Cyclophilin B overexpression predicts a poor prognosis and activates metastatic pathways in colon cancer
Original Article

Cyclophilin B overexpression predicts a poor prognosis and activates metastatic pathways in colon cancer

Xiaojing Zhang1, Jinjing Tan2, Lei Yang3, Guangyu An1

1Oncology Department, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; 2Department of Cellular and Molecular Biology, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China; 3Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China

Contributions: (I) Conception and design: G An; (II) Administrative support: G An, L Yang; (III) Provision of study materials or patients: G An, L Yang; (IV) Collection and assembly of data: X Zhang, J Tan; (V) Data analysis and interpretation: X Zhang, J Tan, L Yang; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors.

Correspondence to: Guangyu An, MD. Oncology Department, Beijing Chao-Yang Hospital, No. 8, Gongti South Road, Chaoyang District, Beijing 100020, China. Email: agybjcy@163.com; Lei Yang, MD. Medical Research Center, Beijing Chao-Yang Hospital, No. 8, Gongti South Road, Chaoyang District, Beijing 100020, China. Email: yl6649084@163.com.

Background: Cyclophilin B (CypB) has been found overexpressed in various malignant tumors. To date, there are few studies on CypB in colon cancer. In this study, we aimed to analyze the CypB expression pattern and to further evaluate its clinical significance, especially its prognostic value for colon cancer.

Methods: CypB expression was investigated in colon cancer tissue microarrays (TMA) by RNAscope in situ hybridization and immunohistochemical (IHC) staining. The correlation between CypB and clinicopathological characteristics was analyzed. The Cancer Genome Atlas (TCGA) RNA-seq dataset of colon adenocarcinoma (COAD) was further analyzed to validate our main findings. Gene Set Enrichment Analysis (GSEA) and Search Tool for the Retrieval of Interacting Genes (STRING) analysis were performed to enrich CypB related biological pathways. In vitro experiments by knockdown of CypB in colon cancer cell HCT116 were performed to verify the bioinformatics results and analyze its role in the metastatic pathways in colon cancer.

Results: We found that CypB expression was highly upregulated in colon cancer tissues (P<0.05). Importantly, the overall survival (OS) time of patients with high CypB expression was significantly shorter than those with low CypB expression, and overexpressed CypB was identified as an independent prognostic indicator for poor survival (P=0.015). Subgroup analysis indicated that a high level of CypB was associated with a shorter OS time, especially for advanced cancer patients, such as later T stage, lymph node metastasis, larger tumor size (P<0.05). Analysis of TCGA RNA-seq dataset of COAD provided us with a larger clinical sample verification. Bioinformatics analysis and the following in vitro study revealed that CypB was involved in tumor metastatic associated signaling pathways.

Conclusions: CypB overexpression predicts a poor prognosis and may activate metastatic pathways in colon cancer.

Keywords: Colon cancer; cyclophilin B (CypB); metastasis; prognosis; RNAscope


Submitted Dec 25, 2019. Accepted for publication Apr 16, 2020.

doi: 10.21037/tcr-19-2960


Introduction

Colorectal cancer is a leading cause of cancer-related death. The incidence of colorectal cancer ranks fourth among all malignant tumors, with approximately 140,000 new cases and 50,000 cases of death each year in the United States (1). In China, due to the huge population base and dramatic changes in the environment, the number of deaths per year is approximately 190,000 (2).

Colonoscopy has been used in the clinic for the early diagnosis of colorectal cancer and has promoted a 5-year survival rate of almost 90%. Unfortunately, many patients lose the chance for early diagnosis and effective treatment and often develop distant metastases, and the 5-year survival rate for those patients is only 12.5% (3). For these distant-stage patients, we more urgently need to find effective biomarkers closely related to prognosis and their pathological mechanisms in order for more precise targeted treatments.

Cyclophilins (Cyps) have been reported to exhibit peptidyl-prolyl isomerase enzymatic activity and are involved in a variety of cell functions (4,5). CypB (cyclophilin B) is a member of the Cyps family, which is predominantly located in the endoplasmic reticulum (ER) and was indicated to act as the target of cyclosporin A (an immunosuppressive drug). CypB has also been shown to be involved in many biological processes, including protein folding (6), virus replication (7), immunosuppression (8) and osteogenesis (9). Recently, a high level of CypB was found in pancreatic, breast, gastric and liver cancer (10-13). CypB was found to promote cancer by accelerating cell proliferation, decreasing cell apoptosis, and facilitating cell migration and invasion (10,14-16). However, the clinical significance of CypB overexpression remains to be investigated in colorectal cancer.

In this study, we analyzed the expression of CypB by RNAscope in situ hybridization and immunohistochemical (IHC) staining in colon cancer. Furthermore, we analyzed the correlation between CypB expression and clinicopathological characteristics. Then, we focused on the prognostic significance and signaling pathways of CypB in colon cancer. Our study demonstrates that CypB was overexpressed in colon cancer tissues and that the upregulation of CypB was associated with poor survival. Bioinformatics analysis and the in vitro study revealed that CypB was involved in tumor metastatic signaling pathways. Hence, we propose that CypB serves as a promising prognostic biomarker and may promote metastasis in colon cancer.


Methods

Patients and tumor tissue microarray (TMA)

The colonic TMA (HCol-Ade180Sur-07, Shanghai Outdo Biotech Co., Shanghai, China) used in RNAscope analysis contained 90 cases of colonic adenocarcinoma and paired adjacent noncancerous tissues. All tissues were retrospectively collected from patients after surgery from January 2009 to October 2009. Before surgery the patients did not receive any chemotherapy or radiotherapy. And the follow-up data of patients were acquired from February 2009 to May 2014. The included patients were followed-up routinely either till their expiry or at least 5 years from their surgery date. Detailed clinicopathological characteristics are listed in supplementary Table S1. The HCol-Ade030PG-01 TMA (Shanghai OUTDO Biotech Co., Shanghai, China) used in IHC analysis consisted of 15 paired colorectal adenocarcinoma tissues and matched normal mucosa; All tissues were retrospectively collected from patients underwent surgery from January 2009 to October 2009. Before surgery the patients did not receive any chemotherapy or radiotherapy. The TMAs were stored in 4 °C before use. This TMA has no clinicopathological or follow-up data. Tumor T staging, N staging and TNM staging were performed based on the 7th Edition of American Joint Committee on Cancer (AJCC) staging system. Histological grading was performed according to the World Health Organization (WHO) classification of tumors of the digestive system of 2010. According to the location of the tumor, tumors located before the splenic flexure of the transverse colon were defined as right colon tumors, and tumors located at or after the splenic flexure of the transverse colon were defined as left colon tumors. Our study design, tissue sample, and data collection were accomplished according to our institutional protocols, which approved by Institutional Ethics Committee, Beijing Chao-Yang Hospital of Capital Medical University (No. 2018-Research-61) and informed consent was taken from all the patients. Our primary endpoint of the study was overall survival (OS) that is stated as the time from the date of surgery to death or the last follow-up date.

RNAscope in situ hybridization and image analysis

RNAscope in situ hybridization analysis was performed on colon cancer TMAs using a probe that targeted human CypB (Cat. No. 476701; Advanced Cell Diagnostics, Hayward, CA, USA) based on the manufacturer’s instruction, and a standard pretreatment protocol was used. RNAscope 2.5 High Definition (HD) Reagent Kit-brown (Cat. No. 322310; Advanced Cell Diagnostics, Hayward, CA, USA) was adopted to amplify and visualize the hybridization signals. Then, the slide image was taken with an Aperio scanner and viewed with AperioImageScope software (v12.3.1.6002, Leica Biosystems). CypB mRNA molecules are shown as brown spots and were counted manually. According to the manufacturer’s guidelines, a 5-tier scoring system was developed for semiquantitative microscopic evaluations: score 0 (−), no staining or less than 1 dot in each of ten cells; score 1 (+), 1–3 dots per cell; score 2 (++), 4–10 dots per cell, very few dot clusters; score 3 (+++), >10 dots per cell and the cells with dot clusters were <10% of all cells; and score 4 (++++), >10 dots per cell and the cells with dot clusters were >10% of all cells. Scores of 0–2 were considered low CypB mRNA expression, and scores of 3–4 were considered high CypB mRNA expression. Bacillus subtilis DapB mRNA (Cat. No. 310043; Advanced Cell Diagnostics, Hayward, CA, USA) was probed as a negative control. All the staining scores were reviewed by two pathologists through blinded-reading.

IHC staining analysis

The TMA slide was deparaffinized and rehydrated and rinsed in water. To quench endogenous peroxidase activity, the TMA slide was treated with 0.3% H2O2 for 10 minutes at room temperature. Antigen retrieval was performed in 0.01 M sodium citrate (pH =6.0) with heating in a pressure cooker. The sections were then blocked in 2% goat serum and were incubated with the primary antibody for 1 hour at room temperature. This study used rabbit polyclonal anti-CypB antibody (ab16045, Abcam Inc., Cambridge, MA, USA) as the primary antibody with 1:500 dilution. Then the second antibody from SP reagent kit (Zhongshan Goldenbridge Biotechnology Co., Beijing, China) was exerted to incubate the TMA sections for 20 minutes at room temperature, followed by further incubation with streptavidin-horseradish peroxidase complex. Staining with 3,3'-diaminobenzidine kit (DAB; Zhongshan Goldenbridge Biotechnology Co.), TMA sections were counter-stained with hematoxylin and evaluated. Score is the combination of staining intensity (0= negative, 1= mild staining, 2= moderate staining and 3= strong staining) and percentage of positive cells (0: <5%, 1: 6% to 25%, 2: 26% to 50%, 3: 51% to 75% and 4: >76%) (17). Finally the CypB staining was assigned to one of 4 levels as follows: negative (−) (score of 0), weak (+) (score of 1–4), moderate (++) (score of 5–8) to strong (+++) (score of 9–12). Negative (−) and weak (+) were considered as low expression, and moderate (++) and strong (+++) were considered as high expression.

