scholarly journals Activation of Intracellular Complement in Lungs of Patients With Severe COVID-19 Disease Decreases T-Cell Activity in the Lungs

2021 ◽  
Vol 12 ◽  
Author(s):  
Mark C. Howell ◽  
Ryan Green ◽  
Andrew R. McGill ◽  
Roukiah M. Kahlil ◽  
Rinku Dutta ◽  
...  
Keyword(s):  
T Cell ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Cell Activity ◽  
Lung Pathology ◽  
Sequencing Data ◽  
Severe Respiratory Distress ◽  
Ventilator Support ◽  
Novel Coronavirus ◽  
Classical Complement

A novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), arose late in 2019, with disease pathology ranging from asymptomatic to severe respiratory distress with multi-organ failure requiring mechanical ventilator support. It has been found that SARS-CoV-2 infection drives intracellular complement activation in lung cells that tracks with disease severity. However, the cellular and molecular mechanisms responsible remain unclear. To shed light on the potential mechanisms, we examined publicly available RNA-Sequencing data using CIBERSORTx and conducted a Ingenuity Pathway Analysis to address this knowledge gap. In complement to these findings, we used bioinformatics tools to analyze publicly available RNA sequencing data and found that upregulation of complement may be leading to a downregulation of T-cell activity in lungs of severe COVID-19 patients. Thus, targeting treatments aimed at the modulation of classical complement and T-cell activity may help alleviate the proinflammatory effects of COVID-19, reduce lung pathology, and increase the survival of COVID-19 patients.

Immunoregulation related gene of CSMD2 and RNA activity as potential predicter of 2-year survival in pancreatic cancer: A DNA and RNA sequencing analysis.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e16212-e16212
Author(s):  
Jiafei Yan ◽  
Si Li ◽  
Wenjing Xi ◽  
Dongsheng Chen ◽  
Mingzhe Xiao
Keyword(s):  
Pancreatic Cancer ◽  
T Cell ◽  
Rna Sequencing ◽  
T Cell Activation ◽  
Cell Activation ◽  
Treatment Options ◽  
Cell Activity ◽  
Sequencing Analysis ◽  
Sequencing Data ◽  
Dna And Rna

e16212 Background: The 5-year survival rate of pancreatic cancer remains as low as 3%-15%. One of the key approaches to enrich current treatment options or improve effectiveness is new biomarker probing. We conducted DNA and RNA sequencing analysis to reveal potential biomarkers related to overall survival. Methods: Whole-exome sequencing, RNA sequencing and clinical data for 209 patients with pancreatic cancer were downloaded from TCGA. Clinical factors and mutational landscape (insertion/ deletion/ single nucleotide variant) were compared between group of OS2+ (OS longer than 2 years) and OS2- (OS longer than 2 years) with T test and Chi-square Test. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted with RNA sequencing data to clarify the functional differences between the two groups. Results: The rates of OS2+ for patients in stage of I/II/III/IV was 43% (9/21), 17.8% (27/152), 0% (0/4), 0% (0/5), respectively. 152 patients in stage II were included for further analysis. No difference of sex and age were found between group of OS2+ and OS2-. Tumor mutation burden was comparable between the two groups. Mutation landscape showed the two groups had the accordance of 50% in top 10 genes. Mutations of CSMD2(18.5% vs. 5.0% , P = 0.026), CMYA5(14.8% vs, 2.5% , P = 0.019) and KCNA6(14.8% vs, 3.3%, P = 0.034) were more frequent in OS2+ group. CSMD2 is thought to be involved in the control of complement cascade of the immune system, and its low expression was significantly associated with differentiation, lymphatic invasion, and tumor size in colorectal cancer. CMYA5 was predicted as novel oncogene in breast cancer with the tool of Moonlight, it may also participate tumor activity in pancreatic cancer. The role of KCNA6 in cancer cell activity is barely known yet. Evaluation of differentially expressed genes between the two groups detected difference in leukocyte differentiation and T cell activation (GO analysis) and MAPK signal pathway (KEGG panalysis), these immunoregulation and MAPK pathways may play critical roles in tumor development and progression and affect the prognosis of pancreatic cancer. Conclusions: Pancreatic cancer with 2-year survival presented significant different DNA and RNA alterations, in which CSMD2 and pathway of leukocyte differentiation and T cell activation are closely associated with immunoregulation. These might provide guidance for prognose management and development of new therapeutic targets. Further mechanistic insights and prospective validation studies are warranted.

