Multi-omics based consensus subtypes, development of prognostic signature, and identification of INHBB as a potential therapeutic target in colorectal cancer.

Purpose: Emerging evidence indicates that a small subpopulation of cancer cells with stem cell-like properties are responsible for acquisition of drug resistance in colorectal cancer (CRC). Intriguingly, the acquisition of such a stem-like state and subsequent drug resistance has been shown to be induced by the tumor microenvironment. In particular, cancer associated fibroblasts (CAFs) have been identified as a key component of tumor microenvironment which promote cancer stemness. Wnt signaling is a well-recognized pathway that drives self-renewal, and recently one of the Wnt-responsive genes, Tiam1, a guanine nucleotide exchange factor specific for Rac1, was shown to be overexpressed in CRC and associated with an aggressive cancer phenotype. Herein, we have investigated Tiam1 as a key modulator of chemoresistance in CRC. Methods: Tiam1 expression was assessed in resected CRC tissues from 300 patients who did or did not respond to chemotherapy. We used siRNA and CRISPR/CAS9 approach in three cell lines and animal models to examine whether inhibition of Tiam1 affects chemosensitivity in CRC. In addition, we established CRC patient derived-CAFs and examined whether the drug sensitivity of CRC cells was altered by supplementation of CAF-derived conditioned medium. Results: High Tiam1 expression significantly correlated with poor prognosis in CRC patients (P=0.032), and emerged as an independent prognostic factor (HR 5.06, 95% CI 1.10-23.2, P=0.038). In addition, Tiam1 overexpression is associated with patients who did not respond to chemotherapy (P=0.0005). We demonstrated that siRNA-mediated inhibition of Tiam1 enhanced sensitivity to three chemotherapeutic drugs (5-fluorouracil, oxaliplatin and irinotecan), and reduced tumor invasiveness in HCT116, SW480 and SW620 cell lines. Silencing of Tiam1 resulted in downregulation of stemness-related genes and spheroid formation ability. Furthermore, we validated that Tiam1-knockdown enhanced drug sensitivity and decreased the expression of stemness-related genes in xenograft tumors. Finally, we illustrated that the conditioned medium (CM) derived from CAFs led to increased stemness and chemoresistance in CRC cells through Tiam1 overexpression, and silencing of Tiam1 in CAFs resulted in reversal of stemness and chemoresistance properties. From a mechanistic standpoint, the target genes of Wnt signaling were also upregulated during co-culture with CM in CRC cells. Conclusion: We have firstly demonstrated that Tiam1 is overexpressed in CRC patients who did not respond to chemotherapeutic drugs; and furthermore, high Tiam1 expression emerged as an independent prognostic factor in CRC. Mechanistically, CAFs enhanced CRC chemoresistance through Tiam1 overexpression. Collectively, these results suggest that Tiam1 suppression in stroma may sensitize CRC cells to chemotherapeutic agents, suggesting that Tiam1 may be an attractive therapeutic target in colorectal cancer. Citation Format: Daisuke Izumi. Tiam1 is a key modulator of chemoresistance in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5226.

Accumulating evidence indicates that dysregulated microRNAs (miRNAs) are involved in cancer development, progression and metastasis. miR‑20a was found to be involved in invasion and epithelial‑mesenchymal transition (EMT) programs, with its aberrant expression having been observed in a variety of malignant tumors. However, the molecular mechanisms underlying the role of miR‑20a in colorectal cancer (CRC) development remain to be fully elucidated. In the present study, the expression of miR‑20a was compared between CRC tissue samples and the normal adjacent mucosa using quantitative polymerase chain reaction. The association of miR‑20a expression with clinicopathological characteristics was assessed using appropriate statistical analysis. The migration and invasion of SW480 cells was examined following transfection of the cells with either miR‑20a precursor or a negative control miRNA precursor. The effect of miR‑20a on the EMT in CRCcells invitro was also analyzed. The regulatory effect of miR‑20a on SMAD family member4 (SMAD4) was evaluated using a dual‑luciferase reporter assay. Relative expression levels of miR‑20a were significantly higher in CRC tissue than those in the normal adjacent mucosa, and high expression of miR‑20a correlated with lymph node metastases and distant metastases. Kaplan‑Meier analysis indicated that patients with increased miR‑20a levels exhibited unfavorable overall survival. Furthermore, multivariate analysis showed that miR‑20a was an independent prognostic factor. The transfection of SW480 CRC cells with miR‑20a promoted migration and invasion invitro, and the upregulation of miR‑20a induced EMT in CRCcells. An inverse correlation between the levels of miR‑20a and SMAD4 was observed in patients with CRC. Overexpression of miR‑20a in CRC cells decreased SMAD4 expression and decreased SMAD4‑driven luciferase reporter activity. The present study revealed that miR‑20a was an independent prognostic factor in CRC. Furthermore, miR‑20a induced EMT and regulated migration and invasion of SW480 cells, at least in part via suppression of SMAD4 expression. The present study suggests that miR‑20a may serve as a novel prognostic marker and therapeutic target for CRC.