Colon Adenocarcinoma (COAD) RNA-seq data from the Cancer Genome Atlas (TCGA)

The COAD RNA-seq datasets of TCGA, which enrolled 286 COAD tissues and 41 adjacent noncancerous tissues, were downloaded through the UCSC cancer genome browser (https://xenabrowser.net). The Illumina HiSeq 2000 RNA Sequencing platform was used to experimentally measure gene expression at the University of North Carolina TCGA genome characterization center. Level 3 data was downloaded from TCGA data coordination center. This dataset shows the gene-level transcription estimates, as in log2(x+1) transformed RSEM normalized count.

Gene set enrichment analysis (GSEA) and network construction

Gene Set Enrichment Analysis (GSEA, http://software.broadinstitute.org/gsea/) was applied for enriching CypB related pathways. At first, the top 50 up-regulated and 50 down-regulated differential genes between normal and cancer tissues from COAD datasets of TCGA were selected using Gene Expression Profiling Interactive Analysis (GEPIA, http://gepia.cancer-pku.cn/) (18). Finally, 87 genes were selected after deleting non-coding RNA. Then CypB related signaling pathways were enriched using GSEA by dividing those differential genes into two sets according to the median value of CypB. The gene set permutations analysis was repeated 1,000 times, according to the default weighted enrichment statistical method. Nominal P value, enrichment score (ES) and false discovery rate (FDR) were calculated to verify the significant difference for GSEA. After gene enrichment, the Search Tool for the Retrieval of Interacting Genes (STRING, https://string-db.org/) was used to construct protein-protein interactions (PPI) and screen the CypB related signaling pathways.

Cell lines, cell culture and cell transfection

The human colon cancer cell line HCT116 purchased from the American Type Culture Collection (ATCC) (Manassas, VA, USA) was used for our experiment. Cells were cultured in RPMI-1640 (Gibco; Thermo Fisher Scientific, Inc., Waltham, MA, USA) containing 10% fetal bovine serum (FBS; HyClone; Thermo Fisher Scientific, Inc., Waltham, MA, USA) at 37 °C in a humidified atmosphere containing 5% CO2. HCT116 cells were seeded in six-well plates and allowed to attach overnight. With the application of lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA), CypB small interfering RNA (siRNA) and control siRNA were transfected into the cells respectively according to the manufacturer’s recommendations. Then the cells were further cultured at 37 °C in a 5% CO2 atmosphere. CypB siRNA-1 sequence was 5'-GCAUGGAGGUGGUGCGG-3', CypB siRNA-2 sequence was 5'-CUUAGCUACAGGAGAGAA-3', and the negative control siRNA sequence was 5'-TTCTCCGAACGTGTCACGT-3'. Both of them were designed and synthesized by the Beijing Hesheng Gene Technology Co., Ltd. (Beijing, China).

RNA extraction and real-time quantitative PCR

Total cellular RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Total RNA was then reverse transcribed to cDNA using the EasyScript® First-Strand cDNA Synthesis kit (Transgene, Beijing, China). Gene expression analysis was performed by qRT-PCR using a SYBR Premix Ex Taq Kit (Takara, Dalian, China). Relative gene expression was quantified using the comparative threshold cycle (2−ΔΔCt) method. The PCR program was as follows: pre-denaturation at 95 °C for 2 min, 40 cycles of denaturation at 95 °C for 5 s, and annealing and elongation at 60 °C for 30 s. The primers used in the experiment were as follows:

CypB: Forward, AAGTCACCGTCAAGGTGTATTTT; Reverse, TGCTGTTTTTGTAGCCAAATCCT.

CNN1: Forward, AGGTTAAGAACAAGCTGGCCC; Reverse, ATGAAGTTGTTGCCGATGCG.

MYL9: Forward, CTCGCTGGGGAAGAACCCC; Reverse, CGTTGCGAATCACATCCTCG.

MYH11: Forward, AGACACAAGTATCACGGGAGAG; Reverse, TTGCCGAATCGTGAGGAGTT.

E-cadherin: Forward, GTCACTGACACCAACGATAATCCT; Reverse, TTTCAGTGTGGTGATTACGACGTTA.

Snail: Forward, GCCATGTCCGGACCCACACTG; Reverse, GGCAGGGGCAGGTATGGAGA.

TWIST: Forward, GTCCGCAGTCTTACGAGGAG; Reverse, GCTTGAGGGTCTGAATCTTGCT.

Vimentin: Forward, CCTGAACCTGAGGGAAACTAA; Reverse, GCAGAAAGGCACTTGAAAGC.

18s: Forward, AAACGGCTACCACATCCA; Reverse, CACCAGACTTGCCCTCCA.

Statistical analysis

Statistical analyses were conducted using SPSS software for Windows, version 17.0 (SPSS, Chicago, IL, USA). GraphPad Prism for Windows, version 5.0 (GraphPad Software, San Diego, CA, USA) was used to create the artwork. Quantitative variables were compared by means of the student t-test. Categorical variables were compared using the χ2 test. The Cox proportional hazards regression model and the Kaplan-Meier test were used to assess the OS rates. The survival curves were plotted by the log-rank test. P<0.05 was considered statistically significant.


Results

RNAscope in situ hybridization and IHC staining present the overexpression of CypB in colon cancer

TMA that contained 90 paired cancer and adjacent normal tissues was used to determine the expression of CypB. Finally, 80 cancer tissues and 84 adjacent normal tissues were successfully stained to show the mRNA levels of CypB by RNAscope. According to the expression level of CypB mRNA (representative images were provided in Figure 1), staining intensities of score 0 (−), score 1 (+) and score 2 (++) were classified as the low expression group, and score 3 (+++) and score 4 (++++) were classified as the high expression group. CypB mRNA was found to be significantly overexpressed in colon cancer tissues compared with adjacent normal tissues (P<0.001; Table 1).

Figure 1 Different expression levels of CypB mRNA in a colon cancer tissue microarray performed by RNAscope in situ hybridization. Score 0 (−), no staining or less than 1 dot in each of ten cells; score 1 (+), 1–3 dots per cell; score 2 (++), 4–10 dots per cell, very few dot clusters; score 3 (+++), >10 dots per cell and the cells with dot clusters were <10% of all cells; score 4 (++++), >10 dots per cell and the cells with dot clusters were >10% of all cells. CypB, cyclophilin B. Red boxes indicate the amplified part of the entire image. Staining method RNAscope in situ hybridization.

Table 1

Expression of CypB mRNA in colon cancer and adjacent noncancerous tissues

Histological type Case numbers CypB expression P value
Low High
Tumor tissues 80 39 41 <0.001*
Nontumor tissues 84 70 14

*, P value less than 0.05. CypB, cyclophilin B.

We also used TMA with a small sample size to detect the expression of CypB protein (Figure 2). As in mRNA level, the expression of CypB protein in colon cancer is significantly higher than that in adjacent tissues (P<0.05; Table 2).

Figure 2 Different expression levels of CypB protein in a colon cancer tissue microarray performed by immunohistochemical (IHC) staining. The levels of CypB range from negative (−) (score of 0), weak (+) (score of 1–4), moderate (++) (score of 5–8) to strong (+++) (score of 9–12). CypB, cyclophilin B.

Table 2

Expression of CypB protein in colon cancer and adjacent noncancerous tissues

Histological type Case numbers CypB expression P value
Low High
Tumor tissues 15 10 5 0.042*
Nontumor tissues 15 15 0

*, P value less than 0.05. CypB, cyclophilin B.

Clinicopathological analysis reveals that CypB is associated with advanced T stage

The correlation between CypB levels and the clinicopathological parameters of 80 colon cancer patients was analyzed. The clinicopathological data of the patients were summarized in the supplementary Table S1. Our analysis indicated that the levels of CypB were significantly higher in patients with T4 stage than in those with T1–3 stage (P=0.043; Table 3). However, there were no significant correlations between the levels of CypB and other parameters, including age, sex, tumor size, N stage, histological grade, TNM stage and tumor position (P>0.05; Table 3).

Table 3

The correlation between CypB expression and clinicopathological characteristics in patients with colon cancer

Parameters Group Case numbers CypB expression P value
Low expression High expression
Age <65 33 18 15 0.385
≥65 47 21 26
Sex Male 43 21 22 0.987
Female 37 18 19
Tumor size <5 cm 33 14 19 0.296
≥5 cm 46 25 21
NA 1 0 1
T stage T1–3 55 31 24 0.043*
T4 25 8 17
N stage N0 53 28 25 0.306
N1–2 27 11 16
Histological grade I–II 69 34 35 0.814
III–V 11 5 6
TNM stage I–II 51 26 25 0.597
III–V 29 13 16
Tumor position Left colon 37 15 22 0.17
Right colon 41 23 18
NA 2 1 1

*, P value less than 0.05. CypB, cyclophilin B; TNM, tumor-node-metastasis.

CypB mRNA overexpression predicts a poor prognosis of colon cancer patients

The prognostic significance of CypB mRNA expression was further investigated in colon cancer patients. In total, 80 patients were followed up for 0.4–64 months (mean ± SD, 47.02±19.48 months). At the end of follow up, 27 patients had died. Kaplan-Meier analysis revealed that the high expression of CypB was associated with a shorter OS (Figure 3A, P=0.0139). Univariate and multivariate Cox regression analyses indicated that TNM stage (P=0.000) and CypB expression (P=0.015) were independent prognostic indicators for poor survival (Table 4). Furthermore, subgroup analysis indicated that high levels of CypB were associated with poor survival for patients with stage T3–4, lymph node metastasis, tumor size ≥5 cm or right colonic cancer (Figure 3B,C,D,E, P<0.05). In addition, our analysis also indicated that patients in TNM stages III–IV with high CypB expression had a shorter survival time, although the difference was not significant (Figure 3F, P=0.0616).

Figure 3 High CypB mRNA expression was correlated with poor prognosis in colon cancer. Kaplan-Meier curves showed that patients with high CypB mRNA expression had significantly shorter OS than those with low CypB mRNA expression in all colon cancer patients (A), T3–4 patients (B), N1–2 patients (C), patients with a tumor size ≥5 cm (D) and patients with right colon cancer (E) (P=0.0139, 0.0311, 0.0247, 0.0078 and 0.0035, respectively; log-rank test). The OS of patients in TNM stage III–IV (F) did not differ significantly according to CypB expression (P=0.0616; log-rank test). CypB, cyclophilin B; OS, overall survival; TNM, tumor-node-metastasis.

