Prediction of overall survival in stage II and III colon cancer beyond TNM system: a retrospective, pooled biomarker study

Development and validation of a survival prediction model for patients with advanced non-small cell lung cancer based on LASSO regression

Introduction: Lung cancer remains a significant global health burden, with non-small cell lung cancer (NSCLC) being the predominant subtype. Despite advancements in treatment, the prognosis for patients with advanced NSCLC remains unsatisfactory, underscoring the imperative for precise prognostic assessment models. This study aimed to develop and validate a survival prediction model specifically tailored for patients diagnosed with NSCLC.

METHODS

A total of 523 patients were randomly divided into a training dataset (n=313) and a validation dataset (n=210). We conducted initial variable selection using three analytical methods: univariate Cox regression, LASSO regression, and random survival forest (RSF) analysis. Multivariate Cox regression was then performed on the variables selected by each method to construct the final predictive models. The optimal model was selected based on the highest bootstrap C-index observed in the validation dataset. Additionally, the predictive performance of the model was evaluated using time-dependent receiver operating characteristic (Time-ROC) curves, calibration plots, and decision curve analysis (DCA).

RESULTS

The LASSO regression model, which included N stage, neutrophil-lymphocyte ratio (NLR), D-dimer, neuron-specific enolase (NSE), squamous cell carcinoma antigen (SCC), driver alterations, and first-line treatment, achieved a bootstrap C-index of 0.668 (95% CI: 0.626-0.722) in the validation dataset, the highest among the three models tested. The model demonstrated good discrimination in the validation dataset, with area under the ROC curve (AUC) values of 0.707 (95% CI: 0.633-0.781) for 1-year survival, 0.691 (95% CI: 0.616-0.765) for 2-year survival, and 0.696 (95% CI: 0.611-0.781) for 3-year survival predictions, respectively. Calibration plots indicated good agreement between predicted and observed survival probabilities. Decision curve analysis demonstrated that the model provides clinical benefit at a range of decision thresholds.

CONCLUSION

The LASSO regression model exhibited robust performance in the validation dataset, predicting survival outcomes for patients with advanced NSCLC effectively. This model can assist clinicians in making more informed treatment decisions and provide a valuable tool for patient risk stratification and personalized management.

Enhancing cisplatin drug sensitivity through PARP3 inhibition: The influence on PDGF and G-coupled signal pathways in cancer

Drug resistance poses a significant challenge in cancer treatment despite the clinical efficacy of cisplatin. Identifying and targeting biomarkers open new ways to improve therapeutic outcomes. In this study, comprehensive bioinformatic analyses were employed, including a comparative analysis of multiple datasets, to evaluate overall survival and mutation hotspots in 27 base excision repair (BER) genes of more than 7,500 tumors across 23 cancer types. By using various parameters influencing patient survival, revealing that the overexpression of 15 distinct BER genes, particularly PARP3, NEIL3, and TDG, consistently correlated with poorer survival across multiple factors such as race, gender, and metastasis. Single nucleotide polymorphism (SNP) analyses within protein-coding regions highlighted the potential deleterious effects of mutations on protein structure and function. The investigation of mutation hotspots in BER proteins identified PARP3 due to its high mutation frequency. Moving from bioinformatics to wet lab experiments, cytotoxic experiments demonstrated that the absence of PARP3 by CRISPR/Cas9-mediated knockdown in MDA-MB-231 breast cancer cells increased drug activity towards cisplatin, carboplatin, and doxorubicin. Pathway analyses indicated the impact of PARP3 absence on the platelet-derived growth factor (PDGF) and G-coupled signal pathways on cisplatin exposure. PDGF, a critical regulator of various cellular functions, was downregulated in the absence of PARP3, suggesting a role in cancer progression. Moreover, the influence of PARP3 knockdown on G protein-coupled receptors (GPCRs) affects their function in the presence of cisplatin. In conclusion, the study demonstrated a synthetic lethal interaction between GPCRs, PDGF signaling pathways, and PARP3 gene silencing. PARP3 emerged as a promising target.

Comprehensive analysis of gene mutations and mismatch repair in Chinese colorectal cancer patients

BACKGROUND

RAS, BRAF, and mismatch repair (MMR)/microsatellite instability (MSI) are crucial biomarkers recommended by clinical practice guidelines for colorectal cancer (CRC). However, their characteristics and influencing factors in Chinese patients have not been thoroughly described.

AIM

To analyze the clinicopathological features of KRAS, NRAS, BRAF, and PIK3CA mutations and the DNA MMR status in CRC.

METHODS

We enrolled 2271 Chinese CRC patients at the China-Japan Friendship Hospital. MMR proteins were tested using immunohistochemical analysis, and the KRAS/NRAS/BRAF/PIK3CA mutations were determined using quantitative polymerase chain reaction. Microsatellite status was determined using an MSI detection kit. Statistical analyses were conducted using SPSS software and logistic regression.

RESULTS

The KRAS, NRAS, BRAF, and PIK3CA mutations were detected in 44.6%, 3.4%, 3.7%, and 3.9% of CRC patients, respectively. KRAS mutations were more likely to occur in patients with moderate-to-high differentiation. BRAF mutations were more likely to occur in patients with right-sided CRC, poorly differentiated, or no perineural invasion. Deficient MMR (dMMR) was detected in 7.9% of all patients and 16.8% of those with mucinous adenocarcinomas. KRAS, NRAS, BRAF, and PIK3CA mutations were detected in 29.6%, 1.1%, 8.1%, and 22.3% of patients with dMMR, respectively. The dMMR was more likely to occur in patients with a family history of CRC, aged < 50 years, right-sided CRC, poorly differentiated histology, no perineural invasion, and with carcinoma in situ, stage I, or stage II tumors.

CONCLUSION

This study analyzed the molecular profiles of KRAS, NRAS, BRAF, PIK3CA, and MMR/MSI in CRC, identifying key influencing factors, with implications for clinical management of CRC.

Comprehensive analysis of gene mutations and mismatch repair in Chinese colorectal cancer patients

BACKGROUND

RAS, BRAF, and mismatch repair (MMR)/microsatellite instability (MSI) are crucial biomarkers recommended by clinical practice guidelines for colorectal cancer (CRC). However, their characteristics and influencing factors in Chinese patients have not been thoroughly described.

AIM

To analyze the clinicopathological features of KRAS, NRAS, BRAF, and PIK3CA mutations and the DNA MMR status in CRC.

METHODS

We enrolled 2271 Chinese CRC patients at the China-Japan Friendship Hospital. MMR proteins were tested using immunohistochemical analysis, and the KRAS/NRAS/BRAF/PIK3CA mutations were determined using quantitative polymerase chain reaction. Microsatellite status was determined using an MSI detection kit. Statistical analyses were conducted using SPSS software and logistic regression.

RESULTS

The KRAS, NRAS, BRAF, and PIK3CA mutations were detected in 44.6%, 3.4%, 3.7%, and 3.9% of CRC patients, respectively. KRAS mutations were more likely to occur in patients with moderate-to-high differentiation. BRAF mutations were more likely to occur in patients with right-sided CRC, poorly differentiated, or no perineural invasion. Deficient MMR (dMMR) was detected in 7.9% of all patients and 16.8% of those with mucinous adenocarcinomas. KRAS, NRAS, BRAF, and PIK3CA mutations were detected in 29.6%, 1.1%, 8.1%, and 22.3% of patients with dMMR, respectively. The dMMR was more likely to occur in patients with a family history of CRC, aged < 50 years, right-sided CRC, poorly differentiated histology, no perineural invasion, and with carcinoma in situ, stage I, or stage II tumors.

CONCLUSION

This study analyzed the molecular profiles of KRAS, NRAS, BRAF, PIK3CA, and MMR/MSI in CRC, identifying key influencing factors, with implications for clinical management of CRC.

Survival Benefits of Postoperative Chemotherapy in Patients With Colorectal Mucinous Adenocarcinoma: An Analysis Utilizing Propensity Score Matching From the Surveillance, Epidemiology, and End Results Database

OBJECTIVE

This study aimed to investigate the characteristics of patients with colorectal mucinous adenocarcinoma (MAC) who benefit from postoperative chemotherapy (POCT) and to develop effective postoperative survival nomograms for predicting overall survival (OS) in colorectal MAC patients.

METHODS

Data of colorectal MAC patients who underwent surgery from the Surveillance, Epidemiology, and End Results (SEER) database between 2010 and 2020 were collected. Patients were grouped based on POCT, and intergroup analysis was performed using 1:1 propensity score matching (PSM). Kaplan-Meier (K-M) curves were used to compare the prognosis between the 2 groups. Cox analysis was employed to identify factors associated with OS in patients with colorectal MAC who underwent POCT. The variance inflation factor (VIF) and bilateral stepwise regression were used to determine factors included in the model. Additionally, a nomogram was constructed to predict postoperative survival outcomes for patients. The discriminative ability of the nomograms was evaluated using the C-index and calibration curve analysis, the decision curve analysis (DCA) assessed the clinical utility of the nomogram, and the receiver operating characteristic (ROC) curve evaluated the nomograms' performance.

