Prognosis and progression of phagocytic regulatory factor-related gene combinations in clear cell renal cell carcinoma (ccRCC)
Highlight box
Key findings
• The prognostic model of a combination of genes associated with phagocytosis regulators had optimal performance in predicting long-term survival.
What is known and what is new?
• Immunotherapy is considered the most promising method to overcome cancer, and macrophages are promising targets in future cancer immunotherapy.
• We explored phagocytosis regulators that could effectively assess clinical prognosis in clear renal cell carcinoma. And phagocytosis regulator genes are closely associated with immune infiltration, phagocytic immune checkpoints and inflammatory factors.
What is the implication, and what should change now?
• In clear renal cell carcinoma, phagocytosis regulators have important prognostic value.
Introduction
Globally, renal cell carcinoma (RCC) accounts for more than 2% of neoplasms in humans worldwide, with the incidence and mortality persistently increasing (1). Gene signatures based on specific characteristic-related to predict prognosis have become a hotspot in cancer research (2-4). The prognostic value of phagocytosis regulators in clear RCC is unclear. Immunotherapy is considered the most promising method to overcome cancer, and macrophages are promising targets in future cancer immunotherapy (5). Phagocytic cells can eliminate cancer cells through phagocytosis, and 173 potential macrophage-regulated genes were obtained by Kamber et al. (6,7). Our study investigated the relationship between phagocytosis regulator gene expression and prognosis in clear cell RCC (ccRCC) patients in the Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) database. Inflammatory cells are a key component in cancer ecology (8). The macrophages are the main component of leukocyte infiltration, and there are different numbers of macrophages in all tumors (9). The macrophages are the key to promoting tumor inflammation. Tumor-associated macrophages (TAMs) promote tumor progression at various levels, including promoting genetic instability, cultivating cancer stem cells, paving the way for metastasis, and taming adaptive protective immunity. TAM expression triggers T cell activation of checkpoints and is the target of checkpoint blockade immunotherapy. Macrophage-centric therapies include strategies to prevent tumor recruitment and survival; anti-tumor function reeducation, M1-like mode; tumor-directed monoclonal antibodies that can cause extracellular killing or phagocytosis of cancer cells (10). Monoclonal antibody therapy targeting tumor antigens largely drives the elimination of cancer cells by triggering macrophage phagocytosis of cancer cells. However, the mechanisms by which cancer cells escape phagocytosis are poorly understood. As a ‘Do not eat me’ signal, CD47 is a known regulator that protects cells from phagocytosis by binding to and activating its receptor SIPRA on macrophages (11). Identifying and characterizing phagocytosis regulators is vital for describing the mechanism of phagocytosis in tumors. Two genome-wide CRISPR articles (6,7) have identified some important phagocytosis regulators. However, the effects of these regulators on tumorigenesis and progression in ccRCC have not been studied. To this end, using data from TCGA, we employed the Cox regression model to evaluate the prognostic relevance of phagocytosis regulator genes in patients with ccRCC. By applying the least absolute shrinkage and selection operator (LASSO) regression, we were able to select the most significant predictors from a vast pool of potential biomarkers. These selected candidates were then used to compute a signature score that assesses patient prognosis and treatment outcomes. This analysis has provided new insights into the role of phagocytosis regulators in the progression and prognosis of ccRCC. We present this article in accordance with the TRIPOD reporting checklist (available at https://tcr.amegroups.com/article/view/10.21037/tcr-24-139/rc).
Methods
Data collection
The study was conducted in accordance with the Declaration of Helsinki (as revised in 2013).
TCGA ccRCC
TCGA database of kidney renal clear cell carcinoma (KIRC) transcriptome data (RNA-Seq) and clinical information data were obtained through Bioconductor package TCGA bio links (12). RNA-Seq data normalized fragments per kilobase of exon model per million mapped fragments (FPKM) expression profile of tumor samples [526] and normal samples [72]. The clinical information included the overall survival time, survival status, and other clinical phenotype data of KIRC patients, including age, gender, tumor grade, tumor stage, and other information (Table 1).