Table 4

Univariate and multivariate analysis of prognostic parameters in patients with colon cancer

Parameters OS
Univariate analysis Multivariate analysis
HR 95% CI P value HR 95% CI P value
Age (<65 vs. ≥65) 1.067 0.495–2.301 0.868
Sex (male vs. female) 1.832 0.822–4.080 0.138
Tumor size (<5 vs. ≥5 cm) 3.183 1.282–7.902 0.013*
T stage (T1–3 vs. T4) 3.432 1.599–7.364 0.002*
N stage (N0 vs. N1–2) 3.702 1.712–8.006 0.001*
Histological grade (I–II vs. III–IV) 3.534 1.485–8.411 0.004
TNM stage (I–II vs. III–IV) 4.805 2.146–10.755 0.000* 4.918 2.193–11.03 0.000*
Tumor position (left vs. right colon) 0.586 0.269–1.277 0.179
CypB mRNA expression (low vs. high) 2.693 1.178–6.155 0.019* 0.36 0.157–0.823 0.015*

*, P value less than 0.05. CI, confidence interval; CypB, cyclophilin B; HR, hazard ratio; OS, overall survival; TNM, tumor-node-metastasis.

Validation of CypB overexpression and its prognostic significance in COAD RNA-seq dataset of TCGA

To further validate our findings, we analyzed the CypB mRNA expressions in COAD RNA-seq dataset of TCGA. First, we compared the CypB mRNA levels between 286 cancerous tissues and 41 normal tissues (Figure 4A). As expected, the CypB levels were significantly higher in cancer tissues than in normal tissues (P<0.0001). Furthermore, in the TCGA 26 paired cancer and corresponding normal tissues, the CypB mRNA levels were also markedly increased in cancer tissues compared to normal tissues (Figure 4B, P=0.0146).

Figure 4 Expression of CypB mRNA was upregulated in COAD patients from TCGA. The analysis of COAD RNA-seq data showed that CypB mRNA was highly upregulated in cancer tissues compared with unpaired (A) and paired (B) adjacent normal tissues (P<0.0001 and P=0.0146, respectively; t-test). COAD, colon adenocarcinoma; CypB, cyclophilin B; TCGA, the Cancer Genome Atlas.

Next, we determined the prognostic significance of CypB mRNA in 286 COAD patients. The CypB mRNA expression levels and clinicopathological parameters are summarized in the supplementary Table S2. OS differences between patients with high or low CypB expression were analyzed by Cox regression models and log-rank tests. As shown by Kaplan-Meier plots, a high level of CypB mRNA was associated with a reduced OS time (P=0.048, Figure 5A). In subgroup analysis, we found that a higher level of CypB mRNA was associated with a shorter OS time for patients with advanced tumors, such as in patients with stage T3–4, lymph node metastasis and TNM stage III-IV (Figure 5B,C,D, P<0.05). Furthermore, Cox multivariate analyses confirmed that CypB mRNA was associated with the OS time of COAD patients (Table 5, P=0.007).

Figure 5 Association between CypB expression and the prognosis of patients with COAD from TCGA and CypB related biological pathways. Kaplan-Meier curves showed that patients with high CypB mRNA expression had significantly shorter OS than those with low CypB mRNA expression in all COAD patients (A), T3–4 patients (B), N1–2 patients (C) and patients in TNM stage III–IV (D) (P=0.048, 0.0360, 0.0214 and 0.0073, respectively; log-rank test). GSEA and STRING analysis of CypB related biological pathways. The gene set of “FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_DN” was enriched with CypB lowly expressed by GSEA (E). STRING analysis was employed to generate a visual image of protein-protein interactions using the enriched genes (F). COAD, colon adenocarcinoma; CypB, cyclophilin B; DN, down; FGFR1, fibroblast growth factor receptor 1; GSEA, Gene set enrichment analysis; OS, overall survival; STRING, the Search Tool for the Retrieval of Interacting Genes; TCGA, the Cancer Genome Atlas; TNM, tumor-node-metastasis.

Table 5

Univariate and multivariate analysis of prognostic parameters in patients with colon cancer in TCGA

Parameters OS
Univariate analysis Multivariate analysis
HR 95% CI P value HR 95% CI P value
Age (<65 vs. ≥65) 1.521 0.914–2.531    0.106
Sex (male vs. female) 0.686 0.420–1.121    0.133
T stage (Tis–2 vs. T3–4) 2.516 1.009–6.271    0.048*
N stage (N0 vs. N1–2) 2.432 1.499–3.947    0.000*
TNM stage (I–II vs. III–IV) 2.548 1.538–4.219    0.000* 2.808 1.688–4.671 0.000*
Tumor position (left vs. right colon) 1.325 0.779–2.254    0.299
CypB mRNA expression (low vs. high) 1.614 0.998–2.612    0.049* 2.007 1.212–3.323 0.007*

*, P value less than 0.05. CI, confidence interval; CypB, cyclophilin B; HR, hazard ratio; OS, overall survival; TNM, tumor-node-metastasis.

GSEA and STRING analyses indicate that CypB is enriched in the metastatic pathways

To identify potential function of CypB, we performed GSEA using TCGA data. The cut-off criterion is set to nominal P value <0.05 and |enrichment score (ES)| >0.55. As shown in Figure 5, the gene set “FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_DN” was enriched with CypB lowly expressed (Figure 5E, P<0.05). This gene set is involved in the regulation of epithelial-to-mesenchymal transition (EMT) and Wnt signaling pathway (19). Furthermore, the enriched genes were analyzed by STRING to generate visual images of PPIs and the potential biological processes (Figure 5F). The results uncovered that CypB was closely involved in tumor metastatic pathways, including cell adhesion, tight junction, cell-cell junction organization, extracellular matrix organization and adherens junctions interactions (Table S3).

CypB is associated with myosin related genes and may involve in Snail-mediated EMT in colon cancer

Based on the enriched gene set with GSEA analysis, we found that the expressions of calponin 1 (CNN1), myosin light chain 9 (MYL9) and myosin heavy chain 11 (MYH11) were positively correlated with the expression of CypB. These three genes are all necessary in cell movement, cytokinesis and spindle formation, which are related to tumor invasion and metastasis. Therefore, in vitro experiments by knockdown of CypB in colon cancer cell HCT116 were performed to verify the bioinformatics results. We found that compared with the NC-siRNA group, CypB silencing significantly reduced the expressions of MYL9, MYH11 and CNN1 (Figure 6A,B,C,D, P<0.05).

Figure 6 CypB is associated with myosin related genes and may involve in Snail-mediated EMT in colon cancer. After transfection of CypB siRNAs, the transcriptional level of CypB (A), MYL9 (B), MYH11 (C), CNN1 (D), Snail (E), E-cadherin (F), Vimentin (G) and TWIST (H) in HCT116 cells were detected by qRT-PCR. *, P<0.05, versus siNC. CNN1, calponin 1; CypB, cyclophilin B; EMT, epithelial-to-mesenchymal transition; MYH11, myosin heavy chain 11; MYL9, myosin light chain 9.

Subsequently, GSEA and STRING analyses revealed that CypB may closely involved in tumor metastatic pathways, such as EMT. During EMT, epithelial cells lose epithelial characteristics and acquire a mesenchymal, highly invasive phenotype. In this process, many transcriptional regulators, such as TWIST, ZEB, Snail and Slug are activated, leading to the downregulation of E-cadherin expression. In HCT116 cells, CypB silencing significantly reduced Snail expression (Figure 6E, P=0.0048). Although there was no statistical significance, the expression of E-cadherin increased (Figure 6F, P>0.05) after CypB decreased. But there were no significant changes in Vimentin and TWIST expressions (Figure 6G,H, P>0.05). These data suggest that Snail-mediated EMT may be associated with CypB in colon cancer.


Discussion

Previous studies have found that CypB was involved in many pathophysiological processes, including osteogenesis, hepatitis virus replication, and immunosuppression. In recent years, CypB overexpression has been observed in stomach, liver, pancreatic, breast and several other types of cancers (10,11,13,20,21). Some in vitro studies have shown that CypB could promote tumor cell proliferation, protect tumor cells against oxidative stress, and stimulate neovascularization (22-24). So far, only one research team has analyzed the relationship between CypB expression and prognosis in colon cancer. Their research was only at the protein level, and the correlation between CypB and clinicopathological parameters was not further explored (12). Our study applied a new technique of RNA in situ hybridization-RNAscope, and explored the expression pattern and clinical significance of CypB in colon cancer at the RNA level. We also detected the CypB protein expression using IHC. Bioinformatics analysis was applied to find out the CypB involved signaling pathways, which provides a new clue to reveal the function of CypB in colon cancer.

For formalin-fixed, paraffin-embedded tissue sections, immunohistochemistry remains the overwhelming technique of choice. However, validations can be complex, with significant specificity, sensitivity and reproducibility issues. Commercial antibodies from many available vendors may also lead to nonstandard approaches. The RNAscope in situ hybridization method enabled a realistic alternative with fewer validation steps and more stringent and reproducible assessment criteria (25,26). In our analyses, we used this method to stain CypB mRNA in single colon cancer cells and adjacent normal cells. We also analyzed the CypB protein expression using IHC. We found that CypB mRNA and protein were distributed in the cytoplasm and nucleus. Furthermore, we observed that CypB was apparently overexpressed in colon cancer tissues compared with adjacent normal tissues. The high expression of CypB mRNA was significantly higher in patients with T4 stage than in those with T1–3 stage. However, there were no significant correlations between CypB mRNA expression and other parameters. To the best of our knowledge, this is the first study to demonstrate the relation between CypB and clinicopathological parameters in colon cancer.

