Peripheral Blood Gene Expression Profiles Research Articles

Clinical Utility of the Molecular Microscope Diagnostic System in a Real-World Transplant Cohort: Moving Towards a New Paradigm.

To evaluate the clinical implications of adjunctive molecular gene expression analysis (MMDx ) of biopsy specimens in heart transplant (HT ) recipients with suspected rejection. Histopathological evaluation remains the standard method for rejection diagnosis in HT. However, the wide interobserver variability combined with a relatively common incidence of "biopsy-negative" rejection has raised concerns about the likelihood of false-negative results. MMDx, which uses gene expression to detect early signs of rejection, is a promising test to further refine the assessment of HT rejection. Single-center prospective study of 418 consecutive for-cause endomyocardial biopsies performed between November 2022 and May 2024. Each biopsy was graded based on histology and assessed for rejection patterns using MMDx. MMDx results were deemed positive if borderline or definitive rejection was present. The impact of MMDx results on clinical management was evaluated. Primary outcomes were 1-year survival and graft dysfunction following MMDx-guided clinical management. Secondary outcomes included changes in donor-specific antibodies, MMDx gene transcripts, and donor-derived cell-free DNA (dd-cfDNA) levels. We analyzed 418 molecular samples from 237 unique patients. Histology identified rejection in 32 cases (7.7%), while MMDx identified rejection in 95 cases (22.7%). Notably, in 79 of the 95 cases where MMDx identified rejection, histology results were negative, with the majority of these cases being antibody-mediated rejection (62.1%). Samples with rejection on MMDx were more likely to show a combined elevation of dd-cfDNA and peripheral blood gene expression profiling than those with borderline or negative MMDx results (36.7% vs 28.0% vs 10.3%; p<0.001). MMDx results led to the implementation of specific antirejection protocols or changes in immunosuppression in 20.4% of cases, and in 73.4% of cases where histology was negative and MMDx showed rejection. 1-year survival was better in the positive MMDx group where clinical management was guided by MMDx results (87.0% vs 78.6%; log rank p=0.0017). In our cohort, MMDx results more frequently indicated rejection than histology, often leading to the initiation of antirejection treatment. Intervention guided by positive MMDx results was associated with improved outcomes.

Peripheral Blood Gene Expression Profiling Reveals Molecular Pathways Associated with Cervical Artery Dissection.

Cervical artery dissection (CeAD) is the primary cause of ischemic stroke in young adults. Monogenic heritable connective tissue diseases account for fewer than 5% of cases of CeAD. The remaining sporadic cases have known risk factors. The clinical, radiological, and histological characteristics of systemic vasculopathy and undifferentiated connective tissue dysplasia are present in up to 70% of individuals with sporadic CeAD. Genome-wide association studies identified CeAD-associated genetic variants in the non-coding genomic regions that may impact the gene transcription and RNA processing. However, global gene expression profile analysis has not yet been carried out for CeAD patients. We conducted bulk RNA sequencing and differential gene expression analysis to investigate the expression profile of protein-coding genes in the peripheral blood of 19 CeAD patients and 18 healthy volunteers. This was followed by functional annotation, heatmap clustering, reports on gene-disease associations and protein-protein interactions, as well as gene set enrichment analysis. We found potential correlations between CeAD and the dysregulation of genes linked to nucleolar stress, senescence-associated secretory phenotype, mitochondrial malfunction, and epithelial-mesenchymal plasticity.

Ensemble Learning for Higher Diagnostic Precision in Schizophrenia Using Peripheral Blood Gene Expression Profile.

