the robust capacity of Seurat in flow cytometric data analysis, which was further validated by Spectre, another high-dimensional cytometric data analysis package, and conventional manual analysis. Importantly, we identified a unique CD8+ T-cell population defined as CD8+CD45RA+CD27+CD161+ T cell that was predominantly present in CB. We characterised its IFN-γ-producing and potential cytotoxic properties using flow cytometry experiments and scRNA-seq analysis from a published dataset. Collectively, we identified a unique human CB CD8+CD45RA+CD27+CD161+ T-cell subset and demonstrated that Seurat, a widely used package for scRNA-seq analysis, possesses great potential to be repurposed for cytometric data analysis. This facilitates an unbiased and thorough interpretation of complicated high-dimensional data using a single analytical pipeline and opens a novel avenue for data-driven investigation in clinical immunology.

• MeSH
• analýza jednotlivých buněk metody   MeSH
• antigeny CD27 metabolismus   imunologie   MeSH
• antigeny CD45 * metabolismus   imunologie   MeSH
• CD8-pozitivní T-lymfocyty * imunologie   MeSH
• dospělí MeSH
• fetální krev * imunologie   cytologie   MeSH
• imunofenotypizace metody   MeSH
• lektinové receptory NK-buněk - podrodina B imunologie   metabolismus   MeSH
• lidé MeSH
• průtoková cytometrie * metody   MeSH
• software MeSH
• T-lymfocyty - podskupiny imunologie   metabolismus   MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

A number of human autoinflammatory diseases manifest with severe inflammatory bone destruction. Mouse models of these diseases represent valuable tools that help us to understand molecular mechanisms triggering this bone autoinflammation. The Pstpip2cmo mouse strain is among the best characterized of these; it harbors a mutation resulting in the loss of adaptor protein PSTPIP2 and development of autoinflammatory osteomyelitis. In Pstpip2cmo mice, overproduction of interleukin-1β (IL-1β) and reactive oxygen species by neutrophil granulocytes leads to spontaneous inflammation of the bones and surrounding soft tissues. However, the upstream signaling events leading to this overproduction are poorly characterized. Here, we show that Pstpip2cmo mice deficient in major regulator of Src-family kinases (SFKs) receptor-type protein tyrosine phosphatase CD45 display delayed onset and lower severity of the disease, while the development of autoinflammation is not affected by deficiencies in Toll-like receptor signaling. Our data also show deregulation of pro-IL-1β production by Pstpip2cmo neutrophils that are attenuated by CD45 deficiency. These data suggest a role for SFKs in autoinflammation. Together with previously published work on the involvement of protein tyrosine kinase spleen tyrosine kinase, they point to the role of receptors containing immunoreceptor tyrosine-based activation motifs, which after phosphorylation by SFKs recruit spleen tyrosine kinase for further signal propagation. We propose that this class of receptors triggers the events resulting in increased pro-IL-1β synthesis and disease initiation and/or progression.

• MeSH
• adaptorové proteiny signální transdukční genetika   imunologie   MeSH
• antigeny CD45 genetika   imunologie   MeSH
• cytoskeletální proteiny genetika   imunologie   MeSH
• diabetes mellitus 1. typu genetika   imunologie   patologie   MeSH
• interleukin-1beta genetika   imunologie   MeSH
• myši knockoutované MeSH
• myši MeSH
• neutrofily imunologie   patologie   MeSH
• osteomyelitida genetika   imunologie   patologie   MeSH
• signální transdukce genetika   imunologie   MeSH
• stupeň závažnosti nemoci MeSH
• toll-like receptory genetika   imunologie   MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The identification and characterization of rare immune cell populations in humans can be facilitated by their growth advantage in the context of specific genetic diseases. Here, we use autoimmune lymphoproliferative syndrome to identify a population of FAS-controlled TCRαβ+ T cells. They include CD4+, CD8+, and double-negative T cells and can be defined by a CD38+CD45RA+T-BET- expression pattern. These unconventional T cells are present in healthy individuals, are generated before birth, are enriched in lymphoid tissue, and do not expand during acute viral infection. They are characterized by a unique molecular signature that is unambiguously different from other known T cell differentiation subsets and independent of CD4 or CD8 expression. Functionally, FAS-controlled T cells represent highly proliferative, noncytotoxic T cells with an IL-10 cytokine bias. Mechanistically, regulation of this physiological population is mediated by FAS and CTLA4 signaling, and its survival is enhanced by mTOR and STAT3 signals. Genetic alterations in these pathways result in expansion of FAS-controlled T cells, which can cause significant lymphoproliferative disease.