Additionally, the patients who had relatively high levels of CypB showed poorer prognoses than their low-level counterparts, and further Cox regression analyses indicated that CypB mRNA expression was an independent prognostic indicator. The expression of CypB is not significantly correlated with clinicopathological parameters, such as T and N stages, but its high expression is related to a poor prognosis, suggesting that CypB may not directly promote the tumor proliferation but may affect the prognosis in other ways. For example, Choi’s study found that the overexpression of CypB could promote oxaliplatin resistance and inhibit oxaliplatin-induced apoptosis in colon cancer cells (27), therefore, further research is needed on this perspective. In addition, in subgroup analysis, we found that CypB had prognostic significance in more advanced tumors, such as in patients with T3–4, lymph node metastasis and clinical stage III-IV, suggesting that CypB may play a vital role in late stage of colon cancer, such as promoting cancer migration.

With the wide application of sequencing technology, TCGA datasets contain differentially expressed transcripts of many cancers (28,29). Here, the COAD RNA-seq dataset in the TCGA was downloaded and analyzed. We confirmed that CypB mRNA was highly upregulated and served as a prognostic biomarker in colon cancer, especially in more advanced tumors. These results further validate our main findings from the TMA.

The mechanism and signaling pathways which CypB is involved in several cancers are studied in depth (10,15,21,30,31). However, the detailed mechanism for CypB in colon cancer progression still needs to be elucidated. In our study, bioinformatic analysis showed that the CypB may be closely associated with metastatic related processes, such as EMT and Wnt signaling pathway. Further cell experiments revealed that compared with the NC-siRNA group, CypB silencing significantly reduced the expressions of MYL9, MYH11 and CNN1. These genes all belong to the myosin family and more and more evidences show that this family may play important roles in tumor invasion and metastasis development, including EMT process (32,33). During EMT, epithelial cells lose epithelial characteristics and acquire a mesenchymal, highly invasive phenotype (34,35). Therefore we next tested several EMT related genes after knockdown of CypB. And results showed that CypB may be associated with Snail-mediated EMT in colon cancer. But further in vivo experiments should be designed to verify our findings in vitro.


Conclusions

Collectively, we report here that CypB is remarkedly overexpressed in human colon cancer. Overexpressed CypB is an independent prognostic indicator for poor survival, especially for advanced tumors. Bioinformatic and in vitro study analysis revealed that CypB is associated with some myosin related genes and may involve in Snail-mediated EMT process in colon cancer. CypB may have an important role in the regulation of tumor metastasis. In this regard, we suggest that CypB could serve as a promising poor prognostic biomarker for colon cancer.

Table S1

CypB mRNA expression levels and clinicopathological parameters of the patients in the colonic tumor tissue microarray (TMA)

Tissue code CypB expression* OS (m) OS# Age (y) Sex& T stage N stage M stage TNM stage Histological grade Tumor position Tumor size (cm3)
D15A1454-B30-C1 1 64 0 72 1 T3 N0 M0 2A II Right colon 6.5×5×1.7
D15A1455-B30-C1 1 1 57 0 T2 N1b M0 3A II Right colon 6.5×5.5×2
D15A1456-B30-C1 1 13 1 76 1 T3 N0 M0 2A II Descending colon 5.5×4.5×2
D15A1458-B30-C1 1 64 0 63 0 T3 N0 M0 2A II Sigmoid colon 4.5×3.5×1.5
D15A1516-B30-C1 76 0 53 1 T4b N0 M0 2C I–II Sigmoid colon 5×3×1.5
D15A1461-B30-C1 2 63 0 78 0 T3 N2b M0 3C II Ascending colon 7×5×1
D15A1464-B30-C1 2 7 1 63 1 T4a N2b M0 3C III Sigmoid colon 5.5×4.5×1.5
D15A1462-B30-C1 1 22 1 78 1 T3 N0 M1b 4B I–II Sigmoid colon 7.5×3×1.5
D15A1502-B30-C1 1 63 0 68 0 T3 N0 M0 2A II Hepatic flexure 6×3×2
D15A1503-B30-C1 1 63 0 39 1 T4a N0 M0 2B II Transverse colon 6×4×3
D15A1504-B30-C1 23 1 68 1 T2 N0 M0 1 I–II Hepatic flexure 5.5×4×2
D15A1505-B30-C1 1 63 0 62 1 T3 N0 M0 2A I–II Ascending colon 2.5×2×0.5
D15A1508-B30-C1 1 63 0 78 1 T3 N0 M0 2A II Ascending colon 5×4×2
D15A1510-B30-C1 2 44 1 50 0 T4a N0 M0 2B II Hepatic flexure 4×3.5×1
D15A1556-B30-C1 2 62 0 73 1 T3 N0 M0 2A I–II Hepatic flexure 11×6×2
D15A1557-B30-C1 2 38 1 68 1 T4a N0 M0 2B II Hepatic flexure 6×4×1
D15A1558-B30-C1 2 13 1 87 0 T4b N1b M0 3C I–II Right colon 6×4×1
D15A1559-B30-C1 2 8 1 52 0 T4a N0 M0 2B II–III Sigmoid colon 7×5×2.5
D15A1560-B30-C1 2 62 0 51 0 T1 N0 M0 1 II Sigmoid colon 2.7×1.7×1.3
D15A1561-B30-C1 2 56 1 55 1 T4a N2a M0 3C II Splenic flexure 3.5×3.5×1
D15A1562-B30-C1 1 17 1 73 1 T4a N0 M1b 4B III–IV Ascending colon 6.5×5×1.5
D15A1563-B30-C1 1 62 0 61 0 T3 N0 M0 2A II Right colon 3×3×2
D15A1564-B30-C1 12 1 48 0 T3 N0 M0 2A II–III Transverse colon 1.5×1×1
D15A1565-B30-C1 1 62 0 59 0 T2 N0 M0 1 II Sigmoid colon 3×2.5×1
D15A1566-B30-C1 40 1 77 0 T2 N0 M0 1 II Sigmoid colon 4×4×3
D15A1567-B30-C1 2 42 1 78 1 T3 N1a M0 3B II Ascending colon 5×5×1.5
D15A1570-B30-C1 1 62 0 31 1 T3 N1b M0 3B I–III Ascending colon 4×3×1
D15A1571-B30-C1 33 1 79 0 T3 N0 M0 2A II Sigmoid colon 7×5×2
D15A1572-B30-P1 1 61 0 81 1 T3 N1b M0 3B II Sigmoid colon 4×3×1
D15A1573-B30-C1 2 61 0 85 1 T3 N0 M0 2A I–II Ascending colon 4.3×2×0.5
D15A1574-B30-C1 2 40 1 90 1 T4a N0 M0 2B II Sigmoid colon 7×5×5
D15A1576-B30-C1 1 61 0 70 0 T2 N0 M0 1 II Sigmoid colon 4.5×2×1
D15A1577-B30-C1 2 23 1 66 0 T4b N1b M0 3C II–III Ascending colon 5×4×1.5
D15A1579-B30-P1 2 61 0 73 1 T3 N0 M0 2A II Descending colon 3.5×3×1
D15A1614-B30-C1 2 61 0 54 0 T3 N0 M0 2A II Descending colon 3.5×3×2
D15A1628-B30-C1 2 25 1 76 0 T3 N1a M0 3B II Ascending colon 8×8×4
D15A1615-B30-C1 1 61 0 50 1 T1 N0 M0 1 I Ascending colon 4×3×3
D15A1616-B30-C1 1 61 0 74 0 T3 N0 M0 2A I Ascending colon 5×2.5×1
D15A1617-B30-C1 1 61 0 80 1 T3 N0 M0 2A II Right colon 8×7×1
D15A1619-B30-C1 2 61 0 65 0 T3 N0 M0 2A I–II Ascending colon 4×3.5×1
D15A1620-B30-C1 1 61 0 59 0 T3 N0 M0 2A II Sigmoid colon 4.5×3.5×1.2
D15A1622-B30-C1 2 61 0 79 1 T3 N0 M0 2A I–II Descending colon 4×4×1
D15A1629-B30-C1 2 61 0 56 1 T3 N0 M0 2A I–II Ascending colon 4×3×1
D15A1624-B30-C1 2 13 1 76 0 T4a N1b M0 3B II Sigmoid colon 3.5×3.5×1
D15A1625-B30-C1 2 60 0 76 0 T3 N0 M0 2A I–II Ascending colon 8×6×1
D15A1626-B30-C1 1 39 1 63 1 T4a N1b M0 3B I–II Sigmoid colon 5×3×1.5
D15A1630-B30-C1 1 60 0 44 0 T2 N0 M0 1 II Ascending colon 8×8×4
D15A1663-B30-C1 1 13 1 73 1 T3 N0 M0 2A II Sigmoid colon 5.5×3.5×2
D15A1668-B30-C1 1 60 0 66 0 T1 N1a M0 3A II Transverse colon 7.5×6.5×0.5
D15A1669-B30-C1 2 1 1 48 0 T3 N0 M0 2A II Right colon 8×7×2
D15A1732-B30-C1 1 59 0 79 1 T3 N0 M0 2A I–II Ascending colon 6×3×1
D15A1733-B30-C1 1 59 0 55 1 T4a N1b M0 3B II–III Hepatic flexure 5×4×1
D15A1735-B30-C1 2 59 0 65 0 T3 N0 M0 2A II Sigmoid colon 4×3×1
D15A1740-B30-C1 2 7 1 73 0 T3 N1a M0 3B II Right colon 8×5×2.5
D15A1741-B30-C1 1 59 0 81 1 T3 N1a M0 3B II Left colon 8×7×1.5
D15A1742-B30-C1 2 59 0 61 1 T2 N0 M0 1 I–II Descending colon 4.5×3.5×1.5
D15A1745-B30-C1 2 59 0 80 1 T3 N0 M0 2A II Ascending colon 4×3×2
D15A1743-B30-C1 2 16 1 65 1 T4b N1b M0 3C III Colon 6×5×1.3
D15A1744-B30-C1 2 16 1 61 1 T4a N2a M1a 4A II–III Sigmoid colon 4×4×3
D15A1756-B30-C1 2 58 0 71 0 T3 N1a M0 3B II Sigmoid colon 3×1.5×1
D15A1758-B30-C1 1 58 0 55 0 T3 N0 M0 2A II–III Ascending colon 11×6×3
D15A1765-B30-C1 2 21 1 55 1 T4a N0 M0 2B II Sigmoid colon 4×2.5×1
D15A1767-B30-C1 1 58 0 83 1 T3 N0 M0 2A I Ascending colon 5×3×2
D15A1762-B30-C1 1 58 0 69 0 T4a N0 M0 2B II Transverse colon 8×5×4
D15A1764-B30-C1 58 0 80 0 T4a N1a M0 3B II–III Ascending colon 6×5.5×1
D15A1990-B30-C1 1 57 0 43 1 T3 N0 M0 2A II Right colon 4×3×1.5
D15A1811-B30-C1 2 57 0 73 1 T4a N0 M0 2B I Ascending colon 7×4×1
D15A1813-B30-C1 1 57 0 82 0 T3 N1a M0 3B II–III Transverse colon 4×4×1
D15A1814-B30-C1 2 57 0 69 0 T2 N0 M0 1 I–II Ascending colon 2×2×1.5
D15A1991-B30-C1 2 57 0 83 1 T4a N0 M0 2B II Descending colon 4×2×1
D15A1815-B30-C1 2 57 0 46 0 T3 N0 M0 2A II Sigmoid colon 6×6×0.7
D15A1819-B30-C1 2 57 0 56 0 T3 N0 M0 2A II Descending colon 4.5×3.5×1.5
D15A1992-B30-C1 56 0 66 1 T3 N0 M0 2A II Ascending colon 4×2.5×0.6
D15A1993-B30-C1 2 0.4 1 82 1 T3 N2b M0 3C III Splenic flexure 7×6×1
D15A1820-B30-P1 1 56 0 78 0 T3 N0 M0 2A II Sigmoid colon 4.5×4×1.5
D15A1836-B30-C1 1 56 0 81 0 T4a N0 M0 2B II Colon 6×5×3.5
D15A1839-B30-C1 2 56 0 73 1 T4a N0 M0 2B II Sigmoid colon 5×5×1.5
D15A1841-B30-C1 1 56 0 50 0 T3 N0 M0 2A II Right colon 6×4×1
D15A1904-B30-C1 19 1 27 0 T4a N2a M0 3C III Descending colon 4×4×1.5
D15A1907-B30-C1 2 35 1 54 1 T3 N0 M0 2A II Right colon 5×5×2
D15A1914-B30-C1 2 55 0 77 0 T4a N1a M0 3B I–II Splenic flexure
D15A1915-B30-C1 1 55 0 55 0 T4a N1b M0 3B II Sigmoid colon 9×6×2
D15A1917-B30-C1 1 55 0 66 1 T2 N0 M0 1 II Sigmoid colon 2.7×2.2×1.3
D15A1918-B30-C1 1 42 1 60 1 T3 N2b M0 3C II Sigmoid colon 3.5×2×1.5
D15A1919-B30-C1 1 19 1 65 1 T3 N2a M0 3B II Sigmoid colon 5×5×1.8
D15A1921-B30-C1 15 1 56 1 T3 N1b M0 3B II Sigmoid colon 6×6×2.5
D15A1923-B30-C1 2 55 0 54 1 T4a N1b M0 3B II Sigmoid colon 6.5×5×2.5
D15A1928-B30-C1 1 55 0 52 0 T2 N0 M0 1 II Transverse colon 5.5×4.5×1.5
D15A1929-B30-C1 1 23 1 62 0 T4a N1b M0 3B I–II Ascending colon 5×4×3
D15A1927-B30-C1 2 19 1 67 1 T3 N1a M0 3B II Sigmoid colon 6×5×1

