scholarly journals Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Won-Chul Lee ◽  
Alexandre Reuben ◽  
Xin Hu ◽  
Nicholas McGranahan ◽  
Runzhe Chen ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Copy Number ◽  
Molecular Mechanisms ◽  
Immune Cell ◽  
Distant Metastases ◽  
Cell Types ◽  
Copy Number Aberration ◽  
Primary Tumors ◽  
Deconvolution Analysis ◽  
Transcriptomic Data

Abstract Background Metastasis is the primary cause of cancer mortality accounting for 90% of cancer deaths. Our understanding of the molecular mechanisms driving metastasis is rudimentary. Results We perform whole exome sequencing (WES), RNA sequencing, methylation microarray, and immunohistochemistry (IHC) on 8 pairs of non-small cell lung cancer (NSCLC) primary tumors and matched distant metastases. Furthermore, we analyze published WES data from 35 primary NSCLC and metastasis pairs, and transcriptomic data from 4 autopsy cases with metastatic NSCLC and one metastatic lung cancer mouse model. The majority of somatic mutations are shared between primary tumors and paired distant metastases although mutational signatures suggest different mutagenesis processes in play before and after metastatic spread. Subclonal analysis reveals evidence of monoclonal seeding in 41 of 42 patients. Pathway analysis of transcriptomic data reveals that downregulated pathways in metastases are mainly immune-related. Further deconvolution analysis reveals significantly lower infiltration of various immune cell types in metastases with the exception of CD4+ T cells and M2 macrophages. These results are in line with lower densities of immune cells and higher CD4/CD8 ratios in metastases shown by IHC. Analysis of transcriptomic data from autopsy cases and animal models confirms that immunosuppression is also present in extracranial metastases. Significantly higher somatic copy number aberration and allelic imbalance burdens are identified in metastases. Conclusions Metastasis is a molecularly late event, and immunosuppression driven by different molecular events, including somatic copy number aberration, may be a common characteristic of tumors with metastatic plasticity.

scholarly journals The miR-582/CD1B Axis Is Involved in Regulation of Dendritic Cells and Is Associated with Clinical Outcomes in Advanced Lung Adenocarcinoma

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Jun Guo ◽  
Hui Jin ◽  
Yanfeng Xi ◽  
Jian Guo ◽  
Yi Jin ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Dendritic Cells ◽  
Lung Adenocarcinoma ◽  
Patient Outcomes ◽  
Molecular Mechanisms ◽  
Immune Cell ◽  
Cell Types ◽  
Independent Dataset ◽  
Immune Genes ◽  
Novel Biomarkers

The involvement of immune dysfunction in the pathogenesis of lung cancer has been extensively studied. However, the potential molecular mechanisms through which the tumor immune response affects drug resistance are still unclear. Accordingly, in this study, we evaluated deviations in the immune cell landscape among patients with different stages of lung adenocarcinoma to identify key microRNAs and their targets associated with patient outcomes. CIBERSORT was used for estimating the proportions of immune cells in various lung tissues. Significantly different adaptive and innate immune cell types, including memory B cells, CD8+ T cells, resting dendritic cells, and resting mast cells, were selected. Comparative studies and survival analyses were carried out. We found that potential genes and microRNAs involved in immune responses were associated with patient outcomes. Specifically, miR-582/CD1B, which are involved in resting and activated dendritic cells, may be potential novel biomarkers for immunotherapy. An independent dataset of miRNA microarray profiles was used to validate the expression of mature miR-582-5p in patients with advanced lung adenocarcinoma. Alternative treatments, including immunotherapies and chemotherapy, are urgently needed to improve outcomes in patients with lung cancer. Thus, our findings could provide insights into the selection of novel microRNAs targeting immune genes and could improve the efficacy of immunotherapy by disrupting tumor function and promoting immune infiltration in patients with advanced lung adenocarcinoma.

scholarly journals Molecular mechanisms governing circulating immune cell heterogeneity across different species revealed by single cell sequencing

2021 ◽  
Author(s):  
Zhibin Li ◽  
chengcheng Sun ◽  
Fei Wang ◽  
Xiran Wang ◽  
Jiacheng Zhu ◽  
...  
Keyword(s):  
Single Cell ◽  
Immune Cells ◽  
Evolutionary Biology ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Mononuclear Cells ◽  
Immune Cell ◽  
Cell Types ◽  
Genetic Regulatory Networks ◽  
Peripheral Blood Mononuclear

