Immune Profiling of Parkinson’s Disease Revealed Its Association With a Subset of Infiltrating Cells and Signature Genes

Parkinson’s disease (PD) is an age-related and second most common neurodegenerative disorder. In recent years, increasing evidence revealed that peripheral immune cells might be able to infiltrate into brain tissues, which could arouse neuroinflammation and aggravate neurodegeneration. This study aimed to illuminate the landscape of peripheral immune cells and signature genes associated with immune infiltration in PD. Several transcriptomic datasets of substantia nigra (SN) from the Gene Expression Omnibus (GEO) database were separately collected as training cohort, testing cohort, and external validation cohort. The immunoscore of each sample calculated by single-sample gene set enrichment analysis was used to reflect the peripheral immune cell infiltration and to identify the differential immune cell types between PD and healthy participants. According to receiver operating characteristic (ROC) curve analysis, the immunoscore achieved an overall accuracy of the area under the curve (AUC) = 0.883 in the testing cohort, respectively. The immunoscore displayed good performance in the external validation cohort with an AUC of 0.745. The correlation analysis and logistic regression analysis were used to analyze the correlation between immune cells and PD, and mast cell was identified most associated with the occurrence of PD. Additionally, increased mast cells were also observed in our in vivo PD model. Weighted gene co-expression network analysis (WGCNA) was used to selected module genes related to a mast cell. The least absolute shrinkage and selection operator (LASSO) analysis and random-forest analysis were used to analyze module genes, and two hub genes RBM3 and AGTR1 were identified as associated with mast cells in the training cohort. The expression levels of RBM3 and AGTR1 in these cohorts and PD models revealed that these hub genes were significantly downregulated in PD. Moreover, the expression trend of the aforementioned two genes differed in mast cells and dopaminergic (DA) neurons. In conclusion, this study not only exhibited a landscape of immune infiltrating patterns in PD but also identified mast cells and two hub genes associated with the occurrence of PD, which provided potential therapeutic targets for PD patients (PDs).

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Classification of Patients With Sepsis According to Immune Cell Characteristics: A Bioinformatic Analysis of Two Cohort Studies

Frontiers in Medicine ◽

10.3389/fmed.2020.598652 ◽

2020 ◽

Vol 7 ◽

Author(s):

Shi Zhang ◽

Zongsheng Wu ◽

Wei Chang ◽

Feng Liu ◽

Jianfeng Xie ◽

...

Keyword(s):

Cohort Studies ◽

Immune Cell ◽

Validation Cohort ◽

Expression Profiles ◽

External Validation ◽

Gene Expression Profiles ◽

Principal Component ◽

Bioinformatic Analysis ◽

Training Cohort ◽

Transcriptomics Data

Background: Sepsis is well-known to alter innate and adaptive immune responses for sustained periods after initiation by an invading pathogen. Identification of immune cell characteristics may shed light on the immune signature of patients with sepsis and further indicate the appropriate immune-modulatory therapy for distinct populations. Therefore, we aimed to establish an immune model to classify sepsis into different immune endotypes via transcriptomics data analysis of previously published cohort studies.Methods: Datasets from two observational cohort studies that included 585 consecutive sepsis patients admitted to two intensive care units were downloaded as a training cohort and an external validation cohort. We analyzed genome-wide gene expression profiles in blood from these patients by using machine learning and bioinformatics.Results: The training cohort and the validation cohort had 479 and 106 patients, respectively. Principal component analysis indicated that two immune subphenotypes associated with sepsis, designated the immunoparalysis endotype, and immunocompetent endotype, could be distinguished clearly. In the training cohort, a higher cumulative 28-day mortality was found in patients classified as having the immunoparalysis endotype, and the hazard ratio was 2.32 (95% CI: 1.53–3.46 vs. the immunocompetent endotype). External validation further demonstrated that the present model could categorize sepsis into the immunoparalysis and immunocompetent type precisely and efficiently. The percentages of 4 types of immune cells (M0 macrophages, M2 macrophages, naïve B cells, and naïve CD4 T cells) were significantly associated with 28-day cumulative mortality (P < 0.05).Conclusion: The present study developed a comprehensive tool to identify the immunoparalysis endotype and immunocompetent status in hospitalized patients with sepsis and provides novel clues for further targeting of therapeutic approaches.