*, CypB (score 0–2 =1, score 3–4 =2); #, OS (event =1); &, Sex (male =1, female =2).

Table S2

CypB mRNA expression levels and clinicopathological parameters of the colon adenocarcinoma (COAD) patients from the Cancer Genome Atlas (TCGA)

Sample CypB mRNA expression OS time (days) OS status (event =1) M stage N stage T stage TNM stage Gender Age (year) Neoplasm_subdivision
TCGA-3L-AA1B-01 13.3798 475 0 M0 N0 T2 I Female 61 Cecum
TCGA-4N-A93T-01 12.6538 146 0 M0 N1b T4a IIIB Male 67 Ascending colon
TCGA-4T-AA8H-01 12.83 385 0 MX N0 T3 IIA Female 42 Descending colon
TCGA-5M-AAT4-01 12.5424 49 1 M1b N0 T3 IV Male 74 Ascending colon
TCGA-5M-AAT5-01 13.5081
TCGA-5M-AAT6-01 13.9539 290 1 M1a N2b T4a IV Female 40 Transverse colon
TCGA-5M-AATA-01 13.2919
TCGA-5M-AATE-01 12.5337 1,200 0 M0 N0 T3 IIA Male 76 Ascending colon
TCGA-A6-2675-01 12.1484 1,321 0 MX N0 T3 IIA Male 78 Sigmoid colon
TCGA-A6-2682-01 13.725 424 1 M1 N1 T4b IV Male 70 [Discrepancy]
TCGA-A6-2684-01 13.1669 1,127 0 M0 N0 T2 I Female 75 Cecum
TCGA-A6-2685-01 12.9514 1,133 0 M0 N0 T3 IIA Female 48 Sigmoid colon
TCGA-A6-2686-01 13.1465 1,126 1 M0 N0 T3 IIA Female 81 Cecum
TCGA-A6-4105-01 13.7982 442 1 M0 N0 T3 IIA Male 79 Ascending colon
TCGA-A6-5656-01 13.305 1,001 0 M0 N0 T2 I Male 74 Sigmoid colon
TCGA-A6-5657-01 12.9149 962 0 M0 N1 T3 IIIB Male 65 [Discrepancy]
TCGA-A6-5659-01 13.0106 926 0 M0 N0 T2 I Male 82 Cecum
TCGA-A6-5660-01 12.8449 888 0 M0 N2b T3 IIIC Male 73 Cecum
TCGA-A6-5661-01 13.3289 1,020 0 M0 N0 T3 IIA Female 80 Ascending colon
TCGA-A6-5662-01 13.254 718 0 M1 N2 T3 IVA Male 46 Splenic flexure
TCGA-A6-5664-01 13.7724 672 0 MX N2a T4a IIIC Male 80 Cecum
TCGA-A6-5665-01 13.7718 671 0 M0 N0 T3 IIA Female 84 Ascending colon
TCGA-A6-5666-01 13.8249 995 0 M0 N0 T4b IIC Male 78 Sigmoid colon
TCGA-A6-5667-01 12.7441 887 0 MX N1a T3 IIIB Female 40 Sigmoid colon
TCGA-A6-6137-01 12.8026 824 0 M0 N1c T3 IIIB Male 55 Hepatic flexure
TCGA-A6-6138-01 12.2254 685 0 M0 N0 T2 I Male 61 Cecum
TCGA-A6-6140-01 13.035 734 0 M0 N0 T3 IIA Male 62 Descending colon
TCGA-A6-6141-01 13.3598 130 0 M0 N0 T3 IIA Male 31 Cecum
TCGA-A6-6142-01 13.4184 763 0 M1a N1a T3 IVA Female 56 Sigmoid colon
TCGA-A6-6648-01 12.4873 766 0 M1a N0 T3 IVA Male 56 [Discrepancy]
TCGA-A6-6649-01 12.9726 735 0 M0 N1b T3 IIIB Male 66 Hepatic flexure
TCGA-A6-6650-01 12.5784 627 0 M0 N0 T3 IIA Female 69 Cecum
TCGA-A6-6651-01 13.1779 662 0 MX N1b T3 IIIB Female 55 Transverse colon
TCGA-A6-6652-01 12.7351 751 0 M1 N0 T3 IVA Male 59 Sigmoid colon
TCGA-A6-6653-01 13.8395 742 0 M0 N0 T2 I Male 82 Ascending colon
TCGA-A6-6654-01 13.3981 726 0 M0 N1 T3 IIIB Female 65 Descending colon
TCGA-A6-6780-01 13.771 612 0 MX N0 T3 IIA Male 74 [Discrepancy]
TCGA-A6-6781-01 14.0498 598 0 MX N1b T4b IIIC Male 43 Transverse colon
TCGA-A6-6782-01 13.0313 617 0 MX N0 T4a IIB Male 82 Transverse colon
TCGA-A6-A565-01 13.0484 494 1 MX N2 T3 IIIC Female 34 Transverse colon
TCGA-A6-A566-01 13.5206 758 1 M0 N1 T4 IIIB Female 55 Descending colon
TCGA-A6-A567-01 12.2014 1,881 1 M1 N1 T3 IV Male 56 Sigmoid colon
TCGA-A6-A56B-01 12.4469 1,711 1 M0 N1 T3 IIIB Male 57 Sigmoid colon
TCGA-A6-A5ZU-01 13.256 293 0 M0 N1 T3 IIIB Male 59 Transverse colon
TCGA-AA-3489-01 12.8667 214 1 M0 N0 T3 II Male 75 Sigmoid colon
TCGA-AA-3492-01 13.3061 92 1 M0 N0 T3 II Female 90 Ascending colon
TCGA-AA-3495-01 13.2578 1,127 0 M0 N0 T2 I Male 79 Hepatic flexure
TCGA-AA-3496-01 13.0737 31 0 M0 N0 T3 II Female 83 Ascending colon
TCGA-AA-3502-01 12.9701 1,065 0 M0 N0 T2 I Male 73 Transverse colon
TCGA-AA-3506-01 13.5302 1,765 0 M0 N0 T2 I Male 77 Hepatic flexure
TCGA-AA-3509-01 13.2673 1,915 0 M0 N0 T3 II Female 54 Sigmoid colon
TCGA-AA-3511-01 12.7691 212 0 M0 N0 T4 II Male 64 Sigmoid colon
TCGA-AA-3526-01 14.0539 580 0 M0 N0 T2 I Male 57 Sigmoid colon
TCGA-AA-3655-01 13.1989 1,856 0 M0 N0 T3 II Male 68 Sigmoid colon
TCGA-AA-3660-01 13.0301 2,375 0 M0 N0 T3 II Female 51 Sigmoid colon
TCGA-AA-3662-01 12.9868 184 0 M1 N2 T4 IV Female 80 Sigmoid colon
TCGA-AA-3663-01 14.2051 212 0 M0 N0 T3 II Male 42 Cecum
TCGA-AA-3675-01 13.3136 1,431 0 M0 N0 T3 II Male 84 Hepatic flexure
TCGA-AA-3685-01 13.8864 1,127 0 M0 N0 T3 II Male 69 Sigmoid colon
TCGA-AA-3697-01 12.3795 2,587 0 M0 N0 T3 II Male 77 Sigmoid colon
TCGA-AA-3712-01 13.2138 M0 N2 T3 III Male 65 Descending colon
TCGA-AA-3713-01 12.8525 579 0 M1 N0 T3 IV Male 68 Ascending colon
TCGA-AA-A01P-01 13.7176 1,158 1 M0 N1 T3 III Female 80 Ascending colon
TCGA-AA-A01X-01 12.6789 791 0 M0 N1 T2 III Female 80 Sigmoid colon
TCGA-AA-A01Z-01 13.3704 1,126 0 M0 N0 T3 II Male 68 Ascending colon
TCGA-AA-A02K-01 12.5992 426 1 M1 N2 T4 IV Male 50 Ascending colon
TCGA-AA-A02Y-01 13.3555 1,216 0 M0 N0 T2 I Male 73 Cecum
TCGA-AD-5900-01 13.3362 370 0 MX N0 T2 I Male 67 Ascending colon
TCGA-AD-6548-01 13.4931 650 0 M0 N0 T2 I Female 81 Splenic flexure
TCGA-AD-6888-01 13.8273 472 1 M0 N1b T3 IIIB Male 73 Hepatic flexure
TCGA-AD-6889-01 15.2878 2,532 1 M0 N0 T3 IIA Male 76 Ascending colon
TCGA-AD-6890-01 13.9953 746 0 MX N0 T1 Male 65 Ascending colon
TCGA-AD-6895-01 13.6519 763 0 M0 N1a T3 IIIB Male 84 Cecum
TCGA-AD-6899-01 12.7928 176 1 MX N2b T4a IIIC Male 84 Cecum
TCGA-AD-6901-01 13.1607 682 1 MX N0 T3 Male 78 Cecum
TCGA-AD-6963-01 12.9269 834 0 MX N0 T3 Male 58 Ascending colon
TCGA-AD-6964-01 13.844 331 1 N2b T4a Male 58 Cecum
TCGA-AD-6965-01 13.391 805 0 M0 N2b T4a IIIC Male 62 Cecum
TCGA-AD-A5EJ-01 14.104 MX N0 T3 IIA Female 74 Cecum
TCGA-AD-A5EK-01 12.9109 500 0 MX N0 T2 I Male 51 Ascending colon
TCGA-AM-5820-01 13.1072 14 0 M1 N2 T4a IVA Female 59 Sigmoid colon
TCGA-AM-5821-01 13.9842 28 0 M0 N0 T3 IIA Female 68 Sigmoid colon
TCGA-AU-3779-01 12.9971 M0 N0 T3 IIA Female 80 Rectosigmoid junction
TCGA-AU-6004-01 12.4943 824 0 M0 N0 T2 I Female 69 Cecum
TCGA-AY-5543-01 12.6835 1,004 0 M1 N1a T3 IVA Female 65 Ascending colon
TCGA-AY-6196-01 12.8902 N2b T3 IIIC Male 47 Cecum
TCGA-AY-6197-01 13.1902 652 0 N0 T3 IIA Male 60 Cecum
TCGA-AY-6386-01 13.7194 542 0 M0 N1a T3 IIIB Female 66 Cecum
TCGA-AY-A54L-01 13.4659 525 0 M0 N0 T2 I Female 74 Transverse colon
TCGA-AY-A69D-01 12.8051 543 0 M0 N0 T3 IIA Female 55 Transverse colon
TCGA-AY-A71X-01 13.3791 588 0 M0 N0 T2 I Female 54 Cecum
TCGA-AY-A8YK-01 12.3245 573 0 M1 N2a T3 IVA Male 44 Sigmoid colon