Background: Immune cells play important roles in mediating immune response and host defense against invading pathogens. However, insights into the molecular mechanisms governing circulating immune cell diversity among multiple species are limited. Methods: In this study, we compared the single-cell transcriptomes of 77 957 immune cells from 12 species using single-cell RNA-sequencing (scRNA-seq). Distinct molecular profiles were characterized for different immune cell types, including T cells, B cells, natural killer cells, monocytes, and dendritic cells. Results: The results revealed the heterogeneity and compositions of circulating immune cells among 12 different species. Additionally, we explored the conserved and divergent cellular cross-talks and genetic regulatory networks among vertebrate immune cells. Notably, the ligand and receptor pair VIM-CD44 was highly conserved among the immune cells. Conclusions: This study is the first to provide a comprehensive analysis of the cross-species single-cell atlas for peripheral blood mononuclear cells (PBMCs). This research should advance our understanding of the cellular taxonomy and fundamental functions of PBMCs, with important implications in evolutionary biology, developmental biology, and immune system disorders

Dynamic plasma extracellular vesicle long RNA profiling changes during the peri-operative period

2020 ◽  
Author(s):  
qing hua ◽  
wenhao xu ◽  
xuefang shen ◽  
xi tian ◽  
Peng Wang ◽  
...  
Keyword(s):  
Immune Cell ◽  
Surgical Stress ◽  
Distant Metastases ◽  
Cell Types ◽  
R Package ◽  
Extracellular Vesicle ◽  
Differentially Expressed ◽  
Dynamic Changes ◽  
Rna Profiling ◽  
Time Points

Abstract Background: Surgery remains the most important treatment strategy for solid tumors, such as colorectal cancer (CRC); However, a number of studies have suggested that surgical stress contributes to tumor recurrence or distant metastases. Extracellular vesicles (EVs), which contain a rich variety of RNAs with specialized functions and clinical applications, have been shown to be an indicator for diagnosis and prognosis of cancers. The effect of surgical stress on the landscape and characteristics of EV long RNA (exLR) in human blood, however, remains largely unknown.Methods: We present an optimized strategy for exLR sequencing (exLR-seq) the plasma from three patients with CRC at 4 time points (before surgery [T0], after extubation [T1], 1 day after surgery [T2], and 3 days after surgery [T4]). The “Limma” R package was used to evaluate the dynamic changes of mRNAs and long non-coding (lnc)RNAs from EVs. We also constructed a protein–protein interaction (PPI) network of hub genes and predicted biological processes, cellular components, and molecular functions of gene ontology (GO) functional analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Results: We observed a sufficient number of exLRs, including 12,924 mRNAs and 2196 lncRNAs. Both mRNAs and lncRNAs underwent dynamic changes during the peri-operative period. Compared with T0, there were 110 mRNAs differentially expressed after extubation, 60 differentially expressed genes（DEGs）1 day after surgery, and 50 DEGs 3 days after surgery. A total of 11 genes changed at all 3 time points and were related to regulation of the membrane potential, receptor complex, and passive transmembrane transporter activity. In addition, 22 lncRNAs were differentially expressed after extubation (T1). Nineteen lncRNAs were differentially expressed between T0 and T2, and 38 lncRNAs were differentially expressed between T0 and T3. In addition, we found that only 3 lncRNAs changed at 3 time points. Interestingly, blood exLRs reflected the tissue origins and relative fractions of different immune cell types. EVs from CD8+ T，CD4+ memory T, and NK cells decreased after surgery and the absolute quality of EVs from immune cells decreased as well. Conclusion: In summary, this study demonstrated abundant exLRs in human plasma and the dynamic changes of these exLRs and exLRs originating from CD8+ T and CD4+ memory T cells were reduced during the peri-operative period.

scholarly journals The Effects of Lung-Moistening Herbal Medicines on Bleomycin-Induced Pulmonary Fibrosis Mouse Model

Processes ◽  
2020 ◽  
Vol 8 (1) ◽  
pp. 102
Author(s):  
Junmo Ahn ◽  
Hyejin Joo ◽  
Jihye Park ◽  
Jae-Woo Park ◽  
Kwan-Il Kim ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Pulmonary Fibrosis ◽  
Mouse Model ◽  
Molecular Mechanisms ◽  
Immune Cell ◽  
Herbal Medicines ◽  
Intratracheal Instillation ◽  
Lavage Fluid ◽  
Septal Thickness ◽  
Different Doses

