Tumor Microenvironment Profiling Identifies Prognostic Signatures and Suggests Immunotherapeutic Benefits in Neuroblastoma
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE182586 | GEO | 2021/09/10
REPOSITORIES: GEO
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Project description:The tumor microenvironment (TME) influences disease initiation and progression. Cross-talks of cells within TME can affect the efficacy of immunotherapies. However, a precise, concise, and comprehensive TME landscape in neuroblastoma (NB) has not been established. Here, we profiled the TME landscape of 498 NB-related patients on a self-curated gene list and identified three prognostic TMEsubgroups. The differentially expressed genes in these three TMEsubgroups were used to construct a genetic signature of the TME landscape and characterize three GeneSubgroups. The subgroup with the worst overall survival prognosis, the TMEsubgroup/GeneSubgroup3, lacked immune cell infiltration and received the highest scores of MYCN- and ALK-related signatures and lowest scores of immune pathways. Additionally, we found that the GeneSubgroup3 might be benefited from anti-GD2 instead of anti-PD-1 therapy. We further created a 48-gene signature, the TMEscore, to infer prognosis and validated it in three independent NB cohorts and a pan-cancer cohort of 9,460 patients. We did RNA-seq on 16 samples and verified that TMEscore was higher in patients with stage 3/4 than stage 1/2 diseases. The TMEscore could also predict responses for several immunotherapies. After adding clinical features, we found that the nomogram-based score system, the TMEIndex, surpassed the current risk system at predicting survivals. Our analysis explained TME at the transcriptome level and paved the way for immunotherapies in NB.
| S-EPMC9047956 | biostudies-literature
Project description:Tumor Microenvironment Profiling Identifies Prognostic Signatures and Suggests Immunotherapeutic Benefits in Neuroblastoma
| PRJNA756972 | ENA
Project description:Neuroblastoma (NB) is the most common extracranial solid tumor during infancy, causing up to 10% of mortality in children. NB shows notable heterogeneity with regard to histology and clinical behavior, ranging from low-risk localized tumors (LR-NB) to high-risk disease (HR-NB), characterized by aggressive metastatic phenotype, resistance to treatment, and fatal relapse occurrence. Risk stratification demands high accuracy, as it will determine the therapeutic treatment. However, the current therapeutic stratification, based on clinical and molecular risk factors, does not allow to discriminate among patients with similar clinical-pathological parameters who receive the same treatment despite showing markedly different clinical courses. The need of novel diagnostic molecular tools in oncology has led to increasing interest in liquid biopsies as a source of biomarkers, as they provide a minimally invasive method. Body fluids are a source of exosomes, nanosized extracellular vesicles that can drive tumor growth and chemoresistance. We previously identified exosomal microRNAs (exo-miRNA) indicative of HR-NB patient sensitivity/resistance to chemotherapy. As exosomes from cancer patients carry proteins that reflect the surface and cytoplasm content of parental cancer cells, including immunosuppressive molecules known to be associated with cancer progression and/or response to therapy, we extended our study to the exosomal proteins (Exo-prot).The purpose of the study is to identify Exo-prot that (i) are specifically expressed in NB patients and (ii) are associated with tumor phenotype and disease stage, in order to improve risk stratification and refine diagnosis.We isolated exosomes from plasma specimens of 24 HR-NB patients and 24 LR-NB patients at diagnosis and of 24 age-matched healthy controls (CTRL). Exo-prot expression was measured by liquid chromatography-mass spectrometry. Missing value distribution and differential expression analysis (performed with two different imputation methods) were applied to identify the most relevant Exo-prot. ROC analysis assessed the diagnostic value of the identified Exo-prot. We demonstrated that NB patients have a different Exo-prot expression profile compared to CTRL. The deregulated Exo-prot in NB specimens act mainly in tumor-associated pathways and build a strictly connected network. Furthermore, HR-NB patients show a different Exo-miR expression profile compared to LR-NB subjects, with the modulation of molecules involved in cell migration, proliferation and metastasis. Importantly, we show that NCAM, NCL, LUM and VASP have a diagnostic value in discriminating NB patients from CTRL; while MYH9, FN1, CALR, AKAP12 and, with a lower performance, LTBP1 can differentiate HR-NB and LR-NB patients with high accuracy. We demonstrated that Exo-prot deregulated in NB vs CTRL subjects and in HR-NB vs LR-NB patients contribute to NB tumor development and to the aggressive metastatic NB phenotype, respectively. We identified Exo-prot with significant diagnostic value for NB patients and able to efficiently identify the HR-NB subset of patients, which can be employed to improve risk stratification. Our results highlight the applicability of Exo-prot evaluation for integrating NB diagnosis and risk assessment.
2024-01-26 | PXD042422 | Pride
Project description:Triple-negative breast cancer represents approximately 15–20% of all reported breast cancer cases, and is characterized by a shorter survival time and higher mortality rates compared to other breast cancer sub-types. Tumor microenvironment (TME) refers to the internal and external environment of tumor tissue. Increasing evidence indicates that a tumor’s microenvironment is tightly associated with the immunological surveillance and defense during the development of breast cancer. Although oncology studies employing digital dissection methodologies have provided some insight on the biological features of TME, the development of methods to investigate the cellular composition of the tumor microenvironment remain an important research priority. In this study, we extracted whole transcriptome from 30 Triple-negative breast cancer (TNBC) patients and then used bioinformatics approaches to characterize cell type content in tumor tissue compared with para-cancerous tissue. We identified 4 types of enriched immune cells and 6 types of downregulated immune cells in the tumor tissue samples. After comprehensive bioinformatics analyses, we developed an ‘immune infiltration score’ (IIS) to quantitatively model immune cell infiltration in TNBC. To demonstrate the utility of the IIS, we used 2 independent datasets for validation. We found that patients with a higher IIS showing a longer progression-free survival time and significantly better prognosis than those with a lower IIS value. In sum, we explored the immune infiltration landscape in 30 TNBC patients and provided a novel and reliable biomarker IIS to evaluate the progression-free survival and prognosis in the TNBC patients.
