Response In Colorectal Cancer Patients Research Articles

Chemokine‑ and chemokine receptor-based subtypes predict prognosis, immunotherapy and chemotherapy response in colorectal cancer patients

BackgroundThe clinical significance and comprehensive characteristics of chemokines and chemokine receptors in colorectal cancer (CRC) have not been previously reported. Our study aims to investigate the expression profiles of chemokines and chemokine receptors, as well as establish subtypes in CRC. Methods1009 CRC samples were enrolled in our study. Consensus unsupervised clustering analysis was conducted to establish subtypes, and a risk score model was developed using univariate Cox regression and least absolute shrinkage and selection operator (LASSO) analyses. 36 pairs of tissue specimens of CRC patients and two CRC cell lines were used to validate the subtypes and risk score in vitro. Quantitative real-time PCR and western blotting were employed to validate mRNA and protein expression levels, respectively. Flow cytometry was utilized for analyzing cell apoptosis, while cell viability assay and EdU assay were conducted to assess cell proliferation ability. ResultsThe Cluster B group shares similarities with the low-risk group in terms of exhibiting a higher level of immune cell infiltration and belonging to hot tumor. Patients CRC in the Cluster B group demonstrate a more favorable prognosis and exhibit better response to immunotherapy and chemotherapy. On the other hand, the Cluster A group resembles the high-risk group as it displays lower levels of immune cell infiltration, indicating a cold tumor phenotype. CRC patients in the Cluster A group have poorer prognoses and show less therapeutic efficacy towards immunotherapy and chemotherapy. Furthermore, we utilized a total of 36 pairs of tissue samples obtained from patients with CRC, along with two CRC cell lines for validation in vitro. This comprehensive approach further enhances the scientific validity and reliability of the identified subtypes and risk score in their ability to predict prognosis, response to immunotherapy, and response to chemotherapy among CRC patients. ConclusionWe first established robust prognostic subtypes based on chemokines and chemokine receptors, which could potentially serve as a novel biomarker for guiding individualized treatment in patients with CRC undergoing immunotherapy and chemotherapy.

Loss of Y in regulatory T lymphocytes in the tumor micro-environment of primary colorectal cancers and liver metastases

Male sex is a risk factor for colorectal cancer (CRC) with higher illness burden and earlier onset. Thus, we hypothesized that loss of chromosome Y (LOY) in the tumor micro-environment (TME) might be involved in oncogenesis. Previous studies show that LOY in circulating leukocytes of aging men was associated with shorter survival and non-hematological cancer, as well as higher LOY in CD4 + T-lymphocytes in men with prostate cancer vs. controls. However, nothing is known about LOY in leukocytes infiltrating TME and we address this aspect here. We studied frequency and functional effects of LOY in blood, TME and non-tumorous tissue. Regulatory T-lymphocytes (Tregs) in TME had the highest frequency of LOY (22%) in comparison to CD4 + T-lymphocytes and cytotoxic CD8 + T-lymphocytes. LOY score using scRNA-seq was also linked to higher expression of PDCD1, TIGIT and IKZF2 in Tregs. PDCD1 and TIGIT encode immune checkpoint receptors involved in the regulation of Tregs function. Our study sets the direction for further functional research regarding a probable role of LOY in intensifying features related to the suppressive phenotype of Tregs in TME and consequently a possible influence on immunotherapy response in CRC patients.

The expression of autophagy-associated protein LC3, metastasis, and chemotherapy response in colorectal cancer patients receiving uracil-based chemotherapy: An observational study

Background: LC3 serves as a marker for assessing autophagy activity in cancer cells, which is a potential focus for therapeutic interventions. It holds the potential to serve as a predictive indicator of resistance to chemotherapy in colorectal cancer. Thus, this study is aimed at finding the association between LC3 expression, metastasis, and chemotherapy response in colorectal patients. Methods: This study was an observational study evaluating the stage and chemotherapy response of a colorectal cancer patient in a tertiary hospital in West Java, Indonesia. The research participants included in this study were 83 subjects. The examination of LC3 was performed with immunohistochemistry. The response evaluation criteria in solid tumors (RECIST) were used for the evaluation of the chemotherapy response. Results: A positive LC3 expression was shown in 58 (69.9%) patients. In positive LC3 expression, 20 subjects (27.4%) showed progressive response, 16 subjects (21.9%) showed stable response, 12 subjects (16.4%) showed partial response, and 1 subject (1.4%) showed complete response. Meanwhile, in negative LC3 expression, 12 subjects (16.4%) showed progressive response, 8 subjects (11%) showed stable response, 3 subjects (4.1%) showed partial response, and 1 subject (1.4%) showed complete response. The LC3 expression showed no significant relationship with age, sex, subtype, grade, tumor location, stage, or chemotherapy response (p > 0.05). Conclusion: The expression of LC3 showed no significant relationship with metastasis or chemotherapy response.