Stigma contributes to a significant part of the burden of schizophrenia (SCZ), therefore reducing false positives from the diagnosis would be liberating for the individuals with SCZ and desirable for the clinicians. The stigmatization associated with schizophrenia advocates the need for high-precision diagnosis. In this study, we present an ensemble learning-based approach for high-precision diagnosis of SCZ using peripheral blood gene expression profiles. The machine learning (ML) models, support vector machines (SVM), and prediction analysis for microarrays (PAM) were developed using differentially expressed genes (DEGs) as features. The SCZ samples were classified based on a voting ensemble classifier of SVM and PAM. Further, microarray-based learning was used to classify RNA sequencing (RNA-Seq) samples from our case-control study (Pune-SCZ) to assess cross-platform compatibility. Ensemble learning using ML models resulted in a significantly higher precision of 80.41% (SD: 0.04) when compared to the individual models (SVM-radial: 71.69%, SD: 0.04 and PAM 77.20%, SD: 0.02). The RNA sequencing samples from our case-control study (Pune-SCZ) resulted in a moderate precision (59.92%, SD: 0.05). The feature genes used for model building were enriched for biological processes such as response to stress, regulation of the immune system, and metabolism of organic nitrogen compounds. The network analysis identified RBX1, CUL4B, DDB1, PRPF19, and COPS4 as hub genes. In summary, this study developed robust models for higher diagnostic precision in psychiatric disorders. Future efforts will be directed towards multi-omic integration and developing "explainable" diagnostic models.

Abstract WP313: Towards Molecular Profiling of Transient Ischemic Attack Mimics for Triage

Peripheral blood gene expression profiles can distinguish ischemic stroke from intracerebral hemorrhage and controls. However, it can be difficult to clinically distinguish “mimics” of transient ischemic attacks (TIA) and minor strokes from true TIAs and minor strokes. Even with imaging this can be a challenging differential diagnosis in the ED and other acute settings. Hence, there is a need for defining a molecular profile from blood that could guide triage of TIA mimics to reduce ED burden. This multi-site project collected peripheral blood from the participants and generated gene-level data from RNA sequencing. The cohort was composed of patients with a) TIA mimic presentation (n= 142 TIA mimics: an acute onset of neurological symptoms lasting &lt;24h, that can be explained by some identifiable process other than cerebral ischemia including migraine, seizure, peripheral vestibular disease, brain tumors, syncope, root or peripheral nerve disease, and others); b) patients with transient ischemic attacks (n= 181 TIA: acute onset of neurological symptoms and signs that last &lt;24h with a likely underlying cause of either large vessel atherosclerosis or cardioembolic origin but with a negative brain DWI-MRI); c) controls (n= 172 VRFC: no acute brain event, usually with one or more vascular risk factors including diabetes, hypertension or hypercholesterolemia). Differential expression (DE) analyses (fold change &gt;

RNA Sequencing of Whole Blood in Premature Coronary Artery Disease: Identification of Novel Biomarkers and Involvement of T Cell Imbalance.

Serum biomarkers were explored based on the peripheral blood gene expression profiles of premature coronary artery disease (PCAD). RNA sequencing (RNA-Seq) was used to detect PCAD-specific differentially expressed genes (DEGs). Quantitative real-time polymerase chain reaction (RT-PCR) was used to validate the most significant DEGs, and enzyme-linked immunosorbent assay (ELISA) was utilized to quantify the effect on corresponding serum proteins. Fifty-nine PCAD-specific DEGs were identified. Functional analysis showed positive regulation of T cell-mediated cytotoxicity, regulation of T cell-mediated immunity, and the regulation of alpha-beta T cell proliferation which were enriched in PCAD. RT-PCR validated the significant difference in the expression of BAG6, MUC5B, and APOA2 between PCAD and late-onset coronary artery disease (LCAD) patients. ELISA validation showed serum MUC5B increased dramatically in PCAD when compared to LCAD. Our study found T cells contribute to the occurrence of PCAD, and the inflammatory factor MUC5B may be a novel serum marker in PCAD patients.