Targeting epigenetic regulators is a promising therapeutic strategy against cancer. However, because of the broad spectrum of targets, selective inhibition of cancer-associated genes remains a major challenge. To address this issue, we focused on the oncogene-regulated histone demethylase, nucleolar protein 66 (NO66 [C14orf169/MAPJD]), which is known to work coordinately with the well-characterized oncogene, c-MYC. To investigate expression patterns and clinical significance of NO66 in colorectal cancer (CRC), we performed immunohistochemical staining in 114 CRC cases. We performed functional analysis of NO66 to evaluate its contribution to proliferation and migration ability in CRC cells in vitro. NO66 was selectively expressed in CRC tissues. Furthermore, high expression levels of NO66 were associated with cancer metastatic potential, including lymphatic duct invasion (p=0.047), venous invasion (p=0.033), and lymph node metastasis (p=0.015). Multivariate analysis indicated that NO66 was an independent prognostic factor for overall survival. In vitro assays revealed that NO66 expression is closely associated with malignant potential, including proliferation, migration and anti-apoptotic activity. NO66 is an independent prognostic factor in CRC. The cancer-selective expression patterns and its involvement in metastatic phenotypes suggest that NO66 is not only a crucial biomarker but is also a promising therapeutic target in CRC.

Background and aim Colorectal cancer (CRC) is a heterogeneous disease, with a diverse immune cell infiltrate. Interferon-stimulating gene 15 (ISG-15) is a type I interferon-regulated gene that is secreted by diverse inflammatory cells. The aim of this work was to evaluate the role of ISG-15 in CRC and to correlate its expression with clinicopathological data and patient survival. Materials and methods This retrospective case–control study included 87 chemo-naive CRC cases, 12 adenomas, and 59 non-neoplastic colonic tissue cases from Egyptian patients; all cases were stained for ISG-15 antibody. Results The present study showed that high expression of ISG-15 was correlated with malignant transformation in colorectal tissues, as higher epithelial H-score of ISG-15 was significantly associated with malignant group in comparison with non-neoplastic group (P=0.004). Epithelial overexpression of ISG-15 in CRC was significantly associated with smaller tumor size (P=0.023 and 0.011). Stromal overexpression of ISG-15 in CRC was significantly associated well-differentiated tumors (P=0.026). Moreover, ISG-15 overexpression in epithelium and stroma was associated with long survival period in CRC (P=0.02 and 0.001, respectively). More importantly, ISG-15 expression, either epithelial or stromal, was an independent prognostic factor in CRC. Conclusion High expression of ISG-15 correlates with malignant transformation in colorectal tissues, as ISG-15 is overexpressed in CRC in comparison with non-neoplastic and is associated with factors of good prognosis. In CRC, ISG-15 overexpression is associated with longer overall survival. Epithelial ISG-15 expression is the most independent prognostic factor in CRC.