In traditional medicine, lung-moistening herbal medicines (LMHM) are regarded as a major option for treating symptoms of pulmonary fibrosis (PF) including dry cough and dyspnea. As PF agents are being applied to the development of lung cancer agents, PF and lung cancer are reported to have high pathological and pharmacological relationships. This study was proposed to identify candidates for the treatment of PF via investigating the effect of LMHM on PF mouse model. PF was induced by intratracheal instillation of bleomycin. Six water extracts of LMHM such as Farfarae Flos (FAF), Trichosanthis Semen (TRS), Lilii Bulbus (LIB), Adenophorae Radix (ADR), Asteris Radix (ASR), and Scrophulariae Radix (SCR) were prepared and administered (300 mg/kg) orally for 10 days after induction. The changes in body weight, histopathology, and immune cell of bronchoalveolar lavage fluid (BALF) were investigated. Among those, LIB and ADR significantly decreased the deposition of collagen and septal thickness of alveolar and terminal bronchiole. Moreover, SCR, TRS, LIB, and ADR decreased total cells, macrophages, and lymphocytes in BALF. Taken together, ADR and LIB could be the candidates to reduce PF. Further studies on their effects at different doses and analysis of their underlying molecular mechanisms are needed.

CDK12 upregulation and adverse correlation with tumor-associated immune cell infiltrates in prostate cancer.

2020 ◽  
Vol 38 (6_suppl) ◽  
pp. 181-181
Author(s):  
Marie C. Hupe ◽  
Anne Offermann ◽  
Cleopatra Schreiber ◽  
Axel Stuart Merseburger ◽  
Sven Perner
Keyword(s):  
Prostate Cancer ◽  
T Cells ◽  
Immune Cell ◽  
Locally Advanced ◽  
Survival Rates ◽  
Distant Metastases ◽  
Genetic Alterations ◽  
Primary Tumors ◽  
Locally Advanced Tumors ◽  
Advanced Tumors

181 Background: Biallelic loss of CDK12 has recently been identified as a novel subtype of prostate cancer (PCa). CDK12 altered PCa associates with elevated neoantigen burden and thus may be suitable for checkpoint inhibition. Up to now, data about CDK12 refer to its genetic alterations in PCa while its characterization on protein level and its association with tumor infiltrating T-cells are lacking. Methods: Immunohistochemistry (IHC) for CDK12 was performed on a PCa cohort including 74 benigns, 391 primary tumors from 222 patients, 63 locally advanced tumors, 92 lymph node (LN) metastases, and 56 distant metastases. CDK12 was categorized into negative, weak, moderate and high expression. Density of tumor associated T-cells per tumor area was assessed by IHC for CD3 and graduated into negative (<1%), slight (1-5%), weak (5-10%), moderate (10-50%) and high (>50%). Results: CDK12 significantly increases during PCa progression showing highest levels in LN and distant metastases while benign samples harbor no or weak CDK12 expression (ANOVA p<0.001). Kaplan-Meier curve reveals 5-year-biochemical recurrence free survival rates of 89.5%, 69.1%, 59.1% and 20.0% for primary tumors expressing no, weak, moderate and high CDK12 (log-rank p=0.05). High CDK12 expression significantly associates with attenuated tumor associated T-cells (p=0.009) revealing CD3 negativity in 64.7% of CDK12 high expressing tumors. Intratumoral CDK12 and density of CD3 positive T-cells correlates adversely in particular in locally advanced tumors (p=0.007). Overall, tumor associated T-cells are significantly reduced in distant metastases compared to local PCa (p<0.001). Conclusions: Our study highlights the prognostic potential of CDK12 for PCa and its overexpression in advanced tumors. Of note, CDK12 overexpressing tumors can be designated as immunologic “cold” tumors which is in line with their more aggressive phenotype. Concordantly, distant metastases show attenuated tumor associated T-cells supporting the poor response to immunotherapy.

scholarly journals Identification of Independent Primary Tumors and Intrapulmonary Metastases Using DNA Rearrangements in Non–Small-Cell Lung Cancer