scholarly journals In-depth transcriptomic analysis of human retina reveals molecular mechanisms underlying diabetic retinopathy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kolja Becker ◽  
Holger Klein ◽  
Eric Simon ◽  
Coralie Viollet ◽  
Christian Haslinger ◽  
...  
Keyword(s):  
Diabetic Retinopathy ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Vision Loss ◽  
Ganglion Cells ◽  
Expression Profiles ◽  
Cell Types ◽  
Sequencing Data ◽  
Disease Stages ◽  
Post Transcriptional Regulation

AbstractDiabetic Retinopathy (DR) is among the major global causes for vision loss. With the rise in diabetes prevalence, an increase in DR incidence is expected. Current understanding of both the molecular etiology and pathways involved in the initiation and progression of DR is limited. Via RNA-Sequencing, we analyzed mRNA and miRNA expression profiles of 80 human post-mortem retinal samples from 43 patients diagnosed with various stages of DR. We found differentially expressed transcripts to be predominantly associated with late stage DR and pathways such as hippo and gap junction signaling. A multivariate regression model identified transcripts with progressive changes throughout disease stages, which in turn displayed significant overlap with sphingolipid and cGMP–PKG signaling. Combined analysis of miRNA and mRNA expression further uncovered disease-relevant miRNA/mRNA associations as potential mechanisms of post-transcriptional regulation. Finally, integrating human retinal single cell RNA-Sequencing data revealed a continuous loss of retinal ganglion cells, and Müller cell mediated changes in histidine and β-alanine signaling. While previously considered primarily a vascular disease, attention in DR has shifted to additional mechanisms and cell-types. Our findings offer an unprecedented and unbiased insight into molecular pathways and cell-specific changes in the development of DR, and provide potential avenues for future therapeutic intervention.

Blood Transcriptome Analysis reveals Age-associated changes in Expression Profile of Immune-Related Gene in Golden snub-nosed Monkey(Rhinopithecus roxellana)

2019 ◽  
Author(s):  
Shao Huanhuan ◽  
Deng Jiabo ◽  
Wu Linfeng ◽  
Li Xuedan ◽  
Niu Lili ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Cell Activity ◽  
Young Group ◽  
Functional Enrichment ◽  
Rhinopithecus Roxellana ◽  
Sequencing Data ◽  
Adult Group ◽  
New Genes ◽  
Age Related ◽  
Differential Genes

Abstract Background Golden snub-nosed monkeys ( Rhinopithecus roxellana ) are an endangered species in China.In the present study, the blood transcriptomes of nine monkeys were characterized by using RNA-Seq technology.Results 57.31 Gb high-quality sequencing data was obtained. The clean data of each sample was >5 Gb, and 86.17% to 94.48% of the reads of each sample could be compared to reference genome of snub-nosed monkey. After assembly, we obtained 24,992 genes, including 3,917 new genes. Many genes were up-regulated or down-regulated with age. In adult group of R. roxellana roxellana, there were 76 differential genes, including 68 up-regulated and 8 down-regulated genes, compared with the young group. While, compared with the adult group, in the old group there were 58 differential genes, including 25 up-regulated genes and 23 down-regulated genes. In R. roxellana qinlingensis , compared with the young group, 117 differential genes were obtained, including 34 up-regulated and 83 down-regulated genes. Functional enrichment analysis indicated that the up-regulated genes were mainly related to innate immune response and T-cell activity, while the down-regulated genes were mainly involved in B-cell activity, suggesting that immune competence of adult group increased gradually compared to young group. However, the adaptive immune function declined gradually in the old group.Conclusions Our findings will contribute to understand on the molecular mechanisms of age-related changes in immune system, which will provide a foundation for future study in snub-nosed monkey.

Mutations in PLCG1 Is a Frequent Event in Cutaneous T-Cell Lymphomas

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 300-300
Author(s):  
Pablo L Ortiz-Romero ◽  
Gonzalo Gomez-Lopez ◽  
Sagrario Gómez de Benito ◽  
Veronica Monsalvez ◽  
Jose P Vaque ◽  
...  
Keyword(s):  
T Cell ◽  
Molecular Mechanisms ◽  
Somatic Mutations ◽  
Catalytic Domain ◽  
Conflicts Of Interest ◽  
Immunohistochemical Analysis ◽  
Sequencing Data ◽  
Coding Region ◽  
Regulatory Pathways ◽  
Frequent Event