Table 1
Characteristics | Type | Patients |
---|---|---|
Gender | Female | 184 |
Male | 342 | |
Stage | I | 263 |
II | 56 | |
III | 122 | |
IV | 82 | |
NA | 3 | |
Grade | G1 | 14 |
G2 | 224 | |
G3 | 205 | |
G4 | 75 | |
NA | 8 | |
Age, years | ≥60 | 261 |
<60 | 265 |
TCGA-KIRC, The Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma; NA, not application.
GEO ccRCC
GEO resource platform (https://www.ncbi.nlm.nih.gov/gds) was used to download a set of renal clear cell carcinoma data (GSE167573, including 62 tumor samples) including log2-transformed TPM (transcripts per million). In addition, transcriptome expression profiles and tumor clinical information (Table S1) were used to validate the analysis.
Feature collection of 28 types of immune cells
The characteristic gene set of 28 immune cells was derived from Clyde et al. (13).
Immune subtypes of TCGA tumors
The immune subtypes of TCGA tumors were derived from Thorsson et al. (14), and TCGA-KIRC included a total of 6 subtypes C1-C6 (Table S2).
Phagocytosis regulators
A total of 90 and 85 phagocytosis-related regulator genes were collected from literature Kamber et al. (6) and Haney et al. (7), respectively. The union of the two sets of 173 genes was used as phagocytosis regulators combined and used for subsequent analysis.
Research methods
Technical route
ssGSEA calculates an immune cell enrichment score
Through the ssGSEA method of Bioconductor package gene set variation analysis (GSVA) (15), we used the log2(FPKM+1) transformed TCGA-KIRC expression profile and 28 immune cell signature gene sets as the input of ssGSEA and calculated each sample in each immune cell ssGSEA enrichment score.
GO/KEGG functional enrichment analysis
The GO/KEGG functional enrichment analysis was performed on the collected phagocytosis regulators using the clusterProfiler (16) of the Bioconductor package, and the functional enrichment was considered to be statistically significant when the calculated result P<0.05 (without multiple test correction).
Differential analysis of tumor and normal samples
Based on the expression data of log2 (FPKM+1) normalized by TCGA-KIRC, we evaluated the model using ImFit, the linear fitting method of limma (17). In addition, we calculated the difference between ccRCC and normal samples using the eBayes method. When fold-change >1.5 and FDR <0.05, the gene expression was significantly different.
Construction and evaluation of phagocytosis regulator genes
First, using R package survival, Cox regression analysis was performed on differentially expressed phagocytosis regulators based on TCGA-KIRC tumor expression profile data, survival time, and survival status (18) to determine the hazard ratio (HR) of genes and significant prognosis, and screened genes with significant P<0.05 as candidate prognostic factors. Subsequently, R package glnmet (19) was used to perform LASSO regression on the candidate prognostic factors, and the factors that significantly impacted survival were selected as phagocytosis regulators. Next, the regression coefficients corresponding to each factor were calculated. Then, the weighted sum of the expression of each prognostic factor and LASSO regression coefficient is used as the sigScore (Signature Score) of each sample, and the calculation formula is as follows: sigScore = ∑ expi × coefi, where i represents the prognostic factor, and exp represents each prognosis The expression level of the factor, and coef represents the LASSO regression coefficient.
To evaluate the correlation between phagocytosis regulator genes and prognosis, the samples were divided into high-risk and low-risk groups according to the median value of sigScore. Then the survival and log-rank test models were constructed using the R package survival, and then survminer (19) demonstrated the Kaplan-Meier survival curve and the significance of the difference between the two groups. Simultaneously, R package timeROC (20) was used to construct the time-dependent receiver operating characteristic (ROC) curve of sigScore to evaluate the performance of phagocytosis regulators.
Finally, univariate and multivariate Cox regression models were used to evaluate whether phagocytosis regulatory factors could be used as independent prognostic factors, and R-package forest model (21) was used to display the forest map of regression analysis.
Immune microenvironment
ESTIMATE (Estimating STromal and Immune cells in MAlignant Tumor tissues using Expression data) can use the unique properties of tumor transcriptional profiles to infer the content of immune cells and stromal cells as well as tumor purity (22). In addition, many algorithms can infer the proportion or score of immune cells in the tumor microenvironment from tumor expression profiles. To this end, we evaluated different immune cell scores using ESTIMATE (23), EPIC (24), quanTIseq (25), and ssGSEA [evaluating 28 immune cells (24)] from R package IOBR (26), respectively.