Micro-inflammation related gene signatures are associated with clinical features and immune status of fibromyalgia

BackgroundFibromyalgia (FM) is a multifaceted disease. Along with the genetic, environmental and neuro-hormonal factors, inflammation has been assumed to have role in the pathogenesis of FM. The aim of the present study was to explore the differences in clinical features and pathophysiology of FM patients under different inflammatory status.MethodsThe peripheral blood gene expression profile of FM patients in the Gene Expression Omnibus database was downloaded. Differentially expressed inflammatory genes were identified, and two molecular subtypes were constructed according to these genes used unsupervised clustering analysis. The clinical characteristics, immune features and pathways activities were compared further between the two subtypes. Then machine learning was used to perform the feature selection and construct a classification model.ResultsThe patients with FM were divided into micro-inflammation and non-inflammation subtypes according to 54 differentially expressed inflammatory genes. The micro-inflammation group was characterized by more major depression (p = 0.049), higher BMI (p = 0.021), more active dendritic cells (p = 0.010) and neutrophils. Functional enrichment analysis showed that innate immune response and antibacterial response were significantly enriched in micro-inflammation subtype (p < 0.050). Then 5 hub genes (MMP8, ENPP3, MAP2K3, HGF, YES1) were screened thought three feature selection algorithms, an accurate classifier based on the 5 hub DEIGs and 2 clinical parameters were constructed using support vector machine model. Model scoring indicators such as AUC (0.945), accuracy (0.936), F1 score (0.941), Brier score (0.079) and Hosmer–Lemeshow goodness-of-fit test (χ2 = 4.274, p = 0.832) proved that this SVM-based classifier was highly reliable.ConclusionMicro-inflammation status in FM was significantly associated with the occurrence of depression and activated innate immune response. Our study calls attention to the pathogenesis of different subtypes of FM.

Bioinformatic identification and experiment validation revealed that ACTG1 is a promising prognostic signature and therapeutic target for sepsis.

In the intensive care unit, sepsis is a prevalent clinical syndrome (i.e. the final pathway to death from most infections). Peripheral blood gene expression profiling is becoming more and more accepted as a potential diagnostic or prognostic tool. This work aimed to recognize genes related to sepsis, providing potential translational therapeutic targets. RNA sequencing was performed on peripheral blood mononuclear cells from 20 healthy control subjects and 51 sepsis patients. Weighted gene coexpression network analysis was employed to pick out sepsis-related and immunocyte-related gene modules. Genes in the yellow module are primarily involved in excessive inflammation and immune suppression. STRING and Cytoscape were combined to identify ACTG1 and IQGAP1 as hub genes with highest connective degree, and prognostic predication value of ACTG1 was confirmed. Both univariate and multivariate logistic regression analyses were carried out. ACTG1 messenger RNA expression was increased in animal and in cell-related sepsis models. Small interfering RNA revealed decreasing ACTG1 can reduce the in vitro sepsis model apoptosis. We have authenticated ACTG1 as a reliable signature of a poor outcome of sepsis and promising therapeutic targets for sepsis.

Multiple abnormal peripheral blood gene expression assay results are correlated with subsequent graft loss after kidney transplantation.

The aim of this study was to correlate peripheral blood gene expression profile (GEP) results during the first post-transplant year with outcomes after kidney transplantation. We conducted a prospective, multicenter observational study of obtaining peripheral blood at five timepoints during the first post-transplant year to perform a GEP assay. The cohort was stratified based on the pattern of the peripheral blood GEP results: Tx-all GEP results normal, 1 Not-TX had one GEP result abnormal and >1 Not-TX two or more abnormal GEP results. We correlated the GEP results with outcomes after transplantation. We enrolled 240 kidney transplant recipients. The cohort was stratified into the three groups: TX n=117 (47%), 1 Not-TX n=59 (25%) and >1 Not-TX n=64 (27%). Compared to the TX group, the >1 Not-TX group had lower eGFR (p<.001) and more chronic changes on 1-year surveillance biopsy (p=.007). Death censored graft survival showed inferior graft survival in the >1 Not-TX group (p<.001) but not in the 1 Not-TX group. All graft losses in the >1 Not-TX group occurred after 1-year post-transplant. We conclude that a pattern of persistently Not-TX GEP assay correlates with inferior graft survival.

