A prognostic classifier for patients with colorectal cancer liver metastasis, based on AURKA, PTGS2 and MMP9

Identifying Key Genes Involved in Axillary Lymph Node Metastasis in Breast Cancer Using Advanced RNA-Seq Analysis: A Methodological Approach with GLMQL and MAS

Our study aims to address the methodological challenges frequently encountered in RNA-Seq data analysis within cancer studies. Specifically, it enhances the identification of key genes involved in axillary lymph node metastasis (ALNM) in breast cancer. We employ Generalized Linear Models with Quasi-Likelihood (GLMQLs) to manage the inherently discrete and overdispersed nature of RNA-Seq data, marking a significant improvement over conventional methods such as the t-test, which assumes a normal distribution and equal variances across samples. We utilize the Trimmed Mean of M-values (TMMs) method for normalization to address library-specific compositional differences effectively. Our study focuses on a distinct cohort of 104 untreated patients from the TCGA Breast Invasive Carcinoma (BRCA) dataset to maintain an untainted genetic profile, thereby providing more accurate insights into the genetic underpinnings of lymph node metastasis. This strategic selection paves the way for developing early intervention strategies and targeted therapies. Our analysis is exclusively dedicated to protein-coding genes, enriched by the Magnitude Altitude Scoring (MAS) system, which rigorously identifies key genes that could serve as predictors in developing an ALNM predictive model. Our novel approach has pinpointed several genes significantly linked to ALNM in breast cancer, offering vital insights into the molecular dynamics of cancer development and metastasis. These genes, including ERBB2, CCNA1, FOXC2, LEFTY2, VTN, ACKR3, and PTGS2, are involved in key processes like apoptosis, epithelial-mesenchymal transition, angiogenesis, response to hypoxia, and KRAS signaling pathways, which are crucial for tumor virulence and the spread of metastases. Moreover, the approach has also emphasized the importance of the small proline-rich protein family (SPRR), including SPRR2B, SPRR2E, and SPRR2D, recognized for their significant involvement in cancer-related pathways and their potential as therapeutic targets. Important transcripts such as H3C10, H1-2, PADI4, and others have been highlighted as critical in modulating the chromatin structure and gene expression, fundamental for the progression and spread of cancer.

Tumor microenvironment derived signature predicting relapse-free survival in I-III cancer and preliminary experiment verification

The recurrence in colon cancer contributed to great difficulties in diagnostic and therapeutic treatment. Tumor microenvironment (TME) gains increasing attention recently. After univariate Cox analysis on relapse-free survival (RFS) and ESTIMATE analysis, WGCNA was further conducted to determine the TME and relapse-related genes in I-III colon cancer. Functional enrichment analyses were conducted. Furthermore, seven genes were screened to build a prognostic signature via LASSO and multivariate Cox analysis. Univariate followed multivariate Cox analysis all showed that the risk group calculated by the signature as a significant predictors. The ROC curves showed great prognostic in the internal training group, internal verification group, and independent external verification group. In the training group, the AUC at 1, 3, and 5 years was 0.737, 0.79, and 0.756. In addition, correlation analysis presented that the signature and genes involved in were significantly associated with the TME. Moreover, 3 of 7 genes (FAM78A, SGIP1, and MMP9) were validated to be associated with PDL1 through qRT-PCR.

Selecting the number of categories of the lymph node ratio in cancer research: A bootstrap-based hypothesis test

The high impact of the lymph node ratio as a prognostic factor is widely established in colorectal cancer, and is being used as a categorized predictor variable in several studies. However, the cut-off points as well as the number of categories considered differ considerably in the literature. Motivated by the need to obtain the best categorization of the lymph node ratio as a predictor of mortality in colorectal cancer patients, we propose a method to select the best number of categories for a continuous variable in a logistic regression framework. Thus, to this end, we propose a bootstrap-based hypothesis test, together with a new estimation algorithm for the optimal location of the cut-off points called BackAddFor, which is an updated version of the previously proposed AddFor algorithm. The performance of the hypothesis test was evaluated by means of a simulation study, under different scenarios, yielding type I errors close to the nominal errors and good power values whenever a meaningful difference in terms of prediction ability existed. Finally, the methodology proposed was applied to the CCR-CARESS study where the lymph node ratio was included as a predictor of five-year mortality, resulting in the selection of three categories.