Organoids as a biomarker for personalized treatment in metastatic colorectal cancer: drug screen optimization and correlation with patient response

BackgroundThe inability to predict treatment response of colorectal cancer patients results in unnecessary toxicity, decreased efficacy and survival. Response testing on patient-derived organoids (PDOs) is a promising biomarker for treatment efficacy. The aim of this study is to optimize PDO drug screening methods for correlation with patient response and explore the potential to predict responses to standard chemotherapies.MethodsWe optimized drug screen methods on 5–11 PDOs per condition of the complete set of 23 PDOs from patients treated for metastatic colorectal cancer (mCRC). PDOs were exposed to 5-fluorouracil (5-FU), irinotecan- and oxaliplatin-based chemotherapy. We compared medium with and without N-acetylcysteine (NAC), different readouts and different combination treatment set-ups to capture the strongest association with patient response. We expanded the screens using the optimized methods for all PDOs. Organoid sensitivity was correlated to the patient’s response, determined by % change in the size of target lesions. We assessed organoid sensitivity in relation to prior exposure to chemotherapy, mutational status and sidedness.ResultsDrug screen optimization involved excluding N-acetylcysteine from the medium and biphasic curve fitting for 5-FU & oxaliplatin combination screens. CellTiter-Glo measurements were comparable with CyQUANT and did not affect the correlation with patient response. Furthermore, the correlation improved with application of growth rate metrics, when 5-FU & oxaliplatin was screened in a ratio, and 5-FU & SN-38 using a fixed dose of SN-38. Area under the curve was the most robust drug response curve metric. After optimization, organoid and patient response showed a correlation coefficient of 0.58 for 5-FU (n = 6, 95% CI -0.44,0.95), 0.61 for irinotecan- (n = 10, 95% CI -0.03,0.90) and 0.60 for oxaliplatin-based chemotherapy (n = 11, 95% CI -0.01,0.88). Median progression-free survival of patients with resistant PDOs to oxaliplatin-based chemotherapy was significantly shorter than sensitive PDOs (3.3 vs 10.9 months, p = 0.007). Increased resistance to 5-FU in patients with prior exposure to 5-FU/capecitabine was adequately reflected in PDOs (p = 0.003).ConclusionsOur study emphasizes the critical impact of the screening methods for determining correlation between PDO drug screens and mCRC patient outcomes. Our 5-step optimization strategy provides a basis for future research on the clinical utility of PDO screens.

Identification of gut microbes-related molecular subtypes and their biomarkers in colorectal cancer.

The role of gut microbes (GM) and their metabolites in colorectal cancer (CRC) development has attracted increasing attention. Several studies have identified specific microorganisms that are closely associated with CRC occurrence and progression, as well as key genes associated with gut microorganisms. However, the extent to which gut microbes-related genes can serve as biomarkers for CRC progression or prognosis is still poorly understood. This study used a bioinformatics-based approach to synthetically analyze the large amount of available data stored in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Through this analysis, this study identified two distinct CRC molecular subtypes associated with GM, as well as CRC markers related to GM. In addition, these new subtypes exhibit significantly different survival outcomes and are characterized by distinct immune landscapes and biological functions. Gut microbes-related biomarkers (GMRBs), IL7 and BCL10, were identified and found to have independent prognostic value and predictability for immunotherapeutic response in CRC patients. In addition, a systematic collection and review of prior research literature on GM and CRC provided additional evidence to support these findings. In conclusion, this paper provides new insights into the underlying pathological mechanisms by which GM promotes the development of CRC and suggests potentially viable solutions for individualized prevention, screening, and treatment of CRC.