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Profiles of Peripheral Immune Cells of Uncomplicated COVID-19 Cases with Distinct Viral RNA Shedding Periods

Viruses ◽

10.3390/v13030514 ◽

2021 ◽

Vol 13 (3) ◽

pp. 514

Author(s):

Denise Utami Putri ◽

Cheng-Hui Wang ◽

Po-Chun Tseng ◽

Wen-Sen Lee ◽

Fu-Lun Chen ◽

...

Keyword(s):

Immune Response ◽

Immune Cells ◽

Mononuclear Cells ◽

Immune Cell ◽

Severe Disease ◽

Viral Rna ◽

Disease Course ◽

Peripheral Blood Mononuclear ◽

Peripheral Immune Cells ◽

Cell Profile

The heterogeneity of immune response to COVID-19 has been reported to correlate with disease severity and prognosis. While so, how the immune response progress along the period of viral RNA-shedding (VRS), which determines the infectiousness of disease, is yet to be elucidated. We aim to exhaustively evaluate the peripheral immune cells to expose the interplay of the immune system in uncomplicated COVID-19 cases with different VRS periods and dynamic changes of the immune cell profile in the prolonged cases. We prospectively recruited four uncomplicated COVID-19 patients and four healthy controls (HCs) and evaluated the immune cell profile throughout the disease course. Peripheral blood mononuclear cells (PBMCs) were collected and submitted to a multi-panel flowcytometric assay. CD19+-B cells were upregulated, while CD4, CD8, and NK cells were downregulated in prolonged VRS patients. Additionally, the pro-inflammatory-Th1 population showed downregulation, followed by improvement along the disease course, while the immunoregulatory cells showed upregulation with subsequent decline. COVID-19 patients with longer VRS expressed an immune profile comparable to those with severe disease, although they remained clinically stable. Further studies of immune signature in a larger cohort are warranted.

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Radiomic nomogram based on MRI to predict grade of branching type intraductal papillary mucinous neoplasms of the pancreas: a multicenter study

Cancer Imaging ◽

10.1186/s40644-021-00395-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Sijia Cui ◽

Tianyu Tang ◽

Qiuming Su ◽

Yajie Wang ◽

Zhenyu Shu ◽

...

Keyword(s):

Calibration Curve ◽

Main Pancreatic Duct ◽

Validation Cohort ◽

External Validation ◽

High Grade ◽

Intraductal Papillary Mucinous Neoplasms ◽

Training Cohort ◽

Independent Validation ◽

Medical Centers ◽

Mucinous Neoplasms

Abstract Background Accurate diagnosis of high-grade branching type intraductal papillary mucinous neoplasms (BD-IPMNs) is challenging in clinical setting. We aimed to construct and validate a nomogram combining clinical characteristics and radiomic features for the preoperative prediction of low and high-grade in BD-IPMNs. Methods Two hundred and two patients from three medical centers were enrolled. The high-grade BD-IPMN group comprised patients with high-grade dysplasia and invasive carcinoma in BD-IPMN (n = 50). The training cohort comprised patients from the first medical center (n = 103), and the external independent validation cohorts comprised patients from the second and third medical centers (n = 48 and 51). Within 3 months prior to surgery, all patients were subjected to magnetic resonance examination. The volume of interest was delineated on T1-weighted (T1-w) imaging, T2-weighted (T2-w) imaging, and contrast-enhanced T1-weighted (CET1-w) imaging, respectively, on each tumor slice. Quantitative image features were extracted using MITK software (G.E.). The Mann-Whitney U test or independent-sample t-test, and LASSO regression, were applied for data dimension reduction, after which a radiomic signature was constructed for grade assessment. Based on the training cohort, we developed a combined nomogram model incorporating clinical variables and the radiomic signature. Decision curve analysis (DCA), a receiver operating characteristic curve (ROC), a calibration curve, and the area under the ROC curve (AUC) were used to evaluate the utility of the constructed model based on the external independent validation cohorts. Results To predict tumor grade, we developed a nine-feature-combined radiomic signature. For the radiomic signature, the AUC values of high-grade disease were 0.836 in the training cohort, 0.811 in external validation cohort 1, and 0.822 in external validation cohort 2. The CA19–9 level and main pancreatic duct size were identified as independent parameters of high-grade of BD-IPMNs using multivariate logistic regression analysis. The CA19–9 level and main pancreatic duct size were then used to construct the radiomic nomogram. Using the radiomic nomogram, the high-grade disease-associated AUC values were 0.903 (training cohort), 0.884 (external validation cohort 1), and 0.876 (external validation cohort 2). The clinical utility of the developed nomogram was verified using the calibration curve and DCA. Conclusions The developed radiomic nomogram model could effectively distinguish high-grade patients with BD-IPMNs preoperatively. This preoperative identification might improve treatment methods and promote personalized therapy in patients with BD-IPMNs.