Effect of Age and Sex on Gene Expression-Based Radiation Biodosimetry Using Mouse Peripheral Blood

Blood-based gene expression profiles that can reconstruct radiation exposure are being developed as a practical approach to radiation biodosimetry. However, age and sex could potentially limit the accuracy of the approach. In this study, we determined the impact of age on the peripheral blood cell gene expression profile of female mice exposed to radiation and identified differences and similarities with a previously obtained transcriptomic signature of male mice. Young (2 months) and old (24 months) female mice were irradiated with 4 Gy X-rays, total RNA was isolated from blood 24 hours later and subjected to whole-genome microarray analysis. Dose reconstruction analyses using a gene signature trained on gene expression data from irradiated young male mice showed accurate reconstruction of 0 or 4 Gy doses with root mean square error of ±0.75 Gy (R2 = 0.90) in young female mice. Although dose reconstruction for irradiated old female mice was less accurate than young female mice, the deviation from the actual radiation dose was not statistically significant. Pathway analysis of differentially expressed genes revealed that after irradiation, apoptosis-related functions were overrepresented, whereas functions related to quantities of various immune cell subtypes were underrepresented, among differentially expressed genes from young female mice, but not older animals. Furthermore, young mice significantly upregulated genes involved in phagocytosis, a process that eliminates apoptotic cells and preserves tissue homeostasis. Both functions were also overrepresented in young, but not old, male mice following 4 Gy X-irradiation. Lastly, functions associated with neutrophil activation that is essential for killing invading pathogens and regulating the inflammatory response were predicted to be uniquely enriched in young but not old female mice. This work supports the concept that peripheral blood gene expression profiles can be identified in mice that accurately predict physical radiation dose exposure irrespective of age and sex.

Peripheral Blood Gene Expression Profile of Infants with Atopic Dermatitis

To enhance the understanding of molecular mechanisms and mine previously unidentified biomarkers of pediatric atopic dermatitis, PBMC gene expression profiles were generated by RNA sequencing in infants with atopic dermatitis and age-matched controls. A total of 178 significantly differentially expressed genes (DEGs) (115 upregulations and 63 downregulations) were seen, compared with those in healthy controls. The DEGs identified included IL1β, TNF, TREM1, IL18R1, and IL18RAP. DEGs were validated by real-time RT- qPCR in a larger number of samples from PBMCs of infants with atopic dermatitis aged <12 months. Using the DAVID (Database for Annotation, Visualization and Integrated Discovery) database, functional and pathway enrichment analyses of DEGs were performed. Gene ontology enrichment analysis showed that DEGs were associated with immune responses, inflammatory responses, regulation of immune responses, and platelet activation. Pathway analysis indicated that DEGs were enriched in cytokine‒cytokine receptor interaction, immunoregulatory interactions between lymphoid and nonlymphoid cells, hematopoietic cell lineage, phosphoinositide 3-kinase‒protein kinase B signaling pathway, NK cell‒mediated cytotoxicity, and platelet activation. Furthermore, the protein‒protein interaction network was predicted using the STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) database and visualized with Cytoscape software. Finally, on the basis of the protein‒protein interaction network, 18 hub genes were selected, and two significant modules were obtained. In conclusion, this study sheds light on the molecular mechanisms of pediatric atopic dermatitis and may provide diagnostic biomarkers and therapeutic targets.

A non-invasive piTreg-related gene signature for spontaneous tolerance in renal transplantation

BackgroundAchieving spontaneous tolerance is the optimal goal in renal transplantation (RT). However, robust biomarkers indicating spontaneous tolerance are still lacking for RT recipients in clinics. MethodsThe peripheral blood gene expression profiles of RT recipients in the state of tolerance and other conditions from four independent cohorts were collected in databases. Immune cell abundance assessment and single-cell analysis were utilized and the peripherally induced regulatory T cell (piTreg) subset was identified as the key cell subtype. Then, a piTreg-related gene set was identified by analyzing cell induction data. Subsequently, selected biomarkers were applied to the Elastic Net for signature construction. The diagnostic ability of the signature was validated in three independent cohorts (Microarray) and our clinical cohort (RT-qPCR). Additionally, time-course analyses during short-term and long-term periods after transplantation were performed to examine whether the gene signature was affected by the administration of immunosuppressive (IS) regimens. ResultsThe piTreg subset was found to possess the best discriminating ability in the peripheral blood for tolerance. After gene set identification and filtering, a two-gene piTreg-related gene signature was constructed in the training cohort (AUC = 0.830). The signature showed robust performance in three independent validation cohorts (AUC = 0.840, 0.826, and 0.859, respectively). The signature was also proved to be not affected by IS regimens in both short-term and long-term periods after RT. ConclusionsWe developed and validated a piTreg-related two-gene signature based on the peripheral blood for tolerance in RT recipients. The non-invasive signature offered a promising potential testing method for individualized immunosuppressant management and immunologic surveillance for RT recipients in clinics.

