scholarly journals Diagnosis of Osteoarthritis Subtypes with Blood Biomarkers

2018 ◽  
Author(s):  
Kun Zhao ◽  
Junxin Lin ◽  
Bingbing Wu ◽  
Guofei Sun ◽  
Chengrui An ◽  
...  

AbstractObjectiveTo identity osteoarthritis(OA) subtypes with gene expression of peripheral blood mononuclear cells.MethodsGene expression data (GSE48556) of Genetics osteoARthritis and Progression (GARP) study was downloaded from Gene Expression Omnibus. Principal component analysis and unsupervised clustering were analyzed to identify subtypes of OA and compare major KEGG pathways and cell type enrichment using GSEA and xCell. Classification of subtypes were explored by the utilization of support vector machine.ResultsUnsupervised clustering identified two distinct OA subtypes: Group A comprised of 60 patients (56.6%) and Group B had 46 patients (43.3%). A classifier including nine genes and CD4+T cell and Regulatory T cell flow cytometry could accurately distinguish patients from each group (area under the curve of 0.99 with gene expression). Group A is typical degenerative OA with glycosaminoglycan biosynthesis and apoptosis. Group B is related to Graft versus host disease and antigen processing and presentation, which indicated OA has a new type of “Antigen processing and presentation” similarly as that of RA.ConclusionOA can be clearly classified into two distinguished subtypes with blood transcriptome, which have important significance on the development of precise OA therapeutics.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 4366-4366
Author(s):  
Nnenna Osuji ◽  
Ilaria Del Giudice ◽  
Tim Dexter ◽  
Estella Matutes ◽  
Vasantha Brito-Babapulle ◽  
...  

Abstract T-cell prolymphocytic leukemia (T-PLL) is rare and presents with widespread disease. Indolent presentations are seen but eventually progress. The disease shows marked chemoresistance and is best treated with the monoclonal anti-CD52 antibody (CAMPATH). Prolymphocytes show a post-thymic phenotype and are CD4+CD8− (65%), CD4−CD8+ (10%) or CD4+CD8+ (25%). This double positive phenotype, raises questions about the putative ontology of T-PLL. Morphological heterogeneity, with typical (75%), small cell (20%) and cerebriform/sezary-like variants (5%) is described. Inversions or reciprocal translocations of chromosome 14 involving breakpoints at q11 (TCR a/d) and q32.1 (TCL1 and TCL1b) are seen (~ 80%). Other common abnormalities involve chromosome 8, translocation (X;14)(q28;q11) and, ATM (11q23). We investigated the clinico-pathological heterogeneity in T-PLL, at the level of the transcriptome and evaluated the ability of gene expression profiling to sub-classify T-PLL. Total RNA was extracted from blood prolymphocytes (>92% purity) of 22 patients. cDNA synthesis followed by biotin-labelled cRNA synthesis was carried out as per Affymetrix protocols. Fragmented cRNA was hybridized to the Human U133 PLUS2 GeneChip array (54K probes). Microarray services were provided by MRC geneservice (UK HGMP Resource Centre). Hierarchical clustering of samples was performed using a filtered gene set (12,456) and >4 different algorithims. Prediction analysis for micoarray (PAM) and significance analysis of microarray (SAM) were used to evaluate class performance, and partition genes using pre-defined labels of immunophenotype, karyotype, response and morphology. Validation was performed by RT-PCR in a subset of genes.Unsupervised analysis robustly and reproducibly partitioned samples into 2 groups; A (n=8) and B (n=14). SAM analysis identified 4487 differentially expressed transcripts (false discovery rates <1%), >40% of which showed >2-fold difference in expression between the groups. There was no statistical difference in age, immunophenotype or karyotype betweeen groups, however, differential response to CAMPATH was seen. PAM analysis refined a sub-group of ~123 genes which most efficiently differentiated these groups. Group A showed significantly higher rates of non-response and progressive disease as compared to group B (n=14, p=0.036). Key differences related to apoptosis and cell-cycle associated gene expression. Down regulation of caspases (CASP1, CASP2,CASP4, CARD8 and CASP8AP2), cyclins (CCNC, CCND2, CCND3, CCNG1, CCNI, CCNT2), bcl-2, HDAC1, HIPK2, IL6R and ATM were frequent in group A with upregulation of genes implicated in NF-kB (TRAF4, SQSTM1) and TNF pathways (LMNA, ARTS-1), as well as transcription factors such as ATF-3. CD52 expression was ~2-fold higher in group B and may explain in part, differential responses to CAMPATH. RT-PCR validated gene expression data for LMNA and ATF-3. Despite the small numbers, algorithim-independent segregation into 2 consistent groups, in conjunction with the magnitude of gene differences, presence of many mutually exclusive divisions, and low prediciton errors, imply that the 2 identified profiles arise from fundamental differences at a regulatory level and thus likely represent a generalisable classification for T-PLL. Differential responses to CAMPATH may be a sub-feature of this grouping.


