Reclassification of Kidney Clear Cell Carcinoma Based on Immune Cell Gene-Related DNA CpG Pairs

Background: A new method was developed based on the relative ranking of gene expression level, overcoming the flaw of the batch effect, and having reliable results in various studies. In the current study, we defined the two methylation sites as a pair. The methylation level in a specific sample was subject to pairwise comparison to calculate a score for each CpGs-pair. The score was defined as a CpGs-pair score. If the first immune-related CpG value was higher than the second one in a specific CpGs-pair, the output score of this immune-related CpGs-pair was 1; otherwise, the output score was 0. This study aimed to construct a new classification of Kidney Clear Cell Carcinoma (KIRC) based on DNA CpGs (methylation sites) pairs. Methods: In this study, the biomarkers of 28 kinds of immune infiltration cells and corresponding methylation sites were acquired. The methylation data were compared between KIRC and normal tissue samples, and differentially methylated sites (DMSs) were obtained. Then, DNA CpGs-pairs were obtained according to the pairs of DMSs. In total, 441 DNA CpGs-pairs were utilized to construct a classification using unsupervised clustering analysis. We also analyzed the potential mechanism and therapy of different subtypes, and validated them in a testing set. Results: The classification of KIRC contained three subgroups. The clinicopathological features were different across three subgroups. The distribution of immune cells, immune checkpoints and immune-related mechanisms were significantly different across the three clusters. The mutation and copy number variation (CNV) were also different. The clinicopathological features and potential mechanism in the testing dataset were consistent with those in the training set. Conclusions: Our findings provide a new accurate and stable classification for developing personalized treatments for the new specific subtypes.

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Comprehensive Analysis of the Immune Infiltrates of Pyroptosis in Kidney Renal Clear Cell Carcinoma

Frontiers in Oncology ◽

10.3389/fonc.2021.716854 ◽

2021 ◽

Vol 11 ◽

Author(s):

Zhuolun Sun ◽

Changying Jing ◽

Xudong Guo ◽

Mingxiao Zhang ◽

Feng Kong ◽

...

Keyword(s):

High Risk ◽

Cell Carcinoma ◽

Poor Prognosis ◽

Immune Cell ◽

Risk Model ◽

Clear Cell ◽

Clear Cell Carcinoma ◽

Renal Clear Cell Carcinoma ◽

The Cancer Genome Atlas ◽

Risk Scores

Kidney renal clear cell carcinoma (KIRC) has long been identified as a highly immune-infiltrated tumor. However, the underlying role of pyroptosis in the tumor microenvironment (TME) of KIRC remains poorly described. Herein, we systematically analyzed the prognostic value, role in the TME, response to ICIs, and drug sensitivity of pyroptosis-related genes (PRGs) in KIRC patients based on The Cancer Genome Atlas (TCGA) database. Cluster 2, by consensus clustering for 24 PRGs, presented a poor prognosis, likely because malignancy-related hallmarks were remarkably enriched. Additionally, we constructed a prognostic prediction model that discriminated well between high- and low-risk patients and was further confirmed in external E-MTAB-1980 cohort and HSP cohort. By further analyzing the TME based on the risk model, higher immune cell infiltration and lower tumor purity were found in the high-risk group, which presented a poor prognosis. Patients with high risk scores also exhibited higher ICI expression, indicating that these patients may be more prone to profit from ICIs. The sensitivity to anticancer drugs that correlated with model-related genes was also identified. Collectively, the pyroptosis-related prognosis risk model may improve prognostic information and provide directions for current research investigations on immunotherapeutic strategies for KIRC patients.

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Tumor antigens and immune subtypes guided mRNA vaccine development for kidney renal clear cell carcinoma

Molecular Cancer ◽

10.1186/s12943-021-01465-w ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Hang Xu ◽

Xiaonan Zheng ◽

Shiyu Zhang ◽

Xianyanling Yi ◽

Tianyi Zhang ◽

...