Differential expression and significance of peripheral blood genes in coronary artery heart disease.

BackgroundThe peripheral blood gene expression profile of patients with coronary artery disease (CAD) has not been fully resolved. The aim of this study was to further analyze the peripheral blood transcriptome information of CAD patients and to uncover key genes and regulatory mechanisms in the pathogenesis and disease progression of CAD.MethodsThe Gene Expression Omnibus (GEO) database was applied to screen out differentially expressed genes (DEGs) in the peripheral blood of CAD patients, and the DEGs were subjected to Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA). The core genes were screened by GO, KEGG, and GSEA, and the gene-gene interaction (GGI) and protein-protein interaction (PPI) networks of DEGs were constructed. The GeneCards database was used to obtain CAD-related genes, and the GEO dataset was used to obtain intersecting genes. The intersecting genes were analyzed for bioenrichment and prediction of potential therapeutic agents, and predictive models were constructed for the intersecting genes. Finally, immune infiltrating cells from the GEO dataset were analyzed.ResultsA total of 79 DEGs were screened in the peripheral blood of CAD patients, of which three were autophagy-related genes. Biological enrichment analysis showed that the DEGs were associated with metabolic pathways, and vascular smooth muscle contraction and were mainly involved the MAPK signaling pathway, metabolic pathways, and the PI3K-Akt signaling pathway. The S100A8, ENTPD1, and MMP9 further screened were screened. A total of 11 CAD crossover genes and 75 potential therapeutic agents were obtained, and the column line graph prediction models constructed for S100A8, HSPB1, F5, MMP9, and PDE9A had good predictive power. There were significant differences in immune cells in CAD patients compared to healthy individuals, especially in T cells regulatory (Tregs) and B cells naïve.ConclusionsThe peripheral blood of CAD patients screened by the GEO dataset was significantly different from that of the healthy population, and the DEGs and intersecting genes were involved in numerous key biological processes that may be involved in the development and progression of CAD and could serve as its regulatory sites and therapeutic drug targets.

Genome-Wide DNA Methylation and Its Effect on Gene Expression During Subclinical Mastitis in Water Buffalo.

Subclinical mastitis (SCM) in buffalo is one of the most challenging paradoxes for the dairy sector with very significant milk production losses and poses an imminent danger to milch animal’s milk-producing ability. We present here the genome-wide methylation specific to SCM in water buffalo and its consequential effect on the gene expression landscape for the first time. Whole-genome DNA methylation profiles from peripheral blood lymphocytes and gene expression profiles from milk somatic cells of healthy and SCM cases were catalogued from the MeDIP-Seq and RNA-Seq data. The average methylation in healthy buffaloes was found to be higher than that in the SCM-infected buffaloes. DNA methylation was abundant in the intergenic region followed by the intronic region in both healthy control and SCM groups. A total of 3,950 differentially methylated regions (DMRs) were identified and annotated to 370 differentially methylated genes (DMGs), most of which were enriched in the promoter region. Several important pathways were activated due to hypomethylation and belonged to the Staphylococcus aureus infection, Th17 cell differentiation, and antigen processing and presentation pathways along with others of defense responses. DNA methylome was compared with transcriptome to understand the regulatory role of DNA methylation on gene expression specific to SCM in buffaloes. A total of 4,778 significant differentially expressed genes (DEGs) were extracted in response to SCM, out of which 67 DMGs were also found to be differentially expressed, suggesting that during SCM, DNA methylation could be one of the epigenetic regulatory mechanisms of gene expression. Genes like CSF2RB, LOC102408349, C3 and PZP like, and CPAMD8 were found to be downregulated in our study, which are known to be involved in the immune response to SCM. Association of DNA methylation with transposable elements, miRNAs, and lncRNAs was also studied. The present study reports a buffalo SCM web resource (BSCM2TDb) available at http://webtom.cabgrid.res.in/BSCM2TDb that catalogues all the mastitis-related information of the analyses results of this study in a single place. This will be of immense use to buffalo researchers to understand the host–pathogen interaction involving SCM, which is required in endeavors of mastitis control and management.

