Digital gene expression analysis of NSCLC-patients reveals strong immune pressure, resulting in an immune escape under immunotherapy

Abstract Background Immune checkpoint inhibitors (ICIs) are currently one of the most promising therapy options in the field of oncology. Although the first pivotal ICI trial results were published in 2011, few biomarkers exist to predict their therapy outcome. PD-L1 expression and tumor mutational burden (TMB) were proven to be sometimes-unreliable biomarkers. We have previously suggested the analysis of processing escapes, a qualitative measurement of epitope structure alterations under immune system pressure, to provide predictive information on ICI response. Here, we sought to further validate this approach and characterize interactions with different forms of immune pressure. Methods We identified a cohort consisting of 48 patients with advanced non-small cell lung cancer (NSCLC) treated with nivolumab as ICI monotherapy. Tumor samples were subjected to targeted amplicon-based sequencing using a panel of 22 cancer-associated genes covering 98 mutational hotspots. Altered antigen processing was predicted by NetChop, and MHC binding verified by NetMHC. The NanoString nCounter® platform was utilized to provide gene expression data of 770 immune-related genes. Patient data from 408 patients with NSCLC were retrieved from The Cancer Genome Atlas (TCGA) as a validation cohort. Results The two immune escape mechanisms of PD-L1 expression (TPS score) (n = 18) and presence of altered antigen processing (n = 10) are mutually non-exclusive and can occur in the same patient (n = 6). Both mechanisms have exclusive influence on different genes and pathways, according to differential gene expression analysis and gene set enrichment analysis, respectively. Interestingly, gene expression patterns associated with altered processing were enriched in T cell and NK cell immune activity. Though both mechanisms influence different genes, they are similarly linked to increased immune activity. Conclusion Pressure from the immune system will lay the foundations for escape mechanisms, leading to acquisition of resistance under therapy. Both PD-L1 expression and altered antigen processing are induced similarly by pronounced immunoactivity but in different context. The present data help to deepen our understanding of the underlying mechanisms behind those immune escapes.

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Gene expression analysis of the innate immune system during early rearing and weaning of meagre (Argyrosomus regius)

Fish & Shellfish Immunology ◽

10.1016/j.fsi.2019.10.009 ◽

2019 ◽

Vol 94 ◽

pp. 819-832

Author(s):

Cindy Campoverde ◽

Douglas J. Milne ◽

Christopher J. Secombes ◽

Alicia Estévez ◽

Enric Gisbert ◽

...

Keyword(s):

Gene Expression ◽

Immune System ◽

Expression Analysis ◽

Innate Immune System ◽

Gene Expression Analysis ◽

Innate Immune ◽

Argyrosomus Regius ◽

Early Rearing

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Multiplexed gene expression analysis of HLA class II-associated podoconiosis implicates chronic immune activation in its pathogenesis

Transactions of the Royal Society of Tropical Medicine and Hygiene ◽

10.1093/trstmh/traa107 ◽

2020 ◽

Vol 114 (12) ◽

pp. 926-936

Author(s):

Diana R Alcantara ◽

Christopher I Jones ◽

Daniel M Altmann ◽

Rosemary J Boyton ◽

Muzlifah Haniffa ◽

...

Keyword(s):

Gene Expression ◽

Expression Analysis ◽

Immune Activation ◽

Antigen Processing ◽

Gene Expression Analysis ◽

Class Ii ◽

Hla Class Ii ◽

Future Research ◽

Pathway Enrichment Analysis ◽

Chronic Immune Activation

Abstract Background Podoconiosis is a tropical lymphoedema of the leg resulting from barefoot exposure to irritant volcanic soils. Approximately 4 million people are affected, mainly in African highland regions. The pathogenesis of this neglected tropical disease is still largely unknown, although HLA class II (HLAII) polymorphisms are associated with the disease. Methods NanoString technology was used to assess expression of 579 immune-related genes in formalin-fixed and paraffin-embedded lymph node archival samples from podoconiosis patients and unaffected controls. Results Forty-eight genes were upregulated and 21 downregulated in podoconiosis samples compared with controls. Gene ontology analysis showed differentially expressed genes to be closely related to major histocompatibility complex protein, cytokine and TNF receptor binding genes. Pathway enrichment analysis revealed involvement of lymphocyte activation, adaptive immunity, cytokine signalling, antigen processing and the IL-12 pathways. Conclusions This exploratory study reports a multiplex gene expression analysis in podoconiosis and shows upregulation of pro-inflammatory transcripts compatible with the notion of local, chronic immune activation in this HLAII-associated disease. Implicated pathways will inform future research into podoconiosis immunopathogenesis.

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Evaluation of the Ankylosing Spondylitis Transcriptome for Oxidative Phosphorylation Pathway: The Shared Pathway with Neurodegenerative Diseases

Iranian Journal of Allergy Asthma and Immunology ◽

10.18502/ijaai.v20i5.7406 ◽

2021 ◽

Author(s):

Arezou Lari ◽

Hamid Gholami Pourbadie ◽

Ali Sharifi-Zarchi ◽

Saeed Aslani ◽

Leila Nejatbakhsh Samimi ◽

...

