
==== Front
Cancer Imaging
Cancer Imaging
Cancer Imaging
1740-5025
1470-7330
BioMed Central London

768
10.1186/s40644-024-00768-7
Research
Radiomics predicts the prognosis of patients with clear cell renal cell carcinoma by reflecting the tumor heterogeneity and microenvironment
Wu Ji 12
Li Jian 3
Huang Bo 4
Dong Sunbin 4
Wu Luyang 4
Shen Xiping shenxiping2022@163.com

12
Zheng Zhigang 17352929252@163.com

5
1 https://ror.org/05t8y2r12 grid.263761.7 0000 0001 0198 0694 Department of General surgery, Suzhou Ninth Hospital Affiliated to Soochow University, Suzhou, Jiangsu Province China
2 https://ror.org/05t8y2r12 grid.263761.7 0000 0001 0198 0694 Department of Radiology, Suzhou Ninth Hospital Affiliated to Soochow University, Suzhou, Jiangsu Province China
3 https://ror.org/02afcvw97 grid.260483.b 0000 0000 9530 8833 Department of Radiology, Changshu No People’s HospitalThe Affiliated Changshu Hospital of Nantong University, Changshu, Jiangsu China
4 grid.89957.3a 0000 0000 9255 8984 Department of Radiology, Municipal Hospital Affiliated to Nanjing Medical University, Suzhou, Jiangsu Province China
5 grid.16821.3c 0000 0004 0368 8293 Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
16 9 2024
16 9 2024
2024
24 12419 6 2024
29 8 2024
© The Author(s) 2024
2024
https://creativecommons.org/licenses/by/4.0/ Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
Purpose

We aimed to develop and externally validate a CT-based deep learning radiomics model for predicting overall survival (OS) in clear cell renal cell carcinoma (ccRCC) patients, and investigate the association of radiomics with tumor heterogeneity and microenvironment.

Methods

The clinicopathological data and contrast-enhanced CT images of 512 ccRCC patients from three institutions were collected. A total of 3566 deep learning radiomics features were extracted from 3D regions of interest. We generated the deep learning radiomics score (DLRS), and validated this score using an external cohort from TCIA. Patients were divided into high and low-score groups by the DLRS. Sequencing data from the corresponding TCGA cohort were used to reveal the differences of tumor heterogeneity and microenvironment between different radiomics score groups. What’s more, univariate and multivariate Cox regression were used to identify independent risk factors of poor OS after operation. A combined model was developed by incorporating the DLRS and clinicopathological features. The SHapley Additive exPlanation method was used for interpretation of predictive results.

Results

At multivariate Cox regression analysis, the DLRS was identified as an independent risk factor of poor OS. The genomic landscape of different radiomics score groups was investigated. The heterogeneity of tumor cell and tumor microenvironment significantly varied between both groups. In the test cohort, the combined model had a great predictive performance, with AUCs (95%CI) for 1, 3 and 5-year OS of 0.879(0.868–0.931), 0.854(0.819–0.899) and 0.831(0.813–0.868), respectively. There was a significant difference in survival time between different groups stratified by the combined model. This model showed great discrimination and calibration, outperforming the existing prognostic models (all p values < 0.05).

Conclusion

The combined model allowed for the prognostic prediction of ccRCC patients by incorporating the DLRS and significant clinicopathologic features. The radiomics features could reflect the tumor heterogeneity and microenvironment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40644-024-00768-7.

Keywords

Overall survival
Clear cell renal cell carcinoma
Deep learning
Radiomics
Tumor microenvironment
Scientific Research Foundation of Suzhou Ninth Hospital Affiliated to Soochow UniversityNo. YK202330 No. YK202330 issue-copyright-statement© International Cancer Imaging Society (ICIS) 2024
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pmcIntroduction

Renal cell carcinoma (RCC) is one of the most deadly urological malignancies [1, 2]. The most common subtype of RCC is clear cell renal cell carcinoma (ccRCC), which accounts for the majority of RCC-related deaths [3]. Radical nephrectomy and nephron-sparing surgery are the primary treatments for localized ccRCC, but the prognosis of ccRCC patients varies among different stages [4]. It is challenging to accurately predict the clinical outcome because of tumor heterogeneity.

To the best of our knowledge, several prognostic models have been proposed for outcome prediction of localized ccRCC after surgery [5–7]. For example, the Stage, Size, Grade, and Necrosis (SSIGN) score and the University of California, Los Angeles, Integrated Staging System (UISS) have been validated and widely used in clinical setting [8, 9]. However, most of these studies were limited to the clinicopathologic level and their predictive performances were unsatisfactory. What’s more, the characteristics of intratumor heterogeneity were not considered in these studies. A more comprehensive prediction could be an intriguing topic for further investigation.

Contrast-enhanced computed tomography (CT) examination is mandatory for detailed assessment of the nature of renal mass [10]. In recent years, a newly established field, converts extracted features into quantitative parameters [11–13]. This method shows huge potential in disease diagnosis and prognosis prediction [14]. However, the association of CT-derived DL radiomics features with clinical outcomes in ccRCC patients remains unclear. We hypothesized that DL radiomics features could provide valuable information for outcome prediction.

Last but not least, previous studies revealed that radiomics features could reflect the tumor heterogeneity [15, 16]. However, the link between imaging subtypes and tumor microenvironment remained unexplored. We aimed to investigate and visualize this relationship.

Overall, we aimed to explore the prognostic implications of CT-derived DL radiomics features, and then generate a prediction model for OS in ccRCC patients. The secondary endpoint was to explore the associations between DL radiomics features and tumor heterogeneity/ microenvironment.

Methods and materials

Study design

This retrospective multicenter cohort study has been reported in line with the STROCSS criteria [17]. We strictly followed the ethical guidelines of the 1975 Declaration of Helsinki. The Research Ethics Committee of Suzhou Ninth Hospital Affiliated to Soochow University had approved it.

Localized ccRCC patients from 3 hospitals between January 2003 and July 2023 were recruited (Fig. 1). Clinical data were collected from the electronic medical record. The inclusion criteria were (1) older than 18-year-old (2) pathologically confirmed ccRCC after radical or partial nephrectomy (3) complete clinicopathological data, follow-up data and contrast-enhanced CT images. Patients with other malignant tumors or history of receiving anti-tumor therapy were excluded. We randomly divided the whole cohort into two groups (i.e., derivation and test cohorts) for model development and validation, with a ratio of 7:3 by the method of random number table.

Fig. 1 Flow chart of the study design. Abbreviation ccRCC clear cell renal cell carcinoma; TCGA the Cancer Genome Atlas; TCIA the Cancer Imaging Archive; KIRC kidney renal clear cell carcinoma; DEG differential expression gene

Primary outcomes

All individuals were followed up every 3 months for the first year and every 6 months thereafter by telephone. The primary outcome for this study was overall survival (OS), which is defined as the period between the date of diagnosis and death or the last follow-up. The secondary outcome was disease-free survival (DFS), defined as the time from primary surgery to first tumor recurrence, progression, death or the last follow-up.

Definitions of potential predictive factors

Eastern Cooperative Oncology Group Performance Status (ECOG-PS) is a questionnaire for functional status assessment. This score showed close correlation with cancer mortality [18].

Charlson Comorbidity Index (CCI), a widely used scoring system, quantifies comorbidities based on the number and severity of diseases [19].

The prognostic role of the microvascular invasion has been reported in ccRCC [20, 21].

World Health Organization/International Society of Urologic Pathologists (WHO/ISUP) classification was used for pathological grading of RCC [22].

Image acquisition and ROI segmentation

Contrast-enhanced CT images were collected from picture archiving and communication system. CT scan protocols are listed in Supplementary Table S1. Contrast-enhanced CT images and detailed clinical information of the external validation cohort (TCGA-KIRC cohort) were collected from The Cancer Imaging Archive (TCIA) (https://www.cancerimagingarchive.net/) [23]. The exclusion criteria were described as follows: (1) no enhanced CT images (2) poor image quality (3) survival time < 30 days. As a result, 96 cases were enrolled. Genomic data matching the TCIA were downloaded from TCGA (https://portal.gdc.cancer.gov/).