RESULTS

This study encompassed 6829 patients with colorectal MAC, among whom 2258 received POCT, and 4571 did not. Whether pre or post PSM, patients in the POCT group consistently exhibited a superior median OS compared to those in the postoperative non-chemotherapy group (P < .0001). For colorectal MAC patients undergoing POCT, OS was correlated with factors such as patient age, carcinoembryonic antigen levels, tumor deposits, perineural invasion (PNI), lymph node examination count, T staging, and Grade staging. Notably, a significant chemotherapy advantage was observed in patients without perineural invasion, those with lymph node examination counts exceeding 12, and patients with moderately differentiated tumors. The overall colorectal MAC patient postoperative OS predictive nomogram demonstrated a C-index of .74, with a calibration curve near the diagonal and a DCA curve indicating positive net benefits. In comparison to TNM staging, the ROC curves of the nomogram at 1 year, 3 years, and 5 years demonstrated superior predictive capabilities (AUC: .80 vs .71, .78 vs .71, .77 vs .70).

CONCLUSION

This study revealed the characteristics of colorectal MAC patients who benefit from POCT and established effective prognostic nomograms, which can aid clinicians in designing personalized treatment plans for individual patients and promote precision medicine.

An invasion front gene expression signature for higher-risk patient selection in stage IIA MSS colon cancer

Stage II colon cancer (CC) encompasses a heterogeneous group of patients with diverse survival experiences: 87% to 58% 5-year relative survival rates for stages IIA and IIC, respectively. While stage IIA patients are usually spared the adjuvant chemotherapy, some of them relapse and may benefit from it; thus, their timely identification is crucial. Current gene expression signatures did not specifically target this group nor did they find their place in clinical practice. Since processes at invasion front have also been linked to tumor progression, we hypothesize that aside from bulk tumor features, focusing on the invasion front may provide additional clues for this stratification. A retrospective matched case-control collection of 39 stage IIA microsatellite-stable (MSS) untreated CCs was analyzed to identify prognostic gene expression-based signatures. The endpoint was defined as relapse within 5 years vs. no relapse for at least 6 years. From the same tumors, three different classifiers (bulk tumor, invasion front, and constrained baseline on bulk tumor) were developed and their performance estimated. The baseline classifier, while the weakest, was validated in two independent data sets. The best performing signature was based on invasion front profiles [area under the receiver operating curve (AUC) = 0.931 (0.815-1.0)] and contained genes associated with KRAS pathway activation, apical junction complex, and heme metabolism. Its combination with bulk tumor classifier further improved the accuracy of the predictions.

Prognostic Impact of Primary Tumor Sidedness in Stage III Colorectal Cancer: Real-World Evidence from a Brazilian Cohort

BACKGROUND

Primary tumor sidedness (PTS) is an independent prognostic factor in patients with metastatic colorectal cancer (CRC), with a worse prognosis for right-sided tumors. There are limited data on the prognostic impact of PTS in stage III CRC. The main objective of this study was to analyze the prognostic impact of PTS in stage III CRC.

PATIENTS AND METHODS

A retrospective and uni-institutional cohort study was performed in an oncology reference center. Patients with stage III CRC treated with a 5-fluorouracil and oxaliplatin-based chemotherapy regimen (mFLOX regimen) from October 2007 to February 2013 were included. The primary outcome was the probability of overall survival (OS) at 5 years stratified by PTS. Secondary outcomes were the probability of disease-free survival (DFS) at 5 years and an analysis of the prognostic impact of clinical and molecular biomarkers. Kaplan‒Meier curves were used, and Cox models were used to evaluate prognostic factors associated with OS and DFS.

RESULTS

Overall, 265 patients were evaluated. Transverse colon tumors, multicentric tumors, and undetermined primary subsites were excluded, resulting in 234 patients classified according to PTS: 95 with right sidedness (40.6%) and 139 with left sidedness (59.4%). The median follow-up time was 66 months [interquartile range (IQR): 39-81]. The 5-year OS probabilities for right-sided and left-sided tumors were 67% (95% CI: 58%-77%) and 82% (75%-89%), respectively [hazard ratio (HR): 2.02, 95% CI: 1.18-3.46; P = .010]. The 5-year probabilities of DFS for right-sided and left-sided tumors were 58% (49%-69%) and 65% (58%-74%), respectively (HR: 1.29, 0.84-1.97; P = 0.248).

CONCLUSION

These data suggest that there may be a worse prognosis (inferior OS at 5 years) for resected right-sided stage III CRC patients treated in the real world. However, these data need to be confirmed by prospective studies with a larger number of participants.

Serum copper status of patients with colorectal cancer: A systematic review and meta-analysis

BACKGROUND

Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide and a public health problem. Several clinical studies have shown that copper (Cu) is involved in carcinogenesis, possibly via cuproptosis, a new form of programmed cell death, but the conclusions from published reports are inconsistent. This study aimed at evaluating the potential of Cu dysregulation as a CRC susceptibility factor.

METHODS

In this systematic review and meta-analysis, we searched Cochrane Library, EBSCOhost, EMBASE, ProQuest, PubMed/MEDLINE, Scopus, and Web of Science for studies reporting serum Cu concentrations in CRC patients and controls from articles published till June 2023. The studies included reported measurements of serum/plasma/blood Cu levels. Meta-analyses were performed as well as study quality, heterogeneity, and small study effects were assessed. Based on a random effects model, summary standardized mean differences (SMDs) and the corresponding 95% confidence intervals (95% CIs) were applied to compare the levels of Cu between CRC patients and controls.

RESULTS

26 studies with a pooled total of9628 participants and 2578 CRC cases were included. The pooled SMD was equal to 0.85 (95% CIs -0.44; 2.14) showing that the CRC patients had higher mean Cu levels than the control subjects, but the difference was not significant (p = 0.185) and the heterogeneity was very high, I2 = 97.9% (95% CIs: 97.5-98.3%; p < 0.001).

CONCLUSION

The pooled results were inconclusive, likely due to discordant results and inaccuracy in reporting data of some studies; further research is needed to establish whether Cu dysregulation might contribute to the CRC risk and whether it might reflect different CRC grades.

Correlation Between DCAMKL-1 Protein Expression and K-ras Gene Mutation in Colorectal Cancer

Aim

To investigate the correlation between doublecortin and CaM kinase-like-1 (DCAMKL-1) protein expression, K-ras gene mutation, and their impact on patient prognosis in colorectal cancer (CRC).

Methods

Immunohistochemistry was used to detect the expression of DCAMKL-1 protein in 60 cases of colorectal adenoma, 82 cases of CRC (including 65 cases of lymph node metastasis) and paraffin-embedded paracancerous intestinal mucosal tissue. K-ras gene mutations in primary CRC lesions were detected using an amplification-refractory mutation system and fluorescent polymerase chain reaction. The relationship between DCAMKL-1 protein expression and K-ras gene mutations with the clinicopathological characteristics of patients with CRC was analyzed. Univariate Kaplan‒Meier survival analysis and multivariate Cox regression analysis were performed using follow-up data.

Results

The mutation rate of the K-ras gene in 82 cases of CRC was 48.8% (40/82). The positivity rate for the presence of DCAMKL-1 protein in CRC was 70.7% (58/82), significantly higher than that for colorectal adenomas (53.3%; 32/60) and paracancerous intestinal mucosa (0%; 0/82) (P<0.05). The positive expression rate for the presence of DCAMKL-1 protein in 65 patients with lymph node metastasis was higher in the primary lesions (69.2%; 45/65) than in the lymph node metastases (52.3%; 34/65) (χ2=12.087, P=0.001). The K-ras gene mutation status was positively correlated with DCAMKL-1 protein expression (r=0.252, P=0.022).

Conclusion

In this study, a potential positive correlation between K-ras gene mutation and DCAMKL-1 protein expression was identified in CRC tissues. The assessment of K-ras gene mutation status and DCAMKL-1 protein expression holds promise for augmenting early diagnosis and prognosis evaluation in CRC. This approach may improve the overall prognosis and survival outcomes for CRC patients.

Detecting colorectal cancer using genetic and epigenetic biomarkers: screening and diagnosis

Colorectal cancer (CRC) is one of the most frequent types of cancer, with high incidence rates and mortality globally. The extended timeframe for developing CRC allows for the potential screening and early identification of the disease. Furthermore, studies have shown that survival rates for patients with cancer are increased when diagnoses are made at earlier stages. Recent research suggests that the development of CRC, including its precancerous lesion, is influenced not only by genetic factors but also by epigenetic variables. Studies suggest epigenetics plays a significant role in cancer development, particularly CRC. While this approach is still in its early stages and faces challenges due to the variability of CRC, it shows promise as a potential method for understanding and addressing the disease. This review examined the current evidence supporting genetic and epigenetic biomarkers for screening and diagnosis. In addition, we also discussed the feasibility of translating these methodologies into clinical settings. Several markers show promising potential, including the methylation of vimentin (VIM), syndecan-2 (SDC2), and septin 9 (SEPT9). However, their application as screening and diagnostic tools, particularly for early-stage CRC, has not been fully optimized, and their effectiveness needs validation in large, multi-center patient populations. Extensive trials and further investigation are required to translate genetic and epigenetic biomarkers into practical clinical use. biomarkers, diagnostic biomarkers.

Comprehensive characterization of PKHD1 mutation in human colon cancer

INTRODUCTION

The PKHD1 (Polycystic Kidney and Hepatic Disease 1) gene is essential for producing fibrocystin or polyductin, which is crucial in various cellular functions. Mutations in PKHD1 have been found to be involved in the development and progression of colorectal cancer (CRC). Along with APC, TP53, and KRAS, PKHD1 is one of the most frequently mutated genes in CRC. PKHD1 expression is governed by the Wnt/PCP pathway, often dysregulated in CRC. Targeting this pathway, crucial for CRC progression, could unveil potential therapeutic strategies for colon cancer treatment.