Keyword(s):

Cell Carcinoma ◽

Topoisomerase Ii ◽

Tumor Antigens ◽

Immune Cell ◽

Vaccine Development ◽

Clear Cell ◽

Clear Cell Carcinoma ◽

Renal Clear Cell Carcinoma ◽

Survival Outcomes ◽

Topoisomerase Ii Alpha

AbstractCurrent treatment strategy for kidney renal clear cell carcinoma (KIRC) is limited. Tumor-associated antigens, especially neoantigen-based personalized mRNA vaccines represent new strategies and manifest clinical benefits in solid tumors, but only a small proportion of patients could benefit from them, which prompts us to identify effective antigens and suitable populations to facilitate mRNA vaccines application in cancer therapy. Through performing expression, mutation, survival and correlation analyses in TCGA-KIRC dataset, we identified four genes including DNA topoisomerase II alpha (TOP2A), neutrophil cytosol factor 4 (NCF4), formin-like protein 1 (FMNL1) and docking protein 3 (DOK3) as potential KIRC-specific neoantigen candidates. These four genes were upregulated, mutated and positively associated with survival and antigen-presenting cells in TCGA-KIRC. Furthermore, we identified two immune subtypes, named renal cell carcinoma immune subtype 1 (RIS1) and RIS2, of KIRC. Distinct clinical, molecular and immune-related signatures were observed between RIS1 and RIS2. Patients of RIS2 had better survival outcomes than those of RIS1. Further comprehensive immune-related analyses indicated that RIS1 is immunologically “hot” and represent an immunosuppressive phenotype, whereas RIS2 represents an immunologically “cold” phenotype. RIS1 and RIS2 also showed differential features with regard to tumor infiltrating immune cells and immune checkpoint-related genes. Moreover, the immune landscape construction identified the immune cell components of each KIRC patient, predicted their survival outcomes, and assisted the development of personalized mRNA vaccines. In summary, our study identified TOP2A, NCF4, FMNL1 and DOK3 as potential effective neoantigens for KIRC mRNA vaccine development, and patients with RIS2 tumor might benefit more from mRNA vaccination.

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Identification of the Prognosis Value and Potential Mechanism of Immune Checkpoints in Renal Clear Cell Carcinoma Microenvironment

Frontiers in Oncology ◽

10.3389/fonc.2021.720125 ◽

2021 ◽

Vol 11 ◽

Author(s):

Guodong Liao ◽

Ping Wang ◽

Yuyong Wang

Keyword(s):

Immune Checkpoint ◽

Prognostic Value ◽

Immune Cell ◽

Clear Cell ◽

Clear Cell Carcinoma ◽

Renal Clear Cell Carcinoma ◽

Immune Checkpoints ◽

Immune Cell Infiltration ◽

Free Survival ◽

Checkpoint Genes

BackgroundKidney Renal Clear Cell Carcinoma (KIRC) is one of the most prevalent types of cancer worldwide. KIRC has a poor prognosis and, to date, immunotherapy based on immune checkpoints is the most promising treatment. However, the role of immune checkpoints in KIRC remains ambiguous.MethodsBioinformatics analyses and qRT-PCR were performed to explore and further confirm the prognostic value of immune checkpoint genes and their correlation with immune infiltration in KIRC samples.ResultsThe expression of the immune checkpoint genes CD274, PDCD1LG2, HAVCR2, CTLA4, TIGFT, LAG3, and PDCD1 was upregulated in KIRC tissues. These genes were involved in the activation of the apoptosis pathway in KIRC. Low expression of CD274 and HAVCR2 and high expression of CTLA4 were associated with poor overall survival (OS), progression-free survival (PFS), and disease-free survival (DFS) of KIRC patients. The univariate and multivariate analyses revealed that CTLA4, HAVCR2, age, pTNM stage, and tumor grade were independent factors affecting the prognosis of KIRC patients. A predictive nomogram demonstrated that the calibration plots for the 3‐year and 5‐year OS probabilities showed good agreement compared to the actual OS of KIRC patients. The expression of CTLA4 and HAVCR2 were positively associated with immune cell infiltration, immune biomarkers, chemokines, and chemokine receptors. Moreover, miR-20b-5p was identified as a potential miRNA target of CTLA4 in KIRC.ConclusionOur study clarified the prognostic value of several immune checkpoint regulators in KIRC, revealing a CTLA4/miR-20b-5p axis in the control of immune cell infiltration in the tumor microenvironment.