3D slicer software (Version 4.11.0) was used for the segmentation of region of interests (ROIs) [24]. The tumor area was outlined slice-by-slice by two experienced radiologists (10-and 15-years’ experience in radiology, respectively) using the “Level Tracing” function of the 3D Slicer. Areas comprising air and non-tumor tissues were manually removed. The boundary is smoothed using the “Smooth” function. The dispute on the region of interest (ROI) delineation would be settled after discussion. The largest cross-sectional slice of the 3D-ROI was selected as the input image for the ResNet50 model. This ROI area was extended outward into a square area. For the image standardization, we resampled all images to a 1 × 1 × 1 mm voxel spacing and performed gray-level discretization. In the gray-level discretization processing, CT images were set to soft tissue window (Window Width:350, Window Level:50), followed by mapping to the grey scale range [0, 255] (bin width, 25; bin count, 11).

Two experts reviewed and manually labelled CT images when blind to clinical information. The intra- and inter-class correlation coefficients (ICCs) were adopted for evaluating the intraobserver and interobserver reproducibility of the DL radiomics features [25]. In our study, 50 patients’ CT images from the derivation cohort were selected at random for ICCs calculation twice, in order to ensure the reproducibility of radiomics analysis.

Feature extraction and selection

The transfer learning framework was introduced to overcome the challenge of small sample size. We extracted the DL radiomics features from the ROIs using the pre-trained classification model ResNet50 (Python 3.6, TensorFlow 2.0.0, Keras 2.3.1). The parameter combinations were listed as follows: activation=’ReLu’, optimizer=’Adam’, classification function=’sigmoid’, learning rate=’0.01’ and epoch = 100. We recorded training and validation loss values, and the corresponding network weights for epochs. During convergence, early stopping was used to prevent overfitting. The final model was determined for radiomics feature extraction, with the highest accuracy and lowest loss value.

The features with ICCs ≤ 0.8 were dropped. Then, we adopted the Spearman correlation coefficient (Rho) to evaluate the correlation between any two CT image features. If two features are highly correlated (i.e., |Rho| > 0.8), either of the two features would be excluded. Next, the univariate Cox analysis was conducted to identify OS-related features. Only features with p value < 0.05 were retained for further analysis. Finally, the least absolute shrinkage and selection operator (LASSO) Cox regression was performed to remove unimportant features. The deep learning radiomics score (DLRS) was then calculated based on weights of their respective coefficients.

Predictive performance and prognostic value of the DLRS

A time-dependent receiver operator characteristic curve (ROC) was used to assess the predictive performance of the DLRS. The optimal cutoff value was calculated based on the maximum of Youden index. Patients were stratified into high- and low-score groups according to the best cutoff. Kaplan-Meier survival curves for OS and DFS were plotted respectively. In addition, the generalization of the DLRS was validated using the CT images from the TCIA (TCGA-KIRC cohort).

Gene set enrichment analysis between high- and low-score groups

We collected CT scans and genomic data from the TCIA (TCGA-KIRC cohort) for revealing the molecular mechanism associated with the DLRS differences. Patients were grouped into high- and low-score groups by the DLRS. Differentially expressed genes (DEGs) were identified between both groups based on the R software “limma” package, with the thresholds of adj p value < 0.05 and |log2FC| > 2 [26].

DEGs were subjected to cell component, molecular function and biological processs studies by Gene Ontology (GO) analysis and Kyoto encyclopedia of Genes and Genomes (KEGG) pathway analysis [27, 28]. Both p and adj p values are set to less than 0.05.

STRING (the Retrieval of Interacting Genes, https://string-db.org/) is web tool to evaluate the potential relationship among these screened DEGs, with a confidence score of ≥ 0.9 [29]. Additionally, survival data from TCGA-KIRC cohort were used to evaluate the prognostic value of DEGs.

Finally, tumor mutation burden (TMB) refers to the sum of gene mutations in tumor cells [30]. In general, tumors with higher TMB may be more likely to respond to immunotherapy. Correlations between DEGs expression and TMB were investigated in our study.

The association of the DLRS with tumor microenvironment

Firstly, the Estimate method was used for estimating tumor purity, stromal score and immune score in high- and low-score groups [31, 32]. Secondly, the CIBERSORT tool was applied to infer the infiltrating immune cells in ccRCC [33, 34]. The immunophenotype differences between different radiomics score groups were analyzed. Thirdly, we compared the immune cell infiltration levels among tumors with different somatic copy number alterations by using the Mann–Whitney U test [35, 36]. TIMER tool, a web server for comprehensive analysis of tumor-infiltrating immune cells, was used to visualize the distributions of each immune subset at each copy number status in ccRCC [35].

Development and validation of the combined model

Clinicopathological data were collected from the electronic medical record including age, gender, body mass index, ECOG-PS, CCI score, TNM stage, tumor size, tumor necrosis, histologic grade, microvascular invasion, laboratory tests and clinical symptoms (hematuria and flank pain).

Univariate and multivariate Cox regression analysis were used to identify independent risk factors of poor OS. In the derivation cohort, eXtreme Gradient Boosting classification (XGBC) algorithm was introduced to generate a combined model by incorporating the DLRS and significant clinicopathological features [37]. The best parameters combination and eligible features were obtained by the method of 10-fold grid-search. We plotted the learning curve for fine-tuning (e.g., n_estimators). The final model with the highest accuracy was determined for the downstream analyses. (Python, version 3.6; scikit-learn package, version 0.24).

Time-dependent ROC analysis was conducted to evaluate the predictive performance. The clinical utility and stability of this combined model were evaluated by decision curve (DCA) and calibration curve analysis [38]. For visualizing the contributions of each feature to outcome prediction, Shapley Additive exPlanations (SHAP) plot was used to explain the impact of selected features on predictions [39].

Furthermore, SSIGN and UISS scores were commonly used for the assessment of long-term prognosis in ccRCC patients in clinical practice. The methods for SSIGN and UISS calculation can be obtained in Supplementary S2.

Statistical analysis

All data analysis were performed with softwares (SPSS, version. 26.0 or R software, version. 4.0). Continuous data was shown as the median ± interquartile range (IQR). The comparison of continuous variables was conducted by the Mann–Whitney U test or Student’s t test. Categorical variables were compared by the chi-square test.

The ICCs were adopted for evaluating the intraobserver and interobserver agreement.

The Spearman correlation coefficient (Rho) was used to evaluate the correlation between variables. We compared the immune cell infiltration levels by using the Mann–Whitney U test. Time-dependent ROC analysis was performed to evaluate the predictive performance of models. Delong test was performed to compare the statistical significance between ROC curves. Univariate and multivariate Cox regression analysis were adopted to screen for independent risk factors of poor OS. The Kaplan–Meier method and log-rank test were used to estimate the survival.

We estimated sample size using pmsampsize package of R software (R2cs = 0.27, parameters = 10, prevalence = 0.15), and then at least 296 cases were required for model development [40]. All significant tests were 2- sided and p values < 0.05.

Results

Patient characteristics

The overall study design is demonstrated in Fig. 2. A total of 512 eligible patients from 3 hospitals were recruited. 358 of 512 patients were randomly assigned to the derivation cohort. The remaining 154 cases and 96 cases from TCGA-KIRC cohort were reserved for model validation. Finally, a novel combined model, namely NHSTM-R, has been developed by integrating the DLRS [R] and independent clinicopathological features (N [tumor necrosis], H [histologic grade], S [tumor size], T [TNM stage] and M [microvascular invasion]).

Fig. 2 Technical flow chart of the study. Abbreviation CCI Charlson Comorbidity Index; MVI microvascular invasion; WHO/ISUP World Health Organization/International Society of Urologic Pathologists; ICC intra- and inter-class correlation coefficients; LASSO least absolute shrinkage and selection operator; XGBC eXtreme Gradient Boosting classification; SHAP SHapley Additive explanation

The details of patient characteristics are shown in Table 1. In the whole cohort, the 5-year OS and DFS rates were 67.9% and 61.2%, respectively. Median OS was 62.2(IQR, 25.3) months for the derivation cohort, 59.7(IQR, 26.8) months for the test cohort. Median DFS was 54.3(IQR, 24.1) months for the derivation cohort, and 52.5(IQR, 23.7) months for the test cohort. In addition, only the OS time of patients in the TCGA cohort could be available, and the median OS was 70.4(IQR, 28.5) months.