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Establishment and Validation of an Integrated Model to Predict Postoperative Recurrence in Patients With Atypical Meningioma

Frontiers in Oncology ◽

10.3389/fonc.2021.754937 ◽

2021 ◽

Vol 11 ◽

Author(s):

Xiao-Yong Chen ◽

Jin-Yuan Chen ◽

Yin-Xing Huang ◽

Jia-Heng Xu ◽

Wei-Wei Sun ◽

...

Keyword(s):

Cox Regression ◽

Validation Cohort ◽

Clinical Laboratory ◽

External Validation ◽

Postoperative Recurrence ◽

Integrated Model ◽

Atypical Meningioma ◽

Tumor Diameter ◽

Roc Curve Analysis ◽

Training Cohort

BackgroundThis study aims to establish an integrated model based on clinical, laboratory, radiological, and pathological factors to predict the postoperative recurrence of atypical meningioma (AM).Materials and MethodsA retrospective study of 183 patients with AM was conducted. Patients were randomly divided into a training cohort (n = 128) and an external validation cohort (n = 55). Univariable and multivariable Cox regression analyses, the least absolute shrinkage and selection operator (LASSO) regression analysis, time-dependent receiver operating characteristic (ROC) curve analysis, and evaluation of clinical usage were used to select variables for the final nomogram model.ResultsAfter multivariable Cox analysis, serum fibrinogen >2.95 g/L (hazard ratio (HR), 2.43; 95% confidence interval (CI), 1.05–5.63; p = 0.039), tumor located in skull base (HR, 6.59; 95% CI, 2.46-17.68; p < 0.001), Simpson grades III–IV (HR, 2.73; 95% CI, 1.01–7.34; p = 0.047), tumor diameter >4.91 cm (HR, 7.10; 95% CI, 2.52–19.95; p < 0.001), and mitotic level ≥4/high power field (HR, 2.80; 95% CI, 1.16–6.74; p = 0.021) were independently associated with AM recurrence. Mitotic level was excluded after LASSO analysis, and it did not improve the predictive performance and clinical usage of the model. Therefore, the other four factors were integrated into the nomogram model, which showed good discrimination abilities in training cohort (C-index, 0.822; 95% CI, 0.759–0.885) and validation cohort (C-index, 0.817; 95% CI, 0.716–0.918) and good match between the predicted and observed probability of recurrence-free survival.ConclusionOur study established an integrated model to predict the postoperative recurrence of AM.

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IL-17+ Mast Cell/T Helper Cell Axis in the Early Stages of Acne

Frontiers in Immunology ◽

10.3389/fimmu.2021.740540 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yoan Eliasse ◽

Edouard Leveque ◽

Lucile Garidou ◽

Louise Battut ◽

Brienne McKenzie ◽

...

