scholarly journals USP8 Status Affects the Immune Landscape of Corticotroph Pituitary Adenomas

2021 ◽  
Author(s):  
Dahlia Greidinger ◽  
Ronit Mor-Cohen ◽  
Roni Zemet ◽  
Nitzan Maixner ◽  
Amit Tirosh
Keyword(s):  
Pituitary Adenomas ◽  
Immune Cell ◽  
Cell Types ◽  
Differentially Expressed ◽  
Toll Like Receptor ◽  
M1 Macrophages ◽  
Mutation Status ◽  
Specific Protease ◽  
Signature Recognition ◽  
Ubiquitin Specific Protease

Abstract Purpose Activating somatic mutations in ubiquitin-specific protease-8 (USP8), encoding a deubiquitinating protein, are found in approximately 30% of corticotroph-derived pituitary adenomas (CPA). USP8 has immunomodulating properties that were demonstrated in non-tumoral diseases. Our study aims to assess the influence of USP8 mutation status on the immune tumor microenvironment (iTME) of CPAs. Methods We analyzed 20 PCAs by RNA sequencing. In six of them, USP8 mutations were detected. We assessed the immune landscape of tumors by quantifying 22 immune cell types based on the CIBERSORT transcriptome signature-recognition algorithms. Also, we performed a pathway analysis for genes that were differentially expressed between groups using the Wikipathways 2019 and Reactome 2016 databases and using the EnrichR platform results. Results CPA with activating USP8 mutations were associated with "cold" iTME compared with wild type USP8 CPA. This "cold" iTME was reflected by lower fractions of B cells, CD4, regulatory and gamma/delta T cells, natural killer cells, M0 and M1 macrophages, dendritic cells and eosinophils (p < 0.05 for all comparisons). Pathways altered by the presence of USP8 mutation, based on the most differentially expressed genes (3,061 genes) included Microglia Pathogen Phagocytosis and multiple toll-like receptor signaling pathways (p < 0.0001). Conclusion USP8 status affects the immune landscape of corticotroph pituitary adenomas, with USP8 mutation associated with "cold" iTME.

PATH-26. EVALUATING THE DISTRIBUTION AND PROGNOSIS OF IMMUNE CELL SIGNATURES OF THE TUMOR MICRO-ENVIRONMENT IN DIFFUSE GLIOMAS

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi120-vi120
Author(s):  
Bharati Mehani ◽  
Saleembhasha Asanigari ◽  
Hye-Jung Chung ◽  
Kenneth Aldape
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Immune Cell ◽  
Tumor Grade ◽  
Cell Types ◽  
Idh Mutation ◽  
Mutation Status ◽  
Cluster Analyses ◽  
Diffuse Gliomas ◽  
Cell Expression

Abstract The tumor micro-environment (TME) plays an important role in the biology of cancer, including gliomas. Single cell studies have highlighted the role of specific TME components in gliomas, and the methods to deconvolve bulk profiling data may serve to complement these studies on clinically annotated tumors. In this study, we estimated cell type proportions in 3 large glioma datasets (TCGA, CGGA-325, CGGA-693) using CIBERSORTx. Using a signature matrix comprising 22 immune cell types, we identified IDH mutation status-specific immune cell distributions and found that the proportions of 10 cell types were significantly different between IDHmut and IDHwt tumors across the 3 datasets. Looking further within IDHmut tumors, we found that monocytes were enriched in 1p/19q non-co-deleted tumors across the 3 glioma datasets, consistent with prior single cell studies. We then examined estimated gene expression among immune cell types relative to IDH mutation status and found clear separation of gene expression in 15 of 22 cell types in all 3 datasets. When we applied these 22 gene expression signatures in each tumor sample onto cluster-of-cluster analyses to identify tumor groups with distinct immune signature patterns, we found that samples were distributed largely according to the IDH status in all 3 datasets, confirming that immune cell expression is distinct based on IDH status. Among IDH-specific groups, cluster-of-cluster analyses showed that immune cell-based cluster groups had distinct survival outcomes, and that IDHwt samples were distributed significantly based on tumor grades as well as based on EGFR overexpression. Among IDHmut tumors, the distributions of tumor grade and 1p/19q co-deletion status were significantly different in the immune-based clusters in 2 of the 3 datasets examined. Overall, these results highlight the biological and clinical significance of the immune cell environment in gliomas, including distinctions based on IDH mutation status as well as prognosis within IDH-specific groups.