• MeSH
• aktivace lymfocytů imunologie   MeSH
• antigeny CD38 imunologie   MeSH
• antigeny CD45 metabolismus   MeSH
• antigeny CD95 imunologie   MeSH
• CD4-pozitivní T-lymfocyty imunologie   MeSH
• CD8-pozitivní T-lymfocyty imunologie   MeSH
• dítě MeSH
• dospělí MeSH
• kojenec MeSH
• lidé středního věku MeSH
• lidé MeSH
• lymfoproliferativní nemoci imunologie   MeSH
• mladiství MeSH
• mladý dospělý MeSH
• novorozenec MeSH
• předškolní dítě MeSH
• senioři MeSH
• signální transdukce imunologie   MeSH
• Check Tag
• dítě MeSH
• dospělí MeSH
• kojenec MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• novorozenec MeSH
• předškolní dítě MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

T cells require the protein tyrosine phosphatase CD45 to detect and respond to antigen because it activates the Src family kinase Lck, which phosphorylates the T cell antigen receptor (TCR) complex. CD45 activates Lck by opposing the negative regulatory kinase Csk. Paradoxically, CD45 has also been implicated in suppressing TCR signaling by dephosphorylating the same signaling motifs within the TCR complex upon which Lck acts. We sought to reconcile these observations using chemical and genetic perturbations of the Csk/CD45 regulatory axis incorporated with computational analyses. Specifically, we titrated the activities of Csk and CD45 and assessed their influence on Lck activation, TCR-associated ζ-chain phosphorylation, and more downstream signaling events. Acute inhibition of Csk revealed that CD45 suppressed ζ-chain phosphorylation and was necessary for a regulatable pool of active Lck, thereby interconnecting the activating and suppressive roles of CD45 that tune antigen discrimination. CD45 suppressed signaling events that were antigen independent or induced by low-affinity antigen but not those initiated by high-affinity antigen. Together, our findings reveal that CD45 acts as a signaling "gatekeeper," enabling graded signaling outputs while filtering weak or spurious signaling events.

• MeSH
• antigeny CD45 genetika   imunologie   MeSH
• C-terminální Src kinasa genetika   MeSH
• Jurkat buňky MeSH
• lidé MeSH
• myši transgenní MeSH
• myši MeSH
• receptory antigenů T-buněk genetika   imunologie   MeSH
• signální transdukce genetika   imunologie   MeSH
• T-lymfocyty cytologie   imunologie   MeSH
• tyrosinkinasa p56(lck), specifická pro lymfocyty genetika   imunologie   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

:Background: Current diagnosis and staging of advanced epithelial ovarian cancer (aEOC) has important limitations and better biomarkers are needed. We investigate the performance of non-haematopoietic circulating cells (CCs) at the time of disease presentation and relapse. Methods: Venous blood was collected prospectively from 37 aEOC patients and 39 volunteers. CCs were evaluated using ImageStream TechnologyTM and specific antibodies to differentiate epithelial cells from haematopoetic cells. qRT-PCR from whole blood of relapsed aEOC patients was carried out for biomarker discovery. Results: Significant numbers of CCs (CK+/WT1+/CD45-) were identified, quantified and characterised from aEOC patients compared to volunteers. CCs are abundant in women with newly diagnosed aEOC, prior to any treatment. Evaluation of RNA from the CCs in relapsed aEOC patients (n = 5) against a 79-gene panel revealed several differentially expressed genes compared to volunteers (n = 14). Size differentiation of CCs versus CD45+ haematopoietic cells was not reliable. Conclusion: CCs of non-haematopoetic origin are prevalent, particularly in patients with newly diagnosed aEOC. Exploiting a CC-rich population in aEOC patients offers insights into a part of the circulating microenvironment.