Keyword(s):

T Cells ◽

Mast Cell ◽

Mast Cells ◽

Immune Cell ◽

T Helper Cell ◽

Helper Cell ◽

T Helper ◽

Cell Axis ◽

Early Stages ◽

Cutibacterium Acnes

Acne is a multifactorial disease driven by physiological changes occurring during puberty in the pilosebaceous unit (PSU) that leads to sebum overproduction and a dysbiosis involving notably Cutibacterium acnes. These changes in the PSU microenvironment lead to a shift from a homeostatic to an inflammatory state. Indeed, immunohistochemical analyses have revealed that inflammation and lymphocyte infiltration can be detected even in the infraclinical acneic stages, highlighting the importance of the early stages of the disease. In this study, we utilized a robust multi-pronged approach that included flow cytometry, confocal microscopy, and bioinformatics to comprehensively characterize the evolution of the infiltrating and resident immune cell populations in acneic lesions, beginning in the early stages of their development. Using a discovery cohort of 15 patients, we demonstrated that the composition of immune cell infiltrate is highly dynamic in nature, with the relative abundance of different cell types changing significantly as a function of clinical lesion stage. Within the stages examined, we identified a large population of CD69+ CD4+ T cells, several populations of activated antigen presenting cells, and activated mast cells producing IL-17. IL-17+ mast cells were preferentially located in CD4+ T cell rich areas and we showed that activated CD4+ T cells license mast cells to produce IL-17. Our study reveals that mast cells are the main IL-17 producers in the early stage of acne, underlying the importance of targeting the IL-17+ mast cell/T helper cell axis in therapeutic approaches.

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Identification of Biomarkers Related to Immune Cell Infiltration in Hepatocellular Carcinoma Using Gene Co-Expression Network

Pathology & Oncology Research ◽

10.3389/pore.2021.601693 ◽

2021 ◽

Vol 27 ◽

Author(s):

Wanbang Zhou ◽

Yiyang Chen ◽

Ruixing Luo ◽

Zifan Li ◽

Guanwei Jiang ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Network Analysis ◽

Tumor Progression ◽

Protein Interactions ◽

Immune Cells ◽

Immune Cell ◽

Immune Microenvironment ◽

Hub Genes ◽

Expression Levels ◽

Immune Infiltration

Hepatocellular carcinoma (HCC) is a common cancer with poor prognosis. Due to the lack of effective biomarkers and its complex immune microenvironment, the effects of current HCC therapies are not ideal. In this study, we used the GSE57957 microarray data from Gene Expression Omnibus database to construct a co-expression network. The weighted gene co-expression network analysis and CIBERSORT algorithm, which quantifies cellular composition of immune cells, were used to identify modules related to immune cells. Four hub genes (EFTUD2, GAPDH, NOP56, PA2G4) were identified by co-expression network and protein-protein interactions network analysis. We examined these genes in TCGA database, and found that the four hub genes were highly expressed in tumor tissues in multiple HCC groups, and the expression levels were significantly correlated with patient survival time, pathological stage and tumor progression. On the other hand, methylation analysis showed that the up-regulation of EFTUD2, GAPDH, NOP56 might be due to the hypomethylation status of their promoters. Next, we investigated the correlations between the expression levels of four hub genes and tumor immune infiltration using Tumor Immune Estimation Resource (TIMER). Gene set variation analysis suggested that the four hub genes were associated with numerous pathways that affect tumor progression or immune microenvironment. Overall, our results showed that the four hub genes were closely related to tumor prognosis, and may serve as targets for treatment and diagnosis of HCC. In addition, the associations between these genes and immune infiltration enhanced our understanding of tumor immune environment and provided new directions for the development of drugs and the monitoring of tumor immune status.

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The Selective Loss of Purkinje Cells Induces Specific Peripheral Immune Alterations

Frontiers in Cellular Neuroscience ◽

10.3389/fncel.2021.773696 ◽

2021 ◽

Vol 15 ◽

Author(s):

Carlos del Pilar ◽

Rafael Lebrón-Galán ◽

Ester Pérez-Martín ◽

Laura Pérez-Revuelta ◽

Carmelo Antonio Ávila-Zarza ◽

...

