Hyaluronan (HA) accumulation in the tumor microenvironment (TME) is increased in colorectal cancer (CRC) and associated with consensus molecular subtypes (CMS) 4 molecular subtype

3577 Background: Transforming growth factor- β pathway (TGF-β) has an established role in promoting growth, invasion, metastasis as well as epithelial to mesenchymal (EMT) transition. Among 4 different described molecular subtypes of colorectal cancer (CRC), consensus molecular subtype 4 (CMS4) comprises up to 25% of CRC pts, distinguished by activation of this pathway, and is associated with higher relapse rate and poor prognosis. Recently, it has also been proposed that TGF-β activation drives immune evasion in murine models, but these findings have not been clinically validated. Methods: Using multi-gene RNA expression profiling, fresh-frozen paraffin-embedded samples of 35 patients with CRC were analyzed to determine TGF-β and EMT expression levels. Multiplexed IHC staining was performed on FFPE tumor blocks by using the Opal 7-Color fIHC Kit and the stained slides were scanned by a Vectra multispectral microscope (PerkinElmer) to measure infiltration of immune cells (i.e., T lymphocytes, cytotoxic T lymphocytes (CTL), T cell antigen-experienced, macrophages, etc.) in the tumor, stroma, and both components. TGF-β and EMT expression levels – as continuous variables - were compared with the infiltration of various immune cells using Spearman’s rank correlation analysis. Results: Among 35 pts, 28 pts had non-CMS1/MSS CRC. TGF-β RNA expression in the tumor microenvironment of these samples was inversely associated with the infiltration of CTL into the tumor (r=-0.43, p= 0.022). In contrast, there was no association of TGF-β with non-cytotoxic T-cells or macrophage infiltration. The tumor and stromal CTL infiltration differed substantially by CMS ( p=0.04, p=0.02, respectively) with tumor infiltration lowest in CMS4 (n=7). Consistent with this, EMT gene signature, which includes TGF-β expression, showed a similar inverse correlation with CTL infiltration (r=-0.48, p=0.009). Conclusions: TGF-β and EMT gene signatures have important roles in the exclusion of CTL in the tumor microenvironment of CRC pts. Inhibiting TGF-β pathway can potentially increase the intratumoral infiltration of CTL, which is a necessary (but not sufficient) step for immunotherapy response in MSS CRC. Clinical trials evaluating this hypothesis are currently ongoing (NCT03436563).

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5mC regulator-mediated molecular subtypes depict the hallmarks of the tumor microenvironment and guide precision medicine in bladder cancer

BMC Medicine ◽

10.1186/s12916-021-02163-6 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Jiao Hu ◽

Belaydi Othmane ◽

Anze Yu ◽

Huihuang Li ◽

Zhiyong Cai ◽

...

Keyword(s):

Bladder Cancer ◽

Tumor Microenvironment ◽

Precision Medicine ◽

Molecular Subtypes ◽

Molecular Subtype ◽

Antiangiogenic Therapy ◽

Principal Component ◽

High Sensitivity ◽

Ppar Γ ◽

Low Sensitivity

Abstract Background Depicting the heterogeneity and functional characteristics of the tumor microenvironment (TME) is necessary to achieve precision medicine for bladder cancer (BLCA). Although classical molecular subtypes effectively reflect TME heterogeneity and characteristics, their clinical application is limited by several issues. Methods In this study, we integrated the Xiangya cohort and multiple external BLCA cohorts to develop a novel 5-methylcytosine (5mC) regulator-mediated molecular subtype system and a corresponding quantitative indicator, the 5mC score. Unsupervised clustering was performed to identify novel 5mC regulator-mediated molecular subtypes. The principal component analysis was applied to calculate the 5mC score. Then, we correlated the 5mC clusters (5mC score) with classical molecular subtypes, immunophenotypes, clinical outcomes, and therapeutic opportunities in BLCA. Finally, we performed pancancer analyses on the 5mC score. Results Two 5mC clusters, including 5mC cluster 1 and cluster 2, were identified. These novel 5mC clusters (5mC score) could accurately predict classical molecular subtypes, immunophenotypes, prognosis, and therapeutic opportunities of BLCA. 5mC cluster 1 (high 5mC score) indicated a luminal subtype and noninflamed phenotype, characterized by lower anticancer immunity but better prognosis. Moreover, 5mC cluster 1 (high 5mC score) predicted low sensitivity to cancer immunotherapy, neoadjuvant chemotherapy, and radiotherapy, but high sensitivity to antiangiogenic therapy and targeted therapies, such as blocking the β-catenin, FGFR3, and PPAR-γ pathways. Conclusions The novel 5mC regulator-based subtype system reflects many aspects of BLCA biology and provides new insights into precision medicine in BLCA. Furthermore, the 5mC score may be a generalizable predictor of immunotherapy response and prognosis in pancancers.

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Risk factors and incidence of colorectal cancer according to major molecular subtypes

JNCI Cancer Spectrum ◽

10.1093/jncics/pkaa089 ◽

2020 ◽

Author(s):

Liang Wang ◽

Xiaosheng He ◽

Tomotaka Ugai ◽

Koichiro Haruki ◽

Chun-Han Lo ◽

...

Keyword(s):

Colorectal Cancer ◽

Risk Factors ◽

Risk Factor ◽

Molecular Subtypes ◽

Cpg Island ◽

Molecular Subtype ◽

Statistical Significance ◽

Dietary Factors ◽

Significant Heterogeneity ◽

Subtype 3

Abstract Background Colorectal cancer (CRC) is a heterogeneous disease that can develop via three major pathways, including the conventional, serrated, and alternate pathways. We aimed to examine whether the risk factor profiles differ according to pathway-related molecular subtypes. Methods We examined the association of 24 risk factors with four CRC molecular subtypes based on a combinatorial status of microsatellite instability (MSI), CpG island methylator phenotype (CIMP), BRAF and KRAS mutations by collecting data from two large US cohorts. We used inverse probability weighted duplication-method Cox proportional hazards regression to evaluate differential associations across subtypes. Results We documented 1,175 CRC cases with molecular subtype data: subtype 1 (n = 498; conventional pathway; non-MSI-high, CIMP-low/negative, BRAF-wildtype, KRAS-wildtype), subtype 2 (n = 138; serrated pathway; any MSI status, CIMP-high, BRAF-mutated, KRAS-wildtype), subtype 3 (n = 367; alternate pathway; non-MSI-high, CIMP-low/negative, BRAF-wildtype, KRAS-mutated), and subtype 4 (n = 172; other marker combinations). Statistically significant heterogeneity in associations with CRC subtypes was found for age, sex, and smoking, with a higher hazard ratio (HR) observed for the subtype 2 (HR per 10 years of age = 2.64, 95% CI = 2.13-3.26; HR for female = 2.65, 95% CI = 1.60-4.39; HR per 20-pack-year of smoking = 1.29, 95% CI = 1.14-1.45) than other CRC subtypes (All P for heterogeneity < 0.005). A stronger association was found for adiposity measures with subtype 1 CRC in men and subtype 3 CRC in women, and for several dietary factors with subtype 1 CRC, although these differences did not achieve statistical significance at α = 0.005 level. Conclusions Risk factor profiles may differ for CRC arising from different molecular pathways.

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Molecular subtyping of colorectal cancer to identify a mesenchymal tumor type that might benefit from TGF-beta pathway inhibition.

Journal of Clinical Oncology ◽

10.1200/jco.2014.32.3_suppl.456 ◽

2014 ◽

Vol 32 (3_suppl) ◽

pp. 456-456 ◽

Cited By ~ 2

Author(s):

Ramon Salazar ◽

Paul Roepman ◽

Stefan M. Willems ◽

Diede Brunen ◽

Udo Kellner ◽

...

Keyword(s):

Colorectal Cancer ◽

Cellular Proliferation ◽

Molecular Subtypes ◽

Molecular Subtype ◽

Tumor Type ◽

Tgf Beta ◽

Chemotherapy Treatment ◽

Treatment Benefit ◽

Mesenchymal Transition ◽

Response To Chemotherapy

456 Background: Currently, most colorectal cancer (CRC) patients receive chemotherapy treatment, even though many patients do not benefit. Therefore, a better understanding of the biology is required to identify those patients who will benefit from chemotherapy and to find a more tailored therapy plan for all other patients. Methods: A molecular subtype classification was developed using full genome expression data of 188 stage I-IV CRC patients and validated in 543 stage II and III patients. Subtypes were correlated to clinical factors, prognosis and treatment benefit (stage III). To determine whether TGF-β signaling is elevated in the tumors, 78 patient biopsies were analyzed for p-SMAD2/3 expression using immunohistochemistry. To analyze the effect of TGF-β activation, we studied the effects of MED12 suppression in SKCO-1 CRC cells under treatment with Cisplatin, Oxaliplatin or 5-FU. Results: We developed a diagnostic test that allows the classification of colorectal cancer tumors into different intrinsic molecular subtypes (A-, B-, C-type). The heterogeneity of these subtypes is largely based on 3 biological hallmarks of the tumor: an epithelial-to-mesenchymal transition, deficiency in mismatch repair genes resulting in a high mutation frequency associated with MSI, and cellular proliferation. Especially the C-type (~15% of CRC tumors) is of clinical interest, as C-type patients have the worst outcome, a mesenchymal phenotype and show no benefit from chemotherapy treatment in our patient set or a public dataset. The C-type subgroup has elevated TGF-β signaling, as shown by TGF-beta and TGF-beta receptor over-expression (TGFB1, p=0.0012; TGFBR1, p=0.0005) and increased phopho-SMAD2/3 staining in the tumor cells (1.9-fold, p=0.0002). In cell line experiments, we show that up-regulation of TGF-β signaling by MED12 knockdown resulted in resistance against chemotherapy by preventing apoptosis. Conclusions: The molecular subtypes differ largely in prognosis and response to chemotherapy. A treatment strategy combining standard drugs with agents suppressing TGF-β signaling might benefit C-type patients.

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Tumor sidedness and intrinsic subtypes in patients with stage II/III colon cancer: Analysis of NSABP C-07 (NRG Oncology).

Journal of Clinical Oncology ◽

10.1200/jco.2017.35.15_suppl.3514 ◽

2017 ◽

Vol 35 (15_suppl) ◽

pp. 3514-3514 ◽

Cited By ~ 1

Author(s):

S. Rim Kim ◽

Nan Song ◽

Greg Yothers ◽

Patrick Gavin ◽

Carmen Joseph Allegra ◽

...

Keyword(s):

Colorectal Cancer ◽

Colon Cancer ◽

Molecular Subtypes ◽

Molecular Subtype ◽

Therapy Response ◽

Stage Ii ◽

Intrinsic Subtypes ◽

Treatment Benefit ◽

Cancer Subtypes ◽

Metastatic Setting

3514 Background: The predictive value of tumor sidedness in colorectal cancer is currently of interest especially in metastatic setting for anti-EGFR therapy response. We tested whether intrinsic molecular subtype classification predictive of treatment benefit in stage II/III colon cancer is an independent novel marker in association with tumor sidedness. Methods: All available cases included in the NSABP/NRG C-07 trial for which we had both gene expression data and anatomical data (n=1603) were used to determine the molecular subtypes using the following classifiers; the Colorectal Cancer Assigner (CRCA), the Colon Cancer Subtypes (CCS) and the Consensus Molecular Subtypes (CMS). Frequency of tumor sidedness in each subtype and recurrence-free survival were analyzed. Results: Intrinsic subtypes were differentially distributed in right- and left-colon tumors with the exception of the stem-like or CMS4 (mesenchymal) subtype (Table 1). Sidedness was not associated with prognosis (p=0.82, HR: 1.022 [CI: 0.851-1.227]) or prediction of patients with greater benefit from oxaliplatin when combined with 5-Fu+LV (interaction p=0.484). Conclusions: Although tumor sidedness is associated with distribution of intrinsic subtypes in stage II/III colon cancer, it is not predictive of survival benefit from oxaliplatin in C-07. Support: -180868, -180822, U24-CA196067; HI13C2162; PA DOH; Sanofi-Synthelabo Clinical trial information: NCT00004931. [Table: see text]

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Unraveling Triple-Negative Breast Cancer Tumor Microenvironment Heterogeneity: Towards an Optimized Treatment Approach

JNCI Journal of the National Cancer Institute ◽

10.1093/jnci/djz208 ◽

2019 ◽

Vol 112 (7) ◽

pp. 708-719 ◽

Cited By ~ 9

Author(s):

Yacine Bareche ◽

Laurence Buisseret ◽

Tina Gruosso ◽

Edwina Girard ◽

David Venet ◽

...

Keyword(s):

Breast Cancer ◽

Androgen Receptor ◽

Tumor Microenvironment ◽

Spatial Pattern ◽

Triple Negative Breast Cancer ◽

Triple Negative ◽

Molecular Subtypes ◽

Molecular Subtype ◽

Statistical Tests ◽

Copy Number Loss

Abstract Background Recent efforts of gene expression profiling analyses recognized at least four different triple-negative breast cancer (TNBC) molecular subtypes. However, little is known regarding their tumor microenvironment (TME) heterogeneity. Methods Here, we investigated TME heterogeneity within each TNBC molecular subtype, including immune infiltrate localization and composition together with expression of targetable immune pathways, using publicly available transcriptomic and genomic datasets from a large TNBC series totaling 1512 samples. Associations between molecular subtypes and specific features were assessed using logistic regression models. All statistical tests were two-sided. Results We demonstrated that each TNBC molecular subtype exhibits distinct TME profiles associated with specific immune, vascularization, stroma, and metabolism biological processes together with specific immune composition and localization. The immunomodulatory subtype was associated with the highest expression of adaptive immune-related gene signatures and a fully inflamed spatial pattern appearing to be the optimal candidate for immune check point inhibitors. In contrast, most mesenchymal stem-like and luminal androgen receptor tumors showed an immunosuppressive phenotype as witnessed by high expression levels of stromal signatures. Basal-like, luminal androgen receptor, and mesenchymal subtypes exhibited an immune cold phenotype associated with stromal and metabolism TME signatures and enriched in margin-restricted spatial pattern. Tumors with high chromosomal instability and copy number loss in the chromosome 5q and 15q regions, including genomic loss of major histocompatibility complex related genes, showed reduced cytotoxic activity as a plausible immune escape mechanism. Conclusions Our results demonstrate that each TNBC subtype is associated with specific TME profiles, setting the ground for a rationale tailoring of immunotherapy in TNBC patients.

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Colony-stimulating factor 3 signaling in colon and rectal cancers: Immune response and CMS classification in TCGA data

PLoS ONE ◽

10.1371/journal.pone.0247233 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0247233

Author(s):

Apryl S. Saunders ◽

Dawn E. Bender ◽

Anita L. Ray ◽

Xiangyan Wu ◽

Katherine T. Morris

Keyword(s):

Colorectal Cancer ◽

Immune Response ◽

Tumor Microenvironment ◽

Immune Cells ◽

Molecular Subtype ◽

Receptor Expression ◽

The Cancer Genome Atlas ◽

Colony Stimulating Factor ◽

Consensus Molecular Subtype ◽

Stimulating Factor

Colorectal cancer is the 2nd leading cause of cancer-related deaths in the world. The mechanisms underlying CRC development, progression, and resistance to treatment are complex and not fully understood. The immune response in the tumor microenvironment has been shown to play a significant role in many cancers, including colorectal cancer. Colony-stimulating factor 3 (CSF3) has been associated with changes to the immune environment in colorectal cancer animal models. We hypothesized that CSF3 signaling would correlate with pro-tumor tumor microenvironment changes associated with immune infiltrate and response. We utilized publicly available datasets to guide future mechanistic studies of the role CSF3 and its receptor (CSF3R) play in colorectal cancer development and progression. Here, we use bioinformatics data and mRNA from patients with colon (n = 242) or rectal (n = 92) cancers, obtained from The Cancer Genome Atlas Firehose Legacy dataset. We examined correlations of CSF3 and CSF3R expression with patient demographics, tumor stage and consensus molecular subtype classification. Gene expression correlations, cell type enrichment, Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data scores and Gene Ontology were used to analyze expression of receptor and ligand, tumor microenvironment infiltration of immune cells, and alterations in biological pathways. We found that CSF3 and CSF3R expression is highest in consensus molecular subtype 1 and consensus molecular subtype 4. Ligand and receptor expression are also correlated with changes in T cell and macrophage signatures. CSF3R significantly correlates with a large number of genes that are associated with poor colorectal cancer prognosis.

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The relationship of tumor microenvironment and clinico-pathological parameters in different molecular subtypes of breast cancer

Journal of Health Sciences ◽

10.17532/jhsci.2021.1121 ◽

2021 ◽

Author(s):

Nina Čamdžić ◽

Suada Kuskunović-Vlahovljak ◽

Svjetlana Radović ◽

Mirsad Dorić ◽

Mirsad Babić ◽

...

Keyword(s):

Breast Cancer ◽

Tumor Microenvironment ◽

Cancer Progression ◽

Molecular Subtypes ◽

Molecular Subtype ◽

Tumor Stroma ◽

Histologic Grade ◽

Clinicopathological Parameters ◽

Immunohistochemical Expression ◽

Ki 67

Introduction: Tumor microenvironment plays a significant role in tumor progression. Tumor stroma is one of the strongest modifiers of tumor cell response, cancer behavior, and cancer progression. This study aimed to investigate the correlation of matrix metalloproteinase-9 (MMP-9) expression and tumor-stroma ratio (TSR) with standard clinicopathological parameters in different molecular subtypes of breast cancer.Methods: Ninety biopsy samples of primary breast cancer diagnosed at the Department of Pathology, School of Medicine, Sarajevo, were selected for this study. The molecular subtype was determined based on the immunohistochemical expression of estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2, and Ki-67. Stromal and tumoral MMP-9 immunohistochemical expression and the TSR were determined for each tumor.Results: Tumoral MMP-9 expression correlated positively with the presence of lymphovascular invasion (p= 0.016). TSR showed significant association and correlation with tumor grade (G) (p= 0.031; p= 0.049) and tumor size (pT) (p = 0.049;p= 0.021, respectively). Stromal MMP-9 expression correlated with histologic type, histologic grade of tumor, and lymphocytic inflammatory infiltrate (p= 0.021;p= 0.047, p= 0.038, respectively). A higher percentage of stromal MMP-9 expression correlated with the strongest lymphocytic response (p = 0.007). Significant correlation was observed between molecular subtypes and histologic grade of the tumor (p= 0.032).Conclusion: Our results, to some extent, confirm the significance of the tumor microenvironment in breast cancer, especially when it is about stromal MMP-9 expression. Although we observed significant association, without linear correlation, we found no significant correlation between molecular subtypes of breast cancer and MMP-9 expression.

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Immune Profile of the Tumor Microenvironment in Colorectal Cancer Corresponds to Molecular Subtype and Pathological Features

Gastroenterology ◽

10.1016/s0016-5085(17)31443-9 ◽

2017 ◽

Vol 152 (5) ◽

pp. S354

Author(s):

Louise A. Elliott ◽

Wendy Moore ◽

Maura Cotter ◽

James J. Phelan ◽

Sandra Van Schaeybroeck ◽

...

Keyword(s):

Colorectal Cancer ◽

Tumor Microenvironment ◽

Molecular Subtype ◽

Pathological Features ◽

Immune Profile

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Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer

10.1101/153809 ◽

2017 ◽

Author(s):

Rachel V Purcell ◽

Martina Visnovska ◽

Patrick J Biggs ◽

Sebastian Schmeier ◽

Frank A Frizelle

Keyword(s):

Colorectal Cancer ◽

16S Rrna ◽

Rna Sequencing ◽

Molecular Mechanisms ◽

Molecular Subtypes ◽

Molecular Subtype ◽

Bacterial Species ◽

Fusobacterium Nucleatum ◽

16S Rrna Analysis ◽

Taxonomic Groups

AbstractColorectal cancer (CRC) is a heterogeneous disease and recent advances in subtype classification have successfully stratified the disease using molecular profiling. The contribution of bacterial species to CRC development is increasingly acknowledged, and here, we sought to analyse CRC microbiomes and relate them to tumour consensus molecular subtypes (CMS), in order to better understand the relationship between bacterial species and the molecular mechanisms associated with CRC subtypes. We classified 34 tumours into CRC subtypes using RNA-sequencing derived gene expression and determined relative abundances of bacterial taxonomic groups using 16S rRNA amplicon metabarcoding. 16S rRNA analysis showed enrichment of Fusobacteria and Bacteroidetes, and decreased levels of Firmicutes and Proteobacteria in CMS1. A more detailed analysis of bacterial taxa using non-human RNA-sequencing reads uncovered distinct bacterial communities associated with each molecular subtype. The most highly enriched species associated with CMS1 included Fusobacterium hwasookii and Porphyromonas gingivalis. CMS2 was enriched for Selenomas and Prevotella species, while CMS3 had few significant associations. Targeted quantitative PCR validated these findings and also showed an enrichment of Fusobacterium nucleatum, Parvimonas micra and Peptostreptococcus stomatis in CMS1. In this study, we have successfully associated individual bacterial species to CRC subtypes for the first time.

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