Abstract Abstract 300 Background: Cutaneous T-cell lymphoma (CTCL) is a heterogeneous group of diseases characterized by clonal expansion of malignant T-cells in the skin. The two predominant clinical forms of CTCL are mycosis fungoides (MF) and Sezary syndrome (SS). Tumor-stage MF has an unfavorable prognosis with a 10-year survival of approximately 40%. The molecular pathogenesis of CTCL is still basically unknown, although some data suggest that signalling from T-cell receptor (TCR) is a driving force. However, the molecular mechanisms responsible for this activation have not been fully clarified. Methods: Based on the hypothesis that TCR activation may depend, at least in part, on somatic mutations, we have investigated this in a selection of genes belonging to TCR, or related pathways, such as NFkB, JAK/STAT, by means of deep sequencing. A Target Enrichment method using SureSelect system (Agilent) has been used to enrich in exons and regulatory regions of 524 genes belonging to these pathways. DNA from 2 tumoral-MF, 5 erythrodermic-MF and 4 SS patients, both normal and tumoral, were processed and sequenced with Genome Analyzer GA2 (Illumina) (PE-42bp). Sequencing data were first checked by FastQC and aligned to the human reference genome (GRCh37) using BWA and BFAST alignments. Somatic variants were identified using GATK. Thus, SNPs available at dbSNP 135 (hg19) and 1000 Genomes Project were filtered out from VCF output files. The GATK-QUAL field was employed for ranking selected somatic variants. Biological impact predictions for detected variants were obtained from Ensembl Variant Effect Predictor. Putative variants were manually reviewed and validated by capillary sequencing. Immunohistochemical analysis for NFAT, p50, p52 and STAT·p was also performed. qPCR-genotyping for specific variants was performed in a new cohort of 60 CTCL patients including SS and tumoral MFs. Results: Several mutations were found in essential genes belonging to pathways implicated in the Treg and Th17 regulatory pathways, NFkB and JAK/STAT, among others. PLCG1 was found mutated in three samples, two of them sharing the same mutation affecting one of the PLCG1 protein catalytic domains. This mutation was further analyzed by qPCR-genotyping in the new series of patients, being detected in 20% of samples. PLCG mutated cases showed a strong paraffin immunostaining for nuclear NFAT, p50 and p52. Additionally, immunological studies performed by flow cytometry in CTCL cell lines show aberrant coexpression of TH17 and Treg phenotypes. Conclusions: Activation of the TCR in CTCL might be partially dependent on the acquisition of somatic mutations in the coding region of genes known to play an essential role in T-cell differentiation processes and acquisition of TH17 and Treg phenotypes. Especially relevant is the finding that the catalytic domain of PLCG1 is frequently mutated in tumoral MF samples. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Comprehensive Integration of Single-Cell Transcriptional Profiling Reveals the Heterogeneities of Non-cardiomyocytes in Healthy and Ischemic Hearts

2020 ◽  
Vol 7 ◽  
Author(s):  
Lingfang Zhuang ◽  
Lin Lu ◽  
Ruiyan Zhang ◽  
Kang Chen ◽  
Xiaoxiang Yan
Keyword(s):  
Myocardial Infarction ◽  
Single Cell ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Developmental Trajectories ◽  
Transcriptional Profiling ◽  
Sequencing Data ◽  
Signature Genes

Advances in single-cell RNA sequencing (scRNA-seq) technology have recently shed light on the molecular mechanisms of the spatial and temporal changes of thousands of cells simultaneously under homeostatic and ischemic conditions. The aim of this study is to investigate whether it is possible to integrate multiple similar scRNA-seq datasets for a more comprehensive understanding of diseases. In this study, we integrated three representative scRNA-seq datasets of 27,349 non-cardiomyocytes isolated at 3 and 7 days after myocardial infarction or sham surgery. In total, seven lineages, including macrophages, fibroblasts, endothelia, and lymphocytes, were identified in this analysis with distinct dynamic and functional properties in healthy and nonhealthy hearts. Myofibroblasts and endothelia were recognized as the central hubs of cellular communication via ligand-receptor interactions. Additionally, we showed that macrophages from different origins exhibited divergent transcriptional signatures, pathways, developmental trajectories, and transcriptional regulons. It was found that myofibroblasts predominantly expand at 7 days after myocardial infarction with pro-reparative characteristics. We identified signature genes of myofibroblasts, such as Postn, Cthrc1, and Ddah1, among which Ddah1 was exclusively expressed on activated fibroblasts and exhibited concordant upregulation in bulk RNA sequencing data and in vivo and in vitro experiments. Collectively, this compendium of scRNA-seq data provides a valuable entry point for understanding the transcriptional and dynamic changes of non-cardiomyocytes in healthy and nonhealthy hearts by integrating multiple datasets.

scholarly journals P03.30 Tumur mutations drive dysfunctional T cell differentiation in lung cancer