Table 1 Patient characteristics

Characteristics	Derivation cohort
n = 358	Test cohort	p value	
n = 154		
Age, year	59 (15)	58 (12)	0.751	
Male gender	236(64.8)	92(59.7)	0.433	
BMI, kg/m2	22.3(3.1)	23.1(2.6)	0.517	
ECOG-PS (0/1/2) a	191/164/3	88/66/1	0.396	
CCI score b	7(6)	7(5)	0.754	
Hematuria	65(18.2)	15(9.7)	0.016	
Flank pain	57(15.9)	25(16.2)	0.682	
Tumor size, cm	5.1(4.3)	5.6(3.5)	0.267	
Tumor necrosis	24(6.7)	13(8.4)	0.363	
TNM stage	0.472	
Stage I	284(79.3)	117(76)		
Stage II	29(8.1)	16(10.4)		
Stage III	42(11.7)	19(12.3)		
Stage IV	3(0.9)	2(1.3)		
Histologic grade	0.395	
G1	42(11.7)	16(10.4)		
G2	211(58.9)	87(56.5)		
G3	95(26.6)	47(30.5)		
G4	10(2.8)	4(2.6)		
Microvascular invasion	
Laboratory tests	
Platelet count, 109/L	234(75)	271(89)	0.051	
Hemoglobin, g/L	127(31)	116(28)	0.152	
Serum calcium, mmol/L	2.63(0.27)	2.46(0.21)	0.202	
Creatinine, umol/L	86(22)	74(19)	0.185	
Mean OS time, month	62.2(25.3)	59.7(26.8)	0.364	
Mean DFS time, month	54.3(24.1)	52.5(23.7)	0.252	
Quantitative values are median (IQR) and categorical variables are n (%)

a ECOG-PS is a questionnaire to assess the functional status

b CCI score is a widely used comorbidity scoring system and quantifies comorbidities based on the number and severity of diseases

Abbreviation BMI body mass index; ECOG-PS Eastern Cooperative Oncology Group Performance Status; CCI Charlson Comorbidity Index

The DLRS calculation and evaluation

Of the 3566 DL radiomics features, 2781 reproducible features were identified based on ICC analysis. Next, of the 2781 features, 1753 DL radiomics features were retained by using the Spearman rank correlation test. Then, 297 DL radiomics features with p value < 0.05 were retained based on the univariate Cox analysis. Finally, by using the LASSO Cox regression method, we selected 7 most valuable DL radiomics features for the DLRS calculation.

DLRS = 0.517*DL_751-0.235* DL_1064 + 0.624* DL_1389 − 0.195* DL_1686 + 0.741* DL_1891 − 0.438* DL_2016 + 0.366* DL_2458 − 0.930.

In the test cohort, the DLRS had a great performance, with AUCs for 1, 3, and 5 year-OS of 0.814(95% CI, 0.775–0.859), 0.796(95% CI, 0.761–0.846) and 0.782(95% CI, 0.749–0.827), respectively (Table 2).

In the TCGA-KIRC cohort, the DLRS also had a great performance, with AUCs for 1, 3, and 5 year-OS of 0.775(95% CI, 0.742–0.801), 0.759(95% CI, 0.735–0.793) and 0.751 (95% CI, 0.730–0.778), respectively.

Table 2 Predictive performance of the models for overall survival prediction in patients with clear cell renal cell carcinoma

Performance	AUCs(95%CI)	
For 1-year OS	For 3-year OS	For 5-year OS	
Derivation cohort	
DLRS	0.839(0.782–0.871)	0.806(0.752–0.863)	0.787(0.749–0.846)	
NHSTM-R	0.903(0.876–0.964)	0.862(0.822–0.905)	0.845(0.817–0.883)	
SSIGN score	0.764(0.701–0.817)	0.752(0.695, 0.796)	0.729(0.674–0.751)	
UISS score	0.722(0.648–0.764)	0.697(0.621–0.749)	0.648(0.592–0.706)	
Test cohort	
DLRS	0.814(0.775–0.859)	0.796(0.761–0.846)	0.782(0.749–0.827)	
NHSTM-R	0.879(0.868–0.931)	0.854(0.819–0.899)	0.831(0.813–0.868)	
SSIGN score	0.745(0.702–0.809)	0.766(0.723–0.803)	0.717(0.654–0.749)	
UISS score	0.725(0.656–0.758)	0.708(0.633–0.758)	0.663(0.614–0.729)	
Abbreviations OS overall survival; DLRS deep learning radiomics score; NHSTM-R a combined model integrating the DLRS and independent clinicopathological features(tumor necrosis, histologic grade, tumor size, TNM stage and microvascular invasion); SSIGN Stage, Size, Grade, and Necrosis; UISS University of California, Los Angeles, Integrated Staging System; UISS University of California, Los Angeles, Integrated Staging System ; AUC area under of ROC curve; CI confidence interval

Patients were classified into high- and low-risk groups on the basis of the best cutoff value (-36.0162). Of the derivation and test datasets, 121 and 47 individuals were classified into the high-risk group, and 237 and 107 individuals were classified into the low-risk group, respectively. Kaplan–Meier survival analysis revealed that ccRCC patients in low-score group had a better OS and DFS compared to those in high-score group (all p values < 0.05) (Fig. 3A-D). The prognostic value of the DLRS was also determined in the external validation cohort (Supplementary Figure S1).

Fig. 3 Kaplan-Meier survival curves for overall survival (A, B) and disease-free survival (C, D) in the derivation and test cohorts. Patients were stratified into high- and low -score groups by the deep learning radiomics score. Red line represents patients with high score and blue line represents patients with low score. We calculated p values using the log-rank test and results revealed that patients in high-score group were prone to poor prognosis (p values < 0.05 for all)

Genomic differences between high- and low-score groups

To further explore the genomic differences between high- and low-score groups, we determined DEGs using RNA-seq data from TCGA cohort, and then generated a volcano plot showing 260 upregulated DEGs and 187 downregulated DEGs (Fig. 4A). Principal components analysis (PCA) revealed significant differences in gene expression level between both groups (Fig. 4B). GO analysis showed that DEGs were enriched in the biological process of immune system regulation: mainly regulation of T cells and lymphocyte (Fig. 4C-E). KEGG analysis indicated that DEGs were intensively enriched in Wnt signaling pathway and JAK-STAT signaling pathway, which were consistent with the findings of previous studies [41–44] (Fig. 4F). Interaction network analysis among DEGs was visualized in Supplementary Figure S2.

To investigate the association of DEGs with prognosis in ccRCC patients, prognostic value of the 10 most significant DEGs were analyzed. We observed that most of DEGs were significantly related to the OS (Supplementary Figure S3). In addition, the correlations between DEGs expression and TMB were visualized with radar chart (Supplementary Figure S4). CLDN8 and KCNJ1 gene expression levels showed significantly negative correlation with TMB (both p values < 0.05).

Fig. 4 The association between radiomics score and gene expression patterns. (A) DEGs are shown in the volcano plot. (B) factor map of the PCA performed on 96 tissue samples and all DEGs. Two cluster groups were identified corresponding to low-score group (blue) and high-score group (red). GO annotation and KEGG pathway enrichment analyses were performed in DEGs. (C) biological process, (D) molecular function, (E) cellular component, and (F) KEGG analysis. The color scale indicates different thresholds of the p value, and the size of the dot indicates the number of genes corresponding to each pathway. Abbreviation DEG differential expression gene; PCA principal component analysis

The association of the DLRS with tumor microenvironment

Firstly, the immune score, stromal score, ESTIMATE score (the sum of immune and stromal scores) and tumor purity were calculated, and significant differences were observed between high- and low-score groups (Fig. 5A, B). This indicated that radiomics score could reflect the immune infiltration levels. Secondly, since multiple immune-related biological processes were enriched, CIBERSORTx was used to calculate the relative proportion of 22 immune cell types of each case (Fig. 5C). We observed that multiple immune cells such as macrophage and regulatory T (Treg) cells varied significantly between different radiomics score groups (Fig. 5D). Finally, box plots were presented to show the distributions of each immune subset at each somatic copy number status of DEGs (Supplementary Figure S5).