Altered mean platelet volume (MPV) is implicated in several malignancies. However, the clinicopathological significance and prognostic value of MPV in colorectal cancer (CRC) is still elusive. The purpose of this study was to elucidate the predictive significance of MPV in CRC. The retrospective study recruited 509 consecutive CRC patients between January 2009 and December 2009. The relationships between MPV and clinicopathological characteristics were analyzed. Kaplan-Meier method and Cox regression were used to evaluate the prognostic impact of MPV. Of the 509 CRC patients, high MPV levels were detected in 150 (29.5%) patients. Elevated MPV was associated with tumor differentiation (p < 0.001). Patients with increased MPV had poor overall survival compared with those with normal level (60.0% vs. 83.6%, log-rank test, p = 0.035). Cox regression analysis showed that MPV was an independent prognostic factor in CRC (HR = 1.452, 95% CI = 1.118–1.884, p = 0.005). In conclusion, MPV is easily available in routine blood test. Elevated MPV might act as a marker of prognosis and therapeutic target for CRC.

Background Inflammation and immune cell dysfunction have been widely known as an essential role in the tumorigenesis of colorectal cancer (CRC). Yet, the role of tumor inflammation signature (TIS) associated with CRC prognosis, immune infiltration, and drug resistance remained unknown. Method The transcriptome sequencing data, as well as clinical data of CRC from the public dataset, were acquired for further investigation. Inflammation-related gene expression patterns were obtained and analyzed. Bioinformatics methods were used to build a prognostic TIS, and its prediction accuracy was verified by using ROC curve analyses. The independent prognostic factors in CRC were identified through multivariable Cox regression analysis. In addition, the specific features of the immunological landscape between low- and high-risk CRC cohorts were analyzed. Results We firstly screened the differentially expressed inflammation-related genes in CRC and constructed a prognostic TIS. We further classified CRC patients into high or low TIS score groups based on the optimal cutoff of prognostic TIS, and patients with high-risk scores had shorter overall survival (OS) than those in the low-risk cohort. The diagnostic accuracy of TIS was evaluated and confirmed with ROC analysis. The result of the univariate and multivariate analysis found that TIS was directly and independently linked to OS of CRC. Otherwise, an optimal nomogram model based on TIS exhibited a better prognostic accuracy in OS. Finally, the immunological status and immune cell infiltration were observed different in the two-risk cohorts. Conclusion In summary, the risk model of the TIS in CRC was found to be useful for predicting patient prognosis and guiding individual treatment. This risk signature could also serve as potential biomarkers and immunotherapeutic targets and indicate immunotherapy response for patients with CRC.

Inflammation is a critical component of tumor progression, and it modifies the tumor microenvironment by various mechanisms. Here, we explore the effect of the inflammatory response on the tumor microenvironment in colorectal cancer (CRC). A prognostic signature consisting of inflammation-related genes (IRGs) was constructed and verified based on the inflammatory response by bioinformatics analysis. IRG risk model was identified as an independent prognostic factor in CRC, and was related to biological processes of extracellular matrix, cell adhesion and angiogenesis. The IRG risk score predicted the clinical benefit of ipilimumab. Weighted correlation network analysis identified TIMP1 as the hub gene of the inflammatory response in the IRG risk model. Coculture experiments with macrophages and CRC cells revealed that TIMP1 promoted macrophage migration, inhibited the expression of M1 markers (CD11C and CD80), and promoted the expression of M2 markers (ARG1 and CD163). TIMP1 promoted the expression of ICAM1 and CCL2 by activating the ERK1/2 signaling pathway to promote macrophage migration and M2-like polarization. These IRGs in the risk model regulated stromal and immune components in the tumor microenvironment and could serve as potential therapeutic targets in CRC. TIMP1 promoted macrophage migration and meditated macrophage M2 polarization by activating ERK1/2/CLAM1 and CCL2.