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Integrated analysis of the underlying immunomodulator and survival signature of STON1 gene in kidney renal clear cell carcinoma

10.21203/rs.3.rs-847345/v1 ◽

2021 ◽

Author(s):

Axiu Zheng ◽

Jianrong Bai ◽

Yanping Ha ◽

Bingshu Wang ◽

Yuan Zou ◽

...

Keyword(s):

Cell Carcinoma ◽

Risk Score ◽

Immune Cell ◽

Cox Regression ◽

Clear Cell ◽

Clear Cell Carcinoma ◽

Renal Clear Cell Carcinoma ◽

Clinicopathological Characteristics ◽

Risk Scores ◽

Integrated Analysis

Abstract Background Stonin 1 (STON1) is an endocytic protein but its role in cancer remains unclear. Here, we investigated the role of STON1 in kidney renal clear cell carcinoma (KIRC). Methods We undertook bioinformatics analyses of a series of public databases to determine the expression and clinical significance of STON1 in KIRC and focused on STON1-related immunomodulator and survival signatures. A nomogram model integrating clinicopathological characteristics and risk scores for KIRC was established and validated. Results Through TGCA and GEO databases, STON1 mRNA was found to be significantly downregulated in KIRC compared with normal controls, and decreased STON1 was related to grade, TNM stage, distant metastasis, and vital status of KIRC. Furthermore, OncoLnc, UALCAN, Kaplan–Meier, and GEPIA2 analyses supported that KIRC patients with high STON1 expression had better overall survival. STON1 was positively associated with mismatch proteins including MLH1, PMS2, MSH2, MSH6 and EpCAM, and was negatively correlated with tumor mutational burden. Interestingly, arm-level deletion of STON1 was clearly related to the abundance of immune cells and the infiltration abundance in the majority of 26 immune cell types that were positively related to STON1 mRNA level in the TIMER database. The TISIDB database revealed 21 immunostimulators and 10 immunoinhibitors that were obviously related to STON1 in KIRC. In univariate and multivariate Cox regression analyses, CTLA4 , KDR , LAG3 , PDCD1 , HHLA2 , TNFRSF25 , and TNFSF14 were screened to establish a risk score model, and the low-risk group had a better prognosis for KIRC. Furthermore, a nomogram integrating clinicopathological characteristics and risk score had better accuracy and practicability in predicating the survival of KIRC patients. Conclusions Decreased STON1 expression in KIRC leads to clinical progression and poor survival. Mechanically, loss of STON1 is associated with the aberrant immune microenvironment in KIRC. Integrated clinicopathological characteristics and risk score derived from STON1 -related immunomodulators can aid the prediction of KIRC survival.

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Expression and Significance of Immune Checkpoints in Clear Cell Carcinoma of the Uterine Cervix

Journal of Immunology Research ◽

10.1155/2020/1283632 ◽

2020 ◽

Vol 2020 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Liju Zong ◽

Qianqian Zhang ◽

Yuncan Zhou ◽

Yujia Kong ◽

Shuangni Yu ◽

...

Keyword(s):