Fig. 5 The association between radiomics score and tumor microenvironment. There were significant differences in stromal score, immune score, ESTIMATE score (A) and tumor purity (B) between high- and low-score groups. The fractions of 22 subsets of immune cells were analyzed and different colors indicate different immune cells (C). 63 samples on the left belong to high-score group, and 33 samples on the right belong to low-score group. The boxplot shows the difference in immune infiltration between high- and low-score groups (D). The horizontal axis indicates 22 immune cells and the vertical axis indicates cell content. The individuals with high score are labeled in red, and those with low score are labeled in blue

Identification of independent risk factors

Univariate Cox regression analysis results are displayed in Fig. 6A. In multivariate Cox regression analysis, the tumor size (HR, 1.66), tumor necrosis (HR, 1.73), TNM stage (HR, 1.95), histologic grade (HR, 1.58), microvascular invasion (HR, 1.96) and DLRS (HR, 2.46) were identified as independent risk factors of poor OS (Fig. 6B).

Fig. 6 Forest plots for the univariate (A) and multivariate (B) Cox regression analysis, describing the association between each feature and poor overall survival. The vertical line represents the value of no effect. Data are presented as the HR value with 95%CI. p values are tested by Cox proportional hazard model. Abbreviation HR hazard ratio; CI confidence interval

Combined model construction and validation

A combined model (namely NHSTM-R) was built based on the DLRS and independent clinicopathological features. The optimal parameter combinations of the NHSTM-R model are described in Supplementary S3. In the test cohort, the NHSTM-R model had the AUCs for 1, 3, and 5 year-OS of 0.879(95% CI, 0.868–0.931), 0.854(95% CI, 0.819–0.899) and 0.831(95% CI, 0.813–0.868), respectively (Table 2). Delong test revealed that the NHSTM-R model significantly outperformed the DLRS and existing prognostic models (all p values < 0.05) (Fig. 7A-C). Kaplan-Meier survival curves for OS and DFS are shown in Fig. 7D-G. There was a significant difference in survival time between different radiomics score groups stratified by the NHSTM-R model.

Furthermore, the feature importance rankings were calculated (Fig. 7H). The NHSTM-R model was well calibrated in both cohorts, and had a larger net benefit than the others in the whole cohort (Fig. 7I, J). As shown in SHAP summary plots, we visualized the contributions of each feature to OS prediction by using the average SHAP values (Fig. 7K). We found that the DLRS acted as a pivot role in the outcome prediction.

Fig. 7 The predictive performance of the models. (A-C) the AUCs of four models for predicting 1, 3 and 5 year-OS were calculated in the derivation and test cohorts. (D-G) patients were stratified into high- and low -score groups by the combined model (namely NHSTM-R). Kaplan–Meier survival curves of the high- (red line) and low-score (blue line) groups showed significant differences. (H) features importance ranking. (I) calibration curves of the NHSTM-R model in the derivation and test cohorts. (J) decision curve analysis revealed that the NHSTM-R model showed great clinical utility. (K) SHAP summary plot explained the detailed contribution of features to prediction at the global level. The colors represent the magnitude of the features values and vary from high to low. Each point on the plot represents a particular feature of an individual. Y-coordinate is determined by the features that the point represents. X-coordinate is determined by the feature’s impact on the model’s output. Abbreviations AUC area under the curve; DLRS deep learning radiomics score; SSIGN the Stage, Size, Grade, and Necrosis score; UISS the University of California, Los Angeles Integrated Staging System; HR hazard ratio; SHAP SHapley Additive explanation

Discussion

In the present study, we generated and externally validated the DLRS for predicting the OS in ccRCC patients. By using multi-omics data from TCGA-KIRC cohort, we revealed the tumor heterogeneity and microenvironment between different radiomics score groups. Furthermore, we developed a novel combined model (namely NHSTM-R) for OS prediction by incorporating the DLRS and independent clinicopathological features. This model showed great discrimination, calibration and clinical utility. SHAP analysis was adopted to help clinicians better understand the predictive results.

Intratumor heterogeneity (ITH), a key driver of tumor progression, can be exhibited on the radiological level [45]. DL techniques can autonomously acquire feature representations of ITH from medical image data on the basis of artificial neural networks [46]. Consequently, these techniques open up a broad scope of future research in the field of disease diagnosis and prognosis prediction for RCC patients. The estimation of OS is important for individualized management of ccRCC patients [5]. Only a few studies have applied DL methodologies to prognosis prediction in ccRCC patients [25, 47, 48]. Nie et al. reported that the DL radiomics model was developed for predicting cancer-specific survival in localized ccRCC patients [47]. This model showed favorable predictive performance. However, the potential value of clinicopathological data has not been explored in their study. In our study, multivariate Cox analysis showed close association between the radiomics score and OS. Schulz et al. also reported that DL radiomics features could stratify ccRCC patients [49].

To the best of our knowledge, previous studies have explored gene expression patterns in different image subtypes. Wang et al. revealed the association between the gene expression level and radiomics features in breast cancer [15]. A few studies have provided insights into that how radiomics reflect the heterogeneity of ccRCC and tumor microenvironment. He et al. and Wang et al. establish CT-based radiomics models for predicting prognosis-related genes expression for ccRCC patients by using CT images [16, 50]. Consistent with above two studies, our study found that lipid metabolism was significantly associated with image subtypes. Meanwhile, Wnt and JAK-STAT signaling pathways were also enriched, and GO analysis for cell component indicated that DEGs were particularly enriched in β-catenin destruction complex which is the heart of the canonical Wnt signaling pathway [51]. Reportedly, WNT signaling pathway played a vital role in the proliferation and self-renewal of cancer stem cells in ccRCC [41]. It has been reported that multiple genes such as CD56 polysialylation and CENPA had great impacts on tumor progression and metastasis via the Wnt/β-catenin signaling pathways in ccRCC [42, 52, 53]. Similarly, JAK-STAT pathway was found associated with the ccRCC progression and OS [43, 54, 55].

Notably, GO analysis for biological process revealed that T cell and lymphocyte apoptotic processes were also enriched in the present study, which suggested that there were significant differences in the tumor microenvironment between image subtypes. This implied that the DL radiomics features could reflect the heterogeneity of tumor microenvironment. The tumor microenvironment plays a key role in the progression of ccRCC. Liu et al. determined the prognostic value of infiltrating immune cells within the tumor microenvironment in ccRCC, and illustrated the underlying mechanism by which infiltrating immune cells promoted cancer progression [56]. What’s more, the close correlation between the radiomics features of ccRCC and tumor-infiltrating immune cells was observed as it is claimed in a previous study [16].

In this study, we also found that tumor purity and the proportion of immune cells significantly varied between high- and low-score groups (p value < 0.05). Macrophage and Treg cells were higher in the high-score group (p value < 0.05), and could be promising targets for cancer immunotherapy. Farha et al. reported that a cluster of ccRCC patients defined by enrichment in M0 macrophages had poor prognosis [57]. Xu et al. reported that ccRCC patients with high Macrophage-M1 fractions had worse prognosis than those with low Macrophage-M1 fractions [58]. Yang et al. reported that SGOL1 promoted ccRCC cell proliferation and invasion by increasing the Treg cells infiltration [59]. In additional, we observed that patients in high-score group had more CD8 T-cell infiltrates compared to those in low-score group (p value > 0.05). Giraldo et al. reported that CD8 + T cells showed positive correlation with unfavorable prognosis in ccRCC [60]. Overall, the poor prognosis of ccRCC patients in high-score group could be caused by the extent of immune cell infiltration. This tumor microenvironment could be reflected by the radiomics features.