TCGA-AZ-4313-01 14.2427 2,310 0 M0 N0 T1 I Female 51 Descending colon
TCGA-AZ-4315-01 13.733 1,776 0 M0 N0 T3 IIA Male 61 Cecum
TCGA-AZ-4323-01 13.2983 43 1 M1 N2 T4 IV Male 37 Cecum
TCGA-AZ-4614-01 13.5968 172 1 M1 N1 T4a IVA Female 71
TCGA-AZ-4615-01 13.3781 1,002 0 M0 N1 T3 IIIB Male 84
TCGA-AZ-4616-01 14.3653 156 1 M1 N2 T3 IV Female 82 Cecum
TCGA-AZ-4682-01 13.873 680 1 M1 N0 T3 IVA Male 61 Sigmoid colon
TCGA-AZ-4684-01 12.7842 1,977 0 M1 N2 T3 IVA Male 49
TCGA-AZ-5403-01 13.307 1,910 1 MX N0 T3 II Male 43 Sigmoid colon
TCGA-AZ-5407-01 12.756 2,683 0 M0 N0 T1 I Female 51 Cecum
TCGA-AZ-6598-01 13.516 1,503 1 MX N0 T3 II Female 77 [Discrepancy]
TCGA-AZ-6599-01 13.5732 206 1 MX N0 T2 I Male 72 Cecum
TCGA-AZ-6600-01 13.2994 M1 N1 T4 IV Male 64 Hepatic flexure
TCGA-AZ-6601-01 13.0715 3,042 1 M0 N0 T3 II Male 68 Sigmoid colon
TCGA-AZ-6603-01 12.8988 899 1 MX N1 T2 Female 77 Sigmoid colon
TCGA-AZ-6605-01 13.3891 159 1 M0 N1 T4 IIIB Male 77 Ascending colon
TCGA-AZ-6606-01 12.7094 357 1 M1 N2 T4 IV Male 81 Cecum
TCGA-AZ-6607-01 12.8187 97 1 M1 N2 T4 IV Male 69 Sigmoid colon
TCGA-AZ-6608-01 13.6897 59 1 M0 N1 T2 IIIA Female 55 Sigmoid colon
TCGA-CA-5254-01 14.2203 386 0 M0 N0 T3 IIA Female 42 Transverse colon
TCGA-CA-5255-01 13.548 376 0 M0 N0 T3 IIA Male 45 Ascending colon
TCGA-CA-5256-01 13.6084 379 0 M0 N0 T3 IIA Female 54 Hepatic flexure
TCGA-CA-5796-01 12.7443 377 0 M0 N0 T3 IIA Female 52 Ascending colon
TCGA-CA-5797-01 13.4717 383 0 M0 N0 T3 IIA Male 56 Sigmoid colon
TCGA-CA-6715-01 13.6661 383 0 M0 N1 T3 IIIB Male 63 Sigmoid colon
TCGA-CA-6716-01 13.0409 371 0 M0 N0 T3 IIA Male 65 Ascending colon
TCGA-CA-6717-01 12.8855 388 0 M0 N0 T3 IIA Male 57 Ascending colon
TCGA-CA-6718-01 13.3607 306 1 M0 N0 T3 IIA Male 46 Ascending colon
TCGA-CA-6719-01 12.9851 435 0 M0 N0 T3 IIA Male 77 Descending colon
TCGA-CK-4947-01 13.2784 534 0 M0 N1 T4 IIIB Female 46 Sigmoid colon
TCGA-CK-4948-01 13.296 4,502 0 M0 N1 T3 III Female 45 Sigmoid colon
TCGA-CK-4950-01 13.4453 2,599 0 M0 N1 T3 IIIB Female 68 Cecum
TCGA-CK-4951-01 13.3511 2,134 1 M0 N0 T3 IIA Female 79 Ascending colon
TCGA-CK-4952-01 13.4197 475 0 M0 N2 T4 IIIC Female 48 Ascending colon
TCGA-CK-5912-01 13.2997 1,493 1 MX N0 T2 I Male 81 Cecum
TCGA-CK-5913-01 13.4065 1,561 0 MX N0 T3 IIA Female 58 Cecum
TCGA-CK-5914-01 13.1163 304 0 MX N1 T3 IIIB Male 81 Sigmoid colon
TCGA-CK-5915-01 12.3319 MX N0 T2 I Male 63 Sigmoid colon
TCGA-CK-5916-01 13.7034 643 1 M0 N0 T1 I Female 71 Cecum
TCGA-CK-6746-01 14.0824 MX N0 T4b IIB Female 84 Cecum
TCGA-CK-6747-01 13.402 2,523 0 MX N0 T3 IIA Female 87 Cecum
TCGA-CK-6748-01 13.2504 58 0 M1 N1 T3 IV Female 45 Sigmoid colon
TCGA-CK-6751-01 13.8717 3,780 0 MX N0 T2 I Female 88 Ascending colon
TCGA-CM-4743-01 14.6461 701 0 M0 N0 T3 IIA Male 69 Hepatic flexure
TCGA-CM-4744-01 14.4513 609 0 M0 N0 T2 I Male 69 Cecum
TCGA-CM-4747-01 12.6867 761 0 M1a N1b T4a IVA Male 47 Cecum
TCGA-CM-4751-01 12.6197 822 0 M0 N1b T3 IIIB Male 62 Cecum
TCGA-CM-5344-01 13.9646 670 0 M0 N1b T3 IIIB Female 39 Sigmoid colon
TCGA-CM-5348-01 12.6828 699 0 M0 N1a T3 IIIB Male 72 Cecum
TCGA-CM-5349-01 13.4487 915 0 M0 N0 T3 IIA Female 68 Cecum
TCGA-CM-5860-01 13.2636 974 0 M0 N0 T3 IIA Male 44 Ascending colon
TCGA-CM-5861-01 13.9718 457 0 M0 N0 T3 IIA Female 63 Cecum
TCGA-CM-5862-01 13.4638 153 1 M1a N1a T3 IVA Male 80 Ascending colon
TCGA-CM-5863-01 13.1017 457 0 M0 N1b T3 IIIB Female 60 Ascending colon
TCGA-CM-5864-01 13.0053 457 0 M0 N0 T2 I Male 60 Cecum
TCGA-CM-5868-01 13.1335 518 0 M1a N1a T4a IVA Female 59 Sigmoid colon
TCGA-CM-6161-01 13.1885 457 0 M0 N0 T2 I Female 36 Sigmoid colon
TCGA-CM-6162-01 13.1823 365 0 M0 N1a T3 IIIB Female 48 Ascending colon
TCGA-CM-6163-01 12.274 427 0 M0 N0 T1 I Male 74 Sigmoid colon
TCGA-CM-6164-01 13.0871 883 0 M0 N0 T3 IIA Female 46 Sigmoid colon
TCGA-CM-6165-01 12.0513 488 0 M0 N0 T3 IIA Male 74 Sigmoid colon
TCGA-CM-6166-01 13.4988 669 0 M0 N0 T2 I Female 48 Ascending colon
TCGA-CM-6167-01 12.9749 456 0 M0 N2b T3 IIIC Female 57 Cecum
TCGA-CM-6168-01 13.2209 395 0 M0 N0 T3 IIA Female 84 Ascending colon
TCGA-CM-6169-01 12.6992 396 0 M0 N0 T3 IIA Male 67 Cecum
TCGA-CM-6170-01 12.3852 457 0 M0 N0 T2 I Female 73 Descending colon
TCGA-CM-6171-01 14.4106 427 0 M0 N0 T2 I Female 77 Ascending colon
TCGA-CM-6172-01 12.7955 335 0 M0 N1a T3 IIIB Female 70 Sigmoid colon
TCGA-CM-6674-01 13.8921 394 0 M0 N0 T3 IIA Male 39 Hepatic flexure
TCGA-CM-6675-01 13.0063 397 0 M1b N2b T3 IVB Male 35 Cecum
TCGA-CM-6676-01 12.8475 337 0 M0 N0 T2 I Male 82 Sigmoid colon
TCGA-CM-6677-01 12.6611 337 0 M0 N0 T3 IIA Female 75 Hepatic flexure
TCGA-CM-6678-01 13.5735 335 0 M1a N1c T4a IVA Female 63 Sigmoid colon
TCGA-CM-6679-01 13.2632 306 0 M0 N0 T3 IIA Male 58 Sigmoid colon
TCGA-CM-6680-01 12.8609 366 0 M0 N2a T3 IIIB Female 78 Cecum
TCGA-D5-5537-01 13.707 1,381 1 MX N2 T3 IIA Male 83 Ascending colon
TCGA-D5-5538-01 13.5236 1,661 1 M0 N1b T3 IIIB Female 60 Cecum
TCGA-D5-5539-01 13.0102 596 0 M0 N1 T3 IIIA Male 60 Ascending colon
TCGA-D5-5540-01 13.899 1,706 0 M0 N0 T3 IIA Male 73 Cecum
TCGA-D5-5541-01 13.097 1,701 0 M0 N1a T3 IIIB Male 63 Sigmoid colon
TCGA-D5-6529-01 12.8576 614 0 M0 N0 T3 IIA Male 69 [Discrepancy]
TCGA-D5-6530-01 13.5343 621 0 M0 N0 T2 I Male 53 [Discrepancy]
TCGA-D5-6531-01 13.5619 540 0 M0 N0 T3 IIA Male 75 Hepatic flexure
TCGA-D5-6532-01 13.2976 555 0 M0 N0 T3 IIA Male 61 Sigmoid colon
TCGA-D5-6533-01 12.4948 775 0 M0 N0 T4b [Discrepancy] Female 68 Transverse colon
TCGA-D5-6534-01 13.1514 1,316 0 M0 N0 T3 IIA Female 62 Ascending colon
TCGA-D5-6535-01 12.3147 460 0 MX N1 T3 IIIB Female 80 Ascending colon
TCGA-D5-6536-01 13.7486 543 0 M0 N0 T3 IIA Male 73 Sigmoid colon
TCGA-D5-6537-01 13.3376 146 1 MX N1a T3 IIIB Male 64 Transverse colon
TCGA-D5-6538-01 13.2516 521 0 M0 N2 T3 IIIB Female 79 Hepatic flexure
TCGA-D5-6539-01 12.3064 380 0 M0 N0 T3 [Discrepancy] Female 45 Transverse colon
TCGA-D5-6540-01 13.827 491 0 M0 N0 T2 I Male 66 Cecum
TCGA-D5-6541-01 13.2981 474 0 M0 N0 T3 IIA Male 49 Splenic flexure
TCGA-D5-6898-01 12.4218 229 0 M0 N0 T2 I Female 51 Sigmoid colon
TCGA-D5-6920-01 13.3308 377 0 M0 N0 T3 IIA Female 77 Sigmoid colon
TCGA-D5-6922-01 12.3456 308 0 M0 N1 T3 IIIA Male 76 Sigmoid colon
TCGA-D5-6923-01 12.909 378 0 M0 N0 T2 I Male 57 Sigmoid colon
TCGA-D5-6924-01 13.2702 435 0 M0 N0 T3 IIA Male 68 Sigmoid colon