Peripheral blood gene expression profiling shows predictive significance for response to mycophenolate in systemic sclerosis-related interstitial lung disease

ObjectivesTo characterise the peripheral blood cell (PBC) gene expression changes ensuing from mycophenolate mofetil (MMF) or cyclophosphamide (CYC) treatment and to determine the predictive significance of baseline PBC transcript scores...

Defining imaging sub-phenotypes of psoriatic arthritis: integrative analysis of imaging data and gene expression in a PsA patient cohort.

To define imaging sub-phenotypes in patients with PsA; determine their association with whole blood gene expression and identify biological pathways characterizing the sub-phenotypes. Fifty-five patients with PsA ready to initiate treatment for active disease were prospectively recruited. We performed musculoskeletal ultrasound assessment of the extent of inflammation in the following domains: synovitis, peritenonitis, tenosynovitis and enthesitis. Peripheral whole blood was profiled with RNAseq, and gene expression data were obtained. First, unsupervised cluster analysis was performed to define imaging sub-phenotypes that reflected the predominant tissue involved. Subsequently, principal component analysis was used to determine the association between imaging-defined sub-phenotypes and peripheral blood gene expression profile. Pathway enrichment analysis was performed to identify underlying mechanisms that characterize individual sub-phenotypes. Cluster analysis revealed three imaging sub-phenotypes: (i) synovitis predominant [n = 31 (56%)]; (ii) enthesitis predominant [n = 13 (24%)]; (iii) peritenonitis predominant [n = 11 (20%)]. The peritenonitis-predominant sub-phenotype had the most severe clinical joint involvement, whereas the enthesitis-predominant sub-phenotype had the highest tender entheseal count. Unsupervised clustering of gene expression data identified three sub-phenotypes that partially overlapped with the imaging sub-phenotypes suggesting biological and clinical relevance of these sub-phenotypes. We therefore characterized enriched differential pathways, which included: immune system (innate system, B cells and neutrophil degranulation), complement system, platelet activation and coagulation function. We identified three sub-phenotypes based on the predominant tissue involved in patients with active PsA. Distinct biological pathways may underlie these imaging sub-phenotypes seen in PsA, suggesting their biological and clinical importance.

Peripheral Blood Transcriptome in Breast Cancer Patients as a Source of Less Invasive Immune Biomarkers for Personalized Medicine, and Implications for Triple Negative Breast Cancer.

Simple SummaryTriple-negative breast cancer (TNBC) is an aggressive and heterogeneous breast cancer (BC) type which is difficult to treat and accompanied by disease recurrence. A better understanding of TNBC and the identification of novel biomarkers is needed to facilitate clinical decisions. Immune-related biomarkers are of particular interest, since immune responses play an important role in BC outcome. Transcriptome studies of peripheral blood cells can help us to understand the systemic immune responses to cancer cells and the mechanisms underlying cancer initiation and progression. They enable the identification of novel immune biomarkers for early cancer detection and personalized BC management and may bring forward new immunotherapy options. Recent transcriptome analyses of peripheral blood cells have delineated novel BC-patient immune subgroups. This categorization has implications for cancer prognosis, the identification of patients likely to benefit from immunotherapy, and treatment efficacy monitoring. Additionally, transcriptome studies have identified TNBC-enriched blood transcriptional signatures that can differentiate TNBC from other classical BC subtypes.Transcriptome studies of peripheral blood cells can advance our understanding of the systemic immune response to the presence of cancer and the mechanisms underlying cancer onset and progression. This enables the identification of novel minimally invasive immune biomarkers for early cancer detection and personalized cancer management and may bring forward new immunotherapy options. Recent blood gene expression analyses in breast cancer (BC) identified distinct patient subtypes that differed in the immune reaction to cancer and were distinct from the clinical BC subtypes, which are categorized based on expression of specific receptors on tumor cells. Introducing new BC subtypes based on peripheral blood gene expression profiles may be appropriate, since it may assist in BC prognosis, the identification of patients likely to benefit from immunotherapy, and treatment efficacy monitoring. Triple-negative breast cancer (TNBC) is an aggressive, heterogeneous, and difficult-to-treat disease, and identification of novel biomarkers for this BC is crucial for clinical decision-making. A few studies have reported TNBC-enriched blood transcriptional signatures, mostly related to strong inflammation and augmentation of altered immune signaling, that can differentiate TNBC from other classical BC subtypes and facilitate diagnosis. Future research is geared toward transitioning from expression signatures in unfractionated blood cells to those in immune cell subpopulations.