Cinobufagin Triggers Defects in Spindle Formation and Cap-Dependent Translation in Liver Cancer Cells by Inhibiting the AURKA-mTOR-eIF4E Axis

Cinobufagin is a Na+/K+-ATPase (NKA) inhibitor with excellent anticancer effects to prolong the survival of patients. The purpose of the present study was to clarify the underlying mechanism of the anticancer effects of cinobufagin using overexpression or inhibition of aurora kinase A (AURKA) signaling. First, high expression of Na+/K+-ATPase alpha 1 subunit (ATP1A1) and AURAK resulted in increased malignant transformation in hepatocellular carcinoma (HCC) patients using the cancer genome atlas (TCGA) data and tissue samples. After treatment with cinobufagin, we successfully screened 202, 249, and 335 changing expression proteins in Huh-7 cells under normal, overexpression, and inhibition of AURKA using tandem mass tags (TMT)-labeled quantitative proteomics coupled to 2D liquid chromatography-tandem mass spectrometry (LC-MS/MS). Bioinformatics analysis revealed that these molecules were closely associated with chromosome segregation, DNA damage, and regulation of translation processes. We further confirmed that cinobufagin induced DNA damage and chromosome segregation disorders and suppresses translational processing in oncogenes by decreasing the expression of AURKA, mechanistic target of rapamycin kinase (mTOR), p-mTOR, p-extracellular regulated protein kinases (ERK), eukaryotic translation initiation factor 4E (eIF4E), and p-eIF4E, while increasing the expression of p-eukaryotic translation initiation factor 4E binding protein 1 (4E-BP1) (S65, T37, T46, T45) and increasing the interaction between eIF4 and 4E-BP1. Our results suggested that cinobufagin performed an antitumor effects in liver cancer cells by inhibiting the AURKA-mTOR-eIF4E axis.

Comprehensive analysis reveals a four-gene signature in colorectal cancer

BACKGROUND

Colorectal cancer (CRC) is one of the major malignant diseases of the gastrointestinal system around the world. However, the current therapeutic regimens were not always effective. This study was designed to identify and depict potential molecular biomarkers and correlated signal pathways in CRC.

METHODS

The gene expression profiles of GSE21510 were obtained on the Gene Expression Omnibus website, we filtered out 44 samples from the GSE21510 to identify different expression genes (DEGs) between CRC tissues and noncancerous tissues. Subsequently, the function and signal pathways enrichment analyses were implemented, the protein-protein interaction (PPI) networks of DEGs were to be carried out, and the hub genes were screened by MCODE built in Cytoscape software. Lastly, we have validated gene expressions and overall survival analyses of these hub genes in related datasets, such as colon adenocarcinoma (COAD) and rectum adenocarcinoma (READ), built in TCGA/GTEx database.

RESULTS

Results showed that a totally of 166 up-regulated genes and 260 down-regulated genes were identified and met the following criteria: |log2 fold change| ≥2 & adjusted P value <0.01. Here, we identified AURKA, BUB1, DLGAP5 and HMMR, which were associated with the regulation of mitotic cycle phase transition and oocyte meiosis pathways.

CONCLUSIONS

The findings of these four genes in this study may shed light on the mechanisms of these four genes as drug-sensitive therapeutic targets for the patients of CRC.

Protective effect of Shaoyao Decoction against colorectal cancer via the Keap1-Nrf2-ARE signaling pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Ulcerative colitis is one of the three high risk factors for colorectal cancer. Studies have found that about 20% of cancers are caused by repeated chronic inflammatory stimuli over a long period of time. Ulcer-related colorectal cancer is one of the main causes of death in patients with ulcerative colitis. At present, surgery is the first choice for the treatment of colorectal cancer, combined with radiotherapy and chemotherapy, which have serious side effects. However, reportedly, a compound prescription of Chinese traditional medicine Shaoyao Decoction (SYD) commonly used to treat damp-heat dysentery has anti-colorectal cancer effect. Thus this study described the effect of SYD to AOM/DSS-induced colon cancer model.