TCGA-D5-6926-01 12.9835 275 0 M0 N1 T4a IIIB Male 65 Sigmoid colon
TCGA-D5-6927-01 13.9284 M0 N0 T3 IIA Male 34 Transverse colon
TCGA-D5-6928-01 13.1599 354 0 M0 N0 T3 IIA Male 80 Ascending colon
TCGA-D5-6929-01 13.5511 408 0 M1 N1 T3 IV Female 49 Sigmoid colon
TCGA-D5-6930-01 13.9947 406 0 M0 N0 T3 IIA Male 67 Ascending colon
TCGA-D5-6931-01 13.1779 365 0 M0 N2 T4b IIIC Male 77 Transverse colon
TCGA-D5-6932-01 13.1223 346 0 M0 N0 T3 IIA Male 69 Transverse colon
TCGA-D5-7000-01 13.1931 312 0 M0 N0 T2 I Female 79 Cecum
TCGA-DM-A0X9-01 13.3966 3,641 0 M0 N0 T3 IIA Female 71 [Discrepancy]
TCGA-DM-A0XD-01 13.9004 743 1 M0 N0 T3 IIA Male 65 [Discrepancy]
TCGA-DM-A0XF-01 13.5163 1,162 1 M0 N2 T3 IIIC Female 68 [Discrepancy]
TCGA-DM-A1D0-01 12.3348 3,974 0 M0 N0 T3 IIA Female 79 Sigmoid colon
TCGA-DM-A1D4-01 12.6627 2,821 1 M0 N0 T3 IIA Male 80 Cecum
TCGA-DM-A1D6-01 12.2639 1,518 1 M0 N0 T3 IIA Male 88 Splenic flexure
TCGA-DM-A1D7-01 13.3092 405 1 M0 N0 T3 IIA Male 82 Sigmoid colon
TCGA-DM-A1D8-01 12.7949 383 1 N1 T3 Female 50 Ascending colon
TCGA-DM-A1D9-01 12.5488 4,270 0 M0 N0 T3 IIA Female 67 Cecum
TCGA-DM-A1DA-01 13.3777 228 1 M0 N2 T3 IIIC Female 71 Cecum
TCGA-DM-A1DB-01 13.8398 1,348 1 M0 N0 T3 IIA Male 68 Sigmoid colon
TCGA-DM-A1HA-01 12.4432 4,000 0 M0 N2 T3 IIIC Male 82 Ascending colon
TCGA-DM-A1HB-01 14.6197 4,126 0 M0 N1 T3 IIIB Male 75 Transverse colon
TCGA-DM-A280-01 14.2422 236 1 M0 N0 T3 IIA Female 70 Ascending colon
TCGA-DM-A282-01 13.9437 4,233 0 M0 N0 T3 IIA Female 60 Hepatic flexure
TCGA-DM-A285-01 13.4791 179 1 M1 N2 T3 IV Female 71 Ascending colon
TCGA-DM-A288-01 13.5002 427 1 M0 N2 T3 IIIC Male 68 Cecum
TCGA-DM-A28A-01 13.7039 805 1 M0 N2 T3 IIIC Male 78 Cecum
TCGA-DM-A28C-01 12.6539 2,475 1 M0 N0 T3 IIA Male 74 Sigmoid colon
TCGA-DM-A28E-01 13.4291 3,648 0 M0 N0 T3 IIA Female 72 Sigmoid colon
TCGA-DM-A28F-01 13.009 1,094 1 M0 N1 T3 IIIB Male 73 Sigmoid colon
TCGA-DM-A28G-01 13.1773 1,849 1 M0 N0 T3 IIA Male 75 Ascending colon
TCGA-DM-A28H-01 13.1818 3,561 0 M0 N2 T3 IIIC Male 50 Cecum
TCGA-DM-A28K-01 13.9535 2,988 0 M0 N0 T3 IIA Male 75 Hepatic flexure
TCGA-DM-A28M-01 12.7494 2,895 0 M0 N0 T3 IIA Male 63 Descending colon
TCGA-F4-6459-01 12.7603 262 1 M0 N2a T3 IIIB Female 61 Sigmoid colon
TCGA-F4-6460-01 12.8791 972 1 M0 N1 T3 IIIB Female 51 Sigmoid colon
TCGA-F4-6461-01 13.4939 338 1 M0 N2 T4b IIIC Female 41 Hepatic flexure
TCGA-F4-6463-01 13.5646 1,087 0 M0 N0 T3 IIA Male 51 Transverse colon
TCGA-F4-6569-01 13.2891 1,087 0 M0 N0 T2 I Male 60 Transverse colon
TCGA-F4-6570-01 13.4011 188 1 M0 N0 T3 IIA Female 78 Transverse colon
TCGA-F4-6703-01 13.3259 1,456 0 M0 N0 T3 IIA Male 64 Ascending colon
TCGA-F4-6704-01 13.5814 47 0 MX N2b T3 IIIC Male 60 Sigmoid colon
TCGA-F4-6805-01 13.2868 1,047 0 M0 N0 T3 IIA Female 58 Descending colon
TCGA-F4-6806-01 13.355 1,260 0 M0 N0 T2 I Female 59 Sigmoid colon
TCGA-F4-6807-01 12.5661 1,309 0 M0 N2b T3 IIIC Female 51 Hepatic flexure
TCGA-F4-6808-01 13.6601 1,024 0 M0 N0 T1 I Female 54 Sigmoid colon
TCGA-F4-6809-01 12.8493 403 1 M1 N1 T3 IVA Female 52 Sigmoid colon
TCGA-F4-6854-01 12.4674 16 0 M0 N0 T3 IIA Female 77 Sigmoid colon
TCGA-F4-6855-01 13.0115 1,442 0 M0 N0 T3 IIA Female 70 Sigmoid colon
TCGA-F4-6856-01 13.9564 1,074 0 M0 N0 T2 I Male 45 Cecum
TCGA-F4-6857-01 13.0872
TCGA-G4-6293-01 13.4778 4,051 0 M0 N1 T3 III Female 49 Transverse colon
TCGA-G4-6294-01 13.2546 858 1 M1 N1 T3 IV Male 75 Cecum
TCGA-G4-6295-01 12.6653 254 0 M0 N0 T3 II Female 70 Cecum
TCGA-G4-6297-01 13.6856 2,506 0 M1 N2 T3 IV Female 55 Cecum
TCGA-G4-6298-01 13.3551 715 1 MX N1 T4a IIIB Male 90 Cecum
TCGA-G4-6299-01 13.2354 2,268 0 M0 N2 T3 IIIC Male 69 Descending colon
TCGA-G4-6302-01 13.2234 2,047 1 M0 N0 T3 IIA Female 90 Cecum
TCGA-G4-6303-01 12.5696 2,003 1 M1 N1 T3 IV Female 54 Sigmoid colon
TCGA-G4-6304-01 14.0855 1,631 0 M0 N0 T4 IIB Female 66 Transverse colon
TCGA-G4-6306-01 13.5552 1,359 0 M0 N0 T2 [Discrepancy] Male 71 Ascending colon
TCGA-G4-6307-01 12.7383 1,674 0 M0 N1 T3 IIIB Female 37 Sigmoid colon
TCGA-G4-6309-01 14.0657 2,600 0 M0 N1 T3 IIIB Female 40 Sigmoid colon
TCGA-G4-6310-01 13.0093 1,935 0 M0 N1 T3 IIIB Male 69 Cecum
TCGA-G4-6311-01 12.8804 1,199 0 MX N1 T3 III Male 80 Ascending colon
TCGA-G4-6314-01 13.0451 1,093 0 M1 N2 T3 IV Female 76 Cecum
TCGA-G4-6315-01 13.0198 1,883 0 M1 N1 T3 IV Male 66 Descending colon
TCGA-G4-6317-01 12.7918 1,095 0 MX N2 T3 IIIC Female 51 Sigmoid colon
TCGA-G4-6320-01 13.278 804 0 MX N1 T3 III Male 73 Hepatic flexure
TCGA-G4-6321-01 12.88 672 0 MX N1 T2 III Female 60 Cecum
TCGA-G4-6322-01 14.2467 792 0 MX N1 T3 IIIB Male 65 Descending colon
TCGA-G4-6323-01 13.1754 419 0 MX N0 Tis IA Male 50 Cecum
TCGA-G4-6586-01 13.683 1,089 0 M0 N0 T3 IIA Female 73 Ascending colon
TCGA-G4-6588-01 13.4753 796 0 M0 N0 T3 IIA Female 58 Cecum
TCGA-G4-6625-01 12.8892 2,792 0 M0 N0 T3 IIA Female 77 Sigmoid colon
TCGA-G4-6626-01 12.547 1,422 1 M0 N0 T3 IIA Male 90 Ascending colon
TCGA-G4-6627-01 12.8671 2,275 0 M0 N0 T3 IIA Male 84 Ascending colon
TCGA-G4-6628-01 13.7375 2,424 0 M0 N0 T2 I Male 78 Cecum
TCGA-NH-A50T-01 13.6842 553 0 MX N0 T3 IIA Female 68 Splenic flexure
TCGA-NH-A50U-01 12.8574 334 1 M1a N0 T4a IVA Male 42 Cecum
TCGA-NH-A50V-01 12.4816 588 0 M0 N2a T3 IIIB Male 69 Cecum
TCGA-NH-A5IV-01 13.1119 588 0 MX N0 T3 IIA Female 90 Transverse colon
TCGA-NH-A6GA-01 12.697 302 1 MX N2a T4a IIIC Male 58 Ascending colon
TCGA-NH-A6GB-01 13.4996 476 0 MX N2b T3 IIIC Female 71 Transverse colon
TCGA-NH-A6GC-01 12.5818 389 0 M1b N1b T4b IVB Female 66 Descending colon
TCGA-NH-A8F7-01 12.7693 543 0 MX N0 T3 IIA Female 53 Sigmoid colon
TCGA-NH-A8F8-01 13.432 511 1 M1 N2b T4a IV Male 79 Ascending colon
TCGA-QG-A5YV-01 13.4551 1,301 0 MX N1a T4b IIIC Female 64 Sigmoid colon
TCGA-QG-A5YW-01 13.0881 896 0 MX N2b T3 IIIC Female 55 Cecum
TCGA-QG-A5YX-01 13.1771 1,003 0 MX N0 T3 IIA Female 61 Sigmoid colon
TCGA-QG-A5Z1-01 12.6054 256 1 MX N1b T3 IIIB Male 71 Sigmoid colon
TCGA-QG-A5Z2-01 13.0875 952 0 M0 N0 T2 I Male 61 Cecum
TCGA-QL-A97D-01 12.3149 666 0 MX N0 T2 I Female 84 Cecum
TCGA-RU-A8FL-01 12.7671 1,177 0 MX N2a T3 IIIB Male 51 Cecum
TCGA-SS-A7HO-01 13.7814 1,829 0 M0 N0 T4a IIB Female 44 Cecum
TCGA-T9-A92H-01 12.5539 362 0 M0 N0 T3 IIA Male 82 Sigmoid colon
TCGA-WS-AB45-01 13.4247 2,130 0 MX N0 T3 IIA Female 52 Cecum