Correlation Between C-Reactive Protein (CRP) Level and Chemotherapy Response in Colorectal Cancer Patients Based on Carcinoembryonic Antigen (CEA) Levels in Post Definitive Operative and Adjuvant Chemotherapy Three Series at Prof. Dr. I.G.N.G Ngoerah Denpasar Hospital

Background: Colorectal cancer is the third leading cause of cancer-related deaths worldwide. Surgical therapy is the primary modality for early-stage cancer with curative goals; chemotherapy is the direct option in advanced cancer with palliative goals; radiotherapy is one of the primary therapy modalities for rectal cancer. The markers for chemotherapy response include CRP and CEA. Elevated CRP and CEA levels in CRC patients are associated with poor chemotherapy response. Objective: to determine the relationship between C-reactive protein (CRP) levels and chemotherapy response measured by Carcinoembryonic Antigen (CEA) levels in colorectal cancer patients at Prof. Dr. IGNG Ngoerah Hospital. Method: analytic observational study with a retrospective cohort study design. The sample in this study used the total consecutive sampling method. The analysis was carried out with the help of SPSS, including descriptive statistical tests, chi-square tests, and correlation tests with Spearman-Rho. Results: 58 patients were divided into 2 groups of 29 each for the group with high CRP levels (≥5 mg/dl) and low CRP levels (<5 mg/dl). The male subjects with the most age <60 years and stage III. Most duration of illness < 2 years. The relationship between CRP levels and chemotherapy response was based on CEA, RR 3.2 [95% CI 1.1-9.6; p 0.030], and the value of the positive correlation coefficient with strong strength is r = 0.722. Conclusion: high CRP levels are significantly associated with a strong correlation to worse chemotherapy response in colorectal cancer patients characterized by a high risk of increasing CEA levels 3.7 times after three series of FOLFIRI adjuvant chemotherapy.

Relationship between Age and The Histopathological Features to Chemotherapy Response in Colorectal Cancer Patients: A Prospective Observational Study

Abstract Introduction Chemotherapy response in early age-onset colorectal cancer patients is still controversial, and the results of chemotherapy response are unknown. Therefore, the purpose of this study is to determine the relationship between the age of colorectal cancer patients and histopathological features and chemotherapy response. Methods This is a prospective observational study. The subjects in this study were colorectal cancer patients in the Digestive Surgery division at Tertiary Hospital in West Java from September 2021 to September 2022. Results There were 86 subjects who underwent chemotherapy in accordance with the inclusion and exclusion criteria. Consisting of 39 patients of early age onset and 44 female patients. The most common histopathological feature in early age onset (EAO) and late age onset (LAO) was adenocarcinoma (25% and 46%, respectively). Stage III colorectal cancer affected 38 patients, while stage IV affected 48 patients. There was a significant relationship between early age onset and late age onset with histological features (p < 0.001). The patients with the highest chemotherapy response had stable diseases in EAO (17 patients) and LAO (20 patients). There was no statistically significant relationship between age, histological features, and stage of colorectal cancer and chemotherapy response (p > 0.05). The results of the ordinal logistic regression test showed no systematic relationship between chemotherapy response and age, histopathological features, gender, or cancer stage (p > 0.05). Conclusion There was no association between age and histopathologic features with chemotherapy response and there is no difference in chemotherapy response between early and late age onset.

Single cell dynamics of tumor specificity vs bystander activity in CD8+ T cells define the diverse immune landscapes in colorectal cancer

CD8+ T cell activation via immune checkpoint blockade (ICB) is successful in microsatellite instable (MSI) colorectal cancer (CRC) patients. By comparison, the success of immunotherapy against microsatellite stable (MSS) CRC is limited. Little is known about the most critical features of CRC CD8+ T cells that together determine the diverse immune landscapes and contrasting ICB responses. Hence, we pursued a deep single cell mapping of CRC CD8+ T cells on transcriptomic and T cell receptor (TCR) repertoire levels in a diverse patient cohort, with additional surface proteome validation. This revealed that CRC CD8+ T cell dynamics are underscored by complex interactions between interferon-γ signaling, tumor reactivity, TCR repertoire, (predicted) TCR antigen-specificities, and environmental cues like gut microbiome or colon tissue-specific ‘self-like’ features. MSI CRC CD8+ T cells showed tumor-specific activation reminiscent of canonical ‘T cell hot’ tumors, whereas the MSS CRC CD8+ T cells exhibited tumor unspecific or bystander-like features. This was accompanied by inflammation reminiscent of ‘pseudo-T cell hot’ tumors. Consequently, MSI and MSS CRC CD8+ T cells showed overlapping phenotypic features that differed dramatically in their TCR antigen-specificities. Given their high discriminating potential for CD8+ T cell features/specificities, we used the single cell tumor-reactive signaling modules in CD8+ T cells to build a bulk tumor transcriptome classification for CRC patients. This “Immune Subtype Classification” (ISC) successfully distinguished various tumoral immune landscapes that showed prognostic value and predicted immunotherapy responses in CRC patients. Thus, we deliver a unique map of CRC CD8+ T cells that drives a novel tumor immune landscape classification, with relevance for immunotherapy decision-making.