2020 ◽  
Vol 8 (Suppl 2) ◽  
pp. A35.1-A35
Author(s):  
E Ghorani ◽  
J Reading ◽  
J Henry ◽  
M Robert de Massy ◽  
R Rosenthal ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
T Cell ◽  
Intellectual Property ◽  
Rna Sequencing ◽  
Stock Options ◽  
Tumour Microenvironment ◽  
Advisory Board ◽  
T Cell Differentiation ◽  
Cell Populations ◽  
Sequencing Data

BackgroundEffective anti-tumour immunity requires cancer antigen expression, but persistent antigen exposure in chronic viral infections and autoimmunity has a detrimental effect on immune function. This is associated with a decline of early differentiated T cell populations in favour of later differentiated, dysfunctional subsets, resulting in an unfavourable skewing of the immune landscape. It is unknown whether this occurs locally within the antigen rich tumour microenvironment, driving immune failure.Materials and MethodsWe combined tumour infiltrating lymphocyte (TIL) high dimensional flow cytometry, bulk exome and RNA sequencing data from multiregional samples obtained from surgically resected tumours of treatment naive patients with non-small cell lung cancer (NSCLC) amongst the first 100 recruited to the prospective, UK-wide lung TRACERx study. Clonal relationship between T cell populations was determined by T cell receptor (TCR) sequencing. We additionally analysed publically available single T cell RNA sequencing data and bulk RNA sequencing data within TCGA.ResultsT cell differentiation skewing (TDS) occurred amongst TILs in association with tumour mutational burden (TMB). Surprisingly, this was most evident within the CD4 compartment that had a greater abundance of central memory cells expressing the key transcription factor TCF7. Amongst CD4 cells, loss of a PD1-CCR7+ T central memory population was accompanied by gain in abundance of PD1+ populations with exhausted (CD57-ICOShiCTLA4hi) and terminally differentiated effector (CD57+Eomes+) features. TCR sequencing revealed early and dysfunctional differentiated populations to be clonally related and CDR3 clustering analysis showed greater similarity of sequences shared vs. non-shared between subsets, consistent with an antigen driven differentiation process. Similar patterns were observed within the CD8 compartment. Identification of these subsets within single T cell RNA sequencing data revealed shared and distinct functional regulators, suggesting the enhanced effector capability of early compared to dysfunctionally differentiated populations. A validated transcriptional signature of TDS generated using TRACERx samples with paired flow cytometry and RNA sequencing data reflected loss of gene expression downstream of TCF7, and predicted worse survival within TRACERx and multiple TCGA cohorts including lung adenocarcinoma (LUAD).ConclusionsOur finding support a model of neoantigen driven T cell differentiation within the tumour microenvironment that drives the depletion of progenitor-like cells and gain in abundance of dysfunctional subsets, resulting in a loss of immune fitness. Our analysis of transcriptomic data elucidates potential regulatory mechanisms and therapeutic targets within the subsets identified.Disclosure InformationE. Ghorani: None. J. Reading: None. J. Henry: None. M. Robert de Massy: None. R. Rosenthal: E. Ownership Interest (stock, stock options, patent or other intellectual property); Modest; Achilles Therapeutics. F. Consultant/Advisory Board; Modest; Achilles Therapeutics. V. Turati: None. A. Furness: None. A. Ben Aissa: None. S. Kumar Saini: None. S. Ramskov: None. A. Georgiou: None. M. Vila De Mucha: None. I. Uddin: None. T. Ronel: None. R. Salgado: None. T. Lund: None. J. Herrero: None. T. Enver: None. S. Hadrup: None. A. Hackshaw: None. K. Peggs: E. Ownership Interest (stock, stock options, patent or other intellectual property); Modest; Achilles Therapeutics. N. McGranahan,: E. Ownership Interest (stock, stock options, patent or other intellectual property); Modest; Achilles Therapeutics. F. Consultant/Advisory Board; Modest; Achilles Therapeutics. B. Chain: None. C. Swanton: B. Research Grant (principal investigator, collaborator or consultant and pending grants as well as grants already received); Modest; Pfizer, AstraZeneca, BMS, Roche–Ventana and Boehringer Ingelheim. E. Ownership Interest (stock, stock options, patent or other intellectual property); Modest; ApoGen Biotechnologies, Epic Bioscience and GRAIL, and has stock options in and is co-founder of Achilles Therapeutics. F. Consultant/Advisory Board; Modest; Pfizer, Novartis, GlaxoSmithKline, MSD, BMS, Celgene, AstraZeneca, Illumina, Genentech, Roche–Ventana, GRAIL, Medicxi and the Sarah Cannon Research Institute. S. Quezada: E. Ownership Interest (stock, stock options, patent or other intellectual property); Modest; Achilles Therapeutics.