AIM OF THE STUDY

In this study, modern biomedical approaches were employed for investigating the protective/preventive effects of SYD in mice with azoxymethane (AOM)/DSS-induced CRC.

MATERIALS AND METHODS

The mice pretreated with AOM/DSS were randomly allocated to SYDL, SYDM, SYDH group and SASP (sulfasalazine) group. Mice without AOM/DSS treatment were randomly divided into PBS control group and SYD control group.

RESULTS

It was found that SYD inhibited the production of inflammatory cytokines, TNF-α, IL-1β, superoxide dismutase (SOD), and malonaldehyde (MDA), and increased the antioxidant indices, as measured by the mRNA expression of GR, TR, HO-1, γ-GCSc, γ-GCSm, NQO-1, UGT1A1, and UGT1A10 in AOM-treated mice. Particularly, the expressions rates of NF-κB and Ki-67 in the SYD-treated experimental groups were significantly lower than those in the model group, indicating that the proliferative ability of the CRC tissues was weaker in the SYD-treated experimental groups. Moreover, the positive levels of Nrf2 in the SYD-treated experimental groups were slightly higher than those in the model group, suggesting that SYD exhibited antioxidant activity.

CONCLUSIONS

To sum up, our results suggest that SYD inhibits the development of acute/chronic colitis and prevents colitis-associated CRC by suppressing inflammation and preventing oxidative stress-induced cellular damage.

Systematic Review of the Prognostic Role of the Immune System After Surgery of Colorectal Liver Metastases

Background: The current prognostication of patient survival after surgery for colorectal liver metastases is based on clinical characteristics, but low accuracy makes it difficult to guide treatment for the individual patient. Rapidly evolving technologies have led to the expectation that biomarkers will be able to outperform the current clinical scoring systems and provide more effective personalised treatment. Two main topics prevail in cancer treatment, namely the role of the immune system and the prediction and prognostication by application of high-throughput methodology. The aim of this review is to examine the evidence for prognostic immunological and molecular markers studied in tumour tissue obtained at surgical resection for colorectal liver metastases.

Methods: First we analysed immunophenotypical protein markers, that are mainly studied by immunohistochemistry. Second, we review molecular markers by analysing high-throughput studies on tumour mRNA and microRNA expression.

Results: CD3, CD4, and CD8 are the most frequently studied protein markers. High intra-tumoural CD3+ T cell infiltration and low CXCR4 expression have the best association with favourable patient survival. Studies that analysed microRNA or mRNA expression data showed very little overlap in prognostic genes.

Conclusions: Patient prognostication after surgery for colorectal liver metastases by analysing the immune system remains difficult. Current data are based on diverse and heterogeneous patient populations which prohibits drawing firm conclusions.

Impacts of AURKA Genetic Polymorphism on Urothelial Cell Carcinoma Development

Urothelial cell carcinoma (UCC) is the most common primary malignancy of the urinary system and the second-most common type of renal cell carcinoma. Aurora kinase A (AURKA), a serine/threonine kinase, has a critical role in centrosome duplication, spindle assembly checkpoint, and cytokinesis. Here, we determined the correlation between UCC susceptibility and AURKA polymorphisms. We used real-time polymerase chain reaction to compare the genotype distributions and allelic frequencies of four single-nucleotide polymorphisms (SNPs) of AURKA, namely rs1047972, rs2273535, rs2064863, and rs6024836, between 431 UCC cases and 862 healthy controls. Logistic regression models demonstrated that the G allele of rs2064863, a genetic polymorphism of AURKA, exhibited a significant protective effect against UCC among the 862 nonsmokers. Moreover, patients with rs2064863 G allele exhibited a slightly lower risk of lymph node metastasis and those with rs6024836 G allele exhibited a lower risk of distant metastases. Our study suggested that several variants of AURKA SNPs rs2064863 and rs6024836 may serve as critical predictors for the clinical status of UCC.