MALAT1 in Liquid Biopsy: The Diagnostic and Prognostic Promise for Colorectal Cancer and Adenomas?

The development of colorectal cancer (CRC) is a multistep process accompanied by the accumulation of mutations that start from specific precancerous lesion - colorectal adenomas (CA). CRC incidence and mortality can be reduced by the early identification of these neoplasm. Colonoscopy is the most widely used screening method for CRC identification. Nowadays, clinical research interest is shifting to the use of liquid biopsy that may help with the early diagnosis of CA and CRC. In our previous study, we identified long non-coding RNA MALAT1 gene amplification associated with the development of CA. This study aimed to describe the potential of MALAT1 expression levels in the adenoma tissue of patients used in the previous study by real-time qPCR. Furthermore, we analysed the plasma samples of an independent group of patients with CA (n=97), CRC (n=101), and cancer-free individuals (CFI, n=48). There was no difference in the MALAT1 expression level between CA patients with or without MALAT1 amplification. However, the plasma MALAT1 expression levels were significantly upregulated in patients with CRC and CA compared to CFI (for both p<0.001). Moreover, a correlation between MALAT1 expression and histological types of adenomas was identified- high-CRC-risk adenomas also displayed the highest MALAT1 expression levels. Furthermore, in CRC patients, MALAT1 levels were associated with a response to therapy. MALAT1 expression levels could serve as a promising circulating biomarker for early CA and CRC diagnosis, and even as a predictor of therapy response in CRC patients.

ERCC1 and MGMT Methylation as a Predictive Marker of Relapse and FOLFOX Response in Colorectal Cancer Patients from South Tunisia.

Genetic and epigenetic modifications present a major cause of relapse and treatment failure in colorectal cancer. This study aims to appreciate the prognostic and predictive value of ERRC1 and MGMT methylation. We also studied the prognostic impact of the ERCC1 rs11615 polymorphism as well as its expression. Methylation profiles of ERCC1 and MGMT were tested by methylation-specific PCR. A polymorphism of ERCC1 was studied using PCR-RFLP and its expression was examined by immunohistochemistry. ERCC1 was methylated in 44.6% of colorectal adenocarcinoma while MGMT was methylated in 69% of cases. MGMT methylation was strongly associated with lymph node metastasis, lymph invasion, venous invasion, perineural invasion, distant metastasis and relapse. Patients with methylation of both genes were more likely to have a poor prognosis and display chemoresistance. IHC analysis revealed that ERCC1 staining was noted in 52.8% of colorectal adenocarcinoma and inversely related to distant metastasis and cancer recurrence. Kaplan Meier analysis revealed that the worst overall survival was significantly associated with ERCC1 and MGMT methylation while decreased ERCC1 expression and T/T genotype exhibited the best overall survival. The methylation of MGMT, alone or combined with ERCC1, is predictive for poor prognosis, short overall survival and chemotherapy response in colorectal cancer.

Predictors of response in advanced colorectal cancer (CRC) patients treated with immune-checkpoint inhibitors (ICI).