METHODS

This study examined an in-house dataset of 3702 colon cancer samples, analyzing mutation landscapes, clinical features, tumor mutational burden (TMB), microsatellite instability (MSI), and chromosomal instability (CIN) score. For the survival analysis of PKHD1 patients, survival data of 436 colon adenocarcinoma samples were obtained from TCGA dataset. Additionally, 433 samples from TCGA with RNA-seq data were used for the assessment of immune cell infiltration and gene set enrichment analysis.

RESULTS

Polycystic Kidney and Hepatic Disease 1 mutation was detected in 424 colon cancer patients from our in-house cohort and was associated with increased TMB, higher MSI, and lower CIN score. Importantly, within the TCGA dataset, PKHD1 mutations were identified as an independent prognostic factor, not merely correlated with established prognostic biomarkers, and were associated with poorer overall survival outcomes. In terms of immune response, these mutations correlated with increased enrichment scores for 12 immune cell types, including B cell plasma, macrophages, and naive CD4+ T cells. Additionally, interferon alpha and interferon-gamma gene sets were significantly down-regulated in patients with PKHD1 mutations (FDA q-value < 0.1).

CONCLUSIONS

Overall, these findings suggest that PKHD1 may be a potential biomarker for the prognosis of colon cancer and provide some insight for personalized immunotherapy.

CRISPR/Cas9: a powerful tool in colorectal cancer research

Colorectal cancer (CRC) is one of the most common malignant cancers worldwide and seriously threatens human health. The clustered regulatory interspaced short palindromic repeat/CRISPR-associate nuclease 9 (CRISPR/Cas9) system is an adaptive immune system of bacteria or archaea. Since its introduction, research into various aspects of treatment approaches for CRC has been accelerated, including investigation of the oncogenes, tumor suppressor genes (TSGs), drug resistance genes, target genes, mouse model construction, and especially in genome-wide library screening. Furthermore, the CRISPR/Cas9 system can be utilized for gene therapy for CRC, specifically involving in the molecular targeted drug delivery or targeted knockout in vivo. In this review, we elucidate the mechanism of the CRISPR/Cas9 system and its comprehensive applications in CRC. Additionally, we discussed the issue of off-target effects associated with CRISPR/Cas9, which serves to restrict its practical application. Future research on CRC should in-depth and systematically utilize the CRISPR/Cas9 system thereby achieving clinical practice.

Prognostic Factors Influencing Survival in Stage II and Stage III Colorectal Cancer Patients

Background Colorectal cancer (CRC) is a global health concern with rising incidence. This study analyzed demographic and clinicopathological factors influencing overall survival (OS) and disease-free survival (DFS) in Jordanian CRC patients. Methodology This retrospective, single-center study collected data from CRC patients at the Royal Medical Services, Jordan, from January 2018 to June 2020. Patient variables included disease stage, stage risk, tumor location, history of chemotherapy, and metastasis status. OS and DFS were defined as the time from surgery to death, last follow-up, or metastasis confirmation. Kaplan-Meier curves and Cox models were used for survival analysis. Results Of 127 CRC patients, 33.3% died during the follow-up period. Most patients were males (55.1%), diagnosed with stage III (55.9%), and classified as high risk (59.2%). Metastasis occurred in 24.4%, and 65.4% received chemotherapy. OS at one, two, and end of the follow-up years was 85.2%, 75.6%, and 66.9%, respectively. Metastasis-free rates were 85%, 78.5%, and 71%, respectively. Multivariate analysis showed that stage III (hazard ratio (HR) = 2.968) and high-risk stage (HR = 2.966) were associated with shorter OS and increased metastasis risk. Right-sided tumors (HR = 2.183) had shorter OS, while chemotherapy recipients (HR = 0.430) had longer OS. Stage III and high-risk stages were strong predictors of mortality, while only stage III and high-risk stages were robust predictors of metastasis. Demographic variables (sex and age) showed no significant associations with survival outcomes. Conclusions Our findings highlight the prognostic significance of disease stage, stage risk, tumor location, and chemotherapy in CRC survival among Jordanian patients. Understanding these factors can guide tailored treatment and improve outcomes.

Specific Mutations in APC, with Prognostic Implications in Metastatic Colorectal Cancer

PURPOSE

Loss-of-function mutations in the adenomatous polyposis coli (APC) gene are common in metastatic colorectal cancer (mCRC). However, the characteristic of APC specific mutations in mCRC is poorly understood. Here, we explored the clinical and molecular characteristics of N-terminal and C-terminal side APC mutations in Chinese patients with mCRC.

MATERIALS AND METHODS

Hybrid capture-based next-generation sequencing was performed on tumor tissues from 275 mCRC pati-ents to detect mutations in 639 tumor-associated genes. The prognostic value and gene-pathway difference between APC specific mutations in mCRC patients were analyzed.

RESULTS

APC mutations were highly clustered, accounting for 73% of all mCRC patients, and most of them were truncating mutations. The tumor mutation burden of the N-terminal side APC mutations group (n=76) was significantly lower than that of the C-terminal side group (n=123) (p < 0.001), further confirmed by the public database. Survival analysis showed that mCRC patients with N-terminus side APC mutations had longer overall survival than C-terminus side. Tumor gene pathway analysis showed that gene mutations in the RTK/RAS, Wnt and transforming growth factor β signaling pathways of the C-terminal group were significantly higher than those of the N-terminal group (p < 0.05). Additionally, KRAS, AMER1, TGFBR2, and ARID1A driver mutations were more common in patients with C-terminal side APC mutations.

CONCLUSION

APC specific mutations have potential function as mCRC prognostic biomarkers. There are obvious differences in the gene mutation patterns between the C-terminus and N-terminus APC mutations group, which may have certain guiding significance for the subsequent precise treatment of mCRC.

A nomogram based on collagen signature for predicting the immunoscore in colorectal cancer

Objectives

The Immunoscore can categorize patients into high- and low-risk groups for prognostication in colorectal cancer (CRC). Collagen plays an important role in immunomodulatory functions in the tumor microenvironment (TME). However, the correlation between collagen and the Immunoscore in the TME is unclear. This study aimed to construct a collagen signature to illuminate the relationship between collagen structure and Immunoscore.

Methods

A total of 327 consecutive patients with stage I-III stage CRC were included in a training cohort. The fully quantitative collagen features were extracted at the tumor center and invasive margin of the specimens using multiphoton imaging. LASSO regression was applied to construct the collagen signature. The association of the collagen signature with Immunoscore was assessed. A collagen nomogram was developed by incorporating the collagen signature and clinicopathological predictors after multivariable logistic regression. The performance of the collagen nomogram was evaluated via calibration, discrimination, and clinical usefulness and then tested in an independent validation cohort. The prognostic values of the collagen nomogram were assessed using Cox regression and the Kaplan-Meier method.

Results

The collagen signature was constructed based on 16 collagen features, which included 6 collagen features from the tumor center and 10 collagen features from the invasive margin. Patients with a high collagen signature were more likely to show a low Immunoscore (Lo IS) in both cohorts (P<0.001). A collagen nomogram integrating the collagen signature and clinicopathological predictors was developed. The collagen nomogram yielded satisfactory discrimination and calibration, with an AUC of 0.925 (95% CI: 0.895-0.956) in the training cohort and 0.911 (95% CI: 0.872-0.949) in the validation cohort. Decision curve analysis confirmed that the collagen nomogram was clinically useful. Furthermore, the collagen nomogram-predicted subgroup was significantly associated with prognosis. Moreover, patients with a low-probability Lo IS, rather than a high-probability Lo IS, could benefit from chemotherapy in high-risk stage II and stage III CRC patients.

Conclusions

The collagen signature is significantly associated with the Immunoscore in the TME, and the collagen nomogram has the potential to individualize the prediction of the Immunoscore and identify CRC patients who could benefit from adjuvant chemotherapy.

Transformers for extracting breast cancer information from Spanish clinical narratives

The wide adoption of electronic health records (EHRs) offers immense potential as a source of support for clinical research. However, previous studies focused on extracting only a limited set of medical concepts to support information extraction in the cancer domain for the Spanish language. Building on the success of deep learning for processing natural language texts, this paper proposes a transformer-based approach to extract named entities from breast cancer clinical notes written in Spanish and compares several language models. To facilitate this approach, a schema for annotating clinical notes with breast cancer concepts is presented, and a corpus for breast cancer is developed. Results indicate that both BERT-based and RoBERTa-based language models demonstrate competitive performance in clinical Named Entity Recognition (NER). Specifically, BETO and multilingual BERT achieve F-scores of 93.71% and 94.63%, respectively. Additionally, RoBERTa Biomedical attains an F-score of 95.01%, while RoBERTa BNE achieves an F-score of 94.54%. The findings suggest that transformers can feasibly extract information in the clinical domain in the Spanish language, with the use of models trained on biomedical texts contributing to enhanced results. The proposed approach takes advantage of transfer learning techniques by fine-tuning language models to automatically represent text features and avoiding the time-consuming feature engineering process.