Collagen IV-conveyed signals can regulate chemokine production and promote liver metastasis

Liver metastases remain a major cause of death from gastrointestinal tract cancers as well as from other malignancies such as breast and lung carcinomas and melanoma. Understanding the underlying biology is essential for the design of effective targeted therapies. We previously reported that collagen IV α1/α2 overexpression in non-metastatic lung carcinoma (M27^colIV) cells increased their metastatic ability, specifically to the liver and documented high collagen IV levels in surgical resections of liver metastases from diverse tumor types. Here, we aimed to elucidate the functional relevance of collagen IV to metastatic outgrowth in the liver. Gene expression profiling revealed in M27^colIVcells significant increases in the expression of chemokines CCL5 (5.7-fold) and CCL7 (2.6-fold) relative to wild-type cells, and this was validated by qPCR and western blotting. Similarly, in human colon carcinoma KM12C and KM12SM cells with divergent liver-colonizing potentials, CCL7 and CCL5 production correlated with type IV collagen expression and the metastatic phenotype. CCL7 silencing by short hairpin RNA (shRNA) reduced experimental liver metastasis in both cell types, whereas CCL5 silencing reduced metastasis of M27^colIV cells, implicating these cytokines in metastatic expansion in the liver. Subsequent functional analyses implicated both MEK/ERK and PI3K signaling upstream of CCL7 upregulation and identified CCL7 (but not CCL5) as a critical migration/invasion factor, acting via the chemokine receptor CCR3. Chemokine CCL5 was identified as a regulator of the T-cell immune response in the liver. Loss of CCL7 in KM12SM cells was also associated with altered E-cadherin and reduced vimentin and Snail expression, implicating it in epithelial-to-mesenchymal transition in these cells. Moreover, in clinical specimens of colon cancer liver metastases analyzed by immunohistochemistry, CCL5 and CCL7 levels paralleled those of collagen IV. The results identify the chemokines CCL5 and CCL7 as type IV collagen-regulated genes that promote liver metastasis by distinct and complementary mechanisms.

Protective effects of Huangqin Decoction against ulcerative colitis and associated cancer in mice

Individuals with ulcerative colitis (UC) are at a high risk for developing colorectal cancer (CRC). Huangqin Decoction (HQD), a traditional Chinese medicinal formula chronicled in the Shang Han Lun, is commonly used to treat gastrointestinal symptoms. However, experimental evidence for supporting the clinical practice is lacking. This study used modern biomedical approaches to investigate the protective/preventive effects of HQD in dextran sulfate sodium (DSS)-induced acute/chronic UC and azoxymethane (AOM)/DSS-induced CRC in mice. HQDs were prepared in 4 different ways: HQD-1 and HQD-2 were prepared in boiling water, whereas HQD-3 and HQD-4 were prepared in heated ethanol (70%). For HQD-1 and HQD-3, the 4 constituent herbs were processed together, whereas for HQD-2 and HQD4, these herbs were processed individually and then combined. The mice were administered 9.1 g/kg HQD via oral gavage daily. HQD-1 significantly inhibited DSS-induced acute UC, whereas HQD-3 and HQD-4 exhibited mild ameliorative effects; but HQD-2 had no protective effect and resulted in a higher mortality rate. This higher mortality rate may be due to the greater abundance of baicalein and wogonin in HQD-2 than HQD-1. Furthermore, HQD-1 protected against DSS-induced chronic UC and significantly inhibited AOM/DSS-induced CRC in mice. HQD-1 also inhibited the production of inflammatory cytokines and increased antioxidant capacity both in chronic DSS and AOM/DSS treated mice. Overall, HQD-1 inhibits the development of acute/chronic colitis and prevents colitis-associated CRC, possibly by inhibiting inflammation and preventing oxidative stress induced cellular damage.