e15579 Background: ICI is reserved for mismatch repair (MMR) deficient and high tumor mutation burden (TMB) CRC patients in the current clinical practice. Identifying clinicopathological factors predicting response to ICI beyond MMR status could help effectively utilize ICI in this population. This is a retrospective review of advanced CRC (recurrent or metastatic) patients treated with ICI at an academic institute to identify the risk factors (RF) for poor outcomes. Methods: CRC patients who received at least one dose of ICI for between 1/1/2015 and 7/31/2021 at the Ohio State University were included in the study. The patient's baseline (BL) characteristics (at the first dose of ICI) were extracted with immune-related adverse events (irAE) details and survival outcomes. Descriptive statistics were used, Fisher exact test to compare categorical variables, log-rank test rank test for survival outcomes, and logistic regression model for categorical outcomes using JMP Pro 16 (SAS Institute Inc., Cary, NC). Results: Our cohort has 46 advanced patients (37 colon and 7 rectal), the median age was 51 years (range 26-82) with 52% females, 95% Caucasians, 76% had metastatic disease (47% and 32% had liver and lung metastases or mets, respectively), 41% were mismatch repair (MMR) deficient, and 30% had KRAS exon two mutations. About 30% and 43% got ICI in the first line and ≥ 4 lines, respectively. Most patients received pembrolizumab (57%), followed by nivolumab (28%), atezolizumab (11%), and durvalumab (4%). Chemotherapy and ICI combination was given in 39%. irAEs were reported in 19% (n = 9). Median overall survival (OS) and progression-free survival (PFS) were 37 months (m) (95% confidence interval [CI], 14-NR) and 15m (95% CI, 7-35), respectively. Baseline (before the first ICI dose) albumin (p = 0.005), hemoglobin or Hb (p = 0.001), and the red cell count or RBC (p = 0.003) were negatively related to OS, while platelet to lymphocyte ratio or PLR (p = 0.01) and alkaline phosphatase levels (p = 0.03) were positively related to OS. High BL white cell count (WBC) (p = 0.04), alkaline phosphatase or ALP (p = 0.01), and low albumin (p = 0.002) and alanine transferase or ALT (p = 0.005) significantly impacted the OS. Other significant predictors are discussed in the table below. Conclusions: Our study provides insights into baseline tumor characteristics (such as lung/liver mets, KRAS exon 2 mutations, and MMR status) and lab values (such as RBC, Hb, PLR, albumin, ALP, and ALT) that could predict tumor response in CRC patients treated with ICI. These associations must be validated in larger studies. [Table: see text]

N6-methyladenosine related gene expression signatures for predicting the overall survival and immune responses of patients with colorectal cancer.

N6-methyladenosine (m6A) modification has been demonstrated to exhibit a crucial prognostic effect on colorectal cancer (CRC). Nonetheless, potential mechanism of m6A in survival rate and immunotherapeutic response remains unknown. Here we investigated the genes associated with m6A regulators and developed a risk score for predicting the overall survival (OS) of CRC patients. RNA-seq transcriptomic profiling data of COAD/READ samples were obtained from The Cancer Genome Atlas (TCGA) database. Absolute Shrinkage and Selection Operator (LASSO)- Cox regression analysis was conducted to identify the m6A-related gene expression signatures and the selected genes were inputted into stepwise regression to develop a prognostic risk score in TCGA, and its predictive performance of CRC survival was further validated in Gene Expression Omnibus (GEO) datasets. According to our results, the risk score comprising 18 m6A-related mRNAs was significantly associated with CRC survival in both TCGA and GEO datasets. And the stratified analysis also confirmed that high-risk score acted as a poor factor in different age, sex, T stage, and tumour, node, metastasis (TNM) stages. The m6A-related prognostic score in combination with clinical characteristics yielded time-dependent area under the receiver operating characteristic curve (AUCs) of 0.85 (95%CI: 0.79-0.91), 0.84 (95%CI: 0.79-0.90) and 0.80 (95%CI: 0.71-0.88) for the prediction of the 1-, 3-, 5-year OS of CRC in TCGA cohort. Furthermore, mutation of oncogenes occurred more frequently in the high-risk group and the composition of immune cells in tumour microenvironment (TME) was significantly distinct between the low- and high-risk groups. The low-risk group had a lower microsatellite instability (MSI) score, T-cell exclusion score and dysfunction score, implying that low-risk patients may have a better immunotherapy response than high-risk patients. In summary, a prognostic risk score derived from m6A-related gene expression signatures could serve as a potential prognostic predictor for CRC survival and indicator for predicting immunotherapy response in CRC patients.

Establishment and external verification of an oxidative stress-related gene signature to predict clinical outcomes and therapeutic responses of colorectal cancer.