Background: CPNE7, a member of copine family, is composed of calcium-dependent membrane-binding proteins. The encoded protein may play a role in calcium-mediated intracellular processes and membrane trafficking mainly. Although this protein was known as tumor suppressor in breast cancer, we identified the possibility as an oncogene in colorectal cancer. In this study, we performed to evaluate the oncogenic functions of CPNE7 in the colorectal cancer cell line and the clinical significance of CPNE7 expression in colorectal cancer patients. Method: The colorectal cancer cell lines (SW480, SW620, HCT116 and HT29) were transfected with siRNA for knockdown CPNE7. The oncogenic functions were identified in the transfected cell lines and compared them with CPNE7 highly expressing control cell lines. In vitro functional studies included cell proliferation assay, migration assay, invasion assay and semisolid agar colony forming assay. The clinical significance of CPNE7 expression was evaluated in 250 cases of colorectal cancer tissue by immunohistochemistry. Results: The knockdowned cell lines significantly showed lower oncogenic function (proliferation, migration, invasion and colony forming) compared to the CPNE7 highly expressing control cell lines (p&amp;lt;0.05). The overall survival rate was decreased in patients of CPNE7 high expression (p=0.03). Multivariate and univariate Cox-regression analysis showed that CPNE7 high expression was an independent prognostic factor in colorectal cancer (HR=1. 54, 95% CI=1. 00-2.38: p=0. 048 / HR=1. 58, 95% CI=1. 03-2.41: p=0. 032). Conclusion: This study announces that CPNE7 is a novel oncogene, an independent prognostic factor and therapeutic target in colorectal cancer. In the future, studies on in vivo assay and identifying oncogenic signal pathways of CPNE7 in colorectal cancer are necessary. Citation Format: DONGJUN JEONG, Seona Ban, Hyungjoo Kim, Seunghyun Oh, Sanghee Ji, Han Jo Kim, Sang Byung Bae, Tae Sung Ahn, Chang-Jin Kim, Moon Soo Lee, Moo-Jun Baek. Identification of novel oncogene, copine-7 (CPNE7), in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4455. doi:10.1158/1538-7445.AM2017-4455

Special AT-rich sequence-binding protein-1 (SATB1) has been identified as a genome organizer that reprograms chromatin organization and transcription profiles. SATB1 promotes tumor growth and metastasis in breast cancer and is associated with poor prognosis in several cancer types. The association between SATB1 and colorectal cancer (CRC) has not been studied intensively. Therefore, this study aimed to investigate the effect of SATB1 on CRC growth and metastasis in vitro and in vivo and its correlation with overall survival and clinicopathological factors in CRC patients. Stable SATB1 knockdown and SATB1-overexpressing cell lines were established. SATB1 knockdown decreased cell growth, colony formation, migration, and invasion and increased apoptosis in CRC cells in vitro (p<0.05), whereas SATB1 overexpression had the opposite effect. SATB1 overexpression increased tumor growth and metastasis to lung and liver in vivo by using xenograft animal models (p<0.05). Thus, SATB1 promoted an aggressive CRC phenotype in vitro and in vivo. Immunohistochemical analysis of 560 CRC specimens showed that SATB1 expression was significantly higher in CRC tissues than in matched non-tumor mucosa (p<0.001). In addition, SATB1 expression was significantly higher in patients with poorly differentiated tumors, higher invasion depth, distant metastasis, and advanced TNM stage. SATB1-positive patients had a poorer prognosis than SATB1-negative patients, and SATB1 was identified as an independent prognostic factor for CRC (p = 0.009). Strikingly, we also evaluated SATB2 expression in CRC and found that SATB2 was more abundantly expressed in non-cancerous mucosa compared to colorectal cancer tissues (p<0.001). However, SATB2 expression had no influence on prognosis of CRC patients (p = 0.836). SATB1 expression was significantly associated with shorter survival time either in SATB2-positive patients or in SATB2-negative patients (p<0.001). In conclusion, our findings indicated an important role for SATB1 in CRC tumorigenesis and metastasis. Therefore, SATB1 may represent an important prognostic biomarker and therapeutic target for CRC.