2014 ◽  
Vol 32 (36) ◽  
pp. 4050-4058 ◽  
Author(s):  
Stephen J. Murphy ◽  
Marie-Christine Aubry ◽  
Faye R. Harris ◽  
Geoffrey C. Halling ◽  
Sarah H. Johnson ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Distant Metastases ◽  
Small Cell ◽  
Genomic Rearrangements ◽  
Next Generation ◽  
Primary Tumors ◽  
Histologic Subtype ◽  
Metastatic Lesions ◽  
Mate Pair ◽  
Clinical Dilemma

PurposeDistinguishing independent primary tumors from intrapulmonary metastases in non–small-cell carcinoma remains a clinical dilemma with significant clinical implications. Using next-generation DNA sequencing, we developed a chromosomal rearrangement–based approach to differentiate multiple primary tumors from metastasis.MethodsTumor specimens from patients with known independent primary tumors and metastatic lesions were used for lineage test development, which was then applied to multifocal tumors. Laser capture microdissection was performed separately for each tumor. Genomic DNA was isolated using direct in situ whole-genome amplification methodology, and next-generation sequencing was performed using an Illumina mate-pair library protocol. Sequence reads were mapped to the human genome, and primers spanning the fusion junctions were used for validation polymerase chain reaction.ResultsA total of 41 tumor samples were sequenced (33 adenocarcinomas [ADs] and eight squamous cell carcinomas [SQCCs]), with a range of three to 276 breakpoints per tumor identified. Lung tumors predicted to be independent primary tumors based on different histologic subtype did not share any genomic rearrangements. In patients with lung primary tumors and paired distant metastases, shared rearrangements were identified in all tumor pairs, emphasizing the patient specificity of identified breakpoints. Multifocal AD and SQCC samples were reviewed independently by two pulmonary pathologists. Concordance between histology and genomic data occurred in the majority of samples. Discrepant tumor samples were resolved by genome sequencing.ConclusionA diagnostic lineage test based on genomic rearrangements from mate-pair sequencing demonstrates promise for distinguishing independent primary from metastatic disease in lung cancer.

scholarly journals Interleukin-4 in the Generation of the AERD Phenotype: Implications for Molecular Mechanisms Driving Therapeutic Benefit of Aspirin Desensitization

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
John W. Steinke ◽  
Spencer C. Payne ◽  
Larry Borish
Keyword(s):  
Molecular Mechanisms ◽  
Immune Cell ◽  
Cell Types ◽  
Therapeutic Benefit ◽  
Interleukin 4 ◽  
Prostaglandin E ◽  
Aspirin Desensitization ◽  
Over Expression ◽  
Cysteinyl Leukotriene ◽  
Cox 2

Aspirin-exacerbated respiratory disease (AERD) is explained in part by over-expression of 5-lipoxygenase, leukotriene C4 synthase (LTC4S) and the cysteinyl leukotriene (CysLT) receptors (CysLT1 and 2), resulting in constitutive over-production of CysLTs and the hyperresponsiveness to CysLTs that occurs with aspirin ingestion. Increased levels of IL-4 have been found in the sinus mucosa and nasal polyps of AERD subjects. Previous studies demonstrated that IL-4 is primarily responsible for the upregulation of LTC4S by mast cells and the upregulation of CysLT1 and 2 receptors on many immune cell types. Prostaglandin E2 (PGE2) acts to prevent CysLT secretion by inhibiting mast cell and eosinophil activation. PGE2 concentrations are reduced in AERD reflecting diminished expression of cyclooxygenase (COX)-2. IL-4 can inhibit basal and stimulated expression of COX-2 and microsomal PGE synthase 1 leading to decreased capacity for PGE2 secretion. Thus, IL-4 plays an important pathogenic role in generating the phenotype of AERD. This review will examine the evidence supporting this hypothesis and describe a model of how aspirin desensitization provides therapeutic benefit for AERD patients.

scholarly journals Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for twelve immune-mediated diseases

2020 ◽  
Author(s):  
Kousik Kundu ◽  
Alice L. Mann ◽  
Manuel Tardaguila ◽  
Stephen Watt ◽  
Hannes Ponstingl ◽  
...  
Keyword(s):  
Fine Mapping ◽  
Molecular Mechanisms ◽  
Immune Cell ◽  
Meta Analysis ◽  
Cell Types ◽  
Genetic Associations ◽  
Sequencing Data ◽  
Immune Mediated ◽  
Causal Genes ◽  
Causal Variants