Objective: Accumulated evidence highlights the biological significance of oxidative stress in tumorigenicity and progression of colorectal cancer (CRC). Our study aimed to establish a reliable oxidative stress-related signature to predict patients' clinical outcomes and therapeutic responses. Methods: Transcriptome profiles and clinical features of CRC patients were retrospectively analyzed from public datasets. LASSO analysis was used to construct an oxidative stress-related signature to predict overall survival, disease-free survival, disease-specific survival, and progression-free survival. Additionally, antitumor immunity, drug sensitivity, signaling pathways, and molecular subtypes were analyzed between different risk subsets through TIP, CIBERSORT, oncoPredict, etc. approaches. The genes in the signature were experimentally verified in the human colorectal mucosal cell line (FHC) along with CRC cell lines (SW-480 and HCT-116) through RT-qPCR or Western blot. Results: An oxidative stress-related signature was established, composed of ACOX1, CPT2, NAT2, NRG1, PPARGC1A, CDKN2A, CRYAB, NGFR, and UCN. The signature displayed an excellent capacity for survival prediction and was linked to worse clinicopathological features. Moreover, the signature correlated with antitumor immunity, drug sensitivity, and CRC-related pathways. Among molecular subtypes, the CSC subtype had the highest risk score. Experiments demonstrated that CDKN2A and UCN were up-regulated and ACOX1, CPT2, NAT2, NRG1, PPARGC1A, CRYAB, and NGFR were down-regulated in CRC than normal cells. In H2O2-induced CRC cells, their expression was notably altered. Conclusion: Altogether, our findings constructed an oxidative stress-related signature that can predict survival outcomes and therapeutic response in CRC patients, thus potentially assisting prognosis prediction and adjuvant therapy decisions.

THE ASSOCIATION BETWEEN B-RAF V600E GENE MUTATION WITH AGE, GRADING, AND CLINICAL RESPONSE IN COLORECTAL CANCER AT THE CENTER GENERAL HOSPITAL (RSUP) PROF. Dr. I GOESTI NGOERAH GDE NGOERAH IN BALI

Background: Colorectal cancer (CRC) is the most common type of cancer found in people over 50 years of age and is a disease associated with aging. CRC is the most preventable and curable cancer due to the pre-clinical phase until it becomes cancer between 10 - 20 years. The B-RAF mutation plays an important role in the prognosis and treatment of CRC patients. The B-RAF V600E mutation is the most common B-RAF mutation. This study aims to analyze the relationship between mutations in the B-RAF V600E gene with age, grading, and clinical response in CRC patients in Bali. Method: We used FFPE samples that were confirmed as CRC tissues by the pathologist. Identification of BRAF V600E mutation was identified using polymerase chain reaction (PCR) and direct sequencing. Data on age, grade, and clinical response were recorded from the patients medical record. Data was analized using Fisher-exact test. Results: The B-RAF V600E mutation samples were identified in 3 out of 74 samples (4.1%). The B-RAF V600E mutation was found in 3/3 of the samples (100%), which aged over 50 years old. All those mutated cases (100%) were low grade. Positive vs. negative clinical response was shown at 2/3 (66.7%) samples vs. 1/3 (33.3%) sample. No significant correlation was found between B-RAF V600E gene mutation and age (p=0.643), grading (p=0.808), and clinical response (p=0.358). Conclusion: We have identified the prevalence and type of BRAF mutation in our cases, however, there is no significant correlation between mutation B-RAF V600E gene and age, grade and clinical response of CRC patients at the center general hospital (RSUP) Prof. Dr. IGNG Ngoerah, Bali.

Effect of gut microbiota on colorectal cancer progression and treatment

Microbiota is a collection of bacteria, archaea, eukaryotes, bacteriophages, viruses, and fungi that cover human body surfaces and cavities. They characterize inside the body due to several factors such as diet, nutrition, xenobiotic substances, and microbial infections. Several studies have shown that gut microbiota can induce resistance against pathogens and regulate the immune system. In addition, their disruption is associated with several physiological and biochemical disorders, including inflammatory bowel disease (IBD), obesity, autoimmune diseases such as diabetes, hypertension, colon cancer, and cardiovascular disease. Colorectal cancer (CRC) is the third-deadliest cancer worldwide, accounting for approximately 900,000 deaths per year globally. Gut microbiota has been heavily linked to CRC incidence and prevention via bacterial metabolites, invasion, translocation, host's defense modulations, and bacterial-immune system interactions. In addition, it can influence the metabolism of chemical compounds such as drugs and xenobiotics to manipulate the treatment response in CRC patients.