Identification of a ferroptosis-related gene signature predicting recurrence in stage II/III colorectal cancer based on machine learning algorithms

Background: Colorectal cancer (CRC) is one of the most prevalent cancer types globally. A survival paradox exists due to the inherent heterogeneity in stage II/III CRC tumor biology. Ferroptosis is closely related to the progression of tumors, and ferroptosis-related genes can be used as a novel biomarker in predicting cancer prognosis. Methods: Ferroptosis-related genes were retrieved from the FerrDb and KEGG databases. A total of 1,397 samples were enrolled in our study from nine independent datasets, four of which were integrated as the training dataset to train and construct the model, and validated in the remaining datasets. We developed a machine learning framework with 83 combinations of 10 algorithms based on 10-fold cross-validation (CV) or bootstrap resampling algorithm to identify the most robust and stable model. C-indice and ROC analysis were performed to gauge its predictive accuracy and discrimination capabilities. Survival analysis was conducted followed by univariate and multivariate Cox regression analyses to evaluate the performance of identified signature. Results: The ferroptosis-related gene (FRG) signature was identified by the combination of Lasso and plsRcox and composed of 23 genes. The FRG signature presented better performance than common clinicopathological features (e.g., age and stage), molecular characteristics (e.g., BRAF mutation and microsatellite instability) and several published signatures in predicting the prognosis of the CRC. The signature was further stratified into a high-risk group and low-risk subgroup, where a high FRG signature indicated poor prognosis among all collected datasets. Sensitivity analysis showed the FRG signature remained a significant prognostic factor. Finally, we have developed a nomogram and a decision tree to enhance prognosis evaluation. Conclusion: The FRG signature enabled the accurate selection of high-risk stage II/III CRC population and helped optimize precision treatment to improve their clinical outcomes.

The Prognostic Significance of Postoperative Adjuvant Chemotherapy in the Population Aged 75 Years and Older with Stage II-III Colorectal Cancer: A Retrospective Multi-Center Cohort Study

Background

It is common for elderly patients to be underrepresented in clinical trials for cancer, which can result in a lack of efficacy data and unclear criteria to guide treatment decisions for clinical doctors. Therefore, one of the common challenges in oncology treatment is determining the extent to which patients aged 75 and older have benefited from postoperative chemotherapy.

Purpose

The study aimed to explore the effect of adjuvant chemotherapy (AC) on 3-year recurrence-free survival (RFS) after curative resection in patients aged 75 years and older with stage II-III colorectal cancer (CRC).

Methods

The retrospective cohort analysis was performed on patients with stage II-III CRC who received curative resection at three cancer centers in China between 2008 and 2017. Kaplan-Meier curves and Multivariable Cox regression models were used to analyze the impact of AC on RFS in patients. Finally, propensity-score matching was used to reduce selection bias and confounding factors in patients aged 75 years and older with stage II-III CRC.

Results

A total of 2885 patients were included (1729 (59.9%) male; 1312 (61.5%) received AC). The pre-matching cohort was comprised of 151 patients aged 75 years and older (median age (IQR)77.00 (76.00, 79.00); 97 (64.2%) male, 51 (72.9%) received AC). Age (P=0.001), postoperative carcinoembryonic antigen (CEA)(P=0.02) level were associated with prognosis. But AC was not associated with 3-year RFS (HR, 1.27; 95% CI, 0.80-2.0; log-rank P=0.37). After a predisposition 1: 1 match (with or without AC, n = 42), AC remains uncorrelated with 3-year RFS (HR, 1.39; 95% CI, 0.52-3.70; log-rank P=0.66).

Conclusion

Patients over the age of 75 with stage II-III CRC who receive AC or do not face the same risk of postoperative recurrence. As a result, patients with stage II-III postoperative adjuvant chemotherapy can make an informed decision regarding whether they want to undergo chemotherapy based on their age and reduce the unnecessary side effects of chemotherapy.

Prediction values of tertiary lymphoid structures in the prognosis of patients with left- and right-sided colon cancer: a multicenter propensity score-matched study

BACKGROUND

Tertiary lymphoid structures (TLS) are the lymphocyte aggregates that play a key role in the vast majority of solid tumors including colon cancer, displaying an antitumor effect under most circumstances. The heterogeneity between left- and right-sided colon cancer (LCC and RCC) encompasses various aspects, such as clinical manifestations, pathological features, and immune responses. However, the function and prognostic significance of TLS within LCC and RCC have yet to be fully understood.

METHODS

A retrospective analysis was performed on 2612 patients who underwent radical resection for LCC or RCC without distant metastasis in multiple medical centers. Utilizing propensity score matching, 121 patients with LCC and 121 patients with RCC were selected for the training set. An external validation set including 64 patients with LCC and 64 patients with RCC were also employed. Hematoxylin-eosin and immunohistochemical staining were used to assess TLS and the proportion of various immune cells. Clinical characteristics and prognostic values of TLS in patients with LCC and RCC were analyzed. Nomograms were constructed for LCC and RCC to predict 3-year and 5-year overall survival (OS), respectively.

RESULTS

For LCC and RCC patients, TLS was located in the interstitial region or outside the tumor tissue and mainly consisted of B cells and T cells. The TLS quantity and density in RCC were higher than those of LCC. In multivariate Cox regression analysis, TLS density ( P =0.014), vascular invasion ( P =0.019), and AJCC stage ( P =0.026) were independent prognostic factors for 5-year OS of RCC. For LCC patients, AJCC stage ( P =0.024), tumor differentiation ( P =0.001), and tumor budding ( P =0.040) emerged as independent prognostic factors for 5-year OS. Similar results were obtained in the external verification set. Separate nomograms for RCC and LCC were developed, displaying improved prediction performance compared to the AJCC 8th edition TNM staging system.

CONCLUSIONS

Differences in TLS quantity and density were observed between LCC and RCC, suggesting that a nomogram based on TLS density could more effectively predict survival for RCC patients. Furthermore, a nomogram based on tumor budding was recommended for better prediction of LCC patient survival. Taken together, these results suggested that the immune and clinical characteristics of colon cancer at left and right side were substantially different, which may lead to the use of different prediction model and the development of individual treatment strategy.

Targeting RAF Isoforms and Tumor Microenvironments in RAS or BRAF Mutant Colorectal Cancers with SJ-C1044 for Anti-Tumor Activity

Colorectal cancer (CRC) is a significant global health issue characterized by a high prevalence of KRAS gene mutations. The RAS/MAPK pathway, involving KRAS, plays a crucial role in CRC progression. Although some RAS inhibitors have been approved, their efficacy in CRC is limited. To overcome these limitations, pan-RAF inhibitors targeting A-Raf, B-Raf, and C-Raf have emerged as promising therapeutic strategies. However, resistance to RAF inhibition and the presence of an immunosuppressive tumor microenvironment (TME) pose additional obstacles to effective therapy. Here, we evaluated the potential of a novel pan-RAF inhibitor, SJ-C1044, for targeting mutant KRAS-mediated signaling and inhibiting CRC cell proliferation. Notably, SJ-C1044 also exhibited inhibitory effects on immunokinases, specifically, CSF1R, VEGFR2, and TIE2, which play crucial roles in immune suppression. SJ-C1044 demonstrated potent antitumor activity in xenograft models of CRC harboring KRAS or BRAF mutations. Importantly, treatment with SJ-C1044 resulted in increased infiltration of T cells and reduced presence of tumor-associated macrophages and regulatory T cells within the TME. Thus, SJ-C1044 shows immunomodulatory potential and the ability to enhance antitumor responses. The study underscores the therapeutic potential of SJ-C1044 as a novel pan-RAF inhibitor capable of targeting oncogenic signaling pathways and overcoming immune suppression in CRC.

Association of collagen deep learning classifier with prognosis and chemotherapy benefits in stage II-III colon cancer

The current tumor-node-metastasis staging system does not provide sufficient prognostic prediction or adjuvant chemotherapy benefit information for stage II-III colon cancer (CC) patients. Collagen in the tumor microenvironment affects the biological behaviors and chemotherapy response of cancer cells. Hence, in this study, we proposed a collagen deep learning (collagen^DL) classifier based on the 50-layer residual network model for predicting disease-free survival (DFS) and overall survival (OS). The collagen^DL classifier was significantly associated with DFS and OS (P < 0.001). The collagen^DL nomogram, integrating the collagen^DL classifier and three clinicopathologic predictors, improved the prediction performance, which showed satisfactory discrimination and calibration. These results were independently validated in the internal and external validation cohorts. In addition, high-risk stage II and III CC patients with high-collagen^DL classifier, rather than low-collagen^DL classifier, exhibited a favorable response to adjuvant chemotherapy. In conclusion, the collagen^DL classifier could predict prognosis and adjuvant chemotherapy benefits in stage II-III CC patients.

Combining of immunotherapeutic approaches with chemotherapy for treatment of gastric cancer: Achievements and limitations

Evidence reveals that gastric cancer (GC) is the fifth most common malignancy in humans, and about 770,000 people die from this cancer yearly. It has been reported that new cases and deaths from GC are more common in men than women. Therapeutic approaches, such as surgery, chemotherapy, and radiotherapy, have been common for treating GC. Nevertheless, due to the complications and limitations of these methods, researchers use novel approaches, such as immunotherapeutic or target therapies, to evaluate the effectiveness of treatment in patients with metastatic GC. Studies have shown that monotherapy is usually associated with unpromising outcomes, and combination therapy can be a more practical option for treating metastatic GC. Therefore, to clarify different aspects of chemotherapy and immunotherapy in patients with metastatic GC, this review discussed the achievements and challenges of combining immunotherapeutic methods with chemotherapeutic agents.