Furthermore, clinicopathological features such as TNM stage and histologic grade showed close correlation with the long-term OS [16, 61, 62], which have been reported in previous studies. Therefore, in order to enhance the predictive capability of the DLRS, we built the NHSTM-R model for outcome prediction by incorporating the DLRS and significant clinicopathological features. The NHSTM-R model showed significantly better discrimination than the DLRS, SSIGN and UISS scores. If the patients are stratified as high-score by the NHSTM-R model, intensive surveillance and systemic therapy are advocated. On the contrary, only regular surveillance is recommended for the low-score patients.

The present study has some limitations. Firstly, the samples size of our study was not large, this study should be validated in a multi-center prospective cohort. Secondly, although we explored the underlying association between radiomics features and prognosis, further validation was necessary.

Conclusion

In conclusion, we developed a combined model for the stratification and prognostic prediction of ccRCC patients by incorporating the DL radiomics features and clinicopathological features. Radiomics could be used for individualized prognosis estimations by reflecting the differences in the tumor heterogeneity and microenvironment.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Material 1

Acknowledgements

The authors have none to declare.

Author contributions

Conceptualization：WJ, LJ, SXP, ZZG. Methodology: WJ, LJ, SXP, WLY, DSB, ZZG, HB. Data collection and analysis: WJ, LJ, WLY, DSB, HB. Original Draft, review and editing: All authors.

Funding

This work was supported by grants from the Scientific Research Foundation of Suzhou Ninth Hospital Affiliated to Soochow University (No. YK202330).

Data availability

No datasets were generated or analysed during the current study.

Declarations

Ethical approval

The ethical guidelines of the 1975 Declaration of Helsinki were strictly followed. The review board has approved our study and Informed consents were waived.

Consent for publication

All authors agree to publish this article.

Competing interests

The authors declare no competing interests.

Abbreviations

CT Computed tomography

ccRCC Clear cell renal cell carcinoma

DL Deep learning

TCIA The Cancer Imaging Archive

TCGA The Cancer Genome Atlas

OS Overall survival

DFS Disease-free survival

ROI Regions of interest

DLRS Deep learning radiomics score

LASSO Least absolute shrinkage and selection operator

ICCs Intra- and inter-class correlation coefficients

AUC Area under the curve

ROC Receiver operating characteristic

IQR Interquartile range

SHAP SHapley Additive explanation

SSIGN Stage, Size, Grade, and Necrosis

UISS University of California, Los Angeles, Integrated Staging System

ECOG-PS Eastern Cooperative Oncology Group

CCI Charlson Comorbidity Index

WHO/ISUP World Health Organization/International Society of Urologic Pathologists

XGBC eXtreme Gradient Boosting classification

DCA Decision curve analysis

DEG Differentially expressed gene

GO Gene Ontology

KEGG Kyoto encyclopedia of Genes and Genomes

TMB Tumor mutation burden

ITH Intratumor heterogeneity

Treg T regulatory cell

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Ji Wu and Jian Li are co-first authors and have contributed equally to this work.
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References