Current Tolerance-Associated Peripheral Blood Gene Expression Profiles After Liver Transplantation Are Influenced by Immunosuppressive Drugs and Prior Cytomegalovirus Infection

Spontaneous operational tolerance to the allograft develops in a proportion of liver transplant (LTx) recipients weaned off immunosuppressive drugs (IS). Several previous studies have investigated whether peripheral blood gene expression profiles could identify operational tolerance in LTx recipients. However, the reported gene expression profiles differed greatly amongst studies, which could be caused by inadequate matching of clinical parameters of study groups. Therefore, the purpose of this study was to validate differentially expressed immune system related genes described in previous studies that identified tolerant LTx recipients after IS weaning. Blood was collected of tolerant LTx recipients (TOL), a control group of LTx recipients with regular IS regimen (CTRL), a group of LTx recipients with minimal IS regimen (MIN) and healthy controls (HC), and groups were matched on age, sex, primary disease, time after LTx, and cytomegalovirus serostatus after LTx. Quantitative Polymerase Chain Reaction was used to determine expression of twenty selected genes and transcript variants in PBMCs. Several genes were differentially expressed between TOL and CTRL groups, but none of the selected genes were differentially expressed between HC and TOL. Principal component analysis revealed an IS drug dosage effect on the expression profile of these genes. These data suggest that use of IS profoundly affects gene expression in peripheral blood, and that these genes are not associated with operational tolerance. In addition, expression levels of SLAMF7 and NKG7 were affected by prior cytomegalovirus infection in LTx recipients. In conclusion, we found confounding effects of IS regimen and prior cytomegalovirus infection, on peripheral blood expression of several selected genes that were described as tolerance-associated genes by previous studies.

Blood transcriptional signatures of gallstone pathogenesis in patients with cholelithiasis and choledocholithiasis Running Title: Blood gene expression gallstone

Objective Disease-specific molecular signalling in peripheral blood has the potential to inform on pathophysiological mechanisms of diseases. Here, we aimed to investigate the blood-based gene expression profiles that reflect disease-specific pathogenic mechanisms of gallstones, such as antioxidant defence, heat-shock responses, DNA damage and repair, ABC pump mechanisms, mucin signals, mitochondrial dysfunction and apoptosis in patients with Cholelithiasis (CHL) and Choledocholithiasis (CHDL) Materials and Methods The relative fold-change in the mRNA expression levels of 73 genes were analysed using a gallstone-related qRT-PCR array in 10 control individuals, 24 CHL patients and 23 CHDL patients. Serum malondialdehyde levels was determined by thiobarbituric-acid reactive substance assays, and 8-hydroxy-2’-deoxyguanosine levels was determined by ELISA assays. Results Our results showed that peripheral whole blood gene expression profile strongly reflects tissue specific molecular signalling in gallstone pathogenesis. The present findings of altered gene expressions including antioxidant defence (CuZn-SOD, CAT), heat shock protein (HSP70), DNA repair (MLH1 and RAD18), pro-apoptotic (P53, BAX, Cyt-c and Caspase 3), ABC transporter (ABCB1, ABCC2, and LRP1) and Mucin signals (MUCIN4, MUCIN5AC and MUCIN5B) point out to DNA damages via oxidative stress as well as deteriorating ABC types pump mechanisms and mucin signals in CHL and CHDL patients. Our findings may also suggest that activation of mitophagy activator, DRP1/hFIS1/PINK1 axis induced by oxidative stress and DNA damage may have a role in the pathogenesis of CHL and CHDL. Conclusions Our results indicate that a blood-based gene expression signature has promising accuracy for monitorize pathogenesis of disease in CHL patients, CHDL patients and unaffected controls.