Background:Immune cell infiltrates are important determinants of colorectal cancer (CRC) outcome. Their presence may be driven by tumour or host-specific factors. From previous studies in mice, senescence, a state of cell cycle arrest, may moderate tumour progression through upregulation of antitumour immune responses. The relationships between senescence and immune infiltrates have not previously been studied in humans. We explore whether a marker of senescence (p16ink4a) in combination with low level expression of a proliferation marker (ki-67) relate to T cell infiltrates in CRC, and whether p16ink4a, Ki-67 and immune infiltrates have similar prognostic value.Methods:Immunostaining of p16inka and Ki-67 was performed within a CRC tissue microarray. Nuclear p16inka and Ki-67 were categorised as high/low. T-cell markers, CD3, CD45RO, CD8 and FOXP3 were scored separately as high/low grade in three areas of the tumour: the invasive margin (IM), tumour stroma and cancer cell nests (CCNs).Results:Two hundred and thirty stage I–III cancers were studied. High nuclear p16ink4a was expressed in 63% and high proliferation (Ki-67 >15%) in 61%. p16ink4a expression was associated with reduced CD45RO+ cells at the IM (P<0.05) and within the stroma (P<0.05) and reduced CD8+ cells at the IM (P<0.01). A low Ki-67 proliferative index was associated with reduced density of CD3+ cells in CCNs (P<0.01), reduced CD45RO+ cells at the IM (P<0.05) and within the CCNs (P<0.001), reduced FOXP3+ cells at the IM (P<0.001), within the stroma (P=0.001) and within CCNs (P<0.001) and reduced CD8+ cells at the IM (P<0.05) and within the CCNs (P<0.05). Tumours with both a low proliferative index and expression of p16ink4a demonstrated similar consistent relationships with reduced densities of T-cell infiltrates. On multivariate analysis, TNM stage (P<0.001), low CD3 cells at the IM (P=0.014), low CD8 cells at the IM (P=0.037), low proliferation (Ki-67; P=0.013) and low senescence (p16ink4a; P=0.002) were independently associated with poorer cancer survival.Conclusion:Senescence, proliferation and immune cell infiltrates are independent prognostic factors in CRC. Although related to survival, p16ink4a-associated senescence is not associated with an upregulation of antitumour T-cell responses.

5-Fluorouracil (5-FU) has been used as a standard first-line treatment for colorectal cancer (CRC) patients. Although 5-FU-based chemotherapy and immune checkpoint blockade (ICB) have achieved success in treating CRC, drug resistance and low response rates remain substantial limitations. Thus, it is necessary to construct a 5-FU resistance-related signature (5-FRSig) to predict patient prognosis and identify ideal patients for chemotherapy and immunotherapy. Using bulk and single-cell RNA sequencing data, we established and validated a novel 5-FRSig model using stepwise regression and multiple CRC cohorts and evaluated its associations with the prognosis, clinical features, immune status, immunotherapy, neoadjuvant therapy, and drug sensitivity of CRC patients through various bioinformatics algorithms. Unsupervised consensus clustering was performed to categorize the 5-FU resistance-related molecular subtypes of CRC. The expression levels of 5-FRSig, immune checkpoints, and immunoregulators were determined using quantitative real-time polymerase chain reaction (RT‒qPCR). Potential small-molecule agents were identified via Connectivity Map (CMap) and molecular docking. The 5-FRSig and cluster were confirmed as independent prognostic factors in CRC, as patients in the low-risk group and Cluster 1 had a better prognosis. Notably, 5-FRSig was significantly associated with 5-FU sensitivity, chemotherapy response, immune cell infiltration, immunoreactivity phenotype, immunotherapy efficiency, and drug selection. We predicted 10 potential compounds that bind to the core targets of 5-FRSig with the highest affinity. We developed a valid 5-FRSig to predict the prognosis, chemotherapeutic response, and immune status of CRC patients, thus optimizing the therapeutic benefits of chemotherapy combined with immunotherapy, which can facilitate the development of personalized treatments and novel molecular targeted therapies for patients with CRC.

Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide, highlighting the urgent need for improved therapeutic strategies. In this study, we identified zinc finger protein 282 (ZNF282), located on chromosome 7q, as a novel gene that contributes to CRC progression through comprehensive expression profiling using data from The Cancer Genome Atlas (TCGA) and single-cell RNA sequencing combined with spatial transcriptomics in clinical CRC datasets. ZNF282 was overexpressed in tumor cells. High ZNF282 mRNA expression was associated with distant metastasis and served as an independent poor prognostic factor in CRC. Invitro and invivo experiments using CRISPR/Cas9-mediated ZNF282 knockout CRC cell lines demonstrated significantly reduced tumor growth and cell proliferation, which were reversed by reexpression of ZNF282. Mechanistically, ZNF282 knockout impaired the G1/S cell cycle transition and downregulated E2F1 and its downstream targets, CCNE1 and CCND1. These findings were supported by single-cell RNA sequencing analysis, which showed ZNF282 enrichment in malignant epithelial cells linked to cell cycle pathways. Motif scanning further identified a putative ZNF282 binding site upstream of the E2F1 transcription start site, suggesting that ZNF282 may enhance E2F1 expression by facilitating the activity of an upstream regulatory region. In conclusion, ZNF282 is a novel gene that promotes CRC progression in part by enhancing cell cycle progression possibly via E2F1 activation. Its high expression is associated with poor prognosis, supporting its potential as a prognostic biomarker and therapeutic target in CRC.

