Cell Infiltration In Colorectal Cancer Research Articles

Abstract NG07: Association between somatic microsatellite instability, hypermutation status, and specific T cell subsets in colorectal cancer tumors

Abstract Background: Colorectal cancer (CRC) is a critical public health concern as the third most commonly diagnosed cancer and second leading cause of cancer death globally. CRC is a heterogeneous disease with many different mechanisms and molecular subtypes. Around 15% of sporadic CRCs are classified as exhibiting high microsatellite instability (MSI-high) due to deficient DNA mismatch repair (dMMR). In the presence of MSI-high, colorectal tumors accumulate somatic mutations, resulting in high neoantigen burden, which, in turn, elicits a strong T cell response. Several previous studies have shown that MSI-high status is associated with overall levels of T cell infiltration in CRC and, specifically, with CD45RO+ T cell density. However, many studies have measured T cell densities using single-plex immunohistochemistry assays of individual T cell markers, which fail to capture the complexity of the T cell response in tumors, and the contributions of different T cell subsets. Using a multiplex immunofluorescence panel, we aimed to characterize the composition of the T cell response in CRC tumors in relation to MSI-high and hypermutation status in CRC. Methods: This study was conducted within a subset of participants from three well-characterized epidemiologic studies included in the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO): the Ontario Family Colon Cancer Registry (OFCCR), the Nurses’ Health Study (NHS), the Health Professionals Follow-up Study (HPFS). In a total of N=637 participants with CRC, we profiled the in-situ T cell landscape of CRC using digital imaging, machine learning, and a multiplexed immunofluorescence panel. Our customized 9-plex panel included antibodies directed against CD3, CD4, CD8, CD45RA, CD45RO, FOXP3, and MKI67, as well as a pan-cytokeratin antibody to identify tumor/epithelial cells and nuclear DAPI (4’, 6-diamidino-2-phenylindole) stain. Assays were conducted using tissue microarrays (TMAs) where all slides were sent to Dana Farber Cancer Institute for analysis. In brief, core selection from donor FFPE blocks was guided by pathologist review of H&E-stained slides. For each CRC case, TMA blocks have 2-4 cores (0.6 mm) from tumor areas. T cell immune microenvironment is assessed for each tumor histologically using a multispectral imaging platform (PerkinElmer Vectra 3.0) for multiplexed immunofluorescence (mIF), where TMAs are stained with all markers concurrently and imaged. With pathologist supervision, a machine learning algorithm segmented tissue into epithelial and stromal area regions as well as phenotyped individual cells. The mIF panel has been validated against traditional chromogenic IHC. Based on these markers, we quantified counts and densities of naive, memory, and regulatory subsets of helper (CD3+CD4+) and cytotoxic (CD3+CD8+) T cells, and looked separately at these subsets within epithelial and stromal tissue, resulting in 12 unique subsets. Microsatellite instability and hypermutation status were determined from one of two targeted sequencing panels that included either 205 or 298 genes. MSI status was called using mSINGS. Hypermutation status was defined by plotting point mutations for all samples and observing different peaks, separately by panel. The minimum value between the two peaks was 23 and 26 point mutations per sample, respectively, which were used as cut-points. We used multivariable ordinal logistic regression to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for the association between MSI/hypermutation status with quantiles of specific T cell densities in CRC. As an alternative approach where counts were modeled directly, we used negative binomial count models with an offset term for area. Ordinal logistic regression either used quartiles or tertiles of T cell densities as the outcome, where different subsets were assessed for zero-inflation considering both epithelial and stromal tissue, so the same subset used the same categorization in each tissue. Subsets with less than 25% zero counts were divided into quartiles, subsets with greater than 25% zero counts into tertiles. Study-specific quantile cut points were used to limit potential batch effects across TMAs. Models were adjusted for age, sex, and study, and p-values were adjusted for multiple testing using the false discovery rate method for 12 independent tests. Results: Among 637 CRC tumors with targeted tumor sequencing and T cell immune profile available, 107 were classified as MSI-high, and 106 were classified as hypermutated. 98 tumors were both MSI-high and hypermutated. Compared to tumors with low microsatellite instability (MSI-low) or microsatellite stable (MSS) tumors, MSI-high tumors were strongly associated (ORs around 2 or higher) with higher T cell densities for all epithelial area CD3+CD4+, epithelial area CD3+CD8+, and stromal area CD3+CD8+ T cells (adjusted p-values <0.001). Compared to MSI-low/MSS tumors, MSI-high tumors had 3 times the odds of greater quantile of epithelial area CD3+CD8+ subsets defined as naive, memory, and regulatory [OR= 3.2 95% CI (2.14, 4.79), OR=3.19 (2.15, 4.72), OR=3.31 (2.20, 4.97), respectively]. MSI-high tumors were not associated with higher densities of stromal area CD3+CD4+ naive, memory, or regulatory cells. Effect estimates for hypermutation status showed consistent results and the same conclusions as MSI. Effect estimates from negative binomial models showed consistent findings with the ordinal logistic results presented. Conclusions: While it is well known that T cells overall are strongly associated with MSI status in CRC, the present study improves our understanding of what specific T cell subsets in what location in the tumor are associated with MSI and hypermutation status. Additionally, given the high level of T cell infiltration in MSI-high/dMMR tumors, these tumors are more likely to respond favorably to immune checkpoint inhibitors (ICIs). A more granular understanding of specific T cell subsets that are associated with these tumor phenotypes may improve our understanding of underlying biology and help inform targeted immunotherapy treatment decision-making for the MSI-high/dMMR CRC subtype. In future work we aim to examine increasing mutation frequency as a continuous variable and with more specific categorization of mutation frequency than binary cut-points in association with T cell profile. Citation Format: Claire Elizabeth Thomas, Yasutoshi Takashima, Tomotaka Ugai, Daniel D. Buchanan, Conghui Qu, Li Hsu, Andressa Dias Costa, Stephen Gallinger, Robert C. Grant, Jeroen R. Huyghe, Sushma S. Thomas, Robert S. Steinfelder, Shuji Ogino, Amanda I. Phipps, Jonathan A. Nowak, Ulrike Peters. Association between somatic microsatellite instability, hypermutation status, and specific T cell subsets in colorectal cancer tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr NG07.

Abstract 285: Targeting TXNDC5 in stromal fibroblasts resolves desmoplasia and resistance to immune checkpoint blockade in mesenchymal-type colorectal cancer

Abstract Objectives: Mesenchymal-type colorectal cancer (CRC), characterized by strong stromal infiltration and immune tolerance, resists immune checkpoint blockade and has poor outcomes. Cancer-associated fibroblasts (CAFs), abundant in tumor stroma, actively remodel the extracellular matrix (ECM), modulate immune evasion, and drive tumor progression. We have recently identified thioredoxin domain-containing protein 5 (TXNDC5), a protein disulfide isomerase (PDI), as a critical mediator of fibroblast activation and ECM remodeling in organ fibrosis. We hypothesized that TXNDC5 could contribute to fibroblast activation, stroma formation and disease progression in cancer, especially in the stroma-enriched fibrogenic mesenchymal-type CRC. Methods: Transcriptome databases of CRC were re-analyzed to determine the clinical relevance of TXNDC5. Experimentally, CRC was induced in mouse lines by azoxymethane (AOM) and dextran sulfate sodium (DSS) stimuli, a model sharing multiple characteristics with human mesenchymal-type CRC. Human colonic fibroblast line CCD-18co was used to investigate the molecular mechanisms by which TXNDC5 regulates colonic fibroblast activities. Fibroblast-specific TXNDC5 knockout (Col1a2-Cre/ERT2*TXNDC5fl/fl) mice were generated, combining with single-cell RNA sequencing analyses on AOM/DSS-induced CRC tumors in these animals, to clarify how fibroblast TXNDC5 impact tumor microenvironment, CRC progression and response to immune checkpoint blockade. Findings: TXNDC5 was predominantly expressed in stromal fibroblasts of human and mouse CRC. Fibroblast-specific deletion of Txndc5 lessened CAF activation, attenuated tumor fibrosis and reduced tumor burden in AOM/DSS-induced CRC. Mechanistically, increased TXNDC5 levels augments TGFβ signaling in CAF by post-translational stabilization of TGFBR1 through its PDI activity. In addition, deletion of Txndc5 in CAFs led to less tumor desmoplasia, decompressed tumor vessels and attenuated intra-tumoral hypoxia, thereby easing immune tolerance and increasing cytotoxic T cell infiltration in CRC. Single-cell transcriptome analysis revealed a marked change of intra-tumoral immune cell populations upon fibroblast-specific deletion of TXNDC5, shifting from myeloid-derived suppressive cells to cytotoxic tumor-infiltrating lymphocytes. Importantly, depletion of TXNDC5 in CAFs potentiated the anti-tumor effects of immune checkpoint blockade with anti-PD1 therapy in CRC. Conclusions: Our data suggest an important yet previously unrecognized role of fibroblast TXNDC5 in CRC progression, through enhancing CAF activation, stroma formation and immune escape. Combining immune checkpoint blockade with TXNDC5 deletion synergistically improved anti-tumor effects in CRC. Targeting TXNDC5, therefore, can be a novel therapeutic approach for CRC patients. Citation Format: Kai-Lin Cheng, Chih-I Chen, Shu-Han Yu, Huai-Wen Liang, Yi-Wei Tsai, Chen-Ting Hung, Yu-Shan Lin, Yi-Shiuan Tzeng, Sung-Jan Lin, Yueh-Feng Wu, Jen-Kuang Lee, Chia-Hui Yu, Shuei-Liong Lin, Shih-Yu Chen, Tzu-Tang Wei, Yun-Ju Huang, Ruey-Hwa Chen, Ching-Chow Chen, Kai-Chien Yang. Targeting TXNDC5 in stromal fibroblasts resolves desmoplasia and resistance to immune checkpoint blockade in mesenchymal-type colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 285.

Abstract 99: Versican regulates T cell abundance within the colorectal cancer microenvironment

Abstract Background: Clinical benefit from immunotherapy is seen in a minority of patients with metastatic colorectal cancer (CRC). Identifying how the tumor microenvironment (TME) influences immune infiltration and treatment response is an unmet need. Versican (VCAN), a chondroitin sulfate proteoglycan, common in the CRC TME has immunoregulatory properties and can be cleaved releasing an immunostimulatory product, versikine (Vkine). Here we evaluate the impact of the abundance of VCAN and Vkine on CD8+ T cell infiltration in CRC. Methods: Samples include 306 primary colon tumors, an additional 176 primary CRCs with matched liver metastases (175 samples), and 328 normal samples (238 colon and 90 liver). Samples were stained via immunohistochemistry (IHC) for VCAN, Vkine, and CD8. CD8+ tumor infiltrating lymphocytes (TILs) were counted per high powered field (HPF, 400X magnification) and presented as averages. Intensity of VCAN and Vkine expression were scored from 0-3+. Samples designated a 0/1 were considered low accumulation and samples scored as a 2/3+ were designated high. Samples scored low for VCAN but high for Vkine were designated VCAN proteolytic predominant (VPP) and all other combinations considered VCAN proteolytic weak (VPW). To create an in vitro model, the mouse MC38 cell line was CRISPR engineered to over-express VCAN. Conditioned media was then concentrated and added to a collagen matrix in a transwell with activated T cells. The number of cells and their subtype that migrated through the matrix were evaluated with flow cytometry. Results: VCAN accumulation was highest in cancerous stroma with 58% of cancers being VCAN high and only 14% of adjacent normal tissues (p<0.001). Vkine accumulation was similar between groups, with 67% of tumors and 54% of adjacent normal samples scored as Vkine high. The VPP phenotype was least common in tumor tissues with only 27% of tumor samples designated VPP versus 43% of adjacent normal samples (p<0.001). VCAN high tumors had significantly fewer TILs with 4 TILs/HPF vs 13 in the VCAN low tumors (p<0.001). High levels of Vkine correlated with greater TIL abundance (Vkine high: 10 TILs/HPF, Vkine low: 5 TILs/HPF; p=0.02). Versican proteolysis had the strongest correlation with TIL abundance in cancers (VPP: 18 TILs/HPF, VPW: 5 TILS/HPF; p<0.001). In vitro, the addition of VCAN containing media into transwell matrices reduced both CD4+ and CD8+ T cell migration through the matrix (Control: 4277 CD8+ T cells, VCAN: 2603 CD8+ T cells; p<0.001 and Control: 7770 CD4+ T cells, VCAN: 5340 CD4+ T cells; p=0.007). Conclusions: VCAN accumulation in human CRCs is common and correlates with reduced TIL abundance, whereas VCAN proteolysis correlates with increased TILs. In vitro, VCAN demonstrated the ability to reduce T cell migration. Future studies will explore the mechanism by which VCAN abundance leads to decreased T cell infiltration and the importance of this as an immunotherapy biomarker. Citation Format: Sean Kraus, Philip Emmerich, Mitch Hayes, Kristina Matkowskyj, Wei Zhang, Cheri Pasch, Fotis Asimakopoulos, Dustin A. Deming. Versican regulates T cell abundance within the colorectal cancer microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 99.

Quantitative Multiplexed Analysis of Indoleamine 2,3-Dioxygenase (IDO) and Arginase-1 (ARG1) Expression and Myeloid Cell Infiltration in Colorectal Cancer

Indoleamine 2,3-dioxygenase (IDO) and arginase-1 (ARG1) are amino acid–metabolizing enzymes, frequently highly expressed in cancer. Their expression may deplete essential amino acids, lead to immunosuppression, and promote cancer growth. Still, their expression patterns, prognostic significance, and spatial localization in the colorectal cancer microenvironment are incompletely understood. Using a custom 10-plex immunohistochemistry assay and supervised machine learning–based digital image analysis, we characterized IDO and ARG1 expression in monocytic cells, granulocytes, mast cells, and tumor cells in 833 colorectal cancer patients. We evaluated the prognostic value and spatial arrangement of IDO- and ARG1-expressing myeloid and tumor cells. IDO was mainly expressed not only by monocytic cells but also by some tumor cells, whereas ARG1 was predominantly expressed by granulocytes. Higher density of IDO+ monocytic cells was an independent prognostic factor for improved cancer-specific survival both in the tumor center (Ptrend = .0002; hazard ratio [HR] for the highest ordinal category Q4 [vs Q1], 0.51; 95% CI, 0.33-0.79) and the invasive margin (Ptrend = .0015). Higher density of granulocytes was associated with prolonged cancer-specific survival in univariable models, and higher FCGR3+ARG1+ neutrophil density in the tumor center also in multivariable analysis (Ptrend = .0020). Granulocytes were, on average, located closer to tumor cells than monocytic cells. Furthermore, IDO+ monocytic cells and ARG1− granulocytes were closer than IDO− monocytic cells and ARG1+ granulocytes, respectively. The mRNA expression of the IDO1 gene was assessed in myeloid and tumor cells using publicly available single-cell RNA sequencing data for 62 colorectal cancers. IDO1 was mainly expressed in monocytes and dendritic cells, and high IDO1 activity in monocytes was associated with enriched immunostimulatory pathways. Our findings provided in-depth information about the infiltration patterns and prognostic value of cells expressing IDO and/or ARG1 in the colorectal cancer microenvironment, highlighting the significance of host immune response in tumor progression.

SLC4A4 moulds the inflammatory tumor microenvironment and predicts therapeutic expectations in colorectal cancer.

In this report, we performed a comprehensive analysis of data in colorectal cancer (CRC), to elucidate the association among Solute Carrier Family 4 Member 4 (SLC4A4) and the abundance of immunological features and immune cell infiltration in CRC, and to explore the impact of SLC4A4 on the CRC tumor microenvironment. Colorectal cancer (CRC) cases with advanced or distal metastases experience a survival rate of less than 20%, with the lack of spectral therapeutic targets and prognostic markers posing a significant challenge for CRC treatment. SLC4A4 may be a CRC-targeted therapy for which there is currently inadequate evidence Objective: To deeply and systematically reveal the characteristics of the tumor microenvironment created by SLC4A4. We downloaded RNA sequencing files (TCGA-COADREAD), clinical data for Colon Cancer (COAD) and Rectal Cancer (READ) from the Cancer Genome Atlas. We evaluated the spearman correlation of SLC4A4 with immune features, Tracking Tumor Immunophenotype (TIP) score, and immune checkpoint gene expression. SLC4A4/immunity-related differentially expressed genes (DEGs) were identified in SLC4A4 expression groups and immune groups, and an assessment system for predicting CRC prognosis was constructed based on univariate COX and multivariate COX analyses. Based on the prognostic factors in CRC, we also constructed a nomogram to assess the survival risk status of CRC. Besides, we evaluated the potential association of SLC4A4 to immunotherapy. We found that SLC4A4 expression trended positively with immune checkpoint expression (PD-L1, CTLA4) and promoted infiltration of 27 immune cells. SLC4A4 promoted the infiltration of CD8 T cells, Dendritic cells, Macrophage, NK cells, and Th1 cells in CRC, shaping the inflammatory tumor microenvironment. Up-regulation of SLC4A4 expression might promote drug response to Anti-FGFR3_therapy, Anti-PPARG_therapy, Nivolumab, Ipilimumab in CRC patients, and down-regulation of SLC4A4 expression might promote drug response to Anti-EGFR_therapy, Aflibercept drug response. Based on the SLC4A4/immunization-related DEGs, we constructed RiskScore to assess the prognosis of CRC, which showed excellent predictive effect and robustness. RiskScore showed a trend of negative correlation with SLC4A4, which was consistent with the trend of the effect of SLC4A4 on CRC survival. Besides, RiskScore could also be useful for predicting patient prognosis. Finally, we constructed a nomogram for predicting CRC survival based on metrics with independent prognostic value (Age, M stage, Stage, RiskScore), which showed potential clinical value. Overall, upregulation of SLC4A4 expression promoted an inflammatory tumor microenvironment in CRC, and RiskScore predicted therapeutic expectancy. SLC4A4 could be a potentially clinically valuable target for CRC therapy.

LOXL1 promotes tumor cell malignancy and restricts CD8 + T cell infiltration in colorectal cancer

BackgroundColorectal cancer (CRC) is a leading cause of cancer mortality globally. Lymph node metastasis and immunosuppression are main factors of poor prognosis in CRC patients. Lysyl oxidase like 1 (LOXL1), part of the lysyl oxidase (LOX) family, plays a yet unclear role in CRC. This study aimed to identify effective biomarkers predictive of prognosis and efficacy of immunotherapy in CRC patients, and to elucidate the prognostic value, clinical relevance, functional and molecular features, and immunotherapy predictive role of LOXL1 in CRC and pan-cancer.MethodsWeighted gene co-expression network analysis (WGCNA) was employed to explore gene modules related to tumor metastasis and CD8 + T cell infiltration. LOXL1 emerged as a hub gene through differential gene expression and survival analysis. The molecular signatures, functional roles, and immunological characteristics affected by LOXL1 were analyzed in multiple CRC cohorts, cell lines and clinical specimens. Additionally, LOXL1's potential as an immunotherapy response indicator was assessed, along with its role in pan-cancer.ResultsTurquoise module in WGCNA analysis was identified as the hub module associated with lymph node metastasis and CD8 + T cell infiltration. Aberrant elevated LOXL1 expression was observed in CRC and correlated with poorer differentiation status and prognosis. Molecular and immunological characterization found that LOXL1 might mediate epithelial-mesenchymal transition (EMT) process and