SCF-FBXL8 contributes to liver metastasis and stem-cell-like features in colorectal cancer cells by mediating ubiquitination and degradation of TP53

BACKGROUND

FBXL8 is a conserved F-box protein, belonging to the ubiquitin ligase complex, which promotes the development and progression of tumours. However, the regulation function and mechanism of FBXL8's involvement in colorectal cancer (CRC) remain unclear.

METHODS

RT-PCR is used to detect gene expression levels. Protein levels were determined by western blotting and flow cytometry. The bindings of FBXL8 and p53 and ubiquitination levels were detected by cell transfection and immunoprecipitation. The transwell assay was used to measure the ability of cells to migrate and invade. Animal studies were used to verify the function of FBXL8 in vivo.

RESULTS

The expression of FBXL8 was up-regulated in CRC tissues, and its overexpression was associated with poor prognosis in CRC patients. The up-regulation of FBXL8 promoted the proliferation, invasion and migration of CRC tumour cells and maintained the stem-cell characteristics of colorectal tumour cells. Further analysis demonstrated that FBXL8 targeted p53 and reduced its stability through ubiquitination. Knockout of FBXL8 down-regulated the proliferation, migration and stem-like properties of tumour cells. CRC mouse xenograft tumour model confirmed that FBXL8 gene knockout inhibited tumour formation and liver metastasis.

CONCLUSION

FBXL8 was highly expressed in CRC. Mechanism studies have shown that FBXL8 degraded tumour suppressor gene p53 by ubiquitination. FBXL8 knockout inhibited the proliferation and stem characteristics of CRC cells, so SCF-FBXL8-TP53 has potential to be used as a therapeutic target for CRC in subsequent studies.

The E3 ubiquitin ligase SCF (FBXW10)-mediated LATS2 degradation regulates angiogenesis and liver metastasis in colorectal cancer

F-box and WD repeat domain containing 10 (FBXW10) is a member of the FBXW subgroup that contains the WD40 domain. FBXW10 has been rarely reported in colorectal cancer (CRC) and its mechanism is unclear. To investigate the role of FBXW10 in CRC, we conducted in vitro and in vivo experiments. Through the database and our clinical samples, we found that FBXW10 expression was up-regulated in CRC, and it was positively correlated with CD31 expression. CRC patients with high FBXW10 expression levels had a poor prognosis. Overexpression of FBXW10 up-regulated cell proliferation, migration and vascular formation, while knockdown of FBXW10 had the opposite effects. Studies on the mechanism of FBXW10 in CRC showed that FBXW10 could ubiquitinate large tumor suppressor kinase 2 (LATS2) and promote its degradation with the Fbox region of FBXW10 played an essential role in this process. In vivo studies demonstrated that knockout of FBXW10 inhibited tumor proliferation and reduced liver metastasis. In conclusion, our study proved that FBXW10 was significantly overexpressed in CRC and was involved in the pathogenesis of CRC by affecting angiogenesis and liver metastasis. Mechanistically, FBXW10 degraded LATS2 through ubiquitination. Therefore, FBXW10-LATS2 can be used as a therapeutic target for CRC in subsequent studies.

Fast and label-free automated detection of microsatellite status in early colon cancer using artificial intelligence integrated infrared imaging

PURPOSE

Microsatellite instability (MSI) due to mismatch repair (MMR) defects accounts for 15-20% of colon cancers (CC). MSI testing is currently standard of care in CC with immunohistochemistry of the four MMR proteins representing the gold standard. Instead, label-free quantum cascade laser (QCL) based infrared (IR) imaging combined with artificial intelligence (AI) may classify MSI/microsatellite stability (MSS) in unstained tissue sections user-independently and tissue preserving.

METHODS

Paraffin-embedded unstained tissue sections of early CC from patients participating in the multicentre AIO ColoPredict Plus (CPP) 2.0 registry were analysed after dividing into three groups (training, test, and validation). IR images of tissue sections using QCL-IR microscopes were classified by AI (convolutional neural networks [CNN]) using a two-step approach. The first CNN (modified U-Net) detected areas of cancer while the second CNN (VGG-Net) classified MSI/MSS. End-points were area under receiver operating characteristic (AUROC) and area under precision recall curve (AUPRC).

RESULTS

The cancer detection in the first step was based on 629 patients (train n = 273, test n = 138, and validation n = 218). Resulting classification AUROC was 1.0 for the validation dataset. The second step classifying MSI/MSS was performed on 547 patients (train n = 331, test n = 69, and validation n = 147) reaching AUROC and AUPRC of 0.9 and 0.74, respectively, for the validation cohort.

CONCLUSION

Our novel label-free digital pathology approach accurately and rapidly classifies MSI vs. MSS. The tissue sections analysed were not processed leaving the sample unmodified for subsequent analyses. Our approach demonstrates an AI-based decision support tool potentially driving improved patient stratification and precision oncology in the future.

NSPA: characterizing the disease association of multiple genetic interactions at single-subject resolution

Motivation

The interaction between genetic variables is one of the major barriers to characterizing the genetic architecture of complex traits. To consider epistasis, network science approaches are increasingly being used in research to elucidate the genetic architecture of complex diseases. Network science approaches associate genetic variables' disease susceptibility to their topological importance in the network. However, this network only represents genetic interactions and does not describe how these interactions attribute to disease association at the subject-scale. We propose the Network-based Subject Portrait Approach (NSPA) and an accompanying feature transformation method to determine the collective risk impact of multiple genetic interactions for each subject.

Results

The feature transformation method converts genetic variants of subjects into new values that capture how genetic variables interact with others to attribute to a subject's disease association. We apply this approach to synthetic and genetic datasets and learn that (1) the disease association can be captured using multiple disjoint sets of genetic interactions and (2) the feature transformation method based on NSPA improves predictive performance comparing with using the original genetic variables. Our findings confirm the role of genetic interaction in complex disease and provide a novel approach for gene-disease association studies to identify genetic architecture in the context of epistasis.

Availability and implementation

The codes of NSPA are now available in: https://github.com/MIB-Lab/Network-based-Subject-Portrait-Approach.

Contact

ting.hu@queensu.ca.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

The Glasgow Microenvironment Score and risk and site of recurrence in TNM I-III colorectal cancer

BACKGROUND

Glasgow Microenvironment Score (GMS) stratifies long-term survival into three groups based on tumour phenotype: peritumoural inflammation (Klintrup-Mäkinen (KM)) and tumour stroma percentage (TSP). However, it is not known if the location of disease recurrence is influenced by the GMS category.

METHODS

Seven hundred and eighty-three TNM I-III colorectal cancers (CRC) were included. GMS (GMS0-high KM; GMS1-low KM, low TSP; GMS2-low KM, high TSP) and cancer-specific survival (CSS), overall survival (OS) and disease recurrence were assessed using Cox regression analysis.

RESULTS

Of the 783 patients, 221 developed CRC recurrence; 65 developed local recurrence + systemic disease. GMS was independent for CSS (HR 1.50, 95% CI 1.17-1.92, p < 0.001) and OS (HR 1.23, 1.05-1.44, p = 0.01). Higher GMS category was associated with T-stage, N-stage, emergency presentation and venous invasion. GMS was independent for local+systemic recurrence (HR 11.53, 95% CI 1.45-91.85, p = 0.04) and distant-only recurrence (HR 3.01, 95% CI 1.59-5.71, p = 0.002). GMS 2 disease did not appear to have statistically better outcomes with adjuvant chemotherapy in high-risk disease.

CONCLUSION

Although confounded by a higher rate of T4 and node-positive disease, GMS 1 and 2 are associated with an increased risk of local and distant recurrence. GMS is an independent poor prognostic indicator for recurrent colorectal cancer. Higher GMS patients may benefit from enhanced postoperative surveillance.

Circumferential Resection Margin is Associated With Distant Metastasis After Rectal Cancer Surgery: A Nation-wide Population-based Study Cohort

OBJECTIVE

To evaluate circumferential resection margin (CRM) as a risk factor for distant metastasis (DM) in rectal cancer.

SUMMARY OF BACKGROUND DATA

The treatment of rectal cancer has evolved over the last decades. Surgical radicality is considered the most important factor in preventing recurrences including local and distant. CRM ≤1.0 mm is considered to increase recurrence risk. This study explores the risk of DM in relation to exact CRM.

METHODS

All patients treated with abdominal resection surgery for rectal cancer between 2005 and 2013 in Sweden were eligible for inclusion in this retrospective study. Primary endpoint was DM.

RESULTS

Twelve thousand one hundred forty-six cases were identified. Eight thousand five hundred ninety-three cases were analyzed after exclusion. Seven hundred seventeen (8.6%) patients had CRM ≤1.0mm and 7577 (91.4%) patients had CRM >1.0 mm. DM recurrence rate at 5 years was 42.1% (95% CI 32.5-50.3), 31.5% (95% CI 27.3-35.5), 25.8% (95% Confidence Interval (CI) 16.2-34.4), and 19.5% (95% CI 18.5-19.5) when CRM was 0.0 mm, 0.1 to 1.0 mm, 1.1 to 1.9 mm, and CRM ≥2mm, respectively. Multivariable analysis revealed higher DM risk in CRM 0.0-1.0 mm versus >1.0 mm (hazard ratio 1.30, 95% CI 1.05-1.60; P = 0.015). No significant difference in DM risk in CRM 1.1-1.9 mm versus ≥2.0 mm (hazard ratio 0.66, 95% CI 0.34-1.28; P = 0.224) could be detected.