2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e15650-e15650
Author(s):  
Kehe Chen ◽  
Haiming Wei ◽  
Tianqi Liu ◽  
Zhenxiang Chen ◽  
Deng Pan ◽  
...  

e15650 Background: Hepatocellular carcinoma (HCC) is one of the most common prevalent fatal cancers worldwide with poor prognosis due to high incidence of recurrence. For patients with HCC, surgical treatment is a potentially cutative therapy. However, the puzzle in the therapy was the rapid recurrence after surgery. The purpose of this study was to integrate the impact of different immune context present in HCC microenvironment on patients’ prognosis, provide the molecular prediction clue of HCC recurrence. Methods: RNA targeted sequencing was performed on 12 primary tumor specimens from HCC patients. Transcripts of 395 immune related genes expressed in FFPE tumor samples were analyzed. The lima package was used to analyze the different expressed genes (DEGs) between patients with different prognosis. The gene set variance analysis (GSVA) analysis was performed to explore gene sets enrichment related to the recurrence post-resection. Results: 15 DEGs were detected in tissue samples between the two groups (group A: patients who relapsed within one year after surgery; group B: patients who hadn't relapsed beyond two years after surgery). The Antigen processing pathway enrichment may associate with the favorable prognosis (p < 0.05). HLA-A gene expression in group A was lower than that in group B; The gene expression of IL23A, TP63, ALOX15B, BUB1, CXCR2, CCL20, CLEC4C, PTK7, MPO, IL1B, MMP9, GAGE2C, GAGE2A, GAGE2E, DMBT1, FOXM1 in group A was higher than that in group B. Additionally, the combination of 3 genes (TP63, IL23A and BUB1) can distinguish the patients recurrent within 1 year or beyond 2 years post-resection. The joint diagnostic equation is logit (Y = 1) = 0.073 +0.740 *(TP63) + 0.589 * (IL23A)+0.959(BUB1), (Optimal threshold: 0.667, specificity: 1, sensitivity: 0.833). Conclusions: Our results suggest that RNA-seq of immune related genes from FFPE sample can effectively profile the specific landscape of tumor immune microenvironment and predict the survival of HCC. 3 genes’ expression (TP63, IL23A and BUB1) might correlate with recurrence in HCC patients after surgery.


2020 ◽  
pp. 2002695 ◽  
Author(s):  
Elliott D. Crouser ◽  
Landon W. Locke ◽  
Mark W. Julian ◽  
Sabahattin Bicer ◽  
Wolfgang Sadee ◽  
...  

IntroductionSarcoidosis and tuberculosis are granulomatous pulmonary diseases characterised by heightened immune reactivity to Mycobacterium tuberculosis (M.tb.) antigens. We hypothesised that an unsupervised analysis comparing the molecular characteristics of granulomas formed in response to M.tb. antigens in patients with sarcoidosis or latent tuberculosis infection (LTBI) would provide novel insights into the pathogenesis of sarcoidosis.MethodsA genomic analysis identified differentially expressed (DE) genes in granuloma-like cell aggregates formed by sarcoidosis (n=12) or LTBI patients (n=5) in an established in vitro human granuloma model wherein peripheral blood mononuclear cells (PBMCs) were exposed to M.tb. antigens (beads coated with purified protein derivative, PPD) and cultured for 7 days. Pathway analysis of DE genes identified canonical pathways, most notably antigen processing and presentation via phagolysosomes, as a prominent pathway in sarcoidosis granuloma formation. The phagolysosomal pathway promoted mTORc1/STAT3 signal transduction. Thus, granuloma formation and related immune mediators were evaluated in the absence or presence of various pre-treatments known to prevent phagolysosome formation (chloroquine) or phagosome acidification (bafilomycin A1) or directly inhibit mTORc1 activation (rapamycin).ResultsIn keeping with genomic analyses indicating enhanced phagolysosomal activation and predicted mTORc1 signalling, it was determined that sarcoidosis granuloma formation and related inflammatory mediator release was dependent upon phagolysosome assembly and acidification and mTORc1/S6/STAT3 signal transduction.ConclusionsSarcoidosis granulomas exhibit enhanced and sustained intracellular antigen processing and presentation capacities, and related phagolysosome assembly and acidification are required to support mTORc1 signalling to promote sarcoidosis granuloma formation.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 1807-1807 ◽  
Author(s):  
Hui Yang ◽  
Zhihong Fang ◽  
Karen Clise-Dwyer ◽  
Kathryn Ruisaard ◽  
Simona Colla ◽  
...  