Keyword(s):

Olfactory Bulb ◽

Antigen Presentation ◽

Purkinje Cells ◽

Immune Cells ◽

Neuronal Death ◽

Immune Cell ◽

Specific Effect ◽

Cell Degeneration ◽

Functional Maturity ◽

Peripheral Immune Cells

The progression of neurodegenerative diseases is reciprocally associated with impairments in peripheral immune responses. We investigated different contexts of selective neurodegeneration to identify specific alterations of peripheral immune cells and, at the same time, discover potential biomarkers associated to this pathological condition. Consequently, a model of human cerebellar degeneration and ataxia -the Purkinje Cell Degeneration (PCD) mouse- has been employed, as it allows the study of different processes of selective neuronal death in the same animal, i.e., Purkinje cells in the cerebellum and mitral cells in the olfactory bulb. Infiltrated leukocytes were studied in both brain areas and compared with those from other standardized neuroinflammatory models obtained by administering either gamma radiation or lipopolysaccharide. Moreover, both myeloid and lymphoid splenic populations were analyzed by flow cytometry, focusing on markers of functional maturity and antigen presentation. The severity and type of neural damage and inflammation affected immune cell infiltration. Leukocytes were more numerous in the cerebellum of PCD mice, being located predominantly within those cerebellar layers mostly affected by neurodegeneration, in a completely different manner than the typical models of induced neuroinflammation. Furthermore, the milder degeneration of the olfactory bulb did not foster leukocyte attraction. Concerning the splenic analysis, in PCD mice we found: (1) a decreased percentage of several myeloid cell subsets, and (2) a reduced mean fluorescence intensity in those myeloid markers related to both antigen presentation and functional maturity. In conclusion, the selective degeneration of Purkinje cells triggers a specific effect on peripheral immune cells, fostering both attraction and functional changes. This fact endorses the employment of peripheral immune cell populations as concrete biomarkers for monitoring different neuronal death processes.

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BATF2 and PDK4 As Diagnostic Molecular Markers of Sarcoidosis and Their Relationship With Immune Infiltration

10.21203/rs.3.rs-557951/v1 ◽

2021 ◽

Author(s):

Xiaoyan Li ◽

Jing Zhou ◽

Jie He

Keyword(s):

Immune Cells ◽

Immune Cell ◽

External Validation ◽

Pulmonary Sarcoidosis ◽

Gene Expression Omnibus ◽

Diagnostic Markers ◽

Cell Infiltration ◽

Immune Cell Infiltration ◽

Immune Disorder ◽

Qpcr Method

Abstract Background: Sarcoidosis (SA) is an immune disorder disease featured with granulomas formation. The work purposed to uncover potential markers for sarcoidosis (SA) diagnosis and explore how immune cell infiltration contributes to the pathogenesis of SA.Methods: Sarcoidosis GSE83456 samples and GSE42834 from Gene Expression Omnibus (GEO) were analyzed as the training and external validation sets, respectively. R statistical software was employed to uncover the differentially expressed genes (DEGs) of GSE83456. SVM algorithms and LASSO logistic regression were applied for screening and verification of the diagnostic markers for key module genes. The infiltration of immune cells in sarcoidosis patients’ blood samples was assessed by CIBERSORT. The expression of serum BATF2 and PDK4 was detected by RT-qPCR method, and the value of BATF2 and PDK4 mRNA expression in the diagnosis of pulmonary sarcoidosis was analyzed.Results: In total, 580 DEGs were identified from the key module. PDK4 (AUC=0.942) and BATF4 (AUC=0.980) were revealed as diagnostic markers of sarcoidosis. We found that monocytes, T cells regulatory (Tregs), mast cells, macrophages，NK cells, and dendritic cells may contribute to sarcoidosis development. In addition, PDK4 and BATF4 were closely associated with these immune cells. BATF2 and PDK4 were highly expressed in pulmonary sarcoidosis. BATF2 and PDK4 combined to predict the area under the ROC curve of pulmonary sarcoidosis was 0.922.Conclusions: PDK4 and BATF4 could be used as diagnostic markers of sarcoidosis, and immune cell infiltration severs an important role in sarcoidosis.