Transcriptomic score: A biomarker index of Alzheimer’s risk and resilience

AbstractBackgroundOne definition of resilience is the absence of disease despite high levels of risk. And in most cases, risk itself is best quantified by a multivariate profile rather than a single risk factor. Thus, multivariate risk profiles may be most appropriate for defining risk and resilience. RNA expression may serve as a risk biomarker, but no method has been proposed to build a whole‐transcriptome risk index of Alzheimer’s disease (AD) that could identify resilient individuals at the highest transcriptomic risk. Here, we derived a novel method for transcriptome‐wide gene expression data called “transcriptomic risk score” (TRS). We also employed the algorithm to build a “transcriptomic resilience score” (TReS) that offsets that risk.MethodAnalogous to a polygenic risk score, TRS is a weighted rank‐sum statistic that represents a subject’s relative expression level across the transcriptome, where the standardized beta coefficients are used as weights. We leveraged the TRS approach on peripheral blood gene expression profiles of 364 normal controls and 188 AD cases from ADNI and AddNeuroMed batch 1. Using TRSas a means of risk quantification, we then identified resilient normal controls as those with the highest percentiles of risk. High‐risk AD cases with matched TRSs range were retained for comparison. Expression levels of individual transcripts not included in the best‐fit TRS were contrasted between the high‐risk normal controls and high‐risk AD cases using mixed‐effect linear models. A TReS was derived using the residual transcriptomic variation that buffers against the transcriptomic risk. The association between TReS and case status was evaluated using a logistic regression model.ResultThe derived TReS differentiated resilient subjects (high‐risk normal controls) and high‐risk AD cases in independent replication samples (216 normal controls and 223 AD cases), with significant differentiation seen at all evaluated p‐value bins and a maximum of 3% variance accounted for at a p‐value threshold of 0.1.ConclusionThis analysis indicated that TRS and TReS analysis of blood has the potential of facilitating the understanding of phenotypic variability and improving clinically useful biomarker profiles for AD.

Effects of Deoxynivalenol and Fumonisins Fed in Combination to Beef Cattle: Immunotoxicity and Gene Expression.

We evaluated the effects of a treatment diet contaminated with 1.7 mg deoxynivalenol and 3.5 mg fumonisins (B1, B2 and B3) per kg ration on immune status and peripheral blood gene expression profiles in finishing-stage Angus steers. The mycotoxin treatment diet was fed for a period of 21 days followed by a two-week washout period during which time all animals consumed the control diet. Whole-blood leukocyte differentials were performed weekly throughout the experimental and washout period. Comparative profiles of CD4+ and CD8+ T cells, along with bactericidal capacity of circulating neutrophils and monocytes were evaluated at 0, 7, 14, 21 and 35 days. Peripheral blood gene expression was measured at 0, 7, 21 and 35 days via RNA sequencing. Significant increases in the percentage of CD4−CD8+ T cells were observed in treatment-fed steers after two weeks of treatment and were associated with decreased CD4:CD8 T-cell ratios at this same timepoint (p ≤ 0.10). No significant differences were observed as an effect of treatment in terms of bactericidal capacity at any timepoint. Dietary treatments induced major changes in transcripts associated with endocrine, metabolic and infectious diseases; protein digestion and absorption; and environmental information processing (inhibition of signaling and processing), as evaluated by dynamic impact analysis. DAVID analysis also suggested treatment effects on oxygen transport, extra-cellular signaling, cell membrane structure and immune system function. These results indicate that finishing-stage beef cattle are susceptible to the immunotoxic and transcript-inhibitory effects of deoxynivalenol and fumonisins at levels which may be realistically encountered in feedlot situations.