Abstract Introduction PD-1 is a negative costimulatory receptor on activated T lymphocytes which counters the activation signal provided by T cell receptor ligation. The expression of PD-1 on T lymphocytes can be dynamically modulated by DNA methylation. A recent study in solid tumors (Kleffel S et al, Cell 2015) suggested that PD-1 was not only expressed by immune cells, but also by a subpopulation of cancer cells, and the cancer intrinsic PD-1 can promote tumorigenesis. Our previous study (Yang H et al, Leukemia 2014) demonstrated an increased PD-1 mRNA expression in peripheral blood mononuclear cells from MDS patients under hypomethylating agent (HMA) treatment, but little is known about detailed PD-1 expression in MDS. PD-1 signaling has been reported to be involved in MDS pathogenesis and resistance mechanisms to HMAs (Yang H et al, Leukemia 2014). Therefore, the PD-1 pathway represents an attractive target and anti-PD-1 monoclonal antibodies are being increasingly used to study MDS. Precise understanding of PD-1 expression in MDS patients may allow for effective treatment. Methods and Human Specimens With this purpose, using multicolor flow cytometry analysis, we studied the PD-1 expression on bone marrow Lin-CD34+ cells (Lineage cells: CD2, CD3, CD4, CD7, CD10, CD11b, CD14, CD19, CD20, CD33, CD56 and CD235a) from 51 patients enrolled in a clinical trial 2014-0930. Based on 5-azacytidine treatment, these patients can be divided into two groups: group A included 29 patients (57%) (22 MDS, 5 CMML, 1 MDS/MPD and 1 AML) which were treated with 5-azacitidine in combination with ipilimumab (N=10), nivolumab (N=16) or ipilimumab + nivolumab (N=2), one patient treated with 5-azacytidine only was also included; group B included 22 patients (43%) (16 MDS, 4 CMML and 2 MDS/MPD) which did not receive 5-azacytidine treatment and were treated with ipilimumab (N=12), nivolumab (N=5) or ipilimumab + nivolumab (N=5) alone. Positive PD-1 expression was considered when the median fluorescence intensity (MFI) ratio between sample and FMO negative control was more than 2. Results In group A, 26 patients (90%) were previously untreated at the time of enrollment. PD-1 expression was not observed in 8 untreated baseline samples collected. We then performed the analysis in samples under different time points of treatment. PD-1 expression was observed in 11 patients (38%, 9 responders, 1 stable disease and 1 non-responder) in at least one time point during treatment. Interestingly, 9 (82%) of them were treated with 5-azacytidine in combination with nivolumab, the other two were treated with 5-azacytidine in combination ipilimumab and ipilimumab + nivolumab separately. PD-1 expression was observed in 56% of the patients under 5-azacytidine in combination with nivolumab treatment. Figure 1 is an example of PD-1 expression in Lin-CD34+ cells from patient treated with 5-azacytidine in combination with nivolumab. In group B, all patients except one (95%) were previously treated at the time of enrollment. PD-1 expression was observed in 2 out of 13 baseline samples collected, and the PD-1 expression was not detected on these two patients after follow-up treatment with ipilimumab. PD-1 expression was observed in two patients (9%, 1 responder, 1 stable disease) in at least one time point during treatment (1 ipilimumab, 1 ipilimumab + nivolumab). Taken together, PD-1 expression was significantly induced in patients treated with 5-azacytidine when compare to patients without 5-azacytidine treatment (38% vs 9%, p=0.023), especially in the group of patients treated with 5-azacytidine in combination with nivolumab (56% vs 10%, p=0.037, compare with 5-azacytidine in combination with ipilimumab). Induction of PD-1 expression may contribute to the response of the treatment (77% vs 46%, p=0.058). Conclusion Our study demonstrates that induced expression of PD-1 on MDS Lin-CD34+ cells may contribute to the response of MDS patients to treatment with 5-azacytidine in combination with nivolumab. PD-1 methylation as well as other biological functions related to this treatment need to be further studied. Figure 1. Figure 1. Disclosures Colla: Abbvie: Research Funding. Daver:Novartis: Research Funding; Incyte: Research Funding; Otsuka: Consultancy; Daiichi-Sankyo: Research Funding; Sunesis: Consultancy; ImmunoGen: Consultancy; Karyopharm: Consultancy; Alexion: Consultancy; Incyte: Consultancy; Kiromic: Research Funding; Pfizer: Consultancy; ARIAD: Research Funding; Pfizer: Research Funding; Novartis: Consultancy; BMS: Research Funding; Karyopharm: Research Funding; Sunesis: Research Funding.