Keyword(s):

Gene Expression ◽

Ankylosing Spondylitis ◽

Oxidative Phosphorylation ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Mononuclear Cells ◽

Differential Expression Analysis ◽

Gene Set Enrichment Analysis ◽

Inflammatory Disorder ◽

Prevalence Of Dementia

Ankylosing spondylitis (AS) is a systemic inflammatory disorder of joints and entheses. Recent studies have reported an increased prevalence of dementia in AS patients. However, data for exploring the association between dementia and AS remain uncertain. In this study, enriched pathways and differentially expressed genes (DEGs) were identified in whole blood transcription data of AS patients obtained from the gene expression omnibus (GEO) database; using gene set enrichment analysis (GSEA) and differential expression analysis. Four pathways, including oxidative phosphorylation, Alzheimer’s, Parkinson’s, and Huntington’s diseases were significantly enriched in AS patients compared to the controls. We identified 22 common genes among the pathways that showed an increasing trend in AS compared to the controls. Five of them including COX7B, NDUFB3, ATP5PF, UQCRB, and NDUFS4 were the most significant genes which were selected for gene expression analysis; using real-time PCR on RNA contents of peripheral blood mononuclear cells (PBMCs) of AS patients and controls (20 samples from each group). The gene expression analysis indicated considerable overexpression of COX7B (p<0.0001) and ATP5J (p=0.0001) genes in AS patients group in comparison to the control samples. The role of oxidative phosphorylation has previously been established in dementia pathogenesis. Given that AS patients have also a remarkably higher prevalence of dementia than the their healthy counterparts, hence our results may propose that the common pathway of oxidative phosphorylation can be regarded as a possible shared contributing factor in the etiopathogenesis of AS and dementia.

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HOXB9 Is Aberrantly Expressed in Blast Cells in a Subset of Acute Myeloid Leukemia Patients and Supports Proliferation of AML Cell Lines

Blood ◽

10.1182/blood.v106.11.1613.1613 ◽

2005 ◽

Vol 106 (11) ◽

pp. 1613-1613 ◽

Cited By ~ 1

Author(s):

Stefan Heinrichs ◽

Claudia Schoch ◽

Donna S. Neuberg ◽

A. Thomas Look

Keyword(s):

Gene Expression ◽

Cell Lines ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Hox Genes ◽

Gene Set Enrichment Analysis ◽

Aberrant Expression ◽

Leukemic Clone ◽

Low Levels ◽

The Absolute

Abstract Studies in mice and humans suggests that HOX genes integrate the myelodysplastic and leukemogenic activities of different oncogenes. HOXA9 has been identified as a major downstream target in patients with MLL translocations and amplifications. Since upregulation of HOXA9 and other specific HOX genes is more frequent than MLL deregulation, additional upstream pathways have to be postulated. Given the fact that HOXA9 is targeted by several yet to be identified mechanisms, we asked whether other members of the HOX9 paralog group are also highly expressed in myeloid malignancies. Microarray gene expression analysis of 449 AML patients revealed that besides HOXA9 (61% of all cases), HOXB9 is upregulated in 15% of the cases, whereas the overexpression of HOXC9 and HOXD9 expression is a very rare event (>1% of all cases). High levels of HOXB9 expression did not correlate with low levels of HOXA9 expression ruling out the possibility that HOXB9 compensates for a lack of HOXA9 activity in the leukemogenesis of a HOXA9 negative AML cases. Moreover, within the cytogenetically defined subgroups inv(16), t(15;17), t(8;21) that have no HOXA9 expression at all, HOXB9 was also low or absent. The analysis of 27 AML cell lines revealed a gene expression pattern of HOXA9 and HOXB9 that reflected the frequency of overexpression found in patient samples (14/27 showed HOXA9 expression; 6/27 showed HOXB9 expression). Interestingly, the absolute expression level of HOXB9 mRNA in cell lines is about 10fold higher than HOXA9 as measured by real-time RT-PCR. Western-blotting with an antibody recognizing both HOXA9 and HOXB9 confirmed this result on the protein level. However, the analysis of the absolute levels in normal CD34+ bone marrow cells revealed an inverse ratio, with very low levels of HOXB9. Taken together these results indicate that HOXB9 expression is aberrant in the leukemic clone. To identify downstream pathways driven by HOXB9 overexpression we designed two highly efficient siRNAs targeting HOXB9 and knocked down its expression by retroviral transduction. In comparison to cells expressing a control siRNA, the resulting cell lines showed <5% of the control HOXB9 protein levels and a reduction in the cellular growth rate. Consequently, HOXB9 expression is required for the rapid growth of these AML cells. To gain insight into the molecular mechanisms underlying this phenotype we are performing global gene expression analysis. Gene set enrichment analysis (GSEA) and related approaches will be used to extract relevant candidate pathways for further analysis. Our results indicate that aberrant expression of HOXB9 inhibits the differentiation of leukemic myeloid progenitor cells and maintains the cells of the leukemic clone in an undifferentiated and rapidly proliferative state.

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GeoDiver: Differential Gene Expression Analysis & Gene-Set Analysis For GEO Datasets

10.1101/127753 ◽

2017 ◽

Cited By ~ 1

Author(s):

Ismail Moghul ◽

Suresh Hewapathirana ◽

Nazrath Nawaz ◽

Anisatu Rashid ◽

Marian Priebe ◽

...

Keyword(s):

Gene Expression ◽

Differential Gene Expression ◽

Expression Analysis ◽

Web Application ◽

Gene Expression Analysis ◽

Gene Set Enrichment Analysis ◽

Differential Gene Expression Analysis ◽

Gene Set ◽

Link Type ◽

Differential Gene

ABSTRACTSummaryGeoDiver is an online web application for performing Differential Gene Expression Analysis (DGEA) and Generally Applicable Gene-set Enrichment Analysis (GAGE) on gene expression datasets from the publicly available Gene Expression Omnibus (GEO). The output produced includes numerous high quality interactive graphics, allowing users to easily explore and examine complex datasets instantly. Furthermore, the results produced can be reviewed at a later date and shared with collaborators.AvailabilityGeoDiver is freely available online at http://www.geodiver.co.uk. The source code is available on Github: https://github.com/GeoDiver/GeoDiver and a docker image is available for easy installation.

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