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 Ubiquitin-Specific Protease 8 Mutant Corticotrope Adenomas Present Unique Secretory and Molecular Features and Shed Light on the Role of Ubiquitylation on ACTH Processing

2019 ◽  
Vol 110 (1-2) ◽  
pp. 119-129 ◽  
Author(s):  
Antonella Sesta ◽  
Maria Francesca Cassarino ◽  
Mariarosa Terreni ◽  
Alberto G. Ambrogio ◽  
Laura Libera ◽  
...  
Keyword(s):  
Protein Degradation ◽  
Pituitary Adenomas ◽  
Expression Profiles ◽  
Primary Cultures ◽  
Acth Secretion ◽  
Specific Protease ◽  
Ubiquitin Proteasome ◽  
Ubiquitin Specific Protease ◽  
Acth Secreting

Background: Somatic mutations in the ubiquitin-specific protease 8 (USP8) gene have recently been shown to occur in ACTH-secreting pituitary adenomas, thus calling attention to the ubiquitin system in corticotrope adenomas. Objectives: Assess the consequences of USP8 mutations and establish the role of ubiquitin on ACTH turnover in human ACTH-secreting pituitary adenomas. Methods: USP8 mutation status was established in 126 ACTH-secreting adenomas. Differences in ACTH secretion and POMC expression from adenoma primary cultures and in microarray gene expression profiles from archival specimens were sought according to USP8 sequence. Ubiquitin/ACTH coimmunoprecipitation and incubation with MG132, a proteasome inhibitor, were performed in order to establish whether ubiquitin plays a role in POMC/ACTH degradation in corticotrope adenomas. Results: USP8 mutations were identified in 29 adenomas (23%). Adenomas presenting USP8 mutations secreted greater amounts of ACTH and expressed POMC at higher levels compared to USP wild-type specimens. USP8 mutant adenomas were also more sensitive to modulation by CRH and dexamethasone in vitro. At microarray analysis, genes associated with endosomal protein degradation and membrane components were downregulated in USP8 mutant adenomas as were AVPR1B, IL11RA, and PITX2. Inhibition of the ubiquitin-proteasome pathway increased ACTH secretion and POMC itself proved a target of ubiquitylation, independently of USP8 sequence status. Conclusions: Our study has shown that USP8 mutant ACTH-secreting adenomas present a more “typical” corticotrope phenotype and reduced expression of several genes associated with protein degradation. Further, ubiquitylation is directly involved in intracellular ACTH turnover, suggesting that the ubiquitin-proteasome system may represent a target for treatment of human ACTH-secreting adenomas.

scholarly journals Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19

2020 ◽  
Author(s):  
Sudhir Ghandikota ◽  
Mihika Sharma ◽  
Anil G. Jegga
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Immune Cell ◽  
Gene Clusters ◽  
Cell Types ◽  
Host Protein ◽  
Differentially Expressed ◽  
Protein Interaction Data ◽  
Neuropsychiatric Diseases

ABSTRACTKnowledge about the molecular mechanisms driving COVID-19 pathophysiology and outcomes is still limited. To learn more about COVID-19 pathophysiology we performed secondary analyses of transcriptomic data from two in vitro (Calu-3 and Vero E6 cells) and one in vivo (Ad5-hACE2-sensitized mice) models of SARS-CoV-2 infection. We found 1467 conserved differentially expressed host genes (differentially expressed in at least two of the three model system transcriptomes compared) in SARS-CoV-2 infection. To find potential genetic factors associated with COVID-19, we analyzed these conserved differentially expressed genes using known human genotype-phenotype associations. Genome-wide association study enrichment analysis showed evidence of enrichment for GWA loci associated with platelet functions, blood pressure, body mass index, respiratory functions, and neurodegenerative and neuropsychiatric diseases, among others. Since human protein complexes are known to be directly related to viral infection, we combined and analyzed the conserved transcriptomic signature with SARS-CoV-2-host protein-protein interaction data and found more than 150 gene clusters. Of these, 29 clusters (with 5 or more genes in each cluster) had at least one gene encoding protein that interacts with SARS-CoV-2 proteome. These clusters were enriched for different cell types in lung including epithelial, endothelial, and immune cell types suggesting their pathophysiological relevancy to COVID-19. Finally, pathway analysis on the conserved differentially expressed genes and gene clusters showed alterations in several pathways and biological processes that could enable in understanding or hypothesizing molecular signatures inducing pathophysiological changes, risks, or sequelae of COVID-19.

scholarly journals Lack of Ubiquitin Specific Protease 8 (USP8) Mutations in Canine Corticotroph Pituitary Adenomas

PLoS ONE ◽  
2016 ◽  
Vol 11 (12) ◽  
pp. e0169009 ◽  
Author(s):  
Silviu Sbiera ◽  
Marianna A. Tryfonidou ◽  
Isabel Weigand ◽  
Guy C. M. Grinwis ◽  
Bart Broeckx ◽  
...  
Keyword(s):  
Pituitary Adenomas ◽  
Specific Protease ◽  
Ubiquitin Specific Protease

scholarly journals SST5 expression and USP8 mutation in functioning and silent corticotroph pituitary tumors