2021-10-18 | E-MTAB-10886 | biostudies-arrayexpress
Project description:A distinctive feature of neuroblastoma (NB) tumors is their ability to secrete neuroendocrine mediators such as catecholamines, which through β-adrenergic receptors ligation may influence different signaling pathways in the tumor microenvironment (TME). Here, we aimed to investigate whether the β3-AR modulation affected the host immune system response to NB tumor. In a murine syngeneic NB model, pharmacological β3-AR antagonism lead to an immune response reactivation and reduced tumor growth through the involvement of PD-1/PD-L1 signaling axis. Indeed, β3-AR blockade on tumor infiltrating lymphocytes (TILs) dampened their ability to secrete IFN-γ and reduced PD-L1 expression on NB tumor cells, preventing the establishment of an immune suppressive TME. Furthermore, genomic analysis on NB patients showed that high ADRB3 gene expression correlates with poor clinical outcome. Overall, these findings indicate that β3-AR is able to sustain an immune suppressive TME in NB via PD-1/PD-L1 crosstalk, and suggest that targeting β-adrenergic signaling in NB could represent a new strategy to overcome immune escape gateway.
2023-07-31 | GSE209634 | GEO
Project description:Tumor endothelial cells (TECs) and corresponding normal endothelial cells (NECs) were isolated from 12 different human colocrectal carcinoma (CRC) patients with different prognostic tumor microenvironments (TME: Th1-TME vs Control-TME).
2023-05-01 | E-MTAB-10465 | biostudies-arrayexpress
Project description:Methylation analysis of 12 corresponding pairs of tumor endothelial cells (TECs) and normal endothelial cells (NECs) isolated from human colorectal carcinoma (CRC) patients with different prognostic tumor microenvironments (TMEs: Th1-TME vs Control-TME): High and low GBP-1 expression in the tumors detected by IHC was used to categorize the patient-derived cells into Th1-TME and Control-TME (compare Naschberger et al, J Clin Invest 2016 and Naschberger et al, Int J Cancer 2008). Isolation of the samples was done according to Naschberger et al, JoVE 2018. The analysis is paralleled by omics-analysis of the same cell cultures at the transcriptome (E-MTAB-10465) and genome level (E-MEXP-3993).
2023-05-01 | E-MTAB-10467 | biostudies-arrayexpress
Project description:Circular RNA (circRNA), a novel class of non-coding RNA, has been reported in various diseases, especially in tumors. However, the key signatures of circRNA-competitive endogenous RNA (ceRNA) network are largely unclear in colorectal cancer (CRC). We first characterized circRNAs profile by using circRNA-seq analysis from real-word dataset. The expression level of hsa_circ_0066351 in CRC tissues and cell lines was detected by quantitative real-time PCR. Then, cell proliferation assay was used to confirm the proliferation function of hsa_circ_0066351. Next, Cytoscape was used to construct circRNA–miRNA–mRNA networks. Last but not least, the landscape of hsa_circ_0066351–miRNA–mRNA in CRC had been investigated in the bulk tissue RNA-Seq level and single-cell Seq level. We proved that hsa_circ_0066351 was significantly downregulated in CRC cell lines and tissues (P < 0.001), and was negatively associated with distant metastasis (P < 0.01). Significantly, the expression of hsa_circ_0066351 was associated with better survival in patients with CRC. Function assays showed that hsa_circ_0066351 could inhibit CRC cells proliferation. In addition, a ceRNA network, including hsa_circ_0066351, two miRNAs, and ten mRNAs, was constructed. Our analyses showed that these ten mRNAs were consistently downregulated in pan-cancer and enriched in tumor suppressive function. A risk score model constructed by these ten downstream genes also indicated that they were related to the prognosis and immune response in CRC. In conclusion, we demonstrated that a novel circRNA (hsa_circ_0066351) inhibited CRC prol
2022-06-15 | GSE205643 | GEO
Project description:With the advent of cancer immunotherapy, intense investigation has been focused on tumor-infiltrating immune cells. With only a fraction of patients responding to these new therapies, a better understanding of all elements of the tumor microenvironment (TME) that may influence therapeutic outcome is needed. Stromal elements of the TME, chiefly fibroblasts, have emerged as potential contributors to tumor progression and most recently resistance to immunotherapy, but their precise composition and clinical relevance remain incompletely understood. Here we use single-cell transcriptomics to chart the fibroblastic landscape during pancreatic ductal adenocarcinoma (PDAC) progression in animal models, identifying two healthy tissue fibroblast subsets that co-evolve along individual trajectories into four subsets of carcinoma-associated fibroblasts (CAFs).
2019-10-31 | E-MTAB-8483 | biostudies-arrayexpress
Project description:RNA sequencing libraries were made for A-498 and 786-O to detect the transcripts regulated by the lincRNA comparing knockdown and the non-targeting control.
2016-12-31 | GSE70602 | GEO