CONCLUSIONS

The risk of DM decreases with increasing CRM. Moreover, CRM ≤1.0 mm is a significant risk factor for DM. Thus, CRM is a dominant factor when discussing risk of DM after rectal cancer surgery.

In silico development and in vitro validation of a novel five-gene signature for prognostic prediction in colon cancer

Colon cancer is one of the most common cancers in digestive system, and its prognosis remains unsatisfactory. Therefore, this study aimed to identify gene signatures that could effectively predict the prognosis of colon cancer patients by examining the data from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. LASSO-Cox regression analysis generated a five-gene signature (DCBLD2, RAB11FIP1, CTLA4, HOXC6 and KRT6A) that was associated with patient survival in the TCGA cohort. The prognostic value of this gene signature was further validated in two independent GEO datasets. GO enrichment revealed that the function of this gene signature was mainly associated with extracellular matrix organization, collagen-containing extracellular matrix, and extracellular matrix structural constituent. Moreover, a nomogram was established to facilitate the clinical application of this signature. The relationships among the gene signature, mutational landscape and immune infiltration cells were also investigated. Importantly, this gene signature also reliably predicted the overall survival in IMvigor210 anti-PD-L1 cohort. In addition to the bioinformatics study, we also conducted a series of in vitro experiments to demonstrate the effect of the signature genes on the proliferation, migration, and invasion of colon cancer cells. Collectively, our data demonstrated that this five-gene signature might serve as a promising prognostic biomarker and shed light on the development of personalized treatment in colon cancer patients.

Transcriptomic Profiling Reveals an Enhancer RNA Signature for Recurrence Prediction in Colorectal Cancer

BACKGROUND

Colorectal cancer (CRC) is one of the most fatal malignancies worldwide, and this is in part due to high rates of tumor recurrence in these patients. Currently, TNM staging remains the gold standard for predicting prognosis and recurrence in CRC patients; however, this approach is inadequate for identifying high-risk patients with the highest likelihood of disease recurrence. Recent evidence has revealed that enhancer RNAs (eRNAs) represent a higher level of cellular regulation, and their expression is frequently dysregulated in several cancers, including CRC. However, the clinical significance of eRNAs as recurrence predictor biomarkers in CRC remains unexplored, which is the primary aim of this study.

RESULTS

We performed a systematic analysis of eRNA expression profiles in colon cancer (CC) and rectal cancer (RC) patients from the TCGA dataset. By using rigorous biomarker discovery approaches by splitting the entire dataset into a training and testing cohort, we identified a 22-eRNA panel in CC and a 19-eRNA panel in RC for predicting tumor recurrence. The Kaplan-Meier analysis showed that biomarker panels robustly stratified low and high-risk CC (p = 7.29 × 10-5) and RC (p = 6.81 × 10-3) patients with recurrence. Multivariate and LASSO Cox regression models indicated that both biomarker panels were independent predictors of recurrence and significantly superior to TNM staging in CC (HR = 11.89, p = 9.54 × 10-4) and RC (HR = 3.91, p = 3.52 × 10-2). Notably, the ROC curves demonstrated that both panels exhibited excellent recurrence prediction accuracy in CC (AUC = 0.833; 95% CI: 0.74-0.93) and RC (AUC = 0.834; 95% CI: 0.72-0.92) patients. Subsequently, a combination signature that included the eRNA panels and TNM staging achieved an even greater predictive accuracy in patients with CC (AUC = 0.85).

CONCLUSIONS

Herein, we report a novel eRNA signature for predicting recurrence in patients with CRC. Further experimental validation in independent clinical cohorts, these biomarkers can potentially improve current risk stratification approaches for guiding precision oncology treatments in patients suffering from this lethal malignancy.

The Prognostic Utilities of DNA Mismatch Repair Status and KRAS and BRAF Mutation in Korean Colorectal Cancer Patients: The KASID Multicenter Study

INTRODUCTION

KRAS, BRAF, and DNA mismatch repair (MMR) mutations aid clinical decision-making for colorectal cancer (CRC) patients. To ensure accurate predictions, the prognostic utilities of these biomarkers and their combinations must be individualized for patients with various TNM stages.

METHODS

Here, we retrospectively analyzed the clinicopathological features of 904 Korean CRC patients who underwent CRC surgery in three teaching hospitals from 2011 to 2013; we also assessed the prognostic utilities of KRAS, BRAF, and MMR mutations in these patients.

RESULTS

The overall frequencies of KRAS and BRAF mutations were 35.8% and 3.2%, respectively. Sixty-nine patients (7.6%) lacking expression of ≥1 MMR protein were considered MMR protein deficient (MMR-D); the remaining patients were considered MMR protein intact. KRAS mutations constituted an independent risk factor for shorter overall survival (OS) in TNM stage I-IV and stage III patients. BRAF mutations were associated with shorter OS in TNM stage I-IV patients. MMR-D status was strongly positive prognostic in TNM stage I-II patients.

DISCUSSION/CONCLUSION

To our knowledge, this is the first multicenter study to explore the prognostic utilities of KRAS, BRAF, and MMR statuses in Korean CRC patients. Various combinations of KRAS, BRAF, and DNA MMR mutations serve as genetic signatures that affect tumor behavior; they are prognostic in CRC patients.

KRAS mutation status between left- and right-sided colorectal cancer: are there any differences in computed tomography?

PURPOSE

To investigate the differences in clinicopathological and imaging features according to KRAS mutation status in left- and right-sided colorectal cancer.

METHOD

A total of 157 patients with pathologically proven colorectal cancer and preoperative contrast-enhanced multidetector CT examinations were enrolled. According to the tumor location and KRAS status, they were divided into two groups: the left-sided colorectal cancer (LCC) group (wild type, mutant type) and the right-sided colorectal cancer (RCC) group (wild type, mutant type). Clinicopathological and imaging features were recorded in each group. The imaging observation indicators included short axis diameter (SAD), longitudinal tumor length (LTL), tumor shape, pericolic fat stranding, bowel stenosis, intratumoral low-density range, enhancement pattern, and bowel obstruction. Univariate and multivariate logistic regression analyses were performed to compare the difference in KRAS mutation status between groups.

RESULTS

In the LCC group, SAD, tumor shape, degree of pericolic fat stranding, and bowel obstruction were significant indicators for predicting KRAS status (P < 0.05). In the RCC group, CA19-9, SAD, and intratumoral low-density range were significant indicators for predicting KRAS status (P < 0.05.). The area under the curve (AUC) of the combination image indicators in the LCC group was 0.802 [cutoff point 0.372, 95% confidence interval (CI) 0.718-0.888, sensitivity 85.4%, specificity 72.0%]. The AUC in the RCC group was 0.828 (cutoff point 0.647, 95% CI 0.726-0.931, sensitivity 79.5%, specificity 75.0%).

CONCLUSION

The CT imaging features associated with KRAS mutation status in the LCC and RCC groups were different. The combination of tumor location and imaging features can help to further improve the predictive value of KRAS status.

Prognostic and predictive molecular biomarkers in advanced colorectal cancer

The revolution of precision medicine has produced unprecedented seismic shifts in the treatment paradigm of advanced cancers. Among the major killers, colorectal cancer (CRC) is far behind the others. In fact, the great successes obtained in breast, NSCLC, melanoma, and genitourinary tract tumors have been observed only in fewer than 5 % metastatic colorectal cancer (mCRC): those with the mismatch repair deficiency (dMMR), a well-known predictive factor for to the outstanding efficacy of checkpoint inhibitors (CPI). The treatment of the remaining vast majority mCRC patients is still based upon only two molecular determinants: the RAS and BRAF mutational status. New promising biomarkers include HER2, tumor mutational burden (TMB) for its possible implications on CPI efficacy, and the extremely rare NTRK fusions. The Consensus Molecular Subtypes classification (CMS) is a good example of the efforts to combine different molecular features of this disease, although its relevance in clinical practice is still under investigation. In this Review, we focus on all these prognostic and predictive biomarkers, analyzing data from the most important clinical trials of the last years. We also try to rank them according to their prognostic and predictive power.

Identification of fatty acid metabolism-related lncRNAs in the prognosis and immune microenvironment of colon adenocarcinoma

BACKGROUND

Cancer metabolism is largely altered compared to normal cells. This study aims to explore critical metabolism pathways in colon adenocarcinoma (COAD), and reveal the possible mechanism of their role in cancer progression.

METHODS

Expression data and sequencing data of COAD samples were obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases. The expression profiles between tumor and normal samples were compared to identify differential metabolism pathways through single sample gene set enrichment analysis.

RESULTS

Fatty acid synthesis was identified as a key metabolism pathway in COAD. Based on fatty acid-related lncRNAs, two molecular subtypes (C1 and C2) were defined. C2 subtype with worse prognosis had higher immune infiltration and higher expression of immune checkpoints. Five transcription factors (TFs) including FOS, JUN, HIF1A, STAT3 and STAT2 were highly expressed in C2 subtype. Five fatty acid-related lncRNAs were identified to be biomarkers for predicting COAD prognosis. Finally, further experients showed that knockdown of lncRNA PAXIP1-AS1 decreased the triglyceride content and the fatty acid synthase and acetyl-CoA carboxylase 1 expressions, which suggested that lncRNA PAXIP1-AS1 plays an important role in fatty acid metabolism of COAD.