1. Chen Y-W Wang L Panian J Treatment Landscape of Renal Cell Carcinoma Curr Treat Options Oncol 2023 24 12 1889 916 10.1007/s11864-023-01161-5 38153686
Chen Y-W, Wang L, Panian J, et al. Treatment Landscape of Renal Cell Carcinoma. Curr Treat Options Oncol. 2023;24(12):1889–916.38153686 10.1007/s11864-023-01161-5
2. Perazella MA Dreicer R Rosner MH Renal cell carcinoma for the nephrologist Kidney Int 2018 94 3 471 83 10.1016/j.kint.2018.01.023 29661544
Perazella MA, Dreicer R, Rosner MH. Renal cell carcinoma for the nephrologist. Kidney Int. 2018;94(3):471–83.29661544 10.1016/j.kint.2018.01.023
3. Rizzo M Caliò A Brunelli M Clinico-pathological implications of the 2022 WHO renal cell carcinoma classification Cancer Treat Rev 2023 116 102558 10.1016/j.ctrv.2023.102558 37060647
Rizzo M, Caliò A, Brunelli M, et al. Clinico-pathological implications of the 2022 WHO renal cell carcinoma classification. Cancer Treat Rev. 2023;116:102558.37060647 10.1016/j.ctrv.2023.102558
4. Li Y, Lih T-SM, Dhanasekaran SM et al. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness. Cancer Cell 2023, 41(1).
5. Leibovich BC Lohse CM Cheville JC Predicting Oncologic outcomes in Renal Cell Carcinoma after surgery Eur Urol 2018 73 5 772 80 10.1016/j.eururo.2018.01.005 29398265
Leibovich BC, Lohse CM, Cheville JC, et al. Predicting Oncologic outcomes in Renal Cell Carcinoma after surgery. Eur Urol. 2018;73(5):772–80.29398265 10.1016/j.eururo.2018.01.005
6. Chen S Jiang L Gao F Machine learning-based pathomics signature could act as a novel prognostic marker for patients with clear cell renal cell carcinoma Br J Cancer 2022 126 5 771 7 10.1038/s41416-021-01640-2 34824449
Chen S, Jiang L, Gao F, et al. Machine learning-based pathomics signature could act as a novel prognostic marker for patients with clear cell renal cell carcinoma. Br J Cancer. 2022;126(5):771–7.34824449 10.1038/s41416-021-01640-2
7. Chen L-X Zeng S-J Liu X-D Cell-cell communications shape tumor microenvironment and predict clinical outcomes in clear cell renal carcinoma J Translational Med 2023 21 1 113 10.1186/s12967-022-03858-x
Chen L-X, Zeng S-J, Liu X-D, et al. Cell-cell communications shape tumor microenvironment and predict clinical outcomes in clear cell renal carcinoma. J Translational Med. 2023;21(1):113.10.1186/s12967-022-03858-x
8. Parker WP Cheville JC Frank I Application of the stage, size, Grade, and necrosis (SSIGN) score for Clear Cell Renal Cell Carcinoma in Contemporary patients Eur Urol 2017 71 4 665 73 10.1016/j.eururo.2016.05.034 27287995
Parker WP, Cheville JC, Frank I, et al. Application of the stage, size, Grade, and necrosis (SSIGN) score for Clear Cell Renal Cell Carcinoma in Contemporary patients. Eur Urol. 2017;71(4):665–73.27287995 10.1016/j.eururo.2016.05.034
9. Yang G Nie P Yan L The radiomics-based tumor heterogeneity adds incremental value to the existing prognostic models for predicting outcome in localized clear cell renal cell carcinoma: a multicenter study Eur J Nucl Med Mol Imaging 2022 49 8 2949 59 10.1007/s00259-022-05773-1 35344062
Yang G, Nie P, Yan L, et al. The radiomics-based tumor heterogeneity adds incremental value to the existing prognostic models for predicting outcome in localized clear cell renal cell carcinoma: a multicenter study. Eur J Nucl Med Mol Imaging. 2022;49(8):2949–59.35344062 10.1007/s00259-022-05773-1
10. Zheng Z Chen Z Xie Y Development and validation of a CT-based nomogram for preoperative prediction of clear cell renal cell carcinoma grades Eur Radiol 2021 31 8 6078 86 10.1007/s00330-020-07667-y 33515086
Zheng Z, Chen Z, Xie Y, et al. Development and validation of a CT-based nomogram for preoperative prediction of clear cell renal cell carcinoma grades. Eur Radiol. 2021;31(8):6078–86.33515086 10.1007/s00330-020-07667-y
11. Lin F Ma C Xu J A CT-based deep learning model for predicting the nuclear grade of clear cell renal cell carcinoma Eur J Radiol 2020 129 109079 10.1016/j.ejrad.2020.109079 32526669
Lin F, Ma C, Xu J, et al. A CT-based deep learning model for predicting the nuclear grade of clear cell renal cell carcinoma. Eur J Radiol. 2020;129:109079.32526669 10.1016/j.ejrad.2020.109079
12. Wang R Dai W Gong J Development of a novel combined nomogram model integrating deep learning-pathomics, radiomics and immunoscore to predict postoperative outcome of colorectal cancer lung metastasis patients J Hematol Oncol 2022 15 1 11 10.1186/s13045-022-01225-3 35073937
Wang R, Dai W, Gong J, et al. Development of a novel combined nomogram model integrating deep learning-pathomics, radiomics and immunoscore to predict postoperative outcome of colorectal cancer lung metastasis patients. J Hematol Oncol. 2022;15(1):11.35073937 10.1186/s13045-022-01225-3
13. Fu N Fu W Chen H A deep-learning radiomics-based lymph node metastasis predictive model for pancreatic cancer: a diagnostic study Int J Surg (London England) 2023 109 8 2196 203 10.1097/JS9.0000000000000469
Fu N, Fu W, Chen H, et al. A deep-learning radiomics-based lymph node metastasis predictive model for pancreatic cancer: a diagnostic study. Int J Surg (London England). 2023;109(8):2196–203.10.1097/JS9.0000000000000469
14. Huang W Wang C Wang Y Predicting malnutrition in gastric cancer patients using computed tomography(CT) deep learning features and clinical data Clin Nutr 2024 43 3 881 91 10.1016/j.clnu.2024.02.005 38377634
Huang W, Wang C, Wang Y, et al. Predicting malnutrition in gastric cancer patients using computed tomography(CT) deep learning features and clinical data. Clin Nutr. 2024;43(3):881–91.38377634 10.1016/j.clnu.2024.02.005
15. Wang X Xie T Luo J Radiomics predicts the prognosis of patients with locally advanced breast cancer by reflecting the heterogeneity of tumor cells and the tumor microenvironment Breast cancer Research: BCR 2022 24 1 20 10.1186/s13058-022-01516-0 35292076
Wang X, Xie T, Luo J, et al. Radiomics predicts the prognosis of patients with locally advanced breast cancer by reflecting the heterogeneity of tumor cells and the tumor microenvironment. Breast cancer Research: BCR. 2022;24(1):20.35292076 10.1186/s13058-022-01516-0
16. He H Jin Z Dai J Computed tomography-based radiomics prediction of CTLA4 expression and prognosis in clear cell renal cell carcinoma Cancer Med 2023 12 6 7627 38 10.1002/cam4.5449 36397666
He H, Jin Z, Dai J, et al. Computed tomography-based radiomics prediction of CTLA4 expression and prognosis in clear cell renal cell carcinoma. Cancer Med. 2023;12(6):7627–38.36397666 10.1002/cam4.5449
17. Mathew G Agha R Albrecht J STROCSS 2021: strengthening the reporting of cohort, cross-sectional and case-control studies in surgery Int J Surg (London England) 2021 96 106165 10.1016/j.ijsu.2021.106165
Mathew G, Agha R, Albrecht J, et al. STROCSS 2021: strengthening the reporting of cohort, cross-sectional and case-control studies in surgery. Int J Surg (London England). 2021;96:106165.10.1016/j.ijsu.2021.106165
18. Neeman E Gresham G Ovasapians N Comparing physician and Nurse Eastern Cooperative Oncology Group Performance Status (ECOG-PS) ratings as predictors of clinical outcomes in patients with Cancer Oncologist 2019 24 12 e1460 6 10.1634/theoncologist.2018-0882 31227648
Neeman E, Gresham G, Ovasapians N, et al. Comparing physician and Nurse Eastern Cooperative Oncology Group Performance Status (ECOG-PS) ratings as predictors of clinical outcomes in patients with Cancer. Oncologist. 2019;24(12):e1460–6.31227648 10.1634/theoncologist.2018-0882
19. Asai N Ohashi W Sakanashi D Combination of sequential organ failure Assessment (SOFA) score and Charlson Comorbidity Index (CCI) could predict the severity and prognosis of candidemia more accurately than the Acute Physiology, Age, Chronic Health evaluation II (APACHE II) score BMC Infect Dis 2021 21 1 77 10.1186/s12879-020-05719-8 33451284
Asai N, Ohashi W, Sakanashi D, et al. Combination of sequential organ failure Assessment (SOFA) score and Charlson Comorbidity Index (CCI) could predict the severity and prognosis of candidemia more accurately than the Acute Physiology, Age, Chronic Health evaluation II (APACHE II) score. BMC Infect Dis. 2021;21(1):77.33451284 10.1186/s12879-020-05719-8
20. Kroeger N Rampersaud EN Patard JJ Prognostic value of microvascular invasion in predicting the cancer specific survival and risk of metastatic disease in renal cell carcinoma: a multicenter investigation J Urol 2012 187 2 418 23 10.1016/j.juro.2011.10.024 22177164