scholarly journals Immune Response Dysfunction in Chronic Lymphocytic Leukemia: Dissecting Molecular Mechanisms and Microenvironmental Conditions

2020 ◽  
Vol 21 (5) ◽  
pp. 1825 ◽  
Author(s):  
Francesca Arruga ◽  
Benjamin Baffour Gyau ◽  
Andrea Iannello ◽  
Nicoletta Vitale ◽  
Tiziana Vaisitti ◽  
...  
Keyword(s):  
Immune Response ◽  
T Cell ◽  
Chronic Lymphocytic Leukemia ◽  
Immune Responses ◽  
T Lymphocyte ◽  
Molecular Mechanisms ◽  
Cell Activity ◽  
Lymphocytic Leukemia ◽  
Leukemic Cells ◽  
Adaptive Immune

Representing the major cause of morbidity and mortality for chronic lymphocytic leukemia (CLL) patients, immunosuppression is a common feature of the disease. Effectors of the innate and the adaptive immune response show marked dysfunction and skewing towards the generation of a tolerant environment that favors disease expansion. Major deregulations are found in the T lymphocyte compartment, with inhibition of CD8+ cytotoxic and CD4+ activated effector T cells, replaced by exhausted and more tolerogenic subsets. Likewise, differentiation of monocytes towards a suppressive M2-like phenotype is induced at the expense of pro-inflammatory sub-populations. Thanks to their B-regulatory phenotype, leukemic cells play a central role in driving immunosuppression, progressively inhibiting immune responses. A number of signaling cascades triggered by soluble mediators and cell–cell contacts contribute to immunomodulation in CLL, fostered also by local environmental conditions, such as hypoxia and derived metabolic acidosis. Specifically, molecular pathways modulating T-cell activity in CLL, spanning from the best known cytotoxic T lymphocyte antigen-4 (CTLA-4) and programmed cell death 1 (PD-1) to the emerging T cell immunoreceptor with immunoglobulin and immunoreceptor tyrosine-based inhibition motif domains (TIGIT)/CD155 axes, are attracting increasing research interest and therapeutic relevance also in the CLL field. On the other hand, in the microenvironment, the B cell receptor (BCR), which is undoubtedly the master regulator of leukemic cell behavior, plays an important role in orchestrating immune responses, as well. Lastly, local conditions of hypoxia, typical of the lymphoid niche, have major effects both on CLL cells and on non-leukemic immune cells, partly mediated through adenosine signaling, for which novel specific inhibitors are currently under development. In summary, this review will provide an overview of the molecular and microenvironmental mechanisms that modify innate and adaptive immune responses of CLL patients, focusing attention on those that may have therapeutic implications.

scholarly journals Versatile workflow for cell type resolved transcriptional and epigenetic profiles from cryopreserved human lung

2020 ◽  
Author(s):  
M Llamazares Prada ◽  
E Espinet ◽  
V Mijosek ◽  
U Schwartz ◽  
SM Waszak ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Human Lung ◽  
Cell Isolation ◽  
Great Promise ◽  
Cell Type ◽  
Sequencing Data ◽  
Chronic Lung Diseases ◽  
Human Lung Cells

AbstractThe complexity of the lung microenvironment together with changes in cellular composition during disease progression make it exceptionally hard to understand the molecular mechanisms leading to the development of chronic lung diseases. Although recent advances in cell type resolved and single-cell sequencing approaches hold great promise for studying complex diseases, their implementation greatly relies on local access to fresh tissue, as traditional methods to process and store tissue do not allow viable cell isolation. To overcome these hurdles, we developed a novel, versatile workflow that allows long-term storage of human lung tissue with high cell viability, permits thorough sample quality check before cell isolation, and is compatible with next generation sequencing-based profiling, including single-cell approaches. We demonstrate that cryopreservation is suitable for isolation of multiple cell types from different lung locations and is applicable to both healthy and diseased tissue, including COPD and tumor samples. Basal cells isolated from cryopreserved airways retain the ability to differentiate, indicating that cellular identity is not altered by cryopreservation. Importantly, using RNA sequencing (RNA-seq) and Illumina EPIC Array, we show that genome-wide gene expression and DNA methylation signatures are preserved upon cryopreservation, emphasizing the suitability of our workflow for -omics profiling of human lung cells. In addition, we obtained high-quality single-cell RNA sequencing data of cells isolated from cryopreserved human lung, demonstrating that cryopreservation empowers single-cell approaches. Overall, thanks to its simplicity, our cryopreservation workflow is well-suited for prospective tissue collection by academic collaborators and biobanks, opening worldwide access to human tissue.

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