• MeSH
• antigeny CD45 metabolismus   MeSH
• karcinom krev   MeSH
• lidé středního věku MeSH
• lidé MeSH
• nádorové biomarkery metabolismus   MeSH
• nádorové buněčné linie MeSH
• nádorové cirkulující buňky metabolismus   patologie   MeSH
• nádory vaječníků krev   MeSH
• proteiny WT1 metabolismus   MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

BACKGROUND: Bone marrow (BM) samples obtained from minimal residual disease (MRD)-negative children with B-cell acute lymphoblastic leukemia (B-ALL) were used in our laboratory as negative biological controls for the development of a neuroblastoma (NBL) flow-cytometric (FC) protocol. The accidental, but systematic, identification of rare cell populations (RCP) mimicking NBL cells (CD45- /CD56+ ) in these samples indicated the need for their thorough immunophenotypic identification, in order to elucidate their possible interference in NBL-MRD assessment. PROCEDURE: RCP observed in BM samples from 14 children recovering from BM aplasia due to intensive chemotherapy for B-ALL were investigated with the following markers: CD81, CD200, CD24, GD2, CD73, CD13, CD90, CD146, CD9, CD117, CD10, CD99, and NG2. BM samples from six newly diagnosed patients with NBL and an NBL cell line were simultaneously investigated as positive controls. RESULTS: The frequency of RCP in B-ALL BM samples was < 1/1 × 104 cells (bulky lysis), and their immunophenotypic profile was indicative of CD56+ mesenchymal stromal cells (MSCs) (CD45- , CD90+ , CD146+ , CD73+ ). Also, RCP expressed CD81 and CD200, simulating NBL cells. The most useful discriminative markers for CD56+ MSCs were CD13 and CD73. An appropriate protocol consisting of two tubes with seven color combinations was further proposed: SYTO-16, GD2 (first tube) or CD73 (second tube)-PE, CD24-ECD, CD13-PC5.5, CD45-PC7, CD81-APC, and CD56-APC700. CONCLUSIONS: RCP that were immunophenotypically similar to NBL were identified as CD56+ MSCs. As these cells might pose an obstacle to accurate NBL disease assessment by FC, especially MRD, an enhanced NBL-FC protocol is proposed for prospective evaluation.

• MeSH
• antigen CD56 metabolismus   MeSH
• antigeny CD45 metabolismus   MeSH
• imunofenotypizace MeSH
• kostní dřeň metabolismus   patologie   MeSH
• lidé MeSH
• mezenchymální kmenové buňky metabolismus   patologie   MeSH
• následné studie MeSH
• neuroblastom diagnóza   etiologie   metabolismus   MeSH
• pre-B-buněčná leukemie komplikace   metabolismus   MeSH
• předškolní dítě MeSH
• prognóza MeSH
• prospektivní studie MeSH
• průtoková cytometrie MeSH
• reziduální nádor etiologie   metabolismus   patologie   MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

AIMS: Immunohistochemical analysis of retraction pocket pars tensa of tympanic membrane in children. Identification of signs typical for cholesteatoma and support of retraction theory of cholesteatoma. STUDY DESIGN: a prospective study analysing 31 surgically removed retraction pockets. DEPARTMENT: University Hospital, Children's Medical Centre Methods: Retraction pockets processed by a standard process for immunohistochemical analysis. The observed findings were specified using antibodies CD45 LCA (leukocyte common antigen), CD31 (platelet endothelial cell adhesion molecule), D2-40 (marker of lymphatic endothelium), MMP9 (marker of degradation of connective tissue extracellular matrix) and Ki67 (cellular marker of proliferation). RESULTS: All observed parameters except for MMP9 had a significantly higher incidence in retraction pocket stage III compared to stage II according to Charachon. CONCLUSION: We described immunohistochemical signs of retraction pocket pars tensa of tympanic membrane in children resulting in cholesteatoma. All the observed signs occur in the structure of matrix and perimatrix of cholesteatoma. A significantly higher incidence of all observed parameters except from MMP9 was proved in retraction pocket stage III, unlike in stage II. This observation proves the fact that retraction pocket is a progressive disease and is a procholesteatoma stage.