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Uncovering the invisible—prevalence, characteristics, and radiomics feature–based detection of visually undetectable intraprostatic tumor lesions in 68GaPSMA-11 PET images of patients with primary prostate cancer

European Journal of Nuclear Medicine and Molecular Imaging ◽

10.1007/s00259-020-05111-3 ◽

2020 ◽

Author(s):

Constantinos Zamboglou ◽

Alisa S. Bettermann ◽

Christian Gratzke ◽

Michael Mix ◽

Juri Ruf ◽

...

Keyword(s):

Prostate Cancer ◽

Validation Cohort ◽

External Validation ◽

Image Interpretation ◽

Receiver Operating Curve ◽

Training Cohort ◽

Primary Prostate Cancer ◽

Psma Pet ◽

Number Of Patients ◽

Clinically Significant

Abstract Introduction Primary prostate cancer (PCa) can be visualized on prostate-specific membrane antigen positron emission tomography (PSMA-PET) with high accuracy. However, intraprostatic lesions may be missed by visual PSMA-PET interpretation. In this work, we quantified and characterized the intraprostatic lesions which have been missed by visual PSMA-PET image interpretation. In addition, we investigated whether PSMA-PET-derived radiomics features (RFs) could detect these lesions. Methodology This study consists of two cohorts of primary PCa patients: a prospective training cohort (n = 20) and an external validation cohort (n = 52). All patients underwent 68Ga-PSMA-11 PET/CT and histology sections were obtained after surgery. PCa lesions missed by visual PET image interpretation were counted and their International Society of Urological Pathology score (ISUP) was obtained. Finally, 154 RFs were derived from the PET images and the discriminative power to differentiate between prostates with or without visually undetectable lesions was assessed and areas under the receiver-operating curve (ROC-AUC) as well as sensitivities/specificities were calculated. Results In the training cohort, visual PET image interpretation missed 134 tumor lesions in 60% (12/20) of the patients, and of these patients, 75% had clinically significant (ISUP > 1) PCa. The median diameter of the missed lesions was 2.2 mm (range: 1–6). Standard clinical parameters like the NCCN risk group were equally distributed between patients with and without visually missed lesions (p < 0.05). Two RFs (local binary pattern (LBP) size-zone non-uniformality normalized and LBP small-area emphasis) were found to perform excellently in visually unknown PCa detection (Mann-Whitney U: p < 0.01, ROC-AUC: ≥ 0.93). In the validation cohort, PCa was missed in 50% (26/52) of the patients and 77% of these patients possessed clinically significant PCa. The sensitivities of both RFs in the validation cohort were ≥ 0.8. Conclusion Visual PSMA-PET image interpretation may miss small but clinically significant PCa in a relevant number of patients and RFs can be implemented to uncover them. This could be used for guiding personalized treatments.

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Immunomodulation of Epithelium

Canadian Journal of Gastroenterology ◽

10.1155/1996/937461 ◽

1996 ◽

Vol 10 (4) ◽

pp. 243-248 ◽

Cited By ~ 1

Author(s):

Mary H Perdue

Keyword(s):

Mast Cell ◽

Immune Cells ◽

Cell Activation ◽

Immune Cell ◽

Regulatory System ◽

Mast Cell Activation ◽

Immune Cell Activation ◽

Inflammatory Conditions ◽

Close Proximity ◽

Antigenic Material

Many studies have provided evidence that the immune system is a key regulatory system of intestinal function. The interaction of immune cells with the gut epithelium plays an important role in host defence, acting to eliminate pathogens, antigens and other noxious material from the lumen of the gastrointestinal tract. During inflammatory conditions of the gut, the mucosa becomes packed with immune cells in close proximity to the enterocytes. Mediators released from these cells have profound effects on epithelial functions. The two main functions of the intestinal epithelium are to transport nutrients, ions and water, and to act as a barrier to prevent unimpeded uptake of antigenic material and microbes from the lumen. Both these functions are altered by immune reactions in response to various stimuli. Topics discussed include mast cells and epithelial function; mast cell-nerve interaction; mast cell activation; neutrophils, eosinophils and macrophages; T cells; and prostaglandins and immune cell activation.

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