Statistical analysis
All statistical analyses were performed by R software (https://www.r-project.org). The Mann-Whitney U test was used to compare the differences between two groups of samples when performing significant analysis between various values (expression level, infiltration ratio, etc.). In the plot presentation, where ns means P>0.05, * means P≤0.05, ** means P≤0.01, *** means P≤0.001, and **** means P≤0.0001.
Results
Phagocytosis regulators are associated with macrophage activity and participate in the occurrence and development of renal clear cell carcinoma
Phagocytosis regulators are associated with macrophage activity
Through mapping, we found that 167 of the 173 phagocytosis regulator genes collected in the literature were expressed in TCGA-KIRC. Subsequently, to explore the association of phagocytosis regulators with macrophages, we calculated the macrophage enrichment score for each sample of TCGA-KIRC using the macrophage gene set and then calculated the enrichment score with each phagocytosis regulator (Figure 1). As a result, we found that many phagocytosis regulators were positively correlated with macrophage scores (Figure 1A), and macrophages could also significantly distinguish the expression abundance of phagocytosis regulators (Figure 1B).
Functional analysis of phagocytosis regulators
We conducted a functional enrichment analysis of 167 phagocytosis regulators and identified significantly enriched Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) sets at P<0.05. In the realm of biological processes, there was an enrichment of gene sets related to the assembly of mitochondrial respiratory chain complexes, particularly complex I. Analysis of cellular components revealed significant enrichment in the mitochondrial inner membrane and the respirasome. Regarding molecular function, the categories predominantly enriched included active transmembrane transporter activity and electron transfer activity (see Figure 2A-2C). The KEGG enrichment analysis indicated associations of phagocytosis regulators with several diseases, prominently with Alzheimer’s disease among neurodegenerative disorders (see Figure 2D). We hypothesize that the functions of phagocytosis regulators are interconnected with the enriched GO categories and KEGG pathways identified in ccRCC.
Identification and prognostic analysis of phagocytosis regulator genes in ccRCC
Based on TCGA-KIRC expression profile, we identified 2094 up- and 2174 down-regulated genes (fold-change >1.5, FDR <0.05), of which 18 were up- and 17 were down-regulated phagocytosis regulators (Figure 3). To ascertain their prognostic significance, we performed univariate Cox regression analyses on these phagocytosis regulator factors. This analysis identified 18 candidates with prognostic value at a P<0.05 level (Figure 4). The Kaplan-Meier curves for the four most significant candidate genes—POU2F2, QPCTL, KLF6, and SLC39A9—indicate that they are capable of effectively distinguishing survival rates, suggesting that these genes may serve as potential biomarkers for the prognosis of ccRCC (Figure 5).
Constructing a prognostic regression model for genes related to phagocytosis regulators
Based on the prognostic candidate regulators, we used LASSO regression model for further screening (Figure 6A,6B). The remaining factors (Figure 6C) were used as phagocytosis regulatory signatures, and the following formula calculated the Signature Score: sigScore = ∑ expi×coefi. Among them, i represents the prognostic phagocytosis regulator, expi represents the expression of the factor, and coef represents the LASSO regression coefficient (Table 2).
Table 2
Signature | Coefficients |
---|---|
BCL6 | 0.337016 |
POU2F2 | 0.154386 |
QPCTL | 0.128073 |
KLF6 | −0.31081 |
SLC39A9 | −0.0464 |
NDUFV1 | −0.17414 |
FOXO1 | −0.1443 |
AIFM1 | −0.09171 |
FDX1 | −0.17718 |
ALAD | −0.24401 |
LASSO, least absolute shrinkage and selection operator.