An Evolutionary Random Forest to measure the Dworak tumor regression grade applied to colorectal cancer

In order to optimize a patient’s cancer treatment, the prediction of the tumor’s response to a planned radiotherapy is vital. For patients with rectal cancer, the quality of life depends heavily on the surgery leaving some patients with a stoma or other problems. If we would be able to predict the response upfront, we would be able to personalize the treatment and therefore preserve the QOL as much as possible. The Dworak tumor regression grade is a typical diagnostic tool to assess the tumor response of colorectal cancer patients. However, the Dworak grade is determined by a pathologist by inspection of the tumor biopsy without a dedicated measurement instrument. The measurement of the Dworak grade in an automated way by using the pre-operative CT scans, is a challenge. In this paper, we propose a novel methodology to measure the Dworak grade based on a customized random forest.We created a new random forest based on the methods from Breiman and Ho. These methods are further enhanced by evolutionary computation. We give the results of both our new method and other classical classification methods and highlight that the choice of classifier and knowledge is crucial.We extracted 111 radiomic features from 141 patients with colorectal cancer, of which 97 bad and 44 good responders. The evaluation gave a 77.507% accuracy and the cross-validation used for validation, gave a 67.081% accuracy. Our results were the best compared with the some other classification methods showing the need of a new method.

MiR-140 leads to MRE11 downregulation and ameliorates oxaliplatin treatment and therapy response in colorectal cancer patients.

Cancer therapy failure is a fundamental challenge in cancer treatment. One of the most common reasons for therapy failure is the development of acquired resistance of cancer cells. DNA-damaging agents are frequently used in first-line chemotherapy regimens and DNA damage response, and DNA repair pathways are significantly involved in the mechanisms of chemoresistance. MRE11, a part of the MRN complex involved in double-strand break (DSB) repair, is connected to colorectal cancer (CRC) patients' prognosis. Our previous results showed that single-nucleotide polymorphisms (SNPs) in the 3' untranslated region (3'UTR) microRNA (miRNA) binding sites of MRE11 gene are associated with decreased cancer risk but with shorter survival of CRC patients, which implies the role of miRNA regulation in CRC. The therapy of colorectal cancer utilizes oxaliplatin (oxalato(trans-l-1,2-diaminocyclohexane)platinum), which is often compromised by chemoresistance development. There is, therefore, a crucial clinical need to understand the cellular processes associated with drug resistance and improve treatment responses by applying efficient combination therapies. The main aim of this study was to investigate the effect of miRNAs on the oxaliplatin therapy response of CRC patients. By the in silico analysis, miR-140 was predicted to target MRE11 and modulate CRC prognosis. The lower expression of miR-140 was associated with the metastatic phenotype (p < 0.05) and poor progression-free survival (odds ratio (OR) = 0.4, p < 0.05). In the in vitro analysis, we used miRNA mimics to increase the level of miR-140 in the CRC cell line. This resulted in decreased proliferation of CRC cells (p < 0.05). Increased levels of miR-140 also led to increased sensitivity of cancer cells to oxaliplatin (p < 0.05) and to the accumulation of DNA damage. Our results, both in vitro and in vivo, suggest that miR-140 may act as a tumor suppressor and plays an important role in DSB DNA repair and, consequently, CRC therapy response.

Multi-perspective comparison of the immune microenvironment of primary colorectal cancer and liver metastases

BackgroundLiver metastases are a major contributor to the poor immunotherapy response in colorectal cancer patients. However, the distinctions in the immune microenvironment between primary tumors and liver metastases are poorly characterized. The goal of this study was to compare the expression profile of multiple immune cells to further analyze the similarities and differences between the microenvironments of liver metastases and the primary tumor.MethodsTissues from 17 patients with colorectal cancer who underwent resection of primary and liver metastases was analyzed using multispectral immunofluorescence. The expression of multiple immune cells (CD8, Foxp3, CD68, CD163, CD20, CD11c, CD66b, CD56, PD-L1, INF-γ, Ki67 and VEGFR-2) in the tumor center (TC), tumor invasive front (< 150 µm from the tumor center, TF) and peritumoral region (≥ 150 µm from the tumor center, PT) was evaluated via comparison. The expression of CD68 and CD163 in different regions was further analyzed based on the cell colocalization method. In addition, different immune phenotypes were studied and compared according to the degree of CD8 infiltration.ResultsThe expression trends of 12 markers in the TF and TC regions were basically the same in the primary tumor and liver metastasis lesions. However, in comparison of the TF and PT regions, the expression trends were not identical between primary and liver metastases, especially CD163, which was more highly expressed in the PT region relative to the TF region. In the contrast of different space distribution, the expression of CD163 was higher in liver metastases than in the primary foci. Further analysis of CD68 and CD163 via colocalization revealed that the distribution of macrophages in liver metastases was significantly different from that in the primary foci, with CD68−CD163+ macrophages predominating in liver metastases. In addition, among the three immunophenotypes, CD163 expression was highest in the immune rejection phenotype.ConclusionsThe immune cells found in the primary tumors of colorectal cancer differed from those in liver metastases in terms of their spatial distribution. More immunosuppressive cells were present in the liver metastases, with the most pronounced differential distribution found for macrophages. CD68−CD163+ macrophages may be associated with intrahepatic immunosuppression and weak immunotherapeutic effects.