Cell Carcinoma ◽

T Cell Activation ◽

Immune Checkpoint ◽

Cell Activation ◽

Clear Cell ◽

Clear Cell Carcinoma ◽

Immune Checkpoint Blockade ◽

Immune Checkpoints ◽

Checkpoint Proteins ◽

Immune Checkpoint Proteins

The purpose of this study was to investigate the expression levels of the immune checkpoint proteins, programmed cell death-ligand 1 (PD-L1), B7-H3, B7-H4, and V-domain Ig suppressor of T cell activation (VISTA), as well as the significance thereof, in clear cell carcinoma (CCC) of the cervix (a rare histological subtype of cervical cancer). We also compared the expression statuses of these biomarkers in cervical CCCs with those in cervical squamous cell carcinomas (SCCs). We evaluated the expression of PD-L1, B7-H3, B7-H4, and VISTA in 50 cervical CCCs and 100 SCCs using immunohistochemical staining and investigated the associations between these markers, clinicopathologic features, and survival in patients with CCCs. Of the cervical CCC samples examined, 22%, 16%, 32%, and 34% were positive for PD-L1, B7-H3, B7-H4, and VISTA, respectively. Nineteen samples (38%) were negative for all 4 of these markers, whereas 31 (62%) expressed at least 1 marker. None of these markers was associated with the investigated clinicopathologic variables or patient survival. PD-L1, B7-H3, and VISTA were observed significantly more frequently in SCCs than in CCCs of the cervix. Our study confirmed the expression of immune checkpoint proteins in cervical CCCs and indicated their nonredundant and complementary roles. As such, our data suggest that monotherapeutic immune checkpoint blockade may not be sufficiently effective in patients with cervical CCC.

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Quantitative Assessment and Prognostic Associations of the Immune Landscape in Ovarian Clear Cell Carcinoma

Cancers ◽

10.3390/cancers13153854 ◽

2021 ◽

Vol 13 (15) ◽

pp. 3854

Author(s):

Saira Khalique ◽

Sarah Nash ◽

David Mansfield ◽

Julian Wampfler ◽

Ayoma Attygale ◽

...

Keyword(s):

Gene Expression ◽

T Cells ◽

Spatial Distribution ◽

Cell Carcinoma ◽

Immune Cell ◽

Clear Cell ◽

Clear Cell Carcinoma ◽

Cell Populations ◽

Ovarian Clear Cell Carcinoma ◽

Risk Patients

Ovarian clear cell carcinoma (OCCC) is a rare subtype of epithelial ovarian cancer characterised by a high frequency of loss-of-function ARID1A mutations and a poor response to chemotherapy. Despite their generally low mutational burden, an intratumoural T cell response has been reported in a subset of OCCC, with ARID1A purported to be a biomarker for the response to the immune checkpoint blockade independent of micro-satellite instability (MSI). However, assessment of the different immune cell types and spatial distribution specifically within OCCC patients has not been described to date. Here, we characterised the immune landscape of OCCC by profiling a cohort of 33 microsatellite stable OCCCs at the genomic, gene expression and histological level using targeted sequencing, gene expression profiling using the NanoString targeted immune panel, and multiplex immunofluorescence to assess the spatial distribution and abundance of immune cell populations at the protein level. Analysis of these tumours and subsequent independent validation identified an immune-related gene expression signature associated with risk of recurrence of OCCC. Whilst histological quantification of tumour-infiltrating lymphocytes (TIL, Salgado scoring) showed no association with the risk of recurrence or ARID1A mutational status, the characterisation of TILs via multiplexed immunofluorescence identified spatial differences in immunosuppressive cell populations in OCCC. Tumour-associated macrophages (TAM) and regulatory T cells were excluded from the vicinity of tumour cells in low-risk patients, suggesting that high-risk patients have a more immunosuppressive microenvironment. We also found that TAMs and cytotoxic T cells were also excluded from the vicinity of tumour cells in ARID1A-mutated OCCCs compared to ARID1A wild-type tumours, suggesting that the exclusion of these immune effectors could determine the host response of ARID1A-mutant OCCCs to therapy. Overall, our study has provided new insights into the immune landscape and prognostic associations in OCCC and suggest that tailored immunotherapeutic approaches may be warranted for different subgroups of OCCC patients.

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SIRT7 is a prognostic biomarker in kidney renal clear cell carcinoma that is correlated with immune cell infiltration

10.21203/rs.3.rs-867349/v1 ◽

2021 ◽

Author(s):

Ming Li ◽

Yue Qian ◽

Lili Mu ◽

Yixian Wang ◽

Xue Jin ◽

...