Phagocytosis regulatory genes are associated with patient prognosis and clinical characteristics
Phagocytosis regulatory genes can predict patient prognosis
Using TCGA-KIRC as a training set for tumor prognosis of phagocytosis regulatory genes and GSE167573 as a validation set, samples were divided into two groups with high and low scores according to the median sigScore. Then, the difference in survival time between the two sample groups was evaluated. Finally, the ROC was used to evaluate phagocytosis regulation. The performance of the factor-related gene model for prognosis prediction (Figure 7, please refer to Figure S1 for the validation set). We can see that the high expression group of phagocytosis regulatory genes has a higher risk of death than the low expression group (Figure 7A). The model had a better prognostic performance at 1, 3, and 5 years with area under the curve (AUC) values of 0.747, 0.706, and 0.704, respectively (Figure 7B).
Phagocytosis regulatory genes are associated with clinical characteristics of patients
Based on the existing clinical features of the training set TCGA-KIRC and the validation set GSE167573, we compared the differences in the sigScore of different clinical feature groups (Figure 8, and the validation set is demonstrated in Figure S2). Some clinical features were significantly correlated with phagocytosis regulatory gene scores. For example, higher tumor grade and stage levels were more likely to have higher phagocytosis regulatory genes, consistent with previous survival analysis showing phagocytosis regulators. In addition, high expression of related genes is associated with poorer prognostic risk.
Multivariate Cox regression to verify the prognostic independence of genes related to phagocytosis regulators
To test the prognostic independence of phagocytosis regulatory genes, based on the training set TCGA-KIRC and the validation set GSE167573, we performed multivariate Cox regression analysis on clinical features and sigScore grouping and found that phagocytosis regulatory genes have prognostic independence (Figure 9, see Figure S3 for the training set).
Different clinical feature groups and prognostic efficacy analyses of phagocytosis factor-related genes
To further explore the prognostic efficacy of phagocytosis factor-related genes, we performed Kaplan-Meier survival analysis for different clinical feature groups and sigScore median groups of TCGA-KIRC and GSE167573 (Figure 10, and the validation set is displayed in Figure S4).
Genes related to phagocytosis regulators are related to the immune microenvironment and immunotherapy of patients
Phagocytosis regulatory genes are related to the immune microenvironment
We assessed the immune microenvironment score of TCGA-KIRC with ESTIMATE and the scores of different immune cells using various methods to investigate the association of phagocytosis regulatory genes with the immune microenvironment. We then assessed the association of phagocytosis regulatory genes with immune infiltration scores and immune cell scores (Figure 11). The figure indicates that phagocytosis regulatory genes can significantly divide samples with different immune infiltration levels into different subgroups (Figure 11A), and sigScore has a significant positive correlation with immune infiltration scores (Figure 11B). Similarly, phagocytosis regulatory genes can significantly divide samples with different degrees of infiltration into different subpopulations based on immune cells, including macrophages (Figure 11C).
Phagocytosis regulatory genes are associated with immune checkpoints and pro-inflammatory factors
Tumor cells usually use immune checkpoint factors to “immune escape”. To further explore the association between phagocytosis signatures and macrophage immune checkpoints (22), we evaluated the relationship between each signature gene and immune checkpoint genes (Figure 12). The figure demonstrates that the high and low grouping of phagocytosis regulatory genes can significantly distinguish the expression levels of immune checkpoints. Concurrently, the genes in phagocytosis regulatory genes are not entirely consistent with their effects, which fully shows that phagocytosis is the combined effect of regulatory genes. In addition, the high and low grouping of phagocytosis regulatory genes depicted a negative relationship between immune checkpoint receptors and ligands, such as PD-1 gene PDCD1 and PD-L1 gene CD274 (Figure 12, more receptor-ligand relationships (Figure S5).
Inflammation and cancer are inextricably linked. Pro-inflammatory factors can often mediate a variety of immune responses. Phagocytic M1 can secrete various cytokines to promote inflammation, while phagocytic M2 can secrete various inhibiting inflammatory responses factor (5). Therefore, we further explored the association between phagocytosis regulators, their genes, and pro-and anti-inflammatory factors (Figure 13). The figure manifests that the expression levels of corresponding genes of IL1A, IL1B, IL-6, IL18, IL23A, and TNF-α are significantly different between high and low groups of phagocytosis regulatory genes and had a consistent trend (Figure 13). The genes in phagocytosis regulators were not identical to their classification effects, fully demonstrating the combined effect of phagocytosis regulatory genes.
