The consensus molecular subtypes of colorectal cancer

Brown B, Chan TA, Chand D, Constanzo J, Demaria S, I. Gabrilovich D, Golden E, Godkin A, Guha C, P. Gupta G, Hasan A, G. Herrera F, Kaufman H, Li D, A. Melcher A, McDonald S, Merghoub T, Monjazeb AM, Paris S, Pitroda S, Sadanandam A, Schaue D, Santambrogio L, Szapary P, Sage J, W. Welsh J, Wilkins A, H. Young K, Wennerberg E, Zitvogel L, Galluzzi L, Deutsch E, C. Formenti S. Updates on radiotherapy-immunotherapy combinations: Proceedings of 8th Annual ImmunoRad Conference

The annual ImmunoRad Conference has established itself as a recurrent occasion to explore the possibility of combining radiation therapy (RT) and immunotherapy (IT) for clinical cancer management. Bringing together a number of preclinical and clinical leaders in the fields of radiation oncology, immuno-oncology and IT, this annual event fosters indeed essential conversations and fruitful exchanges on how to address existing challenges to expand the therapeutic value of RT-IT combinations. The 8th edition of the ImmunoRad Conference, which has been held in October 2024 at the Weill Cornell Medical College of New York City, highlighted exciting preclinical and clinical advances at the interface between RT and IT, setting the stage for extra progress toward extended benefits for patients with an increasing variety of tumor types. Here, we critically summarize the lines of investigation that have been discussed at the occasion of the 8th Annual ImmunoRad Conference.

CRISPR/Cas9-directed epigenetic editing in colorectal cancer

Colorectal cancer (CRC) remains a leading cause of cancer-related illness and death worldwide, arising from a complex interplay of genetic predisposition, environmental influences, and epigenetic dysregulation. Among these factors, epigenetic modifications-reversible and heritable changes in gene expression-serve as crucial regulators of CRC progression. Understanding these modifications is essential for identifying potential biomarkers for early diagnosis and developing targeted therapeutic strategies. Epigenetic drugs (epidrugs) such as DNA methyltransferase inhibitors (e.g., decitabine) and bromodomain inhibitors (e.g., JQ1) have shown promise in modulating aberrant epigenetic changes in CRC. However, challenges such as drug specificity, delivery, and safety concerns limit their clinical application. Advances in CRISPR-Cas9-based epigenetic editing offer a more precise approach to modifying specific epigenetic markers, presenting a potential breakthrough in CRC treatment. Despite its promise, CRISPR-based epigenome editing may result in unintended genetic modifications, necessitating stringent regulations and safety assessments. Beyond pharmacological interventions, lifestyle factors-including diet and gut microbiome composition-play a significant role in shaping the epigenetic landscape of CRC. Nutritional and microbiome-based interventions have shown potential in preventing CRC development by maintaining intestinal homeostasis and reducing tumor-promoting epigenetic changes. This review provides a comprehensive overview of epigenetic alterations in CRC, exploring their implications for diagnosis, prevention, and treatment. By integrating multi-omics approaches, single-cell technologies, and model organism studies, future research can enhance the specificity and efficacy of epigenetic-based therapies. Shortly, a combination of advanced gene-editing technologies, targeted epidrugs, and lifestyle interventions may pave the way for more effective and personalized CRC treatment strategies.

ARID3A inhibits colorectal cancer cell stemness and drug-resistance by targeting a multitude of stemness-associated genes

AIMS

ARID3A is highly expressed in CRC patients. However, the functional role of ARID3A in CRC remains unexplored. We sought to demonstrate ARID3A function in CRC.

MATERIALS AND METHODS

ARID3A was knocked-down using lentiviruses harboring shRNA. CRC patients' tissue cDNA array was used to assess expression of ARID3A. Effect of ARID3A on CSC-associated genes was analysed using real-time PCR array. Western-blot analysis and ChIP assay were used to validate the role of ARID3A. Paclitaxel-resistant CSC-enriched cell population was used to assess correlation between ARID3A, stemness and drug resistance potential. Ex vivo findings were corroborated on preclinical mouse model.

KEY FINDINGS

ARID3A expression was significantly higher throughout CRC stages than normal individuals. ARID3A expression was significantly higher in the aggressive CRC cell line HCT116 compared to HT29, which expressed higher levels of CD44, CD133, and EpCAM, suggesting a reciprocal relationship between ARID3A expression and CRC stemness. Real-time PCR-based stem cell array using ARID3A-knockdown HCT116 cells showed upregulation of 9 cancer stem cell (CSC)-associated genes. ChIP-assay verified binding of ARID3A on transcriptionally active promoter regions of CSC associated genes. ARID3A depletion led to enhanced proliferation, anchorage-independent growth, and ABCG2 upregulation in HCT116 cells. In paclitaxel-resistant HCT116 cells, ARID3A expression was dampened, whereas, CD44 and CD133 increased. ARID3A knockdown accelerated tumor growth and promoted larger tumor formation in nude-mouse xenograft model. Ki67, CD44 and CD133 were highly upregulated in knockdown tumors.

SIGNIFICANCE

This study demonstrated that ARID3A inhibits CRC stemness, anchorage-independent growth, self-renewal, anti-cancer drug resistance of CRC cells and tumor growth in vivo.

CDX2 downregulation regulates intrinsic WNT pathway activation, dictating metastasis in APC and CTNNB1 wildtype colorectal cancer

Colorectal cancer (CRC) can be divided into 4 subtypes of which consensus molecular subtype 4 (CMS4) is associated with metastasis and poor survival. Previously, we reported that the KPN mouse model resembles human CMS4. Strikingly, although tumor formation in this model is slow and limited, effective metastasis is observed. To understand this aggressive behavior, we compared two distinct in vitro KPN models, organoids and tumoroids. The organoid model only carries the original mutations, while the tumoroids are derived from in vivo grown tumors that underwent selection during development. Here, we reveal that tumoroids harbor endogenous WNT pathway activity, which can be driven by tankyrase activity and Cdx2 downregulation. Importantly, WNT pathway activation was heterogeneous in nature, subject to regulation and allowed for a mixture of WNT-driven and YAP-driven cells within tumoroids. This unique type of WNT pathway activation is not crucial for colonic tumor growth, but results in metastatic spreading. Intriguingly, these findings reflect a specific subset of aggressive human CMS4 cancers that display low CDX2 expression and lack of classical WNT pathway mutations, while having a higher tendency to metastasize. Together, these data propose a novel mechanism for WNT pathway activation that drives metastasis formation in aggressive CRC.

Advances in BRAF mutated colorectal cancer-could deoxycholic acid be the culprit?

BRAF mutated colorectal cancer (CRC) often demonstrates distinct molecular profiles characterized by a high methylator phenotype with two different microsatellite statuses (MSI and MSS) and corresponding methylation spectra. Prognostic disparities between these two different BRAF mutated CRC arise from divergent carcinogenic pathways, with BRAF-mutated MSS CRC exhibiting particularly unfavorable clinical outcomes. The underlying mechanism of these phenomena stems from epigenetic heterogeneity in methylation landscapes. Emerging evidences linking cholelithiasis and deoxycholic acid (DCA) to BRAF-mutated CRC pathogenesis warrant systematic investigation into their potential mechanistic relationships. Elucidating these connections could unravel novel pathogenetic pathways and inform targeted strategies for risk mitigation, molecular diagnostics, and therapeutic intervention of BRAF-mutated CRC.

A quantitative tumor-wide analysis of morphological heterogeneity of colorectal adenocarcinoma

The intertumoral and intratumoral heterogeneity of colorectal adenocarcinoma (CRC) at the morphologic level is poorly understood. Previously, we identified morphological patterns associated with CRC molecular subtypes and their distinct molecular motifs. Here we aimed to evaluate the heterogeneity of these patterns across CRC. Three pathologists evaluated dominant, secondary, and tertiary morphology on four sections from four different FFPE blocks per tumor in a pilot set of 22 CRCs. An AI-based image analysis tool was trained on these tumors to evaluate the morphologic heterogeneity on an extended set of 161 stage I-IV primary CRCs (n = 644 H&E sections). We found that most tumors had two or three different dominant morphotypes and the complex tubular (CT) morphotype was the most common. The CT morphotype showed no combinatorial preferences. Desmoplastic (DE) morphotype was rarely dominant and rarely combined with other dominant morphotypes. Mucinous (MU) morphotype was mostly combined with solid/trabecular (TB) and papillary (PP) morphotypes. Most tumors showed medium or high heterogeneity, but no associations were found between heterogeneity and clinical parameters. A higher proportion of DE morphotype was associated with higher T-stage, N-stage, distant metastases, AJCC stage, and shorter overall survival (OS) and relapse-free survival (RFS). A higher proportion of MU morphotype was associated with higher grade, right side, and microsatellite instability (MSI). PP morphotype was associated with earlier T- and N-stage, absence of metastases, and improved OS and RFS. CT was linked to left side, lower grade, and better survival in stage I-III patients. MSI tumors showed higher proportions of MU and TB, and lower CT and PP morphotypes. These findings suggest that morphological shifts accompany tumor progression and highlight the need for extensive sampling and AI-based analysis. In conclusion, we observed unexpectedly high intratumoral morphological heterogeneity of CRC and found that it is not heterogeneity per se, but the proportions of morphologies that are associated with clinical outcomes.