Table S3

The potential CypB related biological processes and signaling pathways generated by the Search Tool for the Retrieval of Interacting Genes (STRING)

#term ID Term description False discovery rate Matching proteins in your network
hsa04514 Cell adhesion molecules (CAMs) 0.00072 CDH1, CDH3, CLDN1, CLDN2, CLDN4
hsa04530 Tight junction 0.00085 CLDN1, CLDN2, CLDN4, MYH11, MYL9
hsa04270 Vascular smooth muscle contraction 0.0019 ACTG2, MYH11, MYL9, PPP1R14A
hsa04670 Leukocyte transendothelial migration 0.0019 CLDN1, CLDN2, CLDN4, MYL9
hsa00480 Glutathione metabolism 0.002 GPX2, GPX3, RRM2
hsa05130 Pathogenic Escherichia coli infection 0.002 CDH1, CLDN1, KRT18
hsa04657 IL-17 signaling pathway 0.0079 CCL20, LCN2, MMP1
hsa05160 Hepatitis C 0.0185 CLDN1, CLDN2, CLDN4
hsa05219 Bladder cancer 0.0209 CDH1, MMP1
hsa00590 Arachidonic acid metabolism 0.0396 GPX2, GPX3
HSA-446728 Cell junction organization 8.90E-06 CDH1, CDH3, CLDN1, CLDN2, CLDN4, LIMS2
HSA-421270 Cell-cell junction organization 2.73E-05 CDH1, CDH3, CLDN1, CLDN2, CLDN4
HSA-445355 Smooth muscle contraction 3.79E-05 ACTG2, LMOD1, MYH11, MYL9
HSA-420029 Tight junction interactions 0.0014 CLDN1, CLDN2, CLDN4
HSA-397014 Muscle contraction 0.0018 ACTG2, DES, LMOD1, MYH11, MYL9
HSA-5625740 RHO GTPases activate PKNs 0.0079 MYH11, MYL9, PPP1R14A
HSA-416572 Sema4D induced cell migration and growth-cone collapse 0.0162 MYH11, MYL9
HSA-5625900 RHO GTPases activate CIT 0.0162 MYH11, MYL9
HSA-5627117 RHO GTPases activate ROCKs 0.0162 MYH11, MYL9
HSA-5627123 RHO GTPases activate PAKs 0.0162 MYH11, MYL9
HSA-2022854 Keratan sulfate biosynthesis 0.0191 B3GNT3, PRELP
HSA-3928663 EPHA-mediated growth cone collapse 0.0191 MYH11, MYL9
HSA-1592389 Activation of matrix metalloproteinases 0.0227 MMP1, MMP7
HSA-195258 RHO GTPase effectors 0.0227 CDH1, MYH11, MYL9, PPP1R14A
HSA-3299685 Detoxification of reactive oxygen species 0.0227 GPX2, GPX3
HSA-418990 Adherens junctions interactions 0.0227 CDH1, CDH3
HSA-202733 Cell surface interactions at the vascular wall 0.0231 CEACAM6, EPCAM, MMP1
HSA-1474228 Degradation of the extracellular matrix 0.0239 CDH1, MMP1, MMP7
HSA-1474244 Extracellular matrix organization 0.026 CDH1, CEACAM6, MMP1, MMP7
HSA-2142753 Arachidonic acid metabolism 0.0465 DPEP1, GPX2

Acknowledgments

Funding: This research was supported by the National Natural Science Foundation of China (No. 81802349).


Footnote

Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at http://dx.doi.org/10.21037/tcr-19-2960). 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 under the approval of the Institutional Ethics Committee, Beijing Chao-Yang Hospital of Capital Medical University (No. 2018-Research-61). Written informed consent was obtained from the patient for publication of this study and any accompanying images. The study outcomes will not affect the future management of the patients.

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/.


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Cite this article as: Zhang X, Tan J, Yang L, An G. Cyclophilin B overexpression predicts a poor prognosis and activates metastatic pathways in colon cancer. Transl Cancer Res 2020;9(5):3573-3585. doi: 10.21037/tcr-19-2960

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