Whether phagocytosis regulatory genes predict the efficacy of immunotherapy in patients
We envisioned that phagocytosis regulatory genes could predict the efficacy of immunotherapy in tumor patients. Therefore, we used a set of immunotherapy data (27) to construct a combination of phagocytosis regulatory genes in the same way as above, but the results were unsatisfactory. To this end, we tried to evaluate its performance in immunotherapy data based on the phagocytosis regulatory genes constructed by TCGA-KIRC and performed survival analysis and drug-corresponding association analysis on the collected immunotherapy data sets. Finally, a survival analysis was carried out. Unfortunately, the correlation of P values with drug response Mann-Whitney U’s P value is less than 0.05 to evaluate its performance, and the results are also not ideal (see Figure S6A-S6D).
Discussion
Cancer cells have long been thought to be associated with regulators of phagocytosis. However, the prognostic value of related genes in ccRCC is unclear. In our study, we investigated the relationship between phagocytosis regulatory gene expression and the prognosis of ccRCC patients in The Cancer Genome Atlas (TCGA) database. Importantly, for the first time, we attempted to construct a prognostic model of a combination of genes associated with phagocytosis regulators using LASSO Cox regression analysis of genes. Kaplan-Meier analysis demonstrated that our model could effectively predict prognosis in TCGA-KIRC cohort and the Clinical Proteomics Cancer Analysis Consortium (cptac_ccrCC) cohort. We found that the model had optimal performance in predicting long-term survival through time-dependent ROC analysis, and multivariate Cox regression analysis revealed that our combined model was an independent prognostic factor. Risk scores for each patient were significantly associated with various clinicopathological parameters. Clinical features were significantly correlated with phagocytosis regulatory gene scores. In contrast, tumors with higher levels of grade and stage were more prone to have higher phagocytosis regulatory genes, which is in contrast to previous survival analysis showing that high expression of phagocytosis regulatory genes has poor expression. Prognostic risks echo each other. Our study suggests that phagocytosis regulatory genes do not play an ideal role in predicting the efficacy of immunotherapy in patients.
Furthermore, research by Gao et al. (28). has shown that KLF6 suppresses ccRCC progression by inhibiting epithelial-mesenchymal transition (EMT) and metastatic capabilities, while Wang et al. (29). found that POU2F2 could enhance EMT and thus promote ccRCC progression. Unlike the findings of Gao and Wang, our study uniquely identifies and confirms the regulatory roles of genes such as POU2F2 and KLF6 in phagocytosis, suggesting them as novel therapeutic targets. This distinction is critical as it highlights potential mechanisms by which these genes could influence tumor progression and patient survival—mechanisms previously unexplored.
Overall, our study provides new insights into the prognostic and progressive roles of phagocytosis regulatory genes in ccRCC, expanding our understanding of their potential impact on treatment outcomes.
Conclusions
We have constructed a prognostic model of a combination of genes associated with phagocytosis regulators and provided new insights into the prognosis and progression of phagocytosis regulatory genes in ccRCC.
Acknowledgments
The authors would like to thank the public database provider in this study.
Funding: This work was supported by
Footnote
Reporting Checklist: The authors have completed the TRIPOD reporting checklist. Available at https://tcr.amegroups.com/article/view/10.21037/tcr-24-139/rc
Peer Review File: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-24-139/prf
Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://tcr.amegroups.com/article/view/10.21037/tcr-24-139/coif). The authors have no conflicts of interest to declare.
Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. The study was conducted in accordance with the Declaration of Helsinki (as revised in 2013).
Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.