Keyword(s):

Cell Carcinoma ◽

Roc Curve ◽

Functional Role ◽

Immune Cell ◽

Clear Cell ◽

Prognostic Biomarker ◽

Clear Cell Carcinoma ◽

Renal Clear Cell Carcinoma ◽

Cancer Type ◽

Immune Cell Infiltration

Abstract Background: SIRT7 has been shown to be expressed in many cancer types, including kidney renal clear cell carcinoma (KIRC), but its functional role in this oncogenic context remains to be firmly defined. This study was designed to explore correlations between SIRT7 and KIRC characteristics using the TCGA database. Methods: Relationships between SIRT7 expression and KIRC patient clinicopathological characteristics were assessed through Kruskal-Wallis tests, Wilcoxon signed-rank tests, and logistic regression analyses. Area under the ROC curve (AUC) values were used to assess the prognostic value of SIRT7 as a means of classifying KIRC patients. The functional role of SIRT7 in this cancer type was assessed through GO/KEGG enrichment analyses and immune cell infiltration analyses. Results: In KIRC patients, higher levels of SIRT7 expression were associated with Race, M stage, T stage (all P < 0.05). SIRT7 offered significant diagnostic value in ROC curve analyses (AUC = 0.912), and elevated SIRT7 levels were linked to worse patient overall survival (OS; P < 0.001). The expression of SIRT7 was independently related with KIRC patient OS (HR: 1.827; 95%CI: 1.346-2.481; P<0.001). In GO/KEGG analyses, SIRT7 was found to be associated with ubiquitin-mediated proteolysis and nucleotide excision repair. Higher SIRT7 expression was related to the enhanced infiltration of certain immune cells.Conclusions: Increased SIRT7 expression was associated with a worse KIRC patient prognosis, and immune infiltrates, suggesting it may offer value as a prognostic biomarker for this cancer type.

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The Evaluation of Clinicopathological and Immunohistochemical Findings of Cervical Clear Cell Carcinoma in a Bitch

Acta Scientiae Veterinariae ◽

10.22456/1679-9216.86433 ◽

2018 ◽

Vol 46 ◽

pp. 5

Author(s):

Kubra Karakas Alkan ◽

Mehmet Eray Alcigir ◽

Hasan Alkan

Keyword(s):