Combining statistical techniques to predict postsurgical risk of 1-year mortality for patients with colon cancer

Introduction

Colorectal cancer is one of the most frequently diagnosed malignancies and a common cause of cancer-related mortality. The aim of this study was to develop and validate a clinical predictive model for 1-year mortality among patients with colon cancer who survive for at least 30 days after surgery.

Methods

Patients diagnosed with colon cancer who had surgery for the first time and who survived 30 days after the surgery were selected prospectively. The outcome was mortality within 1 year. Random forest, genetic algorithms and classification and regression trees were combined in order to identify the variables and partition points that optimally classify patients by risk of mortality. The resulting decision tree was categorized into four risk categories. Split-sample and bootstrap validation were performed. ClinicalTrials.gov Identifier: NCT02488161.

Results

A total of 1945 patients were enrolled in the study. The variables identified as the main predictors of 1-year mortality were presence of residual tumor, American Society of Anesthesiologists Physical Status Classification System risk score, pathologic tumor staging, Charlson Comorbidity Index, intraoperative complications, adjuvant chemotherapy and recurrence of tumor. The model was internally validated; area under the receiver operating characteristic curve (AUC) was 0.896 in the derivation sample and 0.835 in the validation sample. Risk categorization leads to AUC values of 0.875 and 0.832 in the derivation and validation samples, respectively. Optimal cut-off point of estimated risk had a sensitivity of 0.889 and a specificity of 0.758.

Conclusion

The decision tree was a simple, interpretable, valid and accurate prediction rule of 1-year mortality among colon cancer patients who survived for at least 30 days after surgery.

Extracellular translationally controlled tumor protein promotes colorectal cancer invasion and metastasis through Cdc42/JNK/ MMP9 signaling

The translationally controlled tumor protein (TCTP) can be secreted independently of the endoplasmic reticulum/Golgi pathway and has extrinsic activities when it is characterized as the histamine releasing factor (HRF). Despite its important role in allergies and inflammation, little is known about how extracellular TCTP affects cancer progression. In this study, we found that TCTP was overexpressed in the interstitial tissue of colorectal cancer (CRC) and its expression correlated with poor survival, high pathological grades and metastatic TNM stage in CRC patients. TCTP expression was greater in metastatic liver tissue than in primary tumors and was increased in highly invasive CRC cells. We demonstrated that the expression of TCTP was regulated by HIF-1α and its release was increased in response to low serum and hypoxic stress. Recombinant human TCTP (rhTCTP) promoted the migration and invasiveness of CRC cells in vitro and contributed to distant liver metastasis in vivo. Furthermore, rhTCTP activated Cdc42, phosphorylated JNK (p-JNK), increasing the translocation of p-JNK from the cytoplasm to the nucleus, as well as the secretion of MMP9. In addition, the expression of TCTP positively correlated with that of Cdc42 and p-JNK in clinical CRC samples. The silencing of Cdc42, JNK and MMP9 significantly inhibited the Matrigel invasion of rhTCTP-enhanced CRC cells. Collectively, these results identify a new role for extracellular TCTP as a promoter of CRC progression and liver metastases via Cdc42/JNK/MMP9 activation.

Overexpression of Rab1B and MMP9 predicts poor survival and good response to chemotherapy in patients with colorectal cancer

Rab1B has recently been reported to be involved in human cancer, but the role of Rab1B in colorectal cancer (CRC) remains unclear. In this study, we investigated the expression of Rab1B and MMP9 in CRC by qRT-PCR, immunoblot and immunohistochemistry and analyzed the clinical significance. The results show that Rab1B and MMP9 are increased at both mRNA and protein levels in CRC cell lines and tissues, as measured by qRT-PCR and immunoblotting. The high protein expression of Rab1B and MMP9 in 179 CRC tissues is associated with deep tumor invasion, lymph-node metastasis and advanced TNM stage. Survival analysis indicates that patients with overexpression of Rab1B or MMP9 have significantly worse overall survival and progression-free survival, but better response to chemotherapy than those with low expression of proteins, and that Rab1B is an independent prognostic factor for CRC patients. Furthermore, when Rab1B and MMP9 are combined into a new risk model, it has a remarkably better prediction of prognosis than each protein alone. In conclusion, Rab1B and MMP9 are potential prognostic biomarkers and their combination significantly improves predictive power for survival and chemotherapy response in CRC patients.