References
- Siegel RL, Miller KD, Jemal A. Cancer statistics, 2019. CA Cancer J Clin 2019;69:7-34. [Crossref] [PubMed]
- Cheng G, Liu D, Liang H, et al. A cluster of long non-coding RNAs exhibit diagnostic and prognostic values in renal cell carcinoma. Aging (Albany NY) 2019;11:9597-615. [Crossref] [PubMed]
- Song Q, Shang J, Yang Z, et al. Identification of an immune signature predicting prognosis risk of patients in lung adenocarcinoma. J Transl Med 2019;17:70. [Crossref] [PubMed]
- Wang Y, Ruan Z, Yu S, et al. A four-methylated mRNA signature-based risk score system predicts survival in patients with hepatocellular carcinoma. Aging (Albany NY) 2019;11:160-73. [Crossref] [PubMed]
- Duan Z, Luo Y. Targeting macrophages in cancer immunotherapy. Signal Transduct Target Ther 2021;6:127. [Crossref] [PubMed]
- Kamber RA, Nishiga Y, Morton B, et al. Inter-cellular CRISPR screens reveal regulators of cancer cell phagocytosis. Nature 2021;597:549-54. [Crossref] [PubMed]
- Haney MS, Bohlen CJ, Morgens DW, et al. Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens. Nat Genet 2018;50:1716-27. [Crossref] [PubMed]
- Mantovani A, Allavena P, Sica A, et al. Cancer-related inflammation. Nature 2008;454:436-44. [Crossref] [PubMed]
- Noy R, Pollard JW. Tumor-associated macrophages: from mechanisms to therapy. Immunity 2014;41:49-61. [Crossref] [PubMed]
- Mantovani A, Marchesi F, Malesci A, et al. Tumour-associated macrophages as treatment targets in oncology. Nat Rev Clin Oncol 2017;14:399-416. [Crossref] [PubMed]
- Morrissey MA, Kern N, Vale RD. CD47 Ligation Repositions the Inhibitory Receptor SIRPA to Suppress Integrin Activation and Phagocytosis. Immunity 2020;53:290-302.e6. [Crossref] [PubMed]
- Colaprico A, Silva TC, Olsen C, et al. TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res 2016;44:e71. [Crossref] [PubMed]
- Clyde D. Cancer genomics: Keeping score with immunotherapy response. Nat Rev Genet 2017;18:146. [Crossref] [PubMed]
- Thorsson V, Gibbs DL, Brown SD, et al. The Immune Landscape of Cancer. Immunity 2018;48:812-830.e14. [Crossref] [PubMed]
- Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics 2013;14:7. [Crossref] [PubMed]
- Yu G, Wang LG, Han Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 2012;16:284-7. [Crossref] [PubMed]
- Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 2015;43:e47. [Crossref] [PubMed]
- Themeau TM, Lumley T. Package ‘survival’. R Top Doc 2015;128:28-33.
- Friedman J, Hastie T, Tibshirani R, et al. Package ‘glmnef’. Journal of Statistical Software. 2010;33:
- Blanche P, Blanche M P. Package 'timeROC'. 2019. Available online: https://cran.r-project.org/web/packages/timeROC/index.html
- Kennedy N. Package ‘forestmodel’. Forest Plots from Regression Models. (R package version 0.6.2) 2020. Available online: https://cran.r-project.org/web/packages/forestmodel/index.html
- Kassambara A, Kosinski M, Biecek P, et al. Package ‘survminer’. Drawing Survival Curves using ‘ggplot2’(R package version 03-1) 2017. Available online: https://cran.r-project.org/web/packages/survminer/index.html
- Yoshihara K, Shahmoradgoli M, Martínez E, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun 2013;4:2612. [Crossref] [PubMed]
- Racle J, de Jonge K, Baumgaertner P, et al. Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data. Elife 2017;6:e26476. [Crossref] [PubMed]
- Finotello F, Mayer C, Plattner C, et al. Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome Med 2019;11:34. [Crossref] [PubMed]
- Zeng D, Ye Z, Shen R, et al. IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures. Front Immunol 2021;12:687975. [Crossref] [PubMed]
- Braun DA, Hou Y, Bakouny Z, et al. Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma. Nat Med 2020;26:909-18. [Crossref] [PubMed]
- Gao Y, Li H, Ma X, et al. KLF6 Suppresses Metastasis of Clear Cell Renal Cell Carcinoma via Transcriptional Repression of E2F1. Cancer Res 2017;77:330-42. [Crossref] [PubMed]
- Wang T, Wagner RT, Hlady RA, et al. SETD2 loss in renal epithelial cells drives epithelial-to-mesenchymal transition in a TGF-β-independent manner. Mol Oncol 2024;18:44-61. [Crossref] [PubMed]