Kroeger N, Rampersaud EN, Patard JJ, et al. Prognostic value of microvascular invasion in predicting the cancer specific survival and risk of metastatic disease in renal cell carcinoma: a multicenter investigation. J Urol. 2012;187(2):418–23.22177164 10.1016/j.juro.2011.10.024
21. Bedke J Heide J Ribback S Microvascular and lymphovascular tumour invasion are associated with poor prognosis and metastatic spread in renal cell carcinoma: a validation study in clinical practice BJU Int 2018 121 1 84 92 10.1111/bju.13984 28803448
Bedke J, Heide J, Ribback S, et al. Microvascular and lymphovascular tumour invasion are associated with poor prognosis and metastatic spread in renal cell carcinoma: a validation study in clinical practice. BJU Int. 2018;121(1):84–92.28803448 10.1111/bju.13984
22. Warren AY Harrison D WHO/ISUP classification, grading and pathological staging of renal cell carcinoma: standards and controversies World J Urol 2018 36 12 1913 26 10.1007/s00345-018-2447-8 30123932
Warren AY, Harrison D. WHO/ISUP classification, grading and pathological staging of renal cell carcinoma: standards and controversies. World J Urol. 2018;36(12):1913–26.30123932 10.1007/s00345-018-2447-8
23. Zanfardino M, Pane K, Mirabelli P et al. TCGA-TCIA impact on Radiogenomics Cancer Research: a systematic review. Int J Mol Sci 2019, 20(23).
24. Nazari M Shiri I Zaidi H Radiomics-based machine learning model to predict risk of death within 5-years in clear cell renal cell carcinoma patients Comput Biol Med 2021 129 104135 10.1016/j.compbiomed.2020.104135 33254045
Nazari M, Shiri I, Zaidi H. Radiomics-based machine learning model to predict risk of death within 5-years in clear cell renal cell carcinoma patients. Comput Biol Med. 2021;129:104135.33254045 10.1016/j.compbiomed.2020.104135
25. Nie P Yang G Wang Y A CT-based deep learning radiomics nomogram outperforms the existing prognostic models for outcome prediction in clear cell renal cell carcinoma: a multicenter study Eur Radiol 2023 33 12 8858 68 10.1007/s00330-023-09869-6 37389608
Nie P, Yang G, Wang Y, et al. A CT-based deep learning radiomics nomogram outperforms the existing prognostic models for outcome prediction in clear cell renal cell carcinoma: a multicenter study. Eur Radiol. 2023;33(12):8858–68.37389608 10.1007/s00330-023-09869-6
26. Liu T-T Li R Huo C Identification of CDK2-Related Immune Forecast Model and ceRNA in Lung Adenocarcinoma, a Pan-cancer Analysis Front cell Dev Biology 2021 9 682002 10.3389/fcell.2021.682002
Liu T-T, Li R, Huo C, et al. Identification of CDK2-Related Immune Forecast Model and ceRNA in Lung Adenocarcinoma, a Pan-cancer Analysis. Front cell Dev Biology. 2021;9:682002.10.3389/fcell.2021.682002
27. Gene Ontology Consortium Going forward Nucleic Acids Res 2015 43 Database issue D1049 56 10.1093/nar/gku1179 25428369
Gene Ontology Consortium. Going forward. Nucleic Acids Res. 2015;43(Database issue):D1049–56.25428369 10.1093/nar/gku1179
28. Kanehisa M Furumichi M Tanabe M KEGG: new perspectives on genomes, pathways, diseases and drugs Nucleic Acids Res 2017 45 D1 D353 61 10.1093/nar/gkw1092 27899662
Kanehisa M, Furumichi M, Tanabe M, et al. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017;45(D1):D353–61.27899662 10.1093/nar/gkw1092
29. Doncheva NT Morris JH Gorodkin J Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data J Proteome Res 2019 18 2 623 32 10.1021/acs.jproteome.8b00702 30450911
Doncheva NT, Morris JH, Gorodkin J, et al. Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data. J Proteome Res. 2019;18(2):623–32.30450911 10.1021/acs.jproteome.8b00702
30. Jardim DL Goodman A de Melo Gagliato D The challenges of Tumor Mutational Burden as an Immunotherapy Biomarker Cancer Cell 2021 39 2 154 73 10.1016/j.ccell.2020.10.001 33125859
Jardim DL, Goodman A, de Melo Gagliato D, et al. The challenges of Tumor Mutational Burden as an Immunotherapy Biomarker. Cancer Cell. 2021;39(2):154–73.33125859 10.1016/j.ccell.2020.10.001
31. Yoshihara K Shahmoradgoli M Martínez E Inferring tumour purity and stromal and immune cell admixture from expression data Nat Commun 2013 4 2612 10.1038/ncomms3612 24113773
Yoshihara K, Shahmoradgoli M, Martínez E, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun. 2013;4:2612.24113773 10.1038/ncomms3612
32. Su Q Zhu Y He B A novel tumor purity and immune infiltration-related model for predicting distant metastasis-free survival in prostate cancer Eur J Med Res 2023 28 1 545 10.1186/s40001-023-01522-8 38017548
Su Q, Zhu Y, He B, et al. A novel tumor purity and immune infiltration-related model for predicting distant metastasis-free survival in prostate cancer. Eur J Med Res. 2023;28(1):545.38017548 10.1186/s40001-023-01522-8
33. Yao W Liu X He Y ScRNA-seq and bulk RNA-seq reveal the characteristics of ferroptosis and establish a risk signature in cholangiocarcinoma Mol Ther Oncolytics 2022 27 48 60 10.1016/j.omto.2022.09.008 36284715
Yao W, Liu X, He Y, et al. ScRNA-seq and bulk RNA-seq reveal the characteristics of ferroptosis and establish a risk signature in cholangiocarcinoma. Mol Ther Oncolytics. 2022;27:48–60.36284715 10.1016/j.omto.2022.09.008
34. Fang H Sheng S Chen B A Pan-cancer analysis of the oncogenic role of Cell Division Cycle-Associated protein 4 (CDCA4) in human tumors Front Immunol 2022 13 826337 10.3389/fimmu.2022.826337 35251007
Fang H, Sheng S, Chen B, et al. A Pan-cancer analysis of the oncogenic role of Cell Division Cycle-Associated protein 4 (CDCA4) in human tumors. Front Immunol. 2022;13:826337.35251007 10.3389/fimmu.2022.826337
35. Li T Fan J Wang B TIMER: a web server for Comprehensive Analysis of Tumor-infiltrating Immune cells Cancer Res 2017 77 21 e108 10 10.1158/0008-5472.CAN-17-0307 29092952
Li T, Fan J, Wang B, et al. TIMER: a web server for Comprehensive Analysis of Tumor-infiltrating Immune cells. Cancer Res. 2017;77(21):e108–10.29092952 10.1158/0008-5472.CAN-17-0307
36. Tsuyukubo T Ishida K Osakabe M Comprehensive analysis of somatic copy number alterations in clear cell renal cell carcinoma Mol Carcinog 2020 59 4 412 24 10.1002/mc.23164 32039517
Tsuyukubo T, Ishida K, Osakabe M, et al. Comprehensive analysis of somatic copy number alterations in clear cell renal cell carcinoma. Mol Carcinog. 2020;59(4):412–24.32039517 10.1002/mc.23164
37. Liang Y Lee MH Zhou A eXtreme gradient boosting-based classification of bacterial mixtures in water and milk using wireless microscopic imaging of quorum sensing peptide-conjugated particles Biosens Bioelectron 2023 227 115144 10.1016/j.bios.2023.115144 36805271
Liang Y, Lee MH, Zhou A, et al. eXtreme gradient boosting-based classification of bacterial mixtures in water and milk using wireless microscopic imaging of quorum sensing peptide-conjugated particles. Biosens Bioelectron. 2023;227:115144.36805271 10.1016/j.bios.2023.115144
38. Hu C Chen W Li F Deep learning radio-clinical signatures for predicting neoadjuvant chemotherapy response and prognosis from pretreatment CT images of locally advanced gastric cancer patients Int J Surg (London England) 2023 109 7 1980 92
Hu C, Chen W, Li F, et al. Deep learning radio-clinical signatures for predicting neoadjuvant chemotherapy response and prognosis from pretreatment CT images of locally advanced gastric cancer patients. Int J Surg (London England). 2023;109(7):1980–92.
39. Chowdhury SU, Sayeed S, Rashid I et al. Shapley-Additive-explanations-based factor analysis for Dengue Severity Prediction using machine learning. J Imaging 2022, 8(9).
40. Riley RD Ensor J Snell KIE Calculating the sample size required for developing a clinical prediction model BMJ 2020 368 m441 10.1136/bmj.m441 32188600
Riley RD, Ensor J, Snell KIE, et al. Calculating the sample size required for developing a clinical prediction model. BMJ. 2020;368:m441.32188600 10.1136/bmj.m441
41. Fendler A Bauer D Busch J Inhibiting WNT and NOTCH in renal cancer stem cells and the implications for human patients Nat Commun 2020 11 1 929 10.1038/s41467-020-14700-7 32066735
Fendler A, Bauer D, Busch J, et al. Inhibiting WNT and NOTCH in renal cancer stem cells and the implications for human patients. Nat Commun. 2020;11(1):929.32066735 10.1038/s41467-020-14700-7
42. Jian Y Zhang L Gong L CD56 polysialylation promotes the tumorigenesis and progression via the hedgehog and Wnt/β-catenin signaling pathways in clear cell renal cell carcinoma Cancer Cell Int 2023 23 1 319 10.1186/s12935-023-03165-5 38087309
Jian Y, Zhang L, Gong L, et al. CD56 polysialylation promotes the tumorigenesis and progression via the hedgehog and Wnt/β-catenin signaling pathways in clear cell renal cell carcinoma. Cancer Cell Int. 2023;23(1):319.38087309 10.1186/s12935-023-03165-5