CONCLUSIONS

This study demonstrated that fatty acid synthesis was greatly altered in COAD. Fatty acid-related lncRNAs were speculated to be involved in cancer progression through associating with TFs. The five screened TFs may serve as new drug targets for treating COAD.

Mutant RAS and the tumor microenvironment as dual therapeutic targets for advanced colorectal cancer

RAS genes are the most frequently mutated oncogenes in cancer. These mutations occur in roughly half of the patients with colorectal cancer (CRC). RAS mutant tumors are resistant to therapy with anti-EGFR monoclonal antibodies. Therefore, patients with RAS mutant CRC currently have few effective therapy options. RAS mutations lead to constitutively active RAS GTPases, involved in multiple downstream signaling pathways. These alterations are associated with a tumor microenvironment (TME) that drives immune evasion and disease progression by mechanisms that remain incompletely understood. In this review, we focus on the available evidence in the literature explaining the potential effects of RAS mutations on the CRC microenvironment. Ongoing efforts to influence the TME by targeting mutant RAS and thereby sensitizing these tumors to immunotherapy will be discussed as well.

Temporal Trends in Clinical Evidence of 5-Year Survival Within Electronic Health Records Among Patients With Early-Stage Colon Cancer Managed With Laparoscopy-Assisted Colectomy vs Open Colectomy

Importance

Temporal shifts in clinical knowledge and practice need to be adjusted for in treatment outcome assessment in clinical evidence.

Objective

To use electronic health record (EHR) data to (1) assess the temporal trends in treatment decisions and patient outcomes and (2) emulate a randomized clinical trial (RCT) using EHR data with proper adjustment for temporal trends.

Design, Setting, and Participants

The Clinical Outcomes of Surgical Therapy (COST) Study Group Trial assessing overall survival of patients with stages I to III early-stage colon cancer was chosen as the target trial. The RCT was emulated using EHR data of patients from a single health care system cohort who underwent colectomy for early-stage colon cancer from January 1, 2006, to December 31, 2017, and were followed up to January 1, 2020, from Mass General Brigham. Analyses were conducted from December 2, 2019, to January 24, 2022.

Exposures

Laparoscopy-assisted colectomy (LAC) vs open colectomy (OC).

Main Outcomes and Measures

The primary outcome was 5-year overall survival. To address confounding in the emulation, pretreatment variables were selected and adjusted. The temporal trends were adjusted by stratification of the calendar year when the colectomies were performed with cotraining across strata.

Results

A total of 943 patients met key RCT eligibility criteria in the EHR emulation cohort, including 518 undergoing LAC (median age, 63 [range, 20-95] years; 268 [52%] women; 121 [23%] with stage I, 165 [32%] with stage II, and 232 [45%] with stage III cancer; 32 [6%] with colon adhesion; 278 [54%] with right-sided colon cancer; 18 [3%] with left-sided colon cancer; and 222 [43%] with sigmoid colon cancer) and 425 undergoing OC (median age, 65 [range, 28-99] years; 223 [52%] women; 61 [14%] with stage I, 153 [36%] with stage II, and 211 [50%] with stage III cancer; 39 [9%] with colon adhesion; 202 [47%] with right-sided colon cancer; 39 [9%] with left-sided colon cancer; and 201 [47%] with sigmoid colon cancer). Tests for temporal trends in treatment assignment (χ2 = 60.3; P < .001) and overall survival (χ2 = 137.2; P < .001) were significant. The adjusted EHR emulation reached the same conclusion as the RCT: LAC is not inferior to OC in overall survival rate with risk difference at 5 years of -0.007 (95% CI, -0.070 to 0.057). The results were consistent for stratified analysis within each temporal period.

Conclusions and Relevance

These findings suggest that confounding bias from temporal trends should be considered when conducting clinical evidence studies with long time spans. Stratification of calendar time and cotraining of models is one solution. With proper adjustment, clinical evidence may supplement RCTs in the assessment of treatment outcome over time.

The relationship between the Glasgow Microenvironment Score and Markers of Epithelial-to-Mesenchymal Transition in TNM II-III Colorectal Cancer

BACKGROUND

Recently published work on the Glasgow Microenvironment Score (GMS) demonstrated its relevance as a biomarker in TNM II-III colorectal cancer (CRC). Epithelial-to-Mesenchymal Transition (EMT) markers in colorectal cancer have also shown promise as prognostic biomarkers. This study aimed to assess the relationship between GMS and markers of EMT in stage II-III CRC.

PATIENTS AND METHODS

A previously constructed tissue microarray of CRC tumours resected between 2000 and 2007 from the Western Infirmary, Stobhill and Gartnavel General hospitals in Glasgow was used. Immunohistochemistry was performed for five markers of EMT: E-cadherin, B-catenin, Fascin, Snail and Zeb1. Two-hundred and thirty-eight TNM II-III CRC with valid scores for all EMT markers and GMS were assessed. The prognostic significance of markers of EMT in this cohort and relationships between GMS and markers of EMT were determined.

RESULTS

High cytoplasmic and nuclear B-catenin and membrane Zeb-1 were significant for worse CSS (HR 1.67, 95% CI 1.01-2.76, p<0.05; HR 2.22, 95% CI 1.24-3.97, p<0.01; and HR 2.00, 95% CI 1.07-3.77, p=0.03, respectively). GMS 0 associated with low membrane Fascin (p=0.03), whereas membrane and cytoplasmic Fascin were observed to be highest in GMS 1, but lower in GMS 2. Nuclear B-catenin was lowest in GMS 0, but highest in GMS 2 (p=0.03), in keeping with its role in facilitating EMT.

CONCLUSIONS

Novel associations were demonstrated between GMS categories and markers of EMT, particularly B-catenin and Fascin, which require further investigation in independent cohorts.

Microsatellite instability and chemosensitivity in solid tumours

The use of biomarkers that influence a targeted choice in cancer treatments is the future of medical oncology. Within this scenario, in recent years, an important role has been played by knowledge of microsatellite instability (MSI), a molecular fingerprint that identifies defects in the mismatch repair system. This knowledge has changed clinical practice in the adjuvant setting of colon cancer, and its role in the neoadjuvant setting in gastric tumours is becoming increasingly interesting, as well as in endometrial cancers in both early and advanced diseases. Furthermore, it has undoubtedly conditioned the first lines of treatment in the metastatic setting in different types of cancers. The incidence of MSI is different in different cancer types, as well as in early cancers versus metastatic disease. Knowing the incidence of MSI in the various histologies can provide insight into the potential use of this biomarker considering its prognostic value, especially in the early stages, and its predictive role with respect to treatment response. In particular, MSI can guide the choice of chemotherapy treatments in the adjuvant setting of colon and perioperative setting in gastric tumours, which could lead to immunotherapy treatments in these patients in both the early stages of the disease and the metastatic setting where the response to immunotherapy drugs in diseases with MSI is now well established. In this review, we focus on colon, gastric and endometrial cancers, and we briefly discuss other cancer types where MSI could have a potential role in oncological treatment decisions.

Effect of oxaliplatin in elderly colon cancer patients with pathological T4 and/or N2 disease: a multicenter, propensity score-matched analysis

PURPOSE

Although adjuvant chemotherapy (AC) using fluoro-pyrimidine and oxaliplatin (FU + oxaliplatin) is recommended after curative resection for locally advanced colon cancer patients, several randomized controlled trials have shown no additional effect of oxaliplatin in patients aged ≥ 70 years. Here, we examined the effectiveness of FU + oxaliplatin on the long-term outcome of old patients with a high risk of recurrence.

METHODS

This multicenter, retrospective study included 346 colon cancer patients diagnosed with pathological T4 and/or N2 disease from 2016 to 2020. They were divided into an old group (≥ 70 years, n = 197) and a young group (< 70 years, n = 167). Propensity score matching was used to minimize selection bias, and 126 patients per group were matched.

RESULTS

Before matching, the rates of poor performance status (p < 0.001) and the presence of comorbidities (76.1% vs. 47.9%, p < 0.001) were higher in the old group. Although all baseline factors were similar between groups, after matching, the AC rate was lower in the old group (45.2% vs. 65.1%, p = 0.002). In the old group, relapse-free (82.2% vs. 55.6% and 69.6%, p < 0.05) and overall survival (83.1% vs. 80.0% and 44.4%, p < 0.05) rates were significantly higher in the AC patients with FU + oxaliplatin than in the AC patients with only FU and the non-AC patients.

CONCLUSION

The selected old colon cancer patients with a high risk of recurrence gained an additional benefit with respect to prognosis from FU + oxaliplatin as AC.