Single-cell transcriptomic analysis identifies tissue-specific fibroblasts as the main modulators of myeloid cells in peritoneal metastasis of different origin

Colorectal cancer (CRC) peritoneal metastasis (CPM) is related to limited therapy options and poor prognosis. Although stromal cells heavily infiltrate most CPMs, interactions between different cell types in their microenvironment remain unclear. Here, we investigated tumor and distant normal tissue from CPM and CRC patients using single-cell RNA sequencing. Investigating the incoming and outgoing signals between cells revealed that fibroblasts dominate the CPM signaling landscape with myeloid cells as their strongest interaction partner. Using immunohistochemistry, we confirmed that fibroblasts co-localize with macrophages in the CPM microenvironment. A fibroblast sub-population detected only in CPM and normal peritoneum demonstrated immunoregulatory properties in co-culture experiments, and was further detected in additional peritoneal malignancies derived from ovarian and gastric origin. This novel fibroblast type and its communication with macrophages could be attractive targets for therapeutic interventions in CPM and potentially peritoneal surface malignancies in general.

Deep learning-based quantification of eosinophils and lymphocytes shows complementary prognostic effects in colorectal cancer patients

The immune microenvironment of colorectal cancer is a major component of the disease and influences not only tumor progression and patient outcome but also therapy response. Expanding on existing studies which have explored the prognostic value of the adaptive immune response with lymphocytes, our study integrates innate immune cells, specifically eosinophils, in a combined analysis. To evaluate the prognostic significance of eosinophils within the context of lymphocyte infiltration, we analyzed a large collective of 1625 colorectal cancer cases from four different centers. For this purpose, we develop an automatic deep learning pipeline for quantification of these immune cells directly from hematoxylin and eosin-stained whole slide images. Our analysis shows eosinophils in the tumor front (EosF) as independent prognostic factor (HR = 0.70, 95%CI = 0.55 - 0.90, p = 0.005), particularly also in microsatellite instability (MSI) cases (HR = 0.32, 95%CI = 0.14 - 0.74, p = 0.008). Moreover, EosF and intraepithelial lymphocytes (IELs) counts are statistically independent and provide additive prognostic information (EosF: HR = 0.71, 95%CI = 0.55 - 0.90, p = 0.005, IELs HR = 0.59, 95%CI = 0.35 - 0.99, p = 0.047). Our study demonstrates that eosinophils are an independent prognostic factor, which can be automatically quantified, underscoring its high potential for translation to a diagnostic biomarker. Moreover, our work could pave the way towards an integrated immune score directly from hematoxylin and eosin-stained sections.

Spatial Heterogeneity, Stromal Phenotypes, and Therapeutic Vulnerabilities in Colorectal Cancer Peritoneal Metastasis

PURPOSE

Peritoneal metastases (PM) in colorectal cancer portend a poor prognosis. We sought to elucidate molecular features differentiating primary tumors (PT) from PMs and actionable targets facilitating transcoelomic dissemination and progression.

EXPERIMENTAL DESIGN

We performed multiomic profiling of 227 samples from 136 patients, including 56 PTs and 120 synchronous PMs comprising 34 matched PT-PM pairs. Whole-exome and bulk RNA sequencing analyses were conducted to identify underlying genomic aberrations and transcriptomic differences between primary and peritoneal lesions. We spatially characterized the microenvironment of tumor-stroma compartments and studied the roles of stromal phenotypes in promulgating tumorigenesis.

RESULTS

Whole-exome sequencing found that genomic alterations and clonality patterns between PTs and PMs remain broadly similar. Transcriptomic profiles, however, suggest a transition as tumors reach the peritoneum toward a more mesenchymal tumor profile and fibrotic tumor microenvironment. Applying spatial profiling, we identify a fibro-collagenous and immune-infiltrated stromal phenotype [stromal cluster (SC) 2] characterized by increased cancer-associated fibroblasts, memory B cells, M2 macrophages, and T-cell exhaustion. These findings were orthogonally validated by multiplex IHC. Patients with SC2 stroma had poorer survival and were characterized by high SERPINE-1 (PAI-1) expression. PMs in patients with SC2 stroma were associated with enriched oncogenic pathways such as TGF-β. PAI-1 inhibition of colorectal cancer PM cell lines with a novel biologic demonstrated reduced IL2-STAT5 and TGF-β pathways and cell death.

CONCLUSIONS

Our findings unveil distinctive and actionable molecular signatures, offering deeper insights into the intricate cross-talk between tumor cells and stromal microenvironments enabling PM in colorectal cancer.

Evaluation of a novel surrogate panel for classifying human colorectal carcinomas according to consensus molecular subtypes

Clinical triaging of colorectal carcinomas (CRCs) is essential for prognostication and therapeutic decision-making. Consensus Molecular Subtyping (CMS) was developed for this purpose; however, it requires comprehensive genomic and transcriptomic studies and prediction algorithms, restricting its usage. We examined the utility of a limited surrogate panel of markers for classifying CRCs. We investigated the expression of immunohistochemical markers MLH1, PMS2, MSH2, MSH6, CDX2, HTRB2, FRMD6, and GLUT1, along with reverse transcriptase polymerase chain reaction for KRAS mutation in a retrospective cohort of 100 CRCs. MMR-deficient cases were classified as CMS1. Differential expressions of other markers, alongside consideration of KRAS mutation status as per CMS guidelines, were utilized to classify the tumors into three additional groups. A significant correlation was observed between tumor subtypes and TNM stage groups (P 0.04). While most stage I and II tumors were CMS1 (77.1 %, n-27/35) and CMS2 tumors (91.7 %, n-11/12), stage III and IV tumors were mostly CMS3 (50 %, n-6/12) and CMS4 (44.8 %, n = 13/29) tumors. Our algorithm classified the CRCs into prognostically favorable CMS2/CMS3 types, then unfavorable CMS1/CMS4 types. Notably, However, overall survival and disease-free survivals did not differ as per the individual CMS types. This study highlights the potential of surrogate tumor typing for clinical triaging. However, further research, building on the findings of this study and existing IHC-based classifiers, is essential to develop a more effective and practical surrogate classifier.

Chemotherapy plus bevacizumab with or without anti-programmed death 1 immunotherapy as the second-line therapy in colorectal cancer

BACKGROUND

Patients with microsatellite stable (MSS) metastatic colorectal cancer (mCRC) typically exhibit an immunosuppressive tumor microenvironment and demonstrate a low response rate to immunotherapy. Reports suggest that chemotherapy and anti-angiogenic therapy may have the potential to enhance the response to immunotherapy in these patients. This study aims to evaluate the effectiveness and safety of chemotherapy combined with bevacizumab with or without anti-programmed death 1 (PD-1) immunotherapy as the second-line regimen for MSS mCRC.

AIM

To evaluate the effectiveness and safety of chemotherapy combined with bevacizumab with or without anti-PD-1 immunotherapy as the second-line regimen for MSS mCRC.

METHODS

A retrospective analysis was conducted on patients with MSS mCRC diagnosed at Peking University First Hospital and Jilin Cancer Hospital from January 2020 to December 2024. The patients were divided into two groups: The experimental group receiving second-line chemotherapy combined with bevacizumab and anti-PD-1 immunotherapy, and the control group receiving chemotherapy combined with bevacizumab. Propensity score matching was applied to balance potential prognostic factors, including age, gender, Eastern Cooperative Oncology Group score, number of metastases, and primary tumor site. The progression-free survival, overall survival, disease control rate, objective response rate, and treatment-related adverse reactions were compared between the two groups. Kaplan-Meier analysis and log-rank test were used to compare survival outcomes. Inverse probability of treatment weighting was used for sensitivity analysis.

RESULTS

Propensity score matching resulted in 103 matched eligible patients. The median follow-up period was 13.9 months in the matched cohort. The objective response rate was 11.5% and 9% for the experimental and control groups, respectively (P = 0.710), while the disease control rate was 76.9% and 53.2%, respectively (P = 0.058). The median progression-free survival in the experimental group was 8.27 months [95% confidence interval (CI): 6.7-14.7 months], significantly higher than that in the control group, which was 4.63 months (95%CI: 3.9-5.67 months) (hazard ratio = 0.4143, 95%CI: 0.2462-0.6972, P = 0.00066). There was a trend towards the higher median overall survival in the experimental group compared to the control group (hazard ratio = 0.4504, 95%CI: 0.1897-1.07, P = 0.064). The incidences of adverse events were similar between the two groups.

CONCLUSION

Compared with the standard second-line chemotherapy combined with bevacizumab regimen, second-line therapy that combines chemotherapy with bevacizumab and anti-PD-1 immunotherapy has demonstrated promising efficacy in the treatment of MSS mCRC, while exhibiting a similar safety profile.

Recent advances and challenges in colorectal cancer: From molecular research to treatment

Colorectal cancer (CRC) ranks among the top causes of cancer-related fatalities globally. Recent progress in genomics, proteomics, and bioinformatics has greatly improved our comprehension of the molecular underpinnings of CRC, paving the way for targeted therapies and immunotherapies. Nonetheless, obstacles such as tumor heterogeneity and drug resistance persist, hindering advancements in treatment efficacy. In this context, the integration of artificial intelligence (AI) and organoid technology presents promising new avenues. AI can analyze genetic and clinical data to forecast disease risk, prognosis, and treatment responses, thereby expediting drug development and tailoring treatment plans. Organoids replicate the genetic traits and biological behaviors of tumors, acting as platforms for drug testing and the formulation of personalized treatment approaches. Despite notable strides in CRC research and treatment - from genetic insights to therapeutic innovations - numerous challenges endure, including the intricate tumor microenvironment, tumor heterogeneity, adverse effects of immunotherapies, issues related to AI data quality and privacy, and the need for standardization in organoid culture. Future initiatives should concentrate on clarifying the pathogenesis of CRC, refining AI algorithms and organoid models, and creating more effective therapeutic strategies to alleviate the global impact of CRC.

Oncological Outcomes From Cytoreductive Surgery and Heated Intraperitoneal Chemotherapy for Colorectal Cancer Peritoneal Metastases

BACKGROUND

Cytoreductive surgery (CRS) is effective for colorectal cancer peritoneal metastases (CRPM) at increasing overall survival (OS) compared to systemic anticancer treatment (SACT) alone. The addition of Oxaliplatin heated intraperitoneal chemotherapy (HIPEC) has been shown in a randomized controlled trial to result in increased complications without significant OS benefit. This study evaluates outcomes for CRPM patients undergoing CRS+HIPEC with Oxaliplatin (Ox) 368mg/m2 (30 min), versus Mitomycin C (MMC) 35mg/m2 (90min).  METHODS: A prospective CRPM real-world database was used to collect outcomes for patients undergoing CRS+HIPEC at a single center. OS, recurrence-free (RFS), peritoneal RFS (PeRFS) were compared amongst all patients with histologically proven CRPM, those with completeness of cytoreduction (CC) score =0/1, and those with CC score=0/1 who were SACT naïve.  RESULTS: Between April 2005 and April 2021, 409 patients underwent CRS+HIPEC: 271 (66%) had MMC, 138 (34%) Ox. Of these, 395 (97%) had histologically confirmed CRPM, 336 (85%) achieved CC=0/1, 188 (47%) were SACT naïve; median OS =39.5, 44.4, and 47.2 months respectively. MMC versus Ox median OS in CC0/1=43.7 (95% CI 35.9-48.3) versus 50.1 (39.7-70.2) months, P = .28; Median OS in SACT naïve=45.7 (39.4-65.9) versus 59.9 (38.3-82.0) months, P = .31; multivariable analysis for CC0/1, SACT naïve patients showed Ox was comparable to MMC: HR=0.90, (0.64-1.27) P = .55 versus HR=0.88, (0.53-1.44) P = .60, respectively. Ox resulted in a significantly improved PeRFS in CC0/1 patients (MMC=9.0 versus Ox=12.6months, P = .01). A multivariable model for PeRFS showed a HR=0.63, (0.43-0.95), P = .03 for Ox.  CONCLUSION: This study suggests a role for Ox HIPEC in CRPM which should be explored further in clinical trials.

A novel machine learning-based workflow to capture intra-patient heterogeneity through transcriptional multi-label characterization and clinically relevant classification

OBJECTIVES

Patient classification into specific molecular subtypes is paramount in biomedical research and clinical practice to face complex, heterogeneous diseases. Existing methods, especially for gene expression-based cancer subtyping, often simplify patient molecular portraits, neglecting the potential co-occurrence of traits from multiple subtypes. Yet, recognizing intra-sample heterogeneity is essential for more precise patient characterization and improved personalized treatments.

METHODS

We developed a novel computational workflow, named MULTI-STAR, which addresses current limitations and provides tailored solutions for reliable multi-label patient subtyping. MULTI-STAR uses state-of-the-art subtyping methods to obtain promising machine learning-based multi-label classifiers, leveraging gene expression profiles. It modifies standard single-label similarity-based techniques to obtain multi-label patient characterizations. Then, it employs these characterizations to train single-sample predictors using different multi-label strategies and find the best-performing classifiers.

RESULTS

MULTI-STAR classifiers offer advanced multi-label recognition of all the subtypes contributing to the molecular and clinical traits of a patient, also distinguishing the primary from the additional relevant secondary subtype(s). The efficacy was demonstrated by developing multi-label solutions for breast and colorectal cancer subtyping that outperform existing methods in terms of prognostic value, primarily for overall survival predictions, and ability to work on a single sample at a time, as required in clinical practice.

CONCLUSIONS

This work emphasizes the importance of moving to multi-label subtyping to capture all the molecular traits of individual patients, considering also previously overlooked secondary assignments and paving the way for improved clinical decision-making processes in diverse heterogeneous disease contexts. Indeed, MULTI-STAR novel, reproducible and generalizable approach provides comprehensive representations of patient inner heterogeneity and clinically relevant insights, contributing to precision medicine and personalized treatments.

From blockage to biology: Unveiling the role of extracellular matrix dynamics in obstructive colorectal cancer pathogenesis

Colorectal cancer obstruction is a common problem with distinct symptomatic clues on CT/MR images even under incomplete conditions. The choice of management in the emergency setting has a significant effect on the prognosis of obstructive and nonobstructive colorectal cancer patients. Previous studies have demonstrated that obstruction in colorectal cancer is associated with significantly poorer outcomes, alongside distinct alterations in the composition of the extracellular matrix. Based on accumulating evidence, it is hypothesized that ECM remodeling plays a pivotal role in the development of colorectal cancer obstruction. This review explores the pathological features of obstructive colorectal cancer, emphasizing extracellular matrix remodeling as a central process. Key mechanisms include tumor-stromal cell interactions, tumor cell aggregation and migration mediated by the peripheral nervous system, vascular and lymphatic remodeling within the tumor microenvironment, and microbiota-mediated regulation of cancer progression. These findings demonstrate that further remodeling of the extracellular matrix may be a molecular biological feature of obstructive colorectal cancer with poor prognosis.

The multifaceted role of agents counteracting metabolic syndrome: A new hope for gastrointestinal cancer therapy

Metabolic syndrome (MetS) is defined by the presence of at least three of five clinical parameters including abdominal obesity, insulin resistance, elevated triglycerides, reduced high-density lipoprotein (HDL) and hypertension. Major features describing MetS have been recognized risk factors for cancer onset, with an alarming impact on gastrointestinal (GI) tumors. Intriguingly, therapeutic administration of drugs to improve glycemic control and dyslipidemia (including metformin, statins) has been shown to have a preventive role in the development and in prognosis improvement of several cancer types. Overall, these observations highlight the key role of altered metabolism prevalently in cancer risk development and unveil anti-MetS agent repurposing potential beyond their conventional pharmacological action. The objective of this review is to summarize the current knowledge about the antitumor activity of anti-diabetic and anti-lipemic agents in GI cancer onset and progression. Here, pre-clinical evidence of their therapeutic potential and of their integration in novel compelling therapeutic strategies will be discussed. Possible clinical outcomes of these novel therapeutic combined protocols specifically dedicated to GI cancer patients will be put under the spotlight. In the future, these novel therapeutic options should be considered to improve conventional chemotherapy response and prognosis of this group of patients.

Epidemiology, pathogenesis, biology and evolving management of MSI-H/dMMR cancers

Deficiency in DNA mismatch repair (dMMR) is a common pathway of carcinogenesis across different tumour types and confers a characteristic microsatellite instability-high (MSI-H) molecular phenotype. The prevalence of the MSI-H/dMMR phenotype is highest in endometrial and colorectal cancers, and this phenotype is associated with a distinct tumour biology, prognosis and responsiveness to various anticancer treatments. In a minority of patients, MSI-H/dMMR cancers result from an inherited pathogenic variant in the context of Lynch syndrome, which has important implications for familial genetic screening. Whether these hereditary cancers have a different biology and clinical behaviour to their sporadic counterparts remains uncertain. Interest in this tumour molecular subtype has increased following the discovery of the high sensitivity of metastatic MSI-H/dMMR cancers to immune-checkpoint inhibitors (ICIs) in a histology-agnostic manner, which reflects the genomic hypermutation resulting from dMMR that renders these tumours highly immunogenic and immune infiltrated. This vulnerability is now also being exploited in early stage disease settings. Despite this common biological foundation, different MSI-H/dMMR cancers have histotype-specific features that correspond to their particular cell or tissue of origin, which might be associated with differences in prognosis and sensitivity to ICIs. In this Review, we provide an overview of the epidemiology, biology, pathogenesis, clinical diagnosis and treatment of MSI-H/dMMR tumours as a histology-agnostic cancer phenomenon. We also highlight peculiarities associated with specific pathogenetic alterations and histologies of MSI-H/dMMR tumours.

Comparative efficacy of cetuximab combined with FOLFOX or CAPEOX in first-line treatment of RAS/BRAF wild-type metastatic colorectal cancer: a multicenter case-control study

FOLFOX combined with cetuximab is a recommended first-line treatment regimen for RAS/BRAF wild-type metastatic colorectal cancer (mCRC). CAPEOX combined with cetuximab differs from the FOLFOX regimen by using oral capecitabine instead of continuous infusion of fluorouracil, offering greater convenience and cost-effectiveness with higher patient acceptance. However, the comparative efficacy of these two regimens remains debatable, necessitating further evidence to explore any differences in their efficacy. This study collected medical records of mCRC patients who were treated with CAPEOX or FOLFOX combined with cetuximab from 1 October 2021 to 16 October 2023 at Harbin Medical University Cancer Hospital and the First Hospital of Shanxi Medical University. Eligible patients were selected based on inclusion criteria and followed up through the hospital's follow-up system and telephone interviews. Kaplan-Meier survival analysis and Cox proportional hazards regression analysis were used to assess patients' progression-free survival (PFS) and overall survival (OS). A total of 71 eligible patients were enrolled in this study; 43 patients received CAPEOX combined with cetuximab (Group A, n  = 43), and 28 patients received FOLFOX combined with cetuximab (Group B, n  = 28). The two groups achieved similar median PFS (mPFS) and median OS (mOS), with mPFS of 18 months and 12 months, respectively ( P  = 0.23), and mOS of 33 months and 20 months, respectively ( P  = 0.21), with no statistically significant differences. The results of this study demonstrated that CAPEOX combined with cetuximab is an equally viable option for first-line treatment of RAS/BRAF wild-type mCRC as FOLFOX combined with cetuximab.

High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer

A comprehensive understanding of cellular behavior and response to the tumor microenvironment (TME) in colorectal cancer (CRC) remains elusive. Here, we introduce the high-definition Visium spatial transcriptomic technology (Visium HD) and investigate formalin-fixed paraffin-embedded human CRC samples (n = 5). We demonstrate the high sensitivity, single-cell-scale resolution and spatial accuracy of Visium HD, generating a highly refined whole-transcriptome spatial profile of CRC samples. We identify transcriptomically distinct macrophage subpopulations in different spatial niches with potential pro-tumor and anti-tumor functions via interactions with tumor and T cells. In situ gene expression analysis validates our findings and localizes a clonally expanded T cell population close to macrophages with anti-tumor features. Our study demonstrates the power of high-resolution spatial technologies to understand cellular interactions in the TME and paves the way for larger studies that will unravel mechanisms and biomarkers of CRC biology, improving diagnosis and disease management strategies.

Precision oncology in colorectal cancer: An anatomical revolution through molecular-clinical integration across colonic subsites

Colorectal cancer (CRC) exhibits significant heterogeneity across different colonic subsites, which vary in embryological origin, microbiome, metabolome, and molecular profiles, affecting tumorigenesis, treatment response, and prognosis. We emphasize the importance of this subsite heterogeneity to advance precision medicine in CRC.

Comprehensive metabolomic and epigenomic characterization of microsatellite stable BRAF-mutated colorectal cancer

Oncogenic codon V600E mutations of the BRAF gene affect 10-15% of colorectal cancers, resulting in activation of the MAPK/ERK signaling pathway and increased cell proliferation and survival. BRAF-mutated colorectal tumors are often microsatellite unstable and characterized by high DNA methylation levels. However, the mechanistic link between BRAF mutations and hypermethylation remains controversial. Understanding this link, particularly in microsatellite stable tumors is of great interest as these often show poor survival. We characterized the metabolomic, epigenetic and transcriptomic patterns of altogether 39 microsatellite stable BRAF-mutated colorectal cancers. Metabolomic analysis of tumor tissue showed low levels of vitamin C and its metabolites in BRAF-mutated tumors. Gene expression analysis indicated dysregulation of vitamin C antioxidant activity in these lesions. As vitamin C is an important cofactor for the activity of TET DNA demethylase enzymes, low vitamin C levels could directly contribute to the high methylation levels in these tumors by decreasing enzymatic TET activity. Vitamin C transporter gene SLC23A1 expression, as well as vitamin C metabolite levels, were inversely correlated with DNA methylation levels. This work proposes a new mechanistic link between BRAF mutations and hypermethylation, inspiring further work on the role of vitamin C in the genesis of BRAF-mutated colorectal cancer.

SATB2 Expression Affects Chemotherapy Metabolism and Immune Checkpoint Gene Expression in Colorectal Cancer

BACKGROUND

Special AT-rich binding protein-2 (SATB2) is a nuclear matrix associated protein regulating gene expression which is normally expressed in colonic tissue. Loss of SATB2 expression in colorectal cancer (CRC) has negative implications for prognosis and has been associated with chemotherapy resistance. Furthermore, recent evidence suggests SATB2 may influence immune checkpoint (IC) expression. We hypothesized that SATB2 expression may be associated with altered expression of chemotherapy resistance associated and IC genes.

METHODS

Clinicopathologic and gene expression data were extracted from The Cancer Genome Atlas PanCancer Atlas. SATB2 expression was compared by clinicopathologic characteristic and by using multivariate regression analysis to explore associations with chemotherapy and IC gene expression.

RESULTS

About 553 patients were included for analysis. Lower quartile SATB2 expression was associated with worse disease specific survival (P = .04). MSI (P < .001) and mucinous (P < .001) tumors were associated with reduced SATB2 expression independently. SATB2 varied by consensus molecular subtype (P < .001) and was lowest in CMS1. On multivariate analysis, SATB2 was negatively associated with 5-FU related metabolism genes, while more complex but significant relationships were seen with oxaliplatin and irinotecan related genes. Low SATB2 expression was associated with increased expression of PD-1, PD-L1, TIM-3 and CTLA-4 IC genes.

CONCLUSION

The positive prognostic influence of SATB2 expression is reaffirmed in this study. This effect may be explained by the negative association between SATB2 and 5-FU-resistance related gene expression. Enhanced IC gene expression in SATB2 low cases suggests a potential role for IC inhibition in this setting, but further study is required.

Research progress of colorectal cancer in genomic and transcriptomic at multi-level

Colorectal cancer is a common malignant tumor in the gastrointestinal tract, and the mechanisms of its occurrence, development, and metastasis have always been the focus of the medical community's attention. The study of CRC genetic mechanisms began with the identification of oncogenes or tumor suppressor genes and their key pathways. With further research, researchers gradually realized that single genes or pathways alone could not explain the occurrence, development, and metastasis of CRC. The development of bulk sequencing technology has helped us to analyze the occurrence, development, and metastasis mechanisms of CRC from a multi-gene, multi-pathway, and multi-dimensional perspective, but it has not brought significant benefits to the clinical treatment of tumors. The main reason for this is that bulk sequencing technology relies on homogeneous cell grouping and cannot capture the heterogeneity between cells within the tumor and the interactions within the tumor microenvironment. The development of single-cell technology has made it possible to study the mechanisms of heterogeneity between cells within CRC and the interaction within the tumor microenvironment. This review discusses the mechanisms of CRC occurrence and development in three stages: traditional molecular biology level of single gene, bulk sequencing, and single-cell sequencing. These results show that the occurrence of CRC is the result of complex interactions between genetic and non-genetic factors in somatic cell evolution, where the heterogeneity between cells within the tumor and the tumor microenvironment are crucial for CRC progression.

Immunotyping the Tumor Microenvironment Reveals Molecular Heterogeneity for Personalized Immunotherapy in Cancer

The tumor microenvironment (TME) significantly influences cancer prognosis and therapeutic outcomes, yet its composition remains highly heterogeneous, and currently, no highly accessible, high-throughput method exists to define it. To address this complexity, the TMEclassifier, a machine-learning tool that classifies cancers into three distinct subtypes: immune Exclusive (IE), immune Suppressive (IS), and immune Activated (IA), is developed. Bulk RNA sequencing categorizes patient samples by TME subtype, and in vivo mouse model validates TME subtype differences and differential responses to immunotherapy. The IE subtype is marked by high stromal cell abundance, associated with aggressive cancer phenotypes. The IS subtype features myeloid-derived suppressor cell infiltration, intensifying immunosuppression. In contrast, the IA subtype, often linked to EBV/MSI, exhibits robust T-cell presence and improved immunotherapy response. Single-cell RNA sequencing is applied to explore TME cellular heterogeneity, and in vivo experiments demonstrate that targeting IL-1 counteracts immunosuppression of IS subtype and markedly improves its responsiveness to immunotherapy. TMEclassifier predictions are validated in this prospective gastric cancer cohort (TIMES-001) and other diverse cohorts. This classifier could effectively stratify patients, guiding personalized immunotherapeutic strategies to enhance precision and overcome resistance.

Cancer-associated fibroblast-derived SEMA3C facilitates colorectal cancer liver metastasis via NRP2-mediated MAPK activation

Liver metastasis remains the predominant cause of mortality in patients with colorectal cancer (CRC). Nevertheless, the mechanisms underlying the initiation of colorectal cancer liver metastasis remain poorly elucidated. During the metastatic process of CRC cells from the primary site to the liver, we performed time-resolved analyses and identified a subset of tumor cells spatially located in the primary tumor and temporally distributed in the early stages of liver metastasis. These cells were termed liver metastasis-initiating cells (LMICs). LMICs exhibit high stemness, low proliferation, active interaction with surrounding stromal components, and a close association with liver metastasis. Notably, we found significant interactions between cancer-associated fibroblasts (CAFs) and LMICs via the SEMA3C-NRP2 receptor-ligand pair. Further in vivo and in vitro experiments confirmed that CAF-secreted SEMA3C could bind to the NRP2 receptor, which activates the MAPK pathway and promotes colorectal cancer liver metastasis. Our findings suggest potential therapeutic strategies for the early prevention of colorectal cancer liver metastasis.

Pan-cancer analysis of homologous recombination deficiency and homologous recombination repair-associated gene alterations in solid tumors from a large Asian cohort

BACKGROUND

Homologous recombination deficiency (HRD) is associated with sensitivity to platinum-based chemotherapy and PARP inhibitors in BRCA-associated cancers, including ovarian, breast, prostate, and pancreatic cancers. This study explores HRD and homologous recombination repair (HRR) gene alterations in a pan-cancer cohort to guide precision oncology.

METHODS

Clinical and genomic data from 9,262 patients with 17 solid tumor types were analyzed using the OncoScreenTM Plus kit. HRD scores, biallelic HRR and tumor suppressor gene alterations, and their clinical correlations were evaluated.

RESULTS

HRD scores varied across cancer types, all showing a long tail in distribution. The prevalence of pathogenic alterations in pan-cancer HRR was 21.3%, with 13.7% of the cases having an HRD score ≥42. HRD-related events (LOH, LST, and TAI) exhibited similarities and cancer-specific patterns at the chromosomal arm level. Biallelic loss of HRR genes, especially BRCA1, BRCA2, RAD51D, RAD51 C, and PPP2R2 A was linked to higher HRD scores in BRCA-associated cancers, while BARD1, RAD51D, RAD54L, BRCA1, and MRE11 were associated with elevated HRD scores in in other cancer types (non-BRCA cancers). TP53 biallelic alterations, with or without HRR alterations, were linked to increased HRD scores. Higher HRD scores were associated with late-stage, older, metastatic, PD-L1 positive, non-MSI-H/non-POLE samples were correlated with genomic instability indexes, such as structural chromosomal instability (SCIN), weighted genome instability index (WGII), and whole-genome doubling (WGD).

CONCLUSIONS

This is the largest pan-cancer HRD study in an Asian population, providing insights for future HRD testing and targeted therapy.

Mutational Patterns in Colorectal Cancer: Do PDX Models Retain the Heterogeneity of the Original Tumor?

Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, highlighting the need for a deeper understanding of the genetic mechanisms driving its development and progression. Identifying genetic mutations that affect key molecular pathways is crucial for advancing CRC diagnosis, prognosis, and treatment. Patient-derived xenograft (PDX) models are essential tools in precision medicine and preclinical research, aiding in the development of personalized therapeutic strategies. In this study, a comparative analysis was conducted on the most frequently mutated genes-APC, TP53, KRAS, BRAF, NRAS, and ERBB2-using data from publicly available databases (n = 7894) and models from University Medicine Rostock (n = 139). The aim of this study was to evaluate the accuracy of these models in reflecting the mutational landscape observed in patient-derived samples, with a focus on both individual mutations and co-occurring mutational patterns. Our comparative analysis demonstrated that while the ranking of individual mutations remained consistent, their overall frequencies were slightly lower in the PDX models. Interestingly, we observed a notably higher prevalence of BRAF mutations in the PDX cohort. When examining co-occurring mutations, TP53 and APC mutations-both individually and in combination with other alterations-were the most frequent in both datasets. While the PDX models showed a greater prevalence of single mutations and a slightly higher proportion of tumors without detectable mutations compared to the public dataset, these findings present valuable insights into CRC's mutational landscape. The discrepancies highlight important considerations, such as selective engraftment bias favoring more aggressive tumors, differences in sample size between the two cohorts, and potential bottleneck effects during PDX engraftment. Understanding these factors can help refine the use of PDX models in CRC research, enhancing their potential for more accurate and relevant applications in precision oncology.

Comprehensive analysis of the critical role of the epithelial mesenchymal transition subtype - TAGLN-positive fibroblasts in colorectal cancer progression and immunosuppression

Epithelial-mesenchymal transition (EMT) plays a pivotal role in tumor metastasis and immune suppression in colorectal cancer (CRC). However, the specific mechanisms of EMT and its relationship with the clinical prognosis and immunotherapy response in CRC patients remain unclear. In this study, we identified TAGLN-positive fibroblasts (TAGLN⁺Fib) as a cancer-associated fibroblast (CAF) subtype within the tumor microenvironment (TME) that promotes tumor metastasis and immune evasion. High EMT scores, strongly associated with TAGLN expression, were correlated with advanced tumor stages, poor prognosis, and resistance to immunotherapy. Functional experiments demonstrated that TAGLN knockdown significantly reduced CRC cell proliferation, migration, and EMT phenotypes in vitro and suppressed tumor growth in vivo. Furthermore, TAGLN⁺Fib closely interacted with MMP7-positive tumor epithelial cells and SPP1-positive macrophages, forming a pro-metastatic and immunosuppressive network. An EMT-TME risk model constructed using TAGLN⁺Fib exhibited robust predictive power for CRC prognosis and immunotherapy response. This study reveals the association of EMT scores with CRC prognosis and immunotherapy response, highlights TAGLN⁺Fib's critical role in tumor progression, and develops an EMT-TME risk model, offering insights for personalized CRC treatment and precision medicine.

Induction of cell death by the CXCR2 antagonist SB225002 in colorectal cancer and stromal cells

Molecular targeted therapies have had great success in cancer treatment due to their high efficacy and selectivity. Identifying specific prognostic/predictive biomarkers helps clinicians stratify patients according to individual characteristics and improves patient quality of life in terms of disease control and survival. In our previous work, we identified Interleukin-8 as an important prognostic biomarker according to specific genomic alterations of colorectal cancers, leading us to investigate the effects of its axis inhibition, by targeting the Interleukin-8 receptors CXCR1 and CXCR2. Here, we show that dual CXCR1/2 inhibition does not affect colorectal cancer cell viability, whereas CXCR2-selective inhibition by SB225002 reduces cell viability in responder colorectal cancer cell lines. More specifically, these responder cells undergo programmed cell death upon SB225002 treatment, while non responder cell lines incur in a reversible G2/M arrest. Interestingly, the same response in terms of inhibition of cell viability also occurs in the stromal compartment (normal fibroblasts): however, in this compartment, the G2/M block is non reversible, hence leading to non-apoptotic cell death. These findings suggest that SB225002 could be a potential therapeutic agent in colorectal cancer, by affecting not only cell viability, but also tumor-stroma interactions.

Synchronous triple primary colorectal cancer: a rare case report from a rural tibetan population

Synchronous multiple colorectal cancers (SMCRC) are rare and defined as distinct malignant tumors occurring simultaneously in the colon and rectum without evidence of metastasis from one tumor to another. This case report presents a 69 year-old Tibetan male admitted with acute abdominal pain, abdominal distension, nausea, and vomiting. Imaging studies and colonoscopy revealed synchronous cancers in the rectum, sigmoid colon, and transverse colon, all pathologically confirmed as moderately differentiated adenocarcinomas. The patient underwent a multisegment colectomy with complete resection of all tumors. Postoperative recovery was uneventful, and no recurrence was reported during follow-up. This case underscores the importance of thorough diagnostic and surgical strategies for SMCRC, particularly in emergency presentations where limited diagnostic modalities may pose challenges.

Immunotherapy in microsatellite-stable colorectal cancer: Strategies to overcome resistance

Colorectal cancer (CRC) is among the foremost causes of cancer-related mortality worldwide; however, individuals with microsatellite-stable (MSS) disease-who constitute most CRC diagnoses-derive limited benefit from existing immunotherapeutic approaches. Here, we outline emerging methods designed to address the inherent resistance of MSS CRC to immune checkpoint inhibitors (ICIs). Recent findings emphasize how the immunosuppressive tumor microenvironment (TME) in MSS CRC, marked by diminished immunogenicity and high levels of regulatory T cells and myeloid-derived suppressor cells, restricts effective antitumor immune activity. Combination regimens that merge ICIs with chemotherapy, anti-angiogenic agents, or targeted blockade of pathways such as TGF-β and VEGF have shown encouraging early outcomes, including enhanced antigen presentation and T-cell penetration. Novel immunomodulatory platforms-such as epigenetic modifiers, oncolytic viruses, and engineered probiotic vaccines-are under assessment to further reprogram the TME and boost therapeutic efficacy. Concurrently, progress in adoptive cell therapies (for example, chimeric antigen receptor (CAR) T cells) and the development of cancer vaccines targeting tumor-associated and neoantigens promise to extend immune control over MSS CRC. In parallel, improving patient selection through predictive biomarkers-from circulating tumor DNA (ctDNA) to gene expression signatures and specific molecular subtypes-could refine individualized treatment strategies. Finally, interventions that alter the gut microbiome, including probiotics and fecal transplantation, serve as complementary tools to strengthen ICI responses. Taken together, these insights and combined treatment strategies lay the foundation for more successful immunotherapeutic interventions in MSS CRC, ultimately aiming to provide sustained clinical benefits to a broader spectrum of patients.

Prognostic Models From Transcriptomic Signatures of the Tumor Microenvironment and Cell Cycle in Stage III Colon Cancer From PETACC-8 and IDEA-France Trials

PURPOSE

The objective of this work was to establish prognostic models in stage III colon cancer (CC) on the basis of transcriptomic signatures of the tumor microenvironment (TME) and cell cycle from the PETACC-8 (training set) and IDEA-France (validation set) trials.

PATIENTS AND METHODS

3'RNA sequencing was performed in 1,733 patients from the PETACC-8 trial and 1,248 patients from the IDEA-France trial. Four transcriptomic signatures were analyzed: T-cell and macrophage M2 signatures, the expression of CXCL13, and a score on the basis of the Oncotype DX CC Recurrence Score using the same formula from the stromal score and the cell cycle score. The Immune Proliferative Stromal (IPS) score was defined as the number of dichotomized signatures that fall under the category of a dismal prognosis (from 0 to 4). Time to recurrence (TTR) was defined as the time from the date of random assignment to local and/or metastatic relapse and/or death because of CC, whichever occurs first.

RESULTS

High Oncotype-like and M2 scores and low CXCL13 expression and T-cell score were associated with a shorter TTR. A multivariable model including these signatures and all known prognostic factors applied to the IDEA-France cohort by obtaining a value of this model for each patient showed TTR significantly different depending on the quartile of this value and a 3-year rate of patients without recurrence ranging from 56% for the lowest quartile to 89% for the highest quartile (P < .0001). The IPS score was significantly associated with TTR in multivariable analysis.

CONCLUSION

Using transcriptomic data of patients with stage III CC from two large-scale adjuvant trials, a prognostic model on the basis of signatures of the TME and the cell cycle provides important information in addition to known prognostic factors for patient stratification on risk of recurrence.

Perspectives of Targeting Autophagy as an Adjuvant to Anti-PD-1/PD-L1 Therapy for Colorectal Cancer Treatment

Colorectal cancer (CRC) is the third most common cancer in the world, with increasing incidence and mortality rates. Standard conventional treatments for CRC are surgery, chemotherapy, and radiotherapy. Recently, immunotherapy has been introduced as a promising alternative to CRC treatment that utilizes patients' immune system to combat cancer cells. The beneficial effect of immune checkpoint inhibitors, specifically anti-PD-1/ PD-L1, has been ascribed to the abundance of DNA replication errors that result in the formation of neoantigens. Such neoantigens serve as distinct flags that amplify the immune response when checkpoint inhibitors (ICIs) are administered. DNA replication errors in CRC patients are expressed as two statuses: the first is the deficient mismatch repair (MSI-H/dMMR) with a higher overall immune response and survival rate than the second status of patients with proficient mismatch repair (MSS/pMMR). There is a limitation to using anti-PD-1/PD-L1 as it is only confined to MSI-H/dMMR, where there is an abundance of T-cell inhibitory ligands (PD-L1). This calls for investigating new therapeutic interventions to widen the scope of ICIs' role in the treatment of CRC. Autophagy modulation provides a good example. Autophagy is a cellular process that plays a crucial role in maintaining cellular homeostasis and has been studied for its impact on tumor development, progression, and response to treatment. In this review, we aim to highlight autophagy as a potential determinant in tumor immune response and to study the impact of autophagy on the tumor immune microenvironment. Moreover, we aim to investigate the value of a combination of anti-PD-1/PD-L1 agents with autophagy modulators as an adjuvant therapeutic approach for CRC treatment.

TGF-β signaling redirects Sox11 gene regulatory activity to promote partial EMT and collective invasion of oncogenically transformed intestinal organoids

Cancer cells infiltrating surrounding tissue frequently undergo partial epithelial-mesenchymal transitions (pEMT) and employ a collective mode of invasion. How these phenotypic traits are regulated and interconnected remains underexplored. Here, we used intestinal organoids with colorectal cancer (CRC) driver mutations as model system to investigate the mechanistic basis of TGF-β1-induced pEMT and collective invasion. By scRNA-seq we identified multiple cell subpopulations representing a broad pEMT spectrum, where the most advanced pEMT state correlated with the transcriptional profiles of leader cells in collective invasion and a poor prognosis mesenchymal subtype of human CRC. Bioinformatic analyses pinpointed Sox11 as a transcription factor gene whose expression peaked in the potential leader/pEMThigh cells. Immunofluorescence staining confirmed Sox11 expression in cells at the invasive front of TGF-β1-treated organoids. Loss-of-function and overexpression experiments showed that Sox11 is necessary, albeit not sufficient, for TGF-β1-induced pEMT and collective invasion. In human CRC samples, elevated SOX11 expression was associated with advanced tumor stages and worse prognosis. Unexpectedly, aside from orchestrating the organoid response to TGF-β1, Sox11 controlled expression of genes related to normal gut function and tumor suppression. Apparently, Sox11 is embedded in several distinct gene regulatory circuits, contributing to intestinal tissue homeostasis, tumor suppression, and TGF-β-mediated cancer cell invasion.

The Expression and Molecular Roles of MAMDC2 in MSS Colorectal Cancer with a High Tumor Stromal Ratio

Background: Colorectal cancer (CRC) heterogeneity is strongly influenced by molecular subtypes and tumor stroma interactions. The meprin/A5/PTPmu (MAM) domain, a conserved structural motif in transmembrane proteins, remains undercharacterized in CRC pathogenesis. Methods: We analyzed RNA-seq data from TCGA-COAD to evaluate MAM domain gene expression. Immunohistochemistry and Western blotting were conducted to validate the results of the database analysis. Results: Bioinformatics analysis revealed that MAM domain-containing protein 2 (MAMDC2) was enriched in mesenchymal subtype 4 (CMS4) colorectal cancer (p < 0.001). IHC confirmed MAMDC2 overexpression in MSS colorectal cancer with a high tumor stroma ratio (TSR) and peritoneal metastatic lesions (p < 0.01). WB and real-time PCR analyses confirmed that MAMDC2 has a role in regulating epithelial-mesenchymal transition (EMT) development in CRC. Importantly, we identified that cancer cell-derived MAMDC2 promotes MYLK expression in cancer-associated fibroblasts (CAFs) through paracrine signaling. Conclusions: Our findings suggest MAMDC2 may function as a stromal-associated regulator in MSS colorectal cancer with a high tumor stromal ratio (TSR).

Microbial interactions induce the mutational signature of mismatch repair deficiency in colorectal cancer and associated with EPPK1 mutations

To better understand the impact of microbial interactions on the clonal evolution of colorectal cancer (CRC), we conducted high-resolution profiling of the gut microbiome of 101 treatment-naïve primary CRC patients using nanopore sequencing. We performed an integrated analysis of microbiome and tumor exome data to identify symbiotic microbes that interactively influence the mutational processes and the subsequent clonality of CRC. Our results suggested that Dialister pneumosintes and Fusobacterium animalis were both associated with somatic EPPK1 mutations and promote SBS6 (mismatch repair deficiency, dMMR) activity. Notably, we showed that the symbiotic architecture of Dialister pneumosintes and Fusobacterium animalis undergoes significant changes with the mutational status of EPPK1. In addition, we identified specific metabolic pathways involving key metabolites that potentially mediate microbial interactions in CRC. These findings provide new insights into the interplay between the gut microbiome and the mutation landscape of colorectal cancer, thereby informing the clonal evolution of CRC and new strategies for precision medicine.

Clonal dispersal is associated with tumor heterogeneity and poor prognosis in colorectal cancer

Clonal dispersal, resulting from the intermingling of tumor cell subpopulations, is thought to be a key driver of tumor heterogeneity. Despite advances in spatial modeling of cancer biology, quantification of clonal dispersal has been challenging. This study introduces a straightforward method, relying on fluorescent cell barcoding, to quantify clonal dispersal in various in vitro and in vivo models of colorectal cancer (CRC). Our approach allows for precise localization of clones and uncovering the degree of clonal mixing across different CRC models. Our findings suggest that clonal dispersal is correlated with the expression of genes involved in epithelial-mesenchymal transition and CMS4-related signaling pathways. We further identify a dispersal gene signature, associated with intratumor heterogeneity, which is a robust clinical predictor of poor prognosis and recurrence in CRC, highlighting its potential as a prognostic marker and a putative direction for therapeutic targeting.

Phenotypic heterogeneity and plasticity in colorectal cancer metastasis

Phenotypic heterogeneity and plasticity in colorectal cancer (CRC) has a crucial role in tumor progression, metastasis, and therapy resistance. However, the regulatory factors and the extrinsic signals driving phenotypic heterogeneity remain unknown. Using a combination of single-cell multiomics and spatial transcriptomics data from primary and metastatic CRC patients, we reveal cancer cell states with regenerative and inflammatory phenotypes that closely resemble metastasis-initiating cells in mouse models. We identify an intermediate population with a hybrid regenerative and stem phenotype. We reveal the transcription factors AP-1 and nuclear factor κB (NF-κB) as their key regulators and show localization of these states in an immunosuppressive niche both at the invasive edge in primary CRC and in liver metastasis. We uncover ligand-receptor interactions predicted to activate the regenerative and inflammatory phenotype in cancer cells. Together, our findings reveal regulatory and signaling factors that mediate distinct cancer cell states and can serve as potential targets to impair metastasis.

Construction and validation of a prognostic model for colorectal cancer based on migrasome-related long non-coding RNAs

Background

Colon adenocarcinoma (COAD) is a globally prevalent and deadly malignancy of the digestive system. Recently, migrasomes have gained significant attention as important regulators of tumor cell migration and metastasis. The current research developed a highly accurate prognostic model using migrasome-related long non-coding RNAs (lncRNAs) in COAD, providing new insights for prognostic assessment and immunotherapy of COAD patients.

Methods

RNA sequencing data from COAD patients were acquired from The Cancer Genome Atlas Program (TCGA) database to construct a prognostic lncRNA model based on known migrasome-related genes (MRGs). The model's predictive accuracy was then assessed using concordance index (C-index) analysis, nomograms, principal component analysis, and receiver operating characteristic curves. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to identify significant differences in biological functions and signaling pathways associated with differentially expressed genes in the high-risk subgroup. A comprehensive evaluation of the model incorporated clinical-pathological features, tumor microenvironment, and chemotherapy sensitivity. The expression levels of prognostic genes in COAD patients were validated via quantitative reverse transcription polymerase chain reaction (RT-qPCR). Furthermore, the role of LCMT1-AS1 in colorectal cancer was examined through CCK-8 assays, colony formation assays, and Transwell experiments.

Results

Migrasome-related lncRNAs were identified as robust prognostic predictors for COAD. Multivariate analysis revealed that the risk score derived from these lncRNAs is an independent prognostic factor for COAD. Patients in the low-risk group exhibited significantly longer overall survival (OS) compared to those in the high-risk group. Accordingly, the nomogram prediction model we developed, which integrates clinical features and risk scores, demonstrated excellent prognostic performance. In vitro experiments further showed that LCMT1-AS1 promotes the proliferation and migration of COAD cells.

Therapeutic potential of stem cells in colorectal cancer management: Current trends and future prospects

Colorectal cancer (CRC) ranks among the leading causes of cancer-related morbidity and mortality worldwide. Despite progress in understanding its molecular intricacies, the management of CRC, especially in advanced stages, remains a significant clinical hurdle. This review delves into the evolving landscape of stem cell-based therapeutic strategies in CRC, with a specific focus on the interplay between cancer stem cells (CSCs) and CRC pathogenesis and treatment resistance. Highlighting the pivotal roles of CSCs in tumor initiation, progression, metastasis, and recurrence, the review comprehensively examines their involvement in CRC, ranging from normal colonic tissue to cancer initiation. The potential of stem cells for medicinal purposes in CRC management is explored, encompassing diverse modalities such as transplantation, differentiation therapy, immunotherapy, and gene/cell-based approaches. Challenges and opportunities associated with these strategies are also evaluated, providing insights into their clinical potential and limitations. The review also appraises preclinical investigations contributing to the understanding of CRC and stem cells. Current clinical trials, patient stratification strategies, and regulatory considerations related to stem cell-based therapies in CRC are scrutinized. Furthermore, the review explores emerging trends and future directions, including developments in stem cell technologies and ethical considerations. It highlights the transformative potential of stem cell-based therapeutic strategies in CRC.

Prognostic and Predictive Value of SARIFA-status Within Molecular Subgroups of Colorectal Cancer: Insights From the Netherlands Cohort Study

We recently proposed Stroma AReactive Invasion Front Areas (SARIFA), defined as direct tumor-adipocyte interaction at the invasion front, as a novel hematoxylin-and-eosin (H&E)-based histopathological prognostic biomarker in various cancers. Given that microsatellite instability, BRAF, and RAS mutation status are routinely tested for colorectal cancers (CRC), studying SARIFA's additional prognostic value within these molecular subgroups is crucial. In addition, exploring whether the survival benefit from adjuvant therapy differs according to SARIFA-status may enhance patient treatment and outcome. SARIFA-status, BRAF, RAS, and DNA mismatch repair (MMR) status were available for 1726 CRC patients from the prospective Netherlands Cohort Study (NLCS, 1986-2006). In this study, we investigated (1) the relationship between SARIFA-status and CRC molecular characteristics, (2) the prognostic value of SARIFA-status within these molecular subgroups, and (3) whether SARIFA-status was associated with survival benefit from adjuvant therapy. SARIFA-positive CRCs more frequently showed a BRAF mutation compared to SARIFA-negative CRCs (P<0.001). BRAF-mutant/MMR-proficient CRCs were enriched in SARIFA-positive cases. SARIFA-positivity was associated with poor CRC-specific (HRrange: 1.47 to 1.78) and overall survival (HRrange: 1.35 to 1.70) within all molecular subgroups except MMR-deficient CRCs. Patients with SARIFA-positive CRC showed a CRC-specific survival benefit from adjuvant therapy compared to surgery alone (HRCRC-specific: 0.59; 95% CI: 0.44-0.79), while no CRC-specific survival benefit was observed for patients with SARIFA-negative CRC. To conclude, our results indicate that SARIFA-positivity is more common in the aggressive subset of BRAF-mutant and BRAF-mutant/MMR-proficient CRCs. Moreover, SARIFA-positivity provides additional prognostic value within molecular subgroups based on BRAF, RAS, and MMR status, suggesting that it may enhance prognostic stratification of CRC patients.

Identification of the "Collagen-Macrophage" sub-category of patients with colorectal cancer as an extension of the CMS4 subtype with THBS2 as a therapeutic target

We identified a subset of patients with colorectal cancer (CRC) enriched with "collagen-TAMs," designated the CM class, using large integrated colon cancer transcriptome and single-cell transcriptome datasets. This classification system could be used as an extension of the traditional CMS classification system for CRC to guide more accurate classification and treatment.We also screened CAF-derived THBS2 as a potential biomarker for CM and found that it plays an important role in CRC disease models in vitro and in vivo, promoting tumor development and metastasis as well as TAM recruitment. Targeting THBS2 combined with PD-1 therapy effectively improved the therapeutic effect of immunotherapy in vivo. The CM classification provides a new perspective for CRC treatment, and THBS2, which is highly expressed in CM cases, can be used as a new potential combined target for immunotherapy.

Development and validation of a high-throughput screening pipeline of compound libraries to target EMT

Epithelial to Mesenchymal transitions (EMT) drive cell plasticity and are associated with cell features such as invasiveness, migration and stemness. They are orchestrated by select families of EMT-associated transcription factors, which exhibit pleiotropic roles in the malignant progression of various cancer types, such as breast and colorectal cancer (CRC). This has spurred interest in EMT as a promising target for the development of novel therapeutic strategies. In this study, we developed a phenotypic dual EMT Sensor screening assay, amendable to efficient high-throughput identification of small molecules interfering with EMT. In a proof-of-concept screening we identified anti-EMT repurposing drugs. From these, we validated RepSox, a selective inhibitor of the TGF-β type I receptor ALK5, and demonstrated that it is potently blocking EMT in both breast and colorectal cancer cell lines in vitro. In addition, utilizing a Drosophila melanogaster metastatic CRC model we confirmed the ability of the identified anti-EMT hits to suppress metastatic behavior in vivo.

Dipeptidase-1-knockout mice develop invasive tumors with features of microsatellite-unstable colorectal cancer

Dipeptidase-1 (DPEP1) is highly upregulated in colorectal cancer (CRC), with its enzymatic function linked to invasion and metastasis. More recently, DPEP1 was found to serve as a receptor for neutrophils when expressed by activated endothelial cells. It is unknown whether neutrophils bind to DPEP1-expressing CRC cells and whether this impacts features of CRC. Neutrophils have been shown to be tumor promoting in cancers including CRC, where they act to exclude CD8+ T cells. Herein, we show that neutrophils bind DPEP1-expressing CRC cells. In addition, DPEP1 is preferentially expressed in microsatellite-stable (MSS) CRCs, in which there are a paucity of CD8+ T cells, whereas DPEP1 is negatively correlated with microsatellite-unstable (MSI-H) CRCs, which are T cell rich and are more responsive to immunotherapy. Remarkably, carcinogen-treated Dpep1-null mice develop multiple, large, plaque-like, locally invasive adenocarcinomas and squamous cell cancers in the distal colon. These adenocarcinomas exhibit a marked reduction in neutrophils and an influx CD8+ T cells, along with reduced expression of mismatch repair proteins, consistent with features of MSI-H CRC. These results establish DPEP1's importance in maintaining MSS CRC and its ability to shape the tumor microenvironment.

Single-cell and bulk transcriptome sequencing identifies circadian rhythm disruption and cluster-specific clinical insights in colorectal tumorigenesis

BACKGROUND

Colorectal cancer (CRC) is one of the most common malignant tumors in the digestive system worldwide, with its mortality ranking second among all cancers. Studies have indicated that disruptions in circadian rhythm (CR) are associated with the occurrence of various cancers; however, the relationship between CR and CRC requires further evidence, and research on the application of CR in CRC is still limited.

METHODS

In this study, we employed both bulk and single-cell RNA sequencing to explore the dysregulation of CR in patients with CRC. By constructing a CR subtype classifier, we conducted an in-depth analysis of the prognostic significance, the status of the tumor microenvironment, and response to immune checkpoint blockade (ICB) therapy between different CR clusters. Furthermore, we developed a CR scoring system (CRS) using machine learning to predict overall survival and identified several genes as potential targets affecting CRC prognosis.

RESULTS

Our findings revealed significant alterations in CR genes and status between CRC and normal tissues using bulk and single-cell transcriptome sequencing. Patients with CRC could be categorized into two distinct CR clusters (CR cluster 1 and 2). The prognosis of CR cluster 2, with higher epithelial-mesenchymal transition (EMT) and angiogenesis scores, was significantly worser than that of CR cluster 1. These clusters exhibited distinct levels of tumor-infiltrating lymphocytes. CR cluster 2 with a notably higher proportion of patients with microsatellite-instability-high (MSI-H), potentially benefit from ICB therapy. The proportion of patients belonging to consensus molecular subtype 4 (CMS4) in CR cluster 2 was also notably higher than in CR cluster 1. Additionally, the CRS combined with tumor stage demonstrated superior overall survival prediction efficacy compared to traditional tumor stage. We revealed a potential link between model genes (LSAMP, MS4A2, NAV3, RAB3B, SIX4) and the disruption of CR and patient prognosis.

CONCLUSION

This study not only provide new insights into the assessment of CR status in CRC patients but also develop a prognosis model based on CR-related genes, offering a new tool for personalized risk assessment in CRC.

Identification and verification of a combined ferroptosis- and pyroptosis-related signature for a prognostic classifier and immunosuppressive targets in colorectal cancer

BACKGROUND AND STUDY AIMS

Ferroptosis and pyroptosis, two forms of cell death, are increasingly reported for their pivotal roles in cancer biology. However, the understanding of the combined ferroptosis-pyroptosis (FPtosis)-related gene signature in colorectal cancer (CRC) remains limited.

MATERIAL AND METHODS

We conducted a comprehensive investigation of the FPtosis-related signature in CRC. Data integration from both the training and validation cohorts was performed. The FPtosis-related signature was established. We evaluated the prognostic significance of the signature through Kaplan-Meier analysis, as well as univariate and multivariate Cox regression models. Functional analyses were conducted to explore the underlying biological mechanisms. Additionally, we analyzed the correlations between the FPtosis-related signature, immune infiltration, and immune checkpoint blockade (ICB) immunotherapy.

RESULTS

The FPtosis-related signature demonstrated significant prognostic potential and can serve as an independent biomarker for predicting outcomes. The signature showed correlations with advanced tumor stage, invasion depth, lymph node metastasis, and distant metastasis. Subgroup analyses revealed the valuable predictive role of the FPtosis-related signature in predicting survival across different clinical subgroups, including age, gender, tumor stage, invasion depth, lymph node metastasis status, and distant metastasis status. Moreover, the signature exhibited positive associations with inflammation and the infiltration of diverse immune cells, such as neutrophils, M0 and M2 macrophages, and regulatory T cells (Tregs). In microsatellite instable (MSI) CRC, the expression of most ICB genes was higher in the high-FPtosis group compared to the low-FPtosis group.

CONCLUSION

The FPtosis signature can effectively predict the prognosis of CRC and had the potential to improve the development of innovative therapeutic strategies.

Immuno-oncology recapitulates ontogeny: Modern cell and gene therapy for cancer

Immuno-oncology (IO) has had over a century to develop from the original seminal insights of Virchow in 1863, seeing inflammation and lymphoid infiltrates as a common anlage for many adult tumors. That IO has become a central pillar of cancer treatment has come about because of the remarkable clinical and subsequent commercial success of immune checkpoint blockade (ICB) in the last 15 years. This now includes approved cell and gene therapies for patients with cancer, including an armed adenovirus, oncolytic herpesvirus, and adoptive transfer of dendritic cells, chimeric antigen receptor T (CAR-T) cells, and tumor-infiltrating lymphocytes (TILs). The evolution of such applications has required the stepwise development of a deeper understanding of the molecular biology of cancer and the physiology of immunobiology. This also recapitulates, in a broader sense, our evolutionary trajectory with capture of "evolvability," not only across the development of species but also within individuals. This review covers how our foundational understanding of immune system learning and evolvability have facilitated better understanding of the co-evolutionary interactions between the epithelium and the immune system. We highlight examples of this in breast, colon, prostate, pancreas, and lung cancer, and provide examples of next-generation cell and gene therapies that intercept cancer development.

KRAS mutations in colorectal cancer: impacts on tumor microenvironment and therapeutic implications

INTRODUCTION

Despite decreasing trends in incidence, colorectal cancer (CRC) is still a major contributor to malignancy-related morbidities and mortalities. Groundbreaking advances in immunotherapies and targeted therapies benefit a subset of CRC patients, with sub-optimal outcomes. Hence, there is an unmet need to design and manufacture novel therapies, especially for advanced/metastatic disease. KRAS, the most highly mutated proto-oncogene across human malignancies, particularly in pancreatic adenocarcinoma, non-small cell lung cancer, and CRC, is an on-off switch and governs several fundamental cell signaling cascades. KRAS mutations not only propel the progression and metastasis of CRC but also critically modulate responses to targeted therapies.

AREAS COVERED

We discuss the impacts of KRAS mutations on the CRC's tumor microenvironment and describe novel strategies for targeting KRAS and its associated signaling cascades and mechanisms of drug resistance.

EXPERT OPINION

Drug development against KRAS mutations has been challenging, mainly due to structural properties (offering no appropriate binding site for small molecules), critical functions of the wild-type KRAS in non-cancerous cells, and the complex network of its downstream effector pathways (allowing malignant cells to develop resistance). Pre-clinical and early clinical data offer promises for combining KRAS inhibitors with immunotherapies and targeted therapies.