Knockdown of Decoy Receptor 3 Impairs Growth and Invasiveness of Hepatocellular Carcinoma Cell Line of HepG2

Background:

Decoy receptor 3 (DcR3) binds to Fas ligand (FasL) and inhibits FasL-induced apoptosis. The receptor is overexpressed in hepatocellular carcinoma (HCC), and it is associated with the growth and metastatic spread of tumors. DcR3 holds promises as a new target for the treatment of HCC, but little is known regarding the molecular mechanisms underlying the oncogenic properties of DcR3. The present work, therefore, examined the role of DcR3 in regulating the growth and invasive property of liver cancer cell HepG2.

Methods:

HepG2 cells were stably transfected with lentivirus-based short hairpin RNA vector targeting DcR3. After the knockdown of DcR3 was confirmed, cell proliferation, clone formation, ability of migrating across transwell membrane, and wound healing were assessed in vitro. Matrix metalloproteinase-9 (MMP 9) and vascular epithelial growth factor (VEGF)-C and D expressions of the DcR3 knockdown were also studied. Comparisons between multiple groups were done using one-way analysis of variance (ANOVA), while pairwise comparisons were performed using Student's t test. P < 0.05 was regarded statistically significant.

Results:

DcR3 was overexpressed in HepG2 compared to other HCC cell lines and normal hepatocyte Lo-2. Stable knockdown of DcR3 slowed down the growth of HepG2 (P < 0.05) and reduced the number of clones formed by 50% compared to those without DcR3 knockdown (P < 0.05). The knockdown also reduced the migration of HepG2 across transwell matrix membrane by five folds compared to the control (P < 0.05) and suppressed the closure of scratch wound (P < 0.05). In addition, the messenger RNA levels of MMP 9, VEGF-C, and VEGF-D were significantly suppressed by DcR3 knockdown by 90% when compared with the mock control (P < 0.05).

Conclusions:

Loss of DcR3 impaired the growth and invasive property of HCC cell line of HepG2. Targeting DcR3 may be a potential therapeutic approach for the treatment of HCC.

Novel roles of DC-SIGNR in colon cancer cell adhesion, migration, invasion, and liver metastasis

Background

Tumor metastasis is an essential cause of the poor prognosis of colon cancer. DC-SIGNR is a C-type lectin that is frequently found on human liver sinusoidal endothelial cells. LSECtin, which is a homologue of DC-SIGNR, has been demonstrated to participate in colon cancer liver metastasis. Due to the similarities in the expression pattern and structure of the two proteins, we speculated that DC-SIGNR could also be involved in this process.

Methods

Colon cancer cells were treated with the DC-SIGNR protein or control IgG, after which cell migration, invasion, and morphology were assayed. Xenograft mouse models were used to determine the role of DC-SIGNR in colon cancer liver metastasis in vivo. In addition, a human gene expression array was used to detect differential gene expression in colon cancer cells stimulated with the DC-SIGNR protein. The serum level of DC-SIGNR was examined in colon cancer patients by ELISA, and the significance of DC-SIGNR was determined.

Results

In our research, we investigated whether DC-SIGNR promotes colon cancer cell adhesion, migration, and invasion. Knocking down mouse DC-SIGNR decreased the liver metastatic potency of colon cancer cells and increased survival time. Expressing human DC-SIGNR enhanced colon cancer liver metastasis. Furthermore, DC-SIGNR conferred metastatic capability on cancer cells by upregulating various metallothionein isoforms. To validate the above results, we also found that the serum DC-SIGNR level was statistically higher in colon cancer patients with liver metastasis compared with those without metastasis.

Conclusions

These results imply that DC-SIGNR may promote colon carcinoma hepatic metastasis and could serve as a promising therapeutic target for anticancer treatment.

Electronic supplementary material

The online version of this article (doi:10.1186/s13045-016-0383-x) contains supplementary material, which is available to authorized users.