Pan-cancer prognostic genetic mutations and clinicopathological factors associated with survival outcomes: a systematic review

Cancer is a leading cause of death, accounting for almost 10 million deaths annually worldwide. Personalised therapies harnessing genetic and clinical information may improve survival outcomes and reduce the side effects of treatments. The aim of this study is to appraise published evidence on clinicopathological factors and genetic mutations (single nucleotide polymorphisms [SNPs]) associated with prognosis across 11 cancer types: lung, colorectal, breast, prostate, melanoma, renal, glioma, bladder, leukaemia, endometrial, ovarian. A systematic literature search of PubMed/MEDLINE and Europe PMC was conducted from database inception to July 1, 2021. 2497 publications from PubMed/MEDLINE and 288 preprints from Europe PMC were included. Subsequent reference and citation search was conducted and a further 39 articles added. 2824 articles were reviewed by title/abstract and 247 articles were selected for systematic review. Majority of the articles were retrospective cohort studies focusing on one cancer type, 8 articles were on pan-cancer level and 6 articles were reviews. Studies analysing clinicopathological factors included 908,567 patients and identified 238 factors, including age, gender, stage, grade, size, site, subtype, invasion, lymph nodes. Genetic studies included 210,802 patients and identified 440 gene mutations associated with cancer survival, including genes TP53, BRCA1, BRCA2, BRAF, KRAS, BIRC5. We generated a comprehensive knowledge base of biomarkers that can be used to tailor treatment according to patients' unique genetic and clinical characteristics. Our pan-cancer investigation uncovers the biomarker landscape and their combined influence that may help guide health practitioners and researchers across the continuum of cancer care from drug development to long-term survivorship.

Development and external validation of a novel nomogram for predicting cancer-specific survival in patients with ascending colon adenocarcinoma after surgery: a population-based study

Background

This study aimed to develop and validate a novel nomogram to predict the cancer-specific survival (CSS) of patients with ascending colon adenocarcinoma after surgery.

Methods

Patients with ascending colon adenocarcinoma were enrolled from the Surveillance, Epidemiology, and End Results (SEER) database from 1973 to 2015 and randomly divided into a training set (5930) and a validation set (2540). The cut-off values for age, tumour size and lymph node ratio (LNR) were calculated via X-tile software. In the training set, independent prognostic factors were identified using univariate and multivariate Cox analyses, and a nomogram incorporating these factors was subsequently built. Data from the validation set were used to assess the reliability and accuracy of the nomogram and then compared with the 8th edition of the American Joint Committee on Cancer (AJCC) tumour-node-metastasis (TNM) staging system. Furthermore, external validation was performed from a single institution in China.

Results

A total of 8470 patients were enrolled from the SEER database, 5930 patients were allocated to the training set, 2540 were allocated to the internal validation set and a separate set of 473 patients was allocated to the external validation set. The optimal cut-off values of age, tumour size and lymph node ratio were 73 and 85, 33 and 75 and 4.9 and 32.8, respectively. Univariate and multivariate Cox multivariate regression revealed that age, AJCC 8th edition T, N and M stage, carcinoembryonic antigen (CEA), tumour differentiation, chemotherapy, perineural invasion and LNR were independent risk factors for patient CSS. The nomogram showed good predictive ability, as indicated by discriminative ability and calibration, with C statistics of 0.835 (95% CI, 0.823–0.847) and 0.848 (95% CI, 0.830–0.866) in the training and validation sets and 0.732 (95% CI, 0.664–0.799) in the external validation set. The nomogram showed favourable discrimination and calibration abilities and performed better than the AJCC TNM staging system.

Conclusions

A novel validated nomogram could effectively predict patients with ascending colon adenocarcinoma after surgery, and this predictive power may guide clinicians in accurate prognostic judgement.

KRAS: A Druggable Target in Colon Cancer Patients

Mutations in KRAS are among the most frequent aberrations in cancer, including colon cancer. KRAS direct targeting is daunting due to KRAS protein resistance to small molecule inhibition. Moreover, its elevated affinity to cellular guanosine triphosphate (GTP) has made the design of specific drugs challenging. Indeed, KRAS was considered ‘undruggable’. KRASG12C is the most commonly mutated variant of KRAS in non-small cell lung cancer. Currently, the achievements obtained with covalent inhibitors of this variant have given the possibility to assess the best therapeutic approach to KRAS-driven tumors. Mutation-related biochemical assets and the tissue of origin are expected to influence responses to treatment. Further attempts to obtain mutant-specific KRAS (KRASG12C) switch-II covalent inhibitors are ongoing and the results are promising. Drugs targeted to block KRAS effector pathways could be combined with direct KRAS inhibitors, immunotherapy or T cell-targeting approaches in KRAS-mutant tumors. The development of valuable combination regimens will be essential against potential mechanisms of resistance that may arise during treatment.

Microsatellite instability in colon cancer: A single center experience from North India

Background

Due to the defects of mismatch repair (MMR) genes MLH1, PMS2, MSH2, and MSH6, the mutations which occur in microsatellite region are not repaired during deoxyribonucleic acid synthesis, leading to microsatellite instability (MSI). MSI is one of the major molecular changes that occur in colorectal carcinoma (CRC). Studies have shown that MMR deficient CRC has different clinicopathological characteristics and a better stage adjusted survival when compared to microsatellite stable tumors.

Materials and Methods

We have retrospectively analyzed the cases of colon cancers treated in our institute for 3 years from 2017 to 2019. Most of the patients underwent surgery and received adjuvant chemotherapy. MSI testing was done in surgical specimen with immunohistochemistry. The clinical details of the patients were tabulated in Microsoft Excel, and statistical analysis was done using IBM SPSS Statistics for Windows, version 21 (IBM Corp., Armonk, NY, USA).

Results

A total of 52 patients who were treated in our institution from 2017 to 2019 were analyzed. The mean age was 46.8 ± 13.5 (19-72) years. The male-to-female ratio was 8:5. No significant association in patient demographics and clinicopathological parameters was observed between MSI stable and unstable disease. However, lymphovascular invasion showed a significantly higher trend in MSI unstable patients (P = 0.052). The median progression-free survival (PFS) of the entire cohort was 27.8 months (95% confidence interval = 22.7-32.9) and the median overall survival (OS) is not reached. The median PFS is 21.3 months in MSI stable patients whereas it is not reached in MSI unstable patients (P = 0.049). The median OS is 27.1 months in MSI stable patients, but it is not reached in MSI unstable patients and the difference shows a trend towards statistical significance (P = 0.061).

Conclusion

MSI unstable tumors were found to have higher PFS and higher OS in our study. It needs prospective validation in larger studies in Indian scenario.

Comprehensive Analysis of Colorectal Cancer Immunity and Identification of Immune-Related Prognostic Targets

Colorectal cancer (COAD) is ranked as the third most common cancer and second in terms of cancer-related deaths worldwide. Due to its poor overall survival and prognosis, the incidents of COAD are significantly increasing. Although treatment methods have greatly been improved in the last decade, it is still not good enough to have satisfactory treatment outcomes. In recent years, immunotherapy has been successful to some extent in the treatment of many cancers but still, many patients do not respond to immunotherapy. Therefore, it is essential to have a deeper understanding of the immune characteristics of the tumor microenvironment and identify meaningful immune targets. In terms of immune targets, COAD has been poorly explored; thus, in the current study, based on the immune cell infiltration score and differentially expressed genes, COAD tumors were classified into hot and cold tumors. The Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis was used to identify hub genes, construct a prognostic model, and screen potential immune targets. In total, 12 genes (CLK3, CYSLTR2, GJA10, CYP4Z1, FAM185A, LINC00324, EEF1A1P34, EEF1B2P8, PTCSC3, MIR6780A, LINC01666, and RNU6.661P) differentially expressed between hot and cold tumors were screened out. Among them, CYSLTR2 was considered as a potential candidate gene, because it showed a significant positive correlation with immune cell infiltration and immune checkpoints (PDCD1, CD274, and CTLA4). Finally, we constructed and validated a new prognostic model for COAD showing 0.854 AUC for the ROC curve, and these results provide sufficient potential to choose CYSLTR2 as an important immune target for the prognosis of COAD.

Prothrombin time (PT) and CEA as prognostic predictive biomarkers for postoperative recurrence after curative resection in patients with stage I-III colorectal cancer: a retrospective cohort study

There are no ideal biomarkers including the TNM stage that can accurately predict the recurrence of colorectal cancer (CRC) and the benefit of chemotherapy for stage II patients. Here, 451 CRC patients were divided into three groups according to preoperative levels of prothrombin time (PT) and CEA to analyze the value of these indexes in predicting postoperative recurrence in different TNM stages. Preoperatively elevated levels of PT and CEA were significantly associated with a high 5-year cumulative recurrence rate (CRR) and short recurrence-free survival (RFS). According to PT and CEA levels, the 5-year CRR and RFS differed significantly among the High-risk (PT ≥ 12.65 s and CEA ≥ 10.175 ng/ml), Middle-risk (PT ≥ 12.65 s or CEA ≥ 10.175 ng/ml), and Low-risk (PT < 12.65 s and CEA < 10.175 ng/ml) groups (p < 0.001). In the same TNM stage, the 5-year CRR of the High-risk group was significantly higher and the RFS was markedly shorter than those in the Low-risk and even those in stage III (p < 0.001). In the subgroup of early stage (stage I and II), the 5-year CRR of the High-risk group was significantly higher and the RFS was significantly shorter than those in stage IIIA and IIIB (p < 0.001), which is similar to IIIC. In conclusion, preoperatively elevated levels of serum PT and CEA were reliable predictors of postoperative high-risk recurrence in CRC and combined with TNM stage precisely identify postoperative recurrence CRC patients in stage I-III and the benefit of adjuvant chemotherapy for patients with stage II CRC.