43. Deng H Gong X Ji G KIF2C promotes clear cell renal cell carcinoma progression via activating JAK2/STAT3 signaling pathway Mol Cell Probes 2023 72 101938 10.1016/j.mcp.2023.101938 37863123
Deng H, Gong X, Ji G, et al. KIF2C promotes clear cell renal cell carcinoma progression via activating JAK2/STAT3 signaling pathway. Mol Cell Probes. 2023;72:101938.37863123 10.1016/j.mcp.2023.101938
44. Wang S Ma X Ying Y Upregulation of ARNTL2 is associated with poor survival and immune infiltration in clear cell renal cell carcinoma Cancer Cell Int 2021 21 1 341 10.1186/s12935-021-02046-z 34217271
Wang S, Ma X, Ying Y, et al. Upregulation of ARNTL2 is associated with poor survival and immune infiltration in clear cell renal cell carcinoma. Cancer Cell Int. 2021;21(1):341.34217271 10.1186/s12935-021-02046-z
45. Soultati A Stares M Swanton C How should clinicians address intratumour heterogeneity in clear cell renal cell carcinoma? Curr Opin Urol 2015 25 5 358 66 10.1097/MOU.0000000000000204 26125509
Soultati A, Stares M, Swanton C, et al. How should clinicians address intratumour heterogeneity in clear cell renal cell carcinoma? Curr Opin Urol. 2015;25(5):358–66.26125509 10.1097/MOU.0000000000000204
46. Fahmy AS Rowin EJ Arafati A Radiomics and deep learning for myocardial scar screening in hypertrophic cardiomyopathy J Cardiovasc Magn Reson 2022 24 1 40 10.1186/s12968-022-00869-x 35761339
Fahmy AS, Rowin EJ, Arafati A, et al. Radiomics and deep learning for myocardial scar screening in hypertrophic cardiomyopathy. J Cardiovasc Magn Reson. 2022;24(1):40.35761339 10.1186/s12968-022-00869-x
47. Nie P Liu S Zhou R A preoperative CT-based deep learning radiomics model in predicting the stage, size, grade and necrosis score and outcome in localized clear cell renal cell carcinoma: a multicenter study Eur J Radiol 2023 166 111018 10.1016/j.ejrad.2023.111018 37562222
Nie P, Liu S, Zhou R, et al. A preoperative CT-based deep learning radiomics model in predicting the stage, size, grade and necrosis score and outcome in localized clear cell renal cell carcinoma: a multicenter study. Eur J Radiol. 2023;166:111018.37562222 10.1016/j.ejrad.2023.111018
48. Wang S Zhu C Jin Y A multi-model based on radiogenomics and deep learning techniques associated with histological grade and survival in clear cell renal cell carcinoma Insights Imaging 2023 14 1 207 10.1186/s13244-023-01557-9 38010567
Wang S, Zhu C, Jin Y, et al. A multi-model based on radiogenomics and deep learning techniques associated with histological grade and survival in clear cell renal cell carcinoma. Insights Imaging. 2023;14(1):207.38010567 10.1186/s13244-023-01557-9
49. Schulz S Woerl AC Jungmann F Multimodal Deep Learning for Prognosis Prediction in Renal Cancer Front Oncol 2021 11 788740 10.3389/fonc.2021.788740 34900744
Schulz S, Woerl AC, Jungmann F, et al. Multimodal Deep Learning for Prognosis Prediction in Renal Cancer. Front Oncol. 2021;11:788740.34900744 10.3389/fonc.2021.788740
50. Wang J Huang Z Zhou J Radiomics Model for Predicting FOXP3 expression level and survival in Clear Cell Renal Carcinoma Acad Radiol 2024 31 4 1447 59 10.1016/j.acra.2023.10.008 37940428
Wang J, Huang Z, Zhou J. Radiomics Model for Predicting FOXP3 expression level and survival in Clear Cell Renal Carcinoma. Acad Radiol. 2024;31(4):1447–59.37940428 10.1016/j.acra.2023.10.008
51. Kimelman D Xu W beta-catenin destruction complex: insights and questions from a structural perspective Oncogene 2006 25 57 7482 91 10.1038/sj.onc.1210055 17143292
Kimelman D, Xu W. beta-catenin destruction complex: insights and questions from a structural perspective. Oncogene. 2006;25(57):7482–91.17143292 10.1038/sj.onc.1210055
52. Wang Q Xu J Xiong Z CENPA promotes clear cell renal cell carcinoma progression and metastasis via Wnt/β-catenin signaling pathway J Translational Med 2021 19 1 417 10.1186/s12967-021-03087-8
Wang Q, Xu J, Xiong Z, et al. CENPA promotes clear cell renal cell carcinoma progression and metastasis via Wnt/β-catenin signaling pathway. J Translational Med. 2021;19(1):417.10.1186/s12967-021-03087-8
53. Wang L Wang Z Zhu Y SOX17 antagonizes the WNT signaling pathway and is epigenetically inactivated in Clear-Cell Renal Cell Carcinoma OncoTargets Therapy 2021 14 3383 94 10.2147/OTT.S294164 34079284
Wang L, Wang Z, Zhu Y, et al. SOX17 antagonizes the WNT signaling pathway and is epigenetically inactivated in Clear-Cell Renal Cell Carcinoma. OncoTargets Therapy. 2021;14:3383–94.34079284 10.2147/OTT.S294164
54. Wang L Yue Y Zhang L PAQR5 inhibits the growth and metastasis of clear cell renal cell carcinoma by suppressing the JAK/STAT3 signaling pathway Cell Oncol (Dordrecht) 2023 46 5 1317 32 10.1007/s13402-023-00813-w
Wang L, Yue Y, Zhang L, et al. PAQR5 inhibits the growth and metastasis of clear cell renal cell carcinoma by suppressing the JAK/STAT3 signaling pathway. Cell Oncol (Dordrecht). 2023;46(5):1317–32.10.1007/s13402-023-00813-w
55. Zhan C Xu C Chen J Development and validation of an IL6/JAK/STAT3-Related Gene Signature to predict overall survival in Clear Cell Renal Cell Carcinoma Front cell Dev Biology 2021 9 686907 10.3389/fcell.2021.686907
Zhan C, Xu C, Chen J, et al. Development and validation of an IL6/JAK/STAT3-Related Gene Signature to predict overall survival in Clear Cell Renal Cell Carcinoma. Front cell Dev Biology. 2021;9:686907.10.3389/fcell.2021.686907
56. Liu S Li S Wang Y Prognostic value of infiltrating immune cells in clear cell renal cell carcinoma (ccRCC) J Cell Biochem 2020 121 3 2571 81 10.1002/jcb.29479 31823423
Liu S, Li S, Wang Y, et al. Prognostic value of infiltrating immune cells in clear cell renal cell carcinoma (ccRCC). J Cell Biochem. 2020;121(3):2571–81.31823423 10.1002/jcb.29479
57. Farha M, Nallandhighal S, Vince R et al. Analysis of the Tumor Immune Microenvironment (TIME) in Clear Cell Renal Cell Carcinoma (ccRCC) reveals an M0 macrophage-enriched subtype: an exploration of Prognostic and Biological characteristics of this Immune phenotype. Cancers 2023, 15(23).
58. Xu W Jiang X Guan C The prognostic and predictive value of tumor infiltrating Macrophage and Neutrophil in patient with clear cell renal cell carcinoma: Tumor infiltrating lymphocytes in renal cell carcinoma Medicine 2020 99 46 e23181 10.1097/MD.0000000000023181 33181696
Xu W, Jiang X, Guan C, et al. The prognostic and predictive value of tumor infiltrating Macrophage and Neutrophil in patient with clear cell renal cell carcinoma: Tumor infiltrating lymphocytes in renal cell carcinoma. Medicine. 2020;99(46):e23181.33181696 10.1097/MD.0000000000023181
59. Yang Z Jiang Y Wang L Prognosis and biological function of SGOL1 in clear cell renal cell carcinoma: a multiomics analysis BMC Med Genom 2024 17 1 60 10.1186/s12920-024-01825-7
Yang Z, Jiang Y, Wang L, et al. Prognosis and biological function of SGOL1 in clear cell renal cell carcinoma: a multiomics analysis. BMC Med Genom. 2024;17(1):60.10.1186/s12920-024-01825-7
60. Giraldo NA Becht E Pagès F Orchestration and Prognostic significance of Immune checkpoints in the Microenvironment of primary and metastatic renal cell Cancer Clin cancer Research: Official J Am Association Cancer Res 2015 21 13 3031 40 10.1158/1078-0432.CCR-14-2926
Giraldo NA, Becht E, Pagès F, et al. Orchestration and Prognostic significance of Immune checkpoints in the Microenvironment of primary and metastatic renal cell Cancer. Clin cancer Research: Official J Am Association Cancer Res. 2015;21(13):3031–40.10.1158/1078-0432.CCR-14-2926
61. Demirjian NL Varghese BA Cen SY CT-based radiomics stratification of tumor grade and TNM stage of clear cell renal cell carcinoma Eur Radiol 2022 32 4 2552 63 10.1007/s00330-021-08344-4 34757449
Demirjian NL, Varghese BA, Cen SY, et al. CT-based radiomics stratification of tumor grade and TNM stage of clear cell renal cell carcinoma. Eur Radiol. 2022;32(4):2552–63.34757449 10.1007/s00330-021-08344-4
62. Zhanghuang C Wang J Zhang Z A web-based prediction model for Cancer-Specific Survival of Elderly patients with Clear Cell Renal Cell Carcinoma: a Population-based study Front Public Health 2021 9 833970 10.3389/fpubh.2021.833970 35310783
Zhanghuang C, Wang J, Zhang Z, et al. A web-based prediction model for Cancer-Specific Survival of Elderly patients with Clear Cell Renal Cell Carcinoma: a Population-based study. Front Public Health. 2021;9:833970.35310783 10.3389/fpubh.2021.833970