AbstractThe identification of causal genetic variants for common diseases improves understanding of disease biology. Here we use data from the BLUEPRINT project to identify regulatory quantitative trait loci (QTL) for three primary human immune cell types and use these to fine-map putative causal variants for twelve immune-mediated diseases. We identify 340 unique, non major histocompatibility complex (MHC) disease loci that colocalise with high (>98%) posterior probability with regulatory QTLs, and apply Bayesian frameworks to fine-map associations at each locus. We show that fine-mapping applied to regulatory QTLs yields smaller credible set sizes and higher posterior probabilities for candidate causal variants compared to disease summary statistics. We also describe a systematic under-representation of insertion/deletion (INDEL) polymorphisms in credible sets derived from publicly available disease meta-analysis when compared to QTLs based on genome-sequencing data. Overall, our findings suggest that fine-mapping applied to disease-colocalising regulatory QTLs can enhance the discovery of putative causal disease variants and provide insights into the underlying causal genes and molecular mechanisms.

scholarly journals ImSig: A resource for the identification and quantification of immune signatures in blood and tissue transcriptomics data

2016 ◽  
Author(s):  
Ajit Johnson Nirmal ◽  
Tim Regan ◽  
Barbara Bo-Ju Shih ◽  
David Arthur Hume ◽  
Andrew Harvey Sims ◽  
...  
Keyword(s):  
Immune Cell ◽  
Cell Types ◽  
Clinical Samples ◽  
Marker Genes ◽  
Immune Gene ◽  
Gene Signatures ◽  
Transcriptomic Data ◽  
Prognostic Assessment ◽  
The Status ◽  
Transcriptomics Data

AbstractThe outcome of many diseases is commonly correlated with the immune response at the site of pathology. The ability to monitor the status of the immune system in situ provides a mechanistic understanding of disease progression, a prognostic assessment and a guide for therapeutic intervention. Global transcriptomic data can be deconvoluted to provide an indication of the cell types present and their activation state, but the gene signatures proposed to date are either disease-specific or have been derived from data generated from isolated cell populations. Here we describe an improved set of immune gene signatures, ImSig, derived based on their co-expression in blood and tissue datasets. ImSig includes validated lists of marker genes for the main immune cell types and a number of core pathways. When used in combination with network analysis, ImSig is an accurate and easy to use approach for monitoring immune phenotypes in transcriptomic data derived from clinical samples.

scholarly journals Genetic mutations associated with lung cancer metastasis to the brain.

2019 ◽  
Vol 5 (suppl) ◽  
pp. 41-41
Author(s):  
ChunXia Su ◽  
Juan Zhou ◽  
Xiangling Chu ◽  
Jing Zhao
Keyword(s):  
Lung Cancer ◽  
Brain Metastasis ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Cancer Metastasis ◽  
Genetic Alterations ◽  
Mapk Signaling ◽  
Primary Tumors ◽  
Cell Lung Carcinoma ◽  
The Brain

41 Background: Lung cancer is the most common cause of mortality in both men and women, accounting for one-quarter of all cancer deaths. Most lung cancer-associated deaths result from metastasis, especially brain metastasis. Metastasis associated mutations are important biomarkers for metastasis prediction and outcome improvement. The current study aimed to reveal the molecular mechanisms and the genetic alterations involved in metastasis from lung tumors to the brain. Methods: We carried out whole exome sequencing (WES) of the primary tumors and the corresponding brain metastases from 15 patients with metastatic non-small-cell lung carcinoma. Results: We identified novel lung cancer metastases associated genes (CHEK2P2, BAGE2, AHNAK2) and epigenetic factors (miR-4436A, miR-6077). Lung-brain metastasis samples have more similar Ti/Tv(transition/transversion) profile with brain cancer. Focal adhesion, PI3K-Akt signaling pathway, MAPK signaling pathway are some of the most important tumor onset and metastasis pathways. Alternative splicing, Methylation and EGF-like domain are important metabolic abnormal for the lung-metastasis cancers. Conclusions: We conducted a pairwise lung-brain metastasis based WES and identified some novel metastasis related mutations which provided potential biomarkers for prognosis and targeted therapeutics.

Sign in / Sign up

Export Citation Format

Share Document