1999 ◽  
Vol 67 (3) ◽  
pp. 1034-1044 ◽  
Author(s):  
Ernesto Liébana ◽  
Robert M. Girvin ◽  
Michael Welsh ◽  
Sydney D. Neill ◽  
John M. Pollock

ABSTRACT Protective immunity against tuberculosis is considered to be essentially cell mediated, and an important role for CD8+ T lymphocytes has been suggested by several studies of murine and human infections. The present work, using an experimental model of infection with Mycobacterium bovis in cattle, showed that liveM. bovis elicits the activation of CD8+ T cells in vitro. However, a sonic extract prepared from M. bovis (MBSE) and protein purified derivative (PPDb) also induced a considerable degree of activation of the CD8+ T cells. Analysis of proliferative responses of peripheral blood mononuclear cells, purified CD8+ T cells, and CD8+ T-cell clones to M. bovis and to soluble antigenic preparations (MBSE, PPDb) showed that the responses of all three types of cells were always superior for live mycobacteria but that strong responses were also obtained with complex soluble preparations. Furthermore, while cytotoxic capabilities were not investigated, the CD8+ T cells were found to produce and release gamma interferon in response to antigen (live and soluble), which indicated one possible protective mechanism for these cells in bovine tuberculosis. Finally, it was demonstrated by metabolic inhibition with brefeldin A and cytochalasin D at the clonal level that an endogenous pathway of antigen processing is required for presentation to bovine CD8+ cells and that presentation is also dependent on phagocytosis of the antigen.


Author(s):  
Daniel He ◽  
Chen Xi Yang ◽  
Basak Sahin ◽  
Amrit Singh ◽  
Casey P. Shannon ◽  
...  

Abstract Background Blood has proven to be a useful resource for molecular analysis in numerous biomedical studies, with peripheral blood mononuclear cells (PBMCs) and whole blood being the major specimen types. However, comparative analyses between these two major compartments (PBMCs and whole blood) are few and far between. In this study, we compared gene expression profiles of PBMCs and whole blood samples obtained from research subjects with or without mild allergic asthma. Methods Whole blood (PAXgene) and PBMC samples were obtained from 5 mild allergic asthmatics and 5 healthy controls. RNA from both sample types was measured for expression of 730 immune-related genes using the NanoString nCounter platform. Results We identified 64 uniquely expressed transcripts in whole blood that reflected a variety of innate, humoral, and adaptive immune processes, and 13 uniquely expressed transcripts in PBMCs which were representative of T-cell and monocyte-mediated processes. Furthermore, analysis of mild allergic asthmatics versus non-asthmatics revealed 47 differentially expressed transcripts in whole blood compared to 1 differentially expressed transcript in PBMCs (FDR < 0.25). Finally, through simultaneous measurement of PBMC proteins on the nCounter assay, we identified CD28 and OX40 (TNFRSF4), both of which are critical co-stimulatory molecules during T-cell activation, as significantly upregulated in asthmatics. Conclusions Whole blood RNA preserved in PAXgene tubes is excellent for producing gene expression data with minimal variability and good sensitivity, suggesting its utility in multi-centre studies requiring measurement of blood gene expression.


2009 ◽  
Vol 107 (1) ◽  
pp. 168-175 ◽  
Author(s):  
Shlomit Radom-Aizik ◽  
Frank Zaldivar ◽  
Szu-Yun Leu ◽  
Dan M. Cooper

Recent studies show that brief exercise alters circulating neutrophil and peripheral blood mononuclear cell (PBMC) gene expression, ranging from cell growth to both pro-and anti-inflammatory processes. These initial observations were made solely in males, but whether PBMC gene expression is altered by exercise in females is not known. Ten early-pubertal girls (8–11 yr old) and 10 late-pubertal girls (15–17 yr old) performed ten 2-min bouts of cycle ergometry (∼90% peak heart rate) interspersed with 1-min rest intervals. Blood was obtained at rest and after exercise, and microarrays were performed in each individual subject. RNA was hybridized to Affymetrix U133+2.0 Arrays. Exercise induced significant changes in PBMC gene expression in early (1,320 genes)- and late (877 genes)-pubertal girls. The expression of 622 genes changed similarly in both groups. Exercise influenced a variety of established gene pathways (EASE < 0.04) in both older (6 pathways) and younger girls (11 pathways). Five pathways were the same in both groups and were functionally related to inflammation, stress, and apoptosis, such as natural killer cell-mediated cytotoxicity, antigen processing and presentation, B cell receptor signaling, and apoptosis. In summary, brief exercise alters PBMC gene expression in early- and late-pubertal girls. The pattern of change involves diverse genetic pathways, consistent with a global danger-type response, perhaps readying PBMCs for a range of physiological functions from inflammation to tissue repair that would be useful following a bout of physical activity.


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