Upregulation of long noncoding RNA ZFAS1 predicts poor prognosis and prompts invasion and metastasis in colorectal cancer

This study leveraged publicly available databases, including The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO), to investigate the expression patterns of ARL6IP1 in colorectal cancer (CRC) and its prognostic relevance. The results demonstrated that reduced ARL6IP1 expression is strongly associated with poorer overall survival (OS), disease-specific survival (DSS), and progression-free survival (PFS) in CRC patients, establishing ARL6IP1 as an independent prognostic marker for CRC. Further analyses using Gene Set Enrichment Analysis (GSEA) and Protein-Protein Interaction (PPI) network investigations indicated that low ARL6IP1 expression is enriched in cancer-related signaling pathways, suggesting its involvement in CRC pathogenesis through the ferroptosis mechanism. Additionally, the study uncovered a correlation between ARL6IP1 expression and immune cell infiltration within the tumor microenvironment (TME), particularly immunosuppressive cell populations such as regulatory T cells (Tregs) and M2-type macrophages. Diminished ARL6IP1 levels may promote the development of an immunosuppressive TME, thereby aiding tumor immune evasion. Collectively, these findings highlight ARL6IP1 as a critical ferroptosis-related gene that may significantly influence CRC progression and immune escape, offering a potential target for prognostic evaluation and therapeutic intervention in CRC. This study aims to investigate the expression patterns of ARL6IP1 in colorectal cancer (CRC) and its prognostic significance, as well as its correlation with immune cell infiltration in the tumor microenvironment. By leveraging publicly available databases, we sought to determine whether ARL6IP1 could serve as a potential prognostic biomarker and therapeutic target for CRC.

Colorectal cancer (CRC) remains a major cause of cancer-related mortality globally, primarily due to its aggressive progression and poor prognosis in many patients. Despite treatment advances, new therapeutic targets are critically needed to enhance patient outcomes. Although sphingosine kinase 1 (SPHK1) has been linked to various cancers, its role in CRC progression, prognosis, and as a therapeutic target is not well understood. This study aimed to investigate the role and molecular mechanisms through which SPHK1 contributes to CRC progression, with a focus on its potential as a prognostic marker and therapeutic target by bioinformatics and experimental analysis. Multi-omics analysis was conducted using data from TCGA, GEPIA2, and other publicly available databases, as well as single-cell RNA sequencing data, to assess SPHK1 expression and its correlation with immune infiltration in CRC tissues. A Mendelian Randomization (MR) approach was employed to investigate the causal relationship between sphingomyelin levels and CRC risk. Multiplex Fluorescence Immunohistochemistry was used to analyze the expression levels of SPHK1, E-cadherin, and Vimentin in 90 CRC and corresponding normal tissues. Migration, invasion, and apoptosis assays were performed in CRC cell lines to examine the functional impact of SPHK1 modulation. SPHK1 expression was significantly elevated in CRC tissues and correlated with poor prognosis. MR analysis confirmed a causal relationship between sphingomyelin levels and increased CRC risk. SPHK1 gene expression was significantly positively related to methylation levels at sites cg11001059 and cg26442874 and significantly negatively associated with methylation levels at cg02028751. SPHK1 expression was associated with immune cell infiltration and sphingolipid metabolism pathways. SPHK1 was found to modulate the expression of E-cadherin, promoting CRC cell migration and invasion, while inhibiting apoptosis. SPHK1 plays a key role in facilitating the epithelial-to-mesenchymal transition of CRC cells, enhancing their migratory and invasive abilities, and influencing the tumor microenvironment. The findings suggest that SPHK1 could be a potential biomarker and therapeutic target for CRC, with implications for the development of targeted therapies to improve patient outcomes.