Identification of N6-methylandenosine related lncRNA signatures for predicting the prognosis and therapy response in colorectal cancer patients.

Despite recent advances in surgical and multimodal therapies, the overall survival (OS) of advanced colorectal cancer (CRC) patients remains low. Thus, discerning sensitive prognostic biomarkers to give the optimistic treatment for CRC patients is extremely critical. N6-methyladenosine (m6A) and long noncoding RNAs (lncRNAs) play an important role in CRC progression. Nonetheless, few studies have focused on the impact of m6A-related lncRNAs on the prognosis, tumor microenvironment (TME) and treatment of CRC. In this study, 1707 m6A-related lncRNAs were identified through Pearson correlation analysis and Weighted co-expression network analysis (WGCNA) using The Cancer Genome Atlas (TCGA) cohort. Then, 28 m6A-related prognostic lncRNAs were screened by univariate Cox regression analysis, followed by identifying two clusters by consensus clustering analysis. A prognostic model consisted of 8 lncRNA signatures was constructed by the least absolute shrinkage and selection operator (LASSO). Kaplan–Meier curve analysis and a nomogram were performed to investigate the prognostic ability of this model. The risk score of prognostic model act as an independent risk factor for OS rate. Functional enrichment analysis indicated that lncRNA signatures related tumor immunity. The low-risk group characterized by increased microsatellite instability-high (MSI-H), mutation burden, and immunity activation, indicated favorable odds of OS. Moreover, the lncRNA signatures were significantly associated with the cancer stem cell (CSC) index and drug sensitivity. In addition, 3 common immune genes shared by the lncRNA signatures were screened out. We found that these immune genes were widely distributed in 2 cell types of TME. Finally, a ceRNA network was constructed to identify ZEB1-AS1 regulatory axis in CRC. We found that ZEB1-AS1 was significantly overexpressed in tumor tissues, and was related to the metastasis of EMT and the chemoresistance of 5-Fu in CRC. Therefore, our study demonstrated the important role of m6A-related lncRNAs in TME remodeling. Moreover, these results illustrated the levels of ZEB1-AS1 might be valuable for predicting the progression and prognosis of CRC, and further provided a new target for the diagnosis and treatment of CRC patients.

Comprehensive exploration of tumor immune microenvironment feature and therapeutic response in colorectal cancer based on a novel immune-related long non-coding RNA prognostic signature.

Colorectal cancer (CRC) is one of the most common malignant tumors with a high incidence rate and mortality. LncRNA is an important regulator of the immune system. It is of great significance to study immune-related lncRNAs (IR-lncRNAs) for CRC. In this study, we screened IR-lncRNAs differentially expressed in normal and CRC tissues, and Univariate Cox regression and the Least Absolute Shrinkage and Selection Operator were applied to construct IR-lncRNA prognostic signature in TCGA training dataset, and its predictive capability for the prognosis of CRC patients was verified in GSE39582 validation dataset. The novel signature was identified as an independent predictor of prognosis in CRC patients. In addition, the signature could accurately predict the feature of the immune microenvironment and therapeutic response in CRC patients. The CMap database was adopted to screen for small molecule candidate drugs that can reverse and treat high-risk CRC patients. Finally, the expression of six IR-lncRNAs were verified by qRT-PCR in clinical specimens from our patient cohort. In conclusion, we construct an IR-lncRNA prognostic signature, which is a powerful biomarker of CRC and can accurately predict the prognosis, immune microenvironment feature, and therapeutic response of CRC patients.