• MeSH
• antigen Ki-67 metabolismus   MeSH
• antigeny CD31 metabolismus   MeSH
• antigeny CD45 metabolismus   MeSH
• biologické markery metabolismus   MeSH
• cholesteatom středního ucha metabolismus   MeSH
• dítě MeSH
• imunohistochemie MeSH
• lidé MeSH
• matrixová metaloproteinasa 9 metabolismus   MeSH
• membrana tympani metabolismus   MeSH
• prospektivní studie MeSH
• Check Tag
• dítě MeSH
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Monitoring immune responses to solid cancers may be a better prognostic tool than conventional staging criteria, and it can also serve as an important criterion for the selection of individualized therapy. Multiparametric phenotyping by mass cytometry extended possibilities for immunoprofiling. However, careful optimization of each step of such method is necessary for obtaining reliable results. Also, with respect to procedure length and costs, sample preparation, staining, and storage should be optimized. Here, we designed a panel of 31 antibodies which allows for identification of several subpopulations of lymphoid and myeloid cells in a solid tumor and peripheral blood simultaneously. For sample preparation, disaggregation of tumor tissue with two different collagenases combined with DNase I was compared, and removal of dead or tumor cells by magnetic separation was evaluated. Two possible procedures of barcoding for single-tube staining of several samples were examined. While the palladium-based barcoding affected the stability of several antigens, the staining with two differently labeled CD45 antibodies was suitable for cells isolated from a patient's blood and tumor. The storage of samples in the intercalation solution for up to two weeks did not influence results of the analysis, which allowed the measurement of samples collected within this interval on the same day. This procedure optimized on samples from patients with head and neck squamous cell carcinoma enabled identification of various immune cells including rare subpopulations.

• MeSH
• analýza jednotlivých buněk MeSH
• antigeny CD45 imunologie   MeSH
• deoxyribonukleasa I metabolismus   MeSH
• imunofenotypizace metody   MeSH
• kolagenasy metabolismus   MeSH
• lidé MeSH
• lymfocyty fyziologie   MeSH
• monoklonální protilátky metabolismus   MeSH
• myeloidní buňky fyziologie   MeSH
• nádory diagnóza   imunologie   MeSH
• palladium metabolismus   MeSH
• průtoková cytometrie MeSH
• separace buněk MeSH
• taxonomické DNA čárové kódování MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

The purpose of the study was to assess whether the occurrence of restenosis is associated with CD45+ platelet count and neutrophil to lymphocyte ratio in patients with type 2 diabetes mellitus (DM) after drug-eluting stent (DES) implantation for stable coronary artery disease (CAD). The study comprised 126 patients, including 55 patients with type 2 DM and stable CAD who underwent elective coronary artery stenting with DES and follow-up angiography within 6 to 12 months. Blood samples were collected from each patient on the morning of the coronary angiography procedure. The variables related to in-stent restenosis were selected by logistic regression analysis. The logistic regression analysis showed that 2 inflammatory factors, CD45+ platelet count (odds ratio [OR] = 4.51, 95% confidence interval [CI]: 1.50-13.50, P = .007) and neutrophil to lymphocyte ratio (OR = 3.09, 95% CI: 1.05-9.10, P = .04), were significantly associated with the risk of in-stent restenosis after stenting with DES in patients with stable CAD and type 2 DM. A receiver operator characteristic curve analysis indicated that the area under the curve was 0.83% (0.05%; P < .001), which showed that the logistic model had good predictive accuracy (based on CD45+ platelet count and neutrophil to lymphocyte ratio) for the risk of in-stent restenosis development in DES in patients with CAD and type 2 DM. Two novel biomarkers of restenosis, CD45+ platelet count and neutrophil to lymphocyte ratio, may be effectively used to predict in-stent restenosis after DES implantation in patients with CAD and type 2 DM.

• MeSH
• antigeny CD45 krev   MeSH
• biologické markery krev   MeSH
• diabetes mellitus 2. typu krev   patologie   chirurgie   MeSH
• diabetické angiopatie krev   patologie   chirurgie   MeSH
• koronární restenóza krev   patologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• nemoci koronárních tepen krev   patologie   chirurgie   MeSH
• počet trombocytů MeSH
• senioři MeSH
• stenty uvolňující léky * MeSH
• trombocyty metabolismus   patologie   MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• klinické zkoušky MeSH