Cell Carcinoma ◽

Clear Cell ◽

Clear Cell Carcinoma ◽

Cervix Uteri ◽

Vaginal Smear ◽

Total Blood ◽

Abdominal Ultrasonography ◽

Tissue Samples ◽

Cytologic Examination ◽

Estrogenic Effect

Background: Clear cell carcinoma (CCC) of the cervix is a rarely seen malignant tumor which is classified in adenocarcinomas of the endometrium. It is responsible for 2.15-3.0% of endometrial tumors. The diagnosis is difficult and is still controversial in uterine carcinomas. Macroscopically, masses were protruding to endometrial surface. However, the definitive diagnosis was carried by microscopical evaluation. The cells contain clear cytoplasm. The cells are seen in this pattern because there is either glycogenation or secretoric activity in the cells.Case: In the present case, clinicopathologic and immunohistochemical findings of clear cell carcinoma of the cervix were defined in a 3 year-old spayed Golden retriever bitch. Previously spayed bitch, which had vaginal discharge for the last month-long, was submitted to the Department of Obstetrics and Gynecology, Ankara University, Faculty of VeterinaryMedicine. In the general clinical examination, vaginoscopy was performed and vaginal cytology was obtained from smear. The source of discharge was detected as cervix uteri. In vaginal cytologic examination, erythrocyte, neutrophile and superficial cells were observed. In abdominal ultrasonography, a hypoechoic mass was detected at cranial part of the urinary bladder. To evaluate the general health condition of the dog, total blood counting and serum biochemistry were analyzed in addition to assessing its hormone prophlye. Estrogen and progesterone levels were evaluated. Estradiol (E2) level was measured as 23 pg/mL and progesterone level was measured as 1.96 ng/mL from collected serum. The cervical mass in diameters of 3x4x2.5 cm was removed in operation. In macroscopical examination, it had spherical and regularly shape.After the macroscopical examination, tissue samples were fixed in 10% buffered formalin. Then, the samples stained with Haematoxylin-Eosin (H&E), Masson’s trichrome and PAS stainings, respectively. At the macroscopic and histological examinations, the mass was diagnosed as clear cell carcinoma. Immunohistochemically, the tumor was stained with CK19 α-SMA, vimentin, desmin, TGF-β, VEGF, CEA, ER and PR markers. Other markers gave moderate to severe reactions in exception for no or weak ER and PR positivities. In direction of these results, clear cell carcinoma of cervix had been found remarkably due to first description in a spayed bitch on the basis of knowledge.Discussion: Clear cell carcinoma (CCC) is one type of the endometrial carcinomas. It is frequently known to have aggressive behavior and unfavorable prognosis. In human counterparts, clear cell carcinoma is frequently reoccurred in caudoabdominal and pelvic region even after being removed. The occurrence of clear cell carcinoma has highly increasedwith diethylstilbestrol usage during pregnancy. The situation on uterine carcinoma is nearly same in domestic animals. It is related to prolonged estrogenism. In this case, the bitch has been under prolong exposure to estrogenic effect. Indeed the estradiol level was high when compared to spayed female. Also, it is thought that the reason of high estradiol leveldoes not depend on the ovarian remnant. It is believed this situation may be relevant to exogen hormone usage. Vaginal smear confirmed erythrocyte (due to bleeding), predominantly superficial cells to it’s under estrogenic effect even despite being spayed.Keywords: clear cell carcinoma, cervix, clinicopathology, marker, bitch.

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Identification a ceRNA (XIST/miR-10a-5p/SERPINE1) Axis as a Prognostic Biomarker in Kidney Renal Clear Cell Carcinoma.

10.21203/rs.3.rs-717299/v1 ◽

2021 ◽

Author(s):

Rui-ji Liu ◽

Zhi-Peng Xu ◽

Shuying Li ◽

Jun-Jie Yu ◽

Bin Xu ◽

...

Keyword(s):

T Cell ◽

Cell Carcinoma ◽

Immune Cell ◽

Clear Cell ◽

Prognostic Biomarker ◽

Clear Cell Carcinoma ◽

Renal Clear Cell Carcinoma ◽

Immune Cell Infiltration ◽

Cerna Network

Abstract Background: Kidney cancer is one of the most common malignancies, of which the most aggressive subtype was kidney renal clear cell carcinoma (KIRC), accounting for 80% of them. A growing number of studies point to the involvement of competitive endogenous RNAs in tumor development. However, the role of ceRNA network involved in KIRC remains unclear. Thus, the aim of this study was to investigate the BAP1-associated prognostic ceRNA in KIRC. Methods: We downloaded the RNAseq data from TCGA along with the relevant clinical data. We screened the differentially expressed lncRNAs, miRNAs, mRNAs according to the expression of BAP1 and established a ceRNA network. Results: After comprehensive bioinformatics analysis, we identified the XIST-miR-10a-5p-SERPINE1 ceRNA axis. Next, we confirmed the prognostic role of miR-10a-5p/SERPINE1 in KIRC using survival analysis and Cox regression analysis. To investigate the abnormally high expression of SERPINE1, we performed methylation analysis of SERPINE1 and concluded that the methylation level of SERPINE1 in KIRC was significantly lower than that in normal tissues. Furthermore, to study the role of SERPINE1 in the immune microenvironment in KIRC, we performed immune cell infiltration analysis and found that SERPINE1 expression was positively correlated with the level of multiple immune cell infiltration (CD 4+ T cell, CD 8+ T cell, macrophages, dendritic cells, neutrophils). Conclusion: We constructed a ceRNA (XIST/has-miR-10a-5p/SERPINE1) that can be used as prognostic biomarker of KIRC. Furthermore, we found that miR-10a-5p/SERPINE1 were significantly associated with clinical features and were independent prognostic factors of KIRC.

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