2020 ◽  
Vol 9 (3) ◽  
pp. 243-253 ◽  
Author(s):  
Solène Castellnou ◽  
Alexandre Vasiljevic ◽  
Véronique Lapras ◽  
Véronique Raverot ◽  
Eudeline Alix ◽  
...  
Keyword(s):  
Retrospective Cohort ◽  
Sanger Sequencing ◽  
Somatostatin Receptor ◽  
Pituitary Tumors ◽  
Urinary Free Cortisol ◽  
Lower Grade ◽  
Mutation Status ◽  
Free Cortisol ◽  
Specific Protease ◽  
Ubiquitin Specific Protease

Objective Somatostatin receptor type 5 (SST5) is inconsistently expressed by corticotroph tumors, with higher expression found in corticotropinomas having ubiquitin-specific protease 8 (USP8) mutations. Aims were to study the correlation between characteristics of corticotropinomas and SST5 expression/USP8 mutation status and to describe the response to pasireotide in five patients. Design Retrospective cohort study. Methods Clinico-biochemical, radiological and pathological data of 62 patients, operated for a functioning or silent corticotropinoma between 2013 and 2017, were collected. SST5 expression was measured by immunohistochemistry (clone UMB-4, Abcam, IRS > 1 being considered positive), and Sanger sequencing was performed on 50 tumors to screen for USP8 mutations. Results SST5 expression was positive in 26/62 pituitary tumors. A moderate or strong IRS was found in 15/58 corticotropinomas and in 13/35 functioning corticotropinomas. Among functioning tumors, those expressing SST5 were more frequent in women (22/24 vs 9/15, P = 0.04) and had a lower grade (P = 0.04) compared to others. USP8 mutations were identified in 13/50 pituitary tumors and were more frequent in functioning compared to silent tumors (11/30 vs 2/20, P = 0.05). SST5 expression was more frequent in USP8mut vs USP8wt tumors (10/11 vs 7/19, P = 0.007). Among treated patients, normal urinary free cortisol levels were obtained in three patients (IRS 0, 2 and 6), while a four-fold decrease was observed in one patient (IRS 4). Conclusion SST5 expression appears to be associated with functioning, USP8mut and lower grade corticotropinomas. A correlation between SST5 expression or USP8mut and response to pasireotide remains to be confirmed.

scholarly journals Tumor Suppressor Functions of miRNA-375 in Nasopharyngeal Carcinoma through Inhibition of Ubiquitin-Specific Protease 1 Expression

2021 ◽  
Author(s):  
Xu Jiayuan ◽  
Li Bangliang ◽  
Song Wei ◽  
Cao Longhe ◽  
Zhu Chuansai ◽  
...  
Keyword(s):  
Cell Migration ◽  
Nasopharyngeal Carcinoma ◽  
Genetic Alterations ◽  
Differentially Expressed ◽  
Luciferase Assay ◽  
Migration And Invasion ◽  
Tumor Cell Migration ◽  
Differentially Expressed Mirnas ◽  
Specific Protease ◽  
Ubiquitin Specific Protease

Abstract Background: Nasopharyngeal carcinoma (NPC) development involves many genetic alterations. This study profiled differentially expressed miRNAs and selected miR-375 for further study.Methods: Differentially expressed miRNAs (DE-miRNAs) were screened using online databases and subjected to various analyses. miR-375 mimics with negative control cDNA, and ubiquitin-specific protease 1 (USP1) as well as a vector-only control were transfected into NPC cells for analysis by quantitative PCR, western blotting, wound healing, Transwell, cell viability, flow cytometry, and luciferase gene reporter assays.Results: A total of 308 NPC and 23 normal tissues were analyzed, and 67 DE-miRNAs were identified. Among these, miR-375 was downregulated and miR-21-5p was upregulated. Bioinformatical analysis identified USP1 as a potential target gene of miR-375. Furthermore, miR-375 expression was decreased, whereas USP1 expression was increased in NPC. Increased USP1 expression was associated with poor survival of head and neck cancer patients. The luciferase assay confirmed miR-375 binding to the USP1 3'-untranslated region (UTR), while the transfection experiment confirmed miR-375 expression reduced USP1 expression, and USP1 overexpression reversed the anti-tumor activity of miR-375 in NPC cells, determined by tumor cell migration, invasion, apoptosis, and gene expression. In addition, USP1 overexpression activated phosphoinositide 3-kinase (PI3K) signaling, whereas a selective PI3K inhibitor (S2793) could reverse the effects of USP1 on NPC cells in vitro.Conclusions: This study confirmed decreased miR-375 expression and increased miR-21 expression in NPC tissues. Downregulated miR-375 expression led to USP1 upregulation, which in turn activated PI3K/Akt signaling and promoted NPC cell migration and invasion, but inhibited NPC cell apoptosis.

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