Integrating biomarkers in colorectal cancer trials in the West and China. Nat Rev Clin Oncol. 2015;12:553-560. [PMID: 25963094 DOI: 10.1038/nrclinonc.2015.88]

Integration of machine learning for developing a prognostic signature related to programmed cell death in colorectal cancer

BACKGROUND

Colorectal cancer (CRC) presents a significant global health burden, characterized by a heterogeneous molecular landscape and various genetic and epigenetic alterations. Programmed cell death (PCD) plays a critical role in CRC, offering potential targets for therapy by regulating cell elimination processes that can suppress tumor growth or trigger cancer cell resistance. Understanding the complex interplay between PCD mechanisms and CRC pathogenesis is crucial. This study aims to construct a PCD-related prognostic signature in CRC using machine learning integration, enhancing the precision of CRC prognosis prediction.

METHOD

We retrieved expression data and clinical information from the Cancer Genome Atlas and Gene Expression Omnibus (GEO) datasets. Fifteen forms of PCD were identified, and corresponding gene sets were compiled. Machine learning algorithms, including Lasso, Ridge, Enet, StepCox, survivalSVM, CoxBoost, SuperPC, plsRcox, random survival forest (RSF), and gradient boosting machine, were integrated for model construction. The models were validated using six GEO datasets, and the programmed cell death score (PCDS) was established. Further, the model's effectiveness was compared with 109 transcriptome-based CRC prognostic models.

RESULT

Our integrated model successfully identified differentially expressed PCD-related genes and stratified CRC samples into four subtypes with distinct prognostic implications. The optimal combination of machine learning models, RSF + Ridge, showed superior performance compared with traditional methods. The PCDS effectively stratified patients into high-risk and low-risk groups, with significant survival differences. Further analysis revealed the prognostic relevance of immune cell types and pathways associated with CRC subtypes. The model also identified hub genes and drug sensitivities relevant to CRC prognosis.

CONCLUSION

The current study highlights the potential of integrating machine learning models to enhance the prediction of CRC prognosis. The developed prognostic signature, which is related to PCD, holds promise for personalized and effective therapeutic interventions in CRC.

Hsa_circ_0020134 promotes liver metastasis of colorectal cancer through the miR-183-5p-PFN2-TGF-β/Smad axis

Circular RNAs (circRNAs) are a distinct class of non-coding RNAs that play regulatory roles in the initiation and progression of tumors. With advancements in transcriptome sequencing technology, numerous circRNAs that play significant roles in tumor-related genes have been identified. In this study, we used transcriptome sequencing to analyze the expression levels of circRNAs in normal adjacent tissues, primary colorectal cancer (CRC) tissues, and CRC tissues with liver metastasis. We successfully identified the circRNA hsa_circ_0020134 (circ0020134), which exhibited significantly elevated expression specifically in CRC with liver metastasis. Importantly, high levels of circ0020134 were associated with a poor prognosis among patients. Functional experiments demonstrated that circ0020134 promotes the proliferation and metastasis of CRC cells both in vitro and in vivo. Mechanistically, upregulation of circ0020134 was induced by the transcription factor, PAX5, while miR-183-5p acted as a sponge for circ0020134, leading to partial upregulation of PFN2 mRNA and protein levels, thereby further activating the downstream TGF-β/Smad pathway. Additionally, downregulation of circ0020134 inhibited epithelial-mesenchymal transition (EMT) in CRC cells, which could be reversed by miR-183-5p inhibitor treatment. Collectively, our findings confirm that the circ0020134-miR-183-5p-PFN2-TGF-β/Smad axis induces EMT transformation within tumor cells, promoting CRC proliferation and metastasis, thus highlighting its potential as a therapeutic target for patients with CRC liver metastasis.

Circulating cell-free circRNA panel predicted tumorigenesis and development of colorectal cancer

Background

Colorectal cancer (CRC) is reported with high morbidity and mortality. Currently, the sensitivity of diagnostic markers for colorectal cancer is low. Therefore, further exploration of new plasma diagnostic markers for early detection of colorectal cancer is of great value. We aimed to explore potential circRNAs in plasma as biomarkers for early diagnosis of CRC.

Methods

We employed the circRNA microarray to investigate dysregulated circRNAs in plasma samples of CRC patients, colorectal adenoma patients (CRA), and healthy controls. Through in‐depth analysis, significantly differentially expressed circRNAs were screened as candidate targets.

Results

Eight circRNAs (hsa_circ_104885, hsa_circ_100185, hsa_circ_103171, hsa_circ_001978, hsa_circ_105039, hsa_circ_103627, hsa_circ_101717, and hsa_circ_104192) were obtained as candidate circRNAs with upregulation in CRC comparing with both CRA and healthy control. Through detecting the plasma expression levels of eight candidate targets, we identified three circRNA (hsa_circ_001978, hsa_circ_105039, and hsa_circ_103627) with increased level which were consistent with the microarray results in training set. Further validation found the circRNA panel was consistent with training set. The ROC curve also revealed a high diagnostic ability of hsa_circ_001978, hsa_circ_105039, and hsa_circ_103627 in predicted the CRC from CRA patients (AUC = 0.966) as well as healthy controls (AUC = 0.969).

Conclusion

Our data suggest that hsa_circ_001978, hsa_circ_105039, and hsa_circ_103627 might be a CRC‐specific biomarker for early diagnosis.

Role of exosomal long non-coding RNAs in colorectal cancer

Exosomes are a class of small extracellular vesicles, 30-150 nm in diameter, that transfer biological information (e.g., DNA, RNA, and protein) via cell-to-cell communication. Exosomes play critical roles in the occurrence and development of human cancers, including colorectal cancer (CRC). Recent studies have shown that long non-coding RNAs (lncRNAs) can be encapsulated in exosomes, which transfer lncRNAs from secretory cells into recipient cells. This process affects the progression of CRC, since exosomal lncRNAs display special and extensive functions in CRC tumorigenesis, including malignant proliferation, metastasis, chemoresistance, and inflammatory response. Moreover, due to their specificity and sensitivity, exosomal lncRNAs are released into body fluids (e.g., urine, sputum, and plasma), which have the potential to be biomarkers of CRC tumorigenesis within screening efforts and medical and epidemiologic research. In this review, we aim to clarify the function and mechanism of exosomal lncRNAs in CRC tumorigenesis and provide a strategy for early diagnosis and medical treatment of this malignancy.

Disheveled-associated activator of morphogenesis 2 promotes invasion of colorectal cancer by activating PAK1 and promoting MMP7 expression

BACKGROUND

Disheveled-associated activator of morphogenesis (DAAM) family, including DAAM1 and DAAM2, is key regulators in Wnt signaling pathway. Although the oncogenic role of Wnt signaling pathway in colorectal cancer (CRC) was investigated in several lines, the expression and function of DAAM in CRC are still obscure.

OBJECTIVE

To investigate the expression and function of DAAM in CRC.

METHODS

DAAM1 and DAAM2 expression in high grade dysplasia (HGD), CRCs and corresponding adjacent tissues were detected with qRT-PCR and immunohistochemistry (IHC). The prognostic significance of DAAM1/2 were estimated with univariate and multivariate analyses. Moreover, the correlations between clinicopathological factors and DAAM were evaluated with the χ² test. With experiments in vitro, we investigated the function of DAAM2 in CRC cell proliferation and invasion, and investigated the underlying mechanism of how DAAM2 facilitated CRC invasion.

RESULTS

DAAM2, instead of DAAM1, was substantially up-regulated in CRCs compared with paired adjacent normal tissues and HGDs. The ratio of high DAAM1 and DAAM2 expression accounted for 44.83% and 46.31%, respectively. High DAAM2, instead of DAAM1, was a risk factor indicating an unfavorable prognosis of CRC. In multivariate analysis, high DAAM2 was identified as an independent prognostic biomarker of CRC predicting poor prognosis. With experiments in vitro, DAAM2 promoted invasion of CRC cells via activating PAK1 and promoting the expression of MMP7, suggesting an essential role of DAAM2 in CRC invasion.

CONCLUSIONS

High expression of DAAM2, instead of DAAM1, indicated an unfavorable prognosis of CRC independently, which suggested that detecting DAAM2 can help define the high-risk patients. DAAM2 activated PAK1 and promoted MMP7 expression and facilitated the invasion of CRC cells, indicating that DAAM2 may be a potential drug target of CRC.

Circ_ 0115744 acts as miR-144 sponge to promote and predict the metastasis of colorectal cancer

Colorectal cancer (CRC) is one of the most common human malignant tumors in recent years. Although multiple approaches have been developed for the diagnosis and therapy of CRC, the overall survival rates of patients with metastatic and recurrent CRC remain poor. In the present study, we used the high-throughput microarray technology to screen circular RNAs (circRNAs) as a potential fingerprint for CRC. We mainly aimed to screen potential biomarkers for liver metastasis by performing risk score analysis. We detected the upregulated expression of circ_0115744 in patients with CRC with liver metastasis (CRLM). Further investigation using a validation set indicated that circ_0115744 might be considered as a fingerprint for CRLM. Functionally, the overexpression of circ_0115744 significantly promoted the invasion of CRC cell lines, while decreased expression of circ_0115744 suppressed cell invasion in vitro. Mechanistic analysis showed that circ_0115744 acted as a competing endogenous RNA of miR-144 to diminish the repressive effect of miR-144 on its target EZH2. In conclusion, we found that increased expression of circ_0115744 could differentiate CRLM from CRC and that the newly identified circ_0115744/miR-144/EZH2 axis was involved in the progression of CRC, which might be used as a potential diagnostic and therapeutic target for patients with CRC.

The prognostic value of p53 positive in colorectal cancer: A retrospective cohort study

This retrospective cohort study aimed to discuss the prognostic value of p53 positive in colorectal cancer. A total of 124 consecutive patients diagnosed with colorectal cancer were evaluated at the National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College from 1 January 2009 to 31 December 2010. The expression of p53 in colorectal cancer was examined by immunohistochemistry. Based on the expression levels of p53, the 124 patients were divided into a p53 positive group and a p53 negative group. In this study, 72 patients were in the p53 positive group and 52 in the p53 negative group. The two groups were well balanced in gender, age, body mass index, American Society of Anesthesiologists scores, and number of lymph nodes harvested. p53 positive was associated with carcinoembryonic antigen ≥5 ng/mL ( p = 0.036), gross type ( p = 0.037), degree of tumor differentiation ( p = 0.026), pathological tumor stage ( p = 0.019), pathological node stage ( p = 0.004), pathological tumor–node–metastasis stage ( p = 0.017), nerve invasion ( p = 0.008), and vessel invasion ( p = 0.018). Tumor site, tumor size, and pathological pattern were not significantly different between these two groups. Disease-free survival and overall survival in the p53 positive group were significantly shorter than the p53 negative group ( p = 0.021 and 0.025, respectively). Colorectal cancer patients with p53 positive tended to be related to a higher degree of malignancy, advanced tumor–node–metastasis stage, and shorter disease-free survival and overall survival. p53 positive was independently an unfavorable prognostic marker for colorectal cancer patients.

Novel therapeutics in metastatic colorectal cancer: molecular insights and pharmacogenomic implications

Although the survival of metastatic colorectal cancer (mCRC) patients has improved five-fold over the last century, CRC remains a significant global health burden. Impressive strides have been made in identifying new regimens, employing maintenance strategies to limit treatment toxicities, and combining multidisciplinary approaches to achieve cure in oligometastatic disease. Attempts at personalized integration of targeted agents have been limited by the ability to identify molecularly enriched patient populations most likely to benefit. In this review, we discuss novel therapeutics and regimens recently approved and in development for mCRC. In addition, we discuss using older agents in novel combination and maintenance strategies, and highlight evidence for implementing pharmacogenomic data and non-invasive monitoring into the personalized management of mCRC patients.

Activation of focal adhesion kinase through an interaction with β4 integrin contributes to tumorigenicity of colon cancer

High expression of either β4 integrin or focal adhesion kinase (FAK) has been reported in human colon cancer. However, it remains unclear how β4 integrin together with FAK contributes to the tumorigenicity of colon cancer. Here, we demonstrate that the co-overexpression of β4 integrin and FAK positively correlates with advanced stages of human colon cancer. Activated β4 integrin interacts with FAK and subsequently induces FAK phosphorylation at Tyr397. Furthermore, ablation of the β4 integrin/FAK complex and/or FAK activation impair colon cancer cell proliferation, anchorage-independent growth, and tumorigenicity. Our data indicate that the β4 integrin/FAK complex and subsequent FAK activation are essential regulators during the tumorigenicity of colon cancer, and we suggest an alternative strategy for colon cancer therapy.

EZH2 Expression and its Correlation with Clinicopathological Features in Patients with Colorectal Carcinoma

Objective

To explore the correlation between the enhancer of zeste homolog 2 (EZH2) expression and clinicopathological features in colorectal cancer patients.

Methods

A total of sixty-six patients with colorectal carcinoma were admitted to our general surgery department from January 2011 to December 2014. The EZH2 expression levels in the cancer tissues (CTs) from the 66 patients with colorectal cancer and those in distant normal colorectal tissues from 30 cases were examined through immunohistochemistry and western blotting assays. The relationship between the expression of EZH2 and the clinicopathological features and prognosis of the patients was analyzed.

Results

EZH2 in colorectal carcinoma tissues is granularly brown, predominantly expressed and diffused in the nuclei of tumor cells. Positive rates of EZH2 in intestinal CTs and in distant normal intestinal tissues are 62.12% (41/66) and 6.67% (2/30), respectively with significant difference (P < 0.05). Western blotting also confirmed its elevated expression in colorectal CTs. EZH2-positive expression in CTs was related to degree of differentiation, Duke staging, and tumor size (P < 0.05) but was unrelated to the patient’s gender, age or tumor site (P = 0.05). The 3-year progression-free survival (PFS) rates of the EZH2-positive group and the EZH2-negative group were 43.8% and 67.5%, respectively. The risk of disease progression of the EZH2-positive patients in the follow-up period was significantly higher than that of the EZH2-negative patients (HR = 2.49, 95% CI = 1.04–4.80, P < 0.05).

Conclusion

EZH2 is closely related to colorectal carcinoma development and disease progression, and thus could be used as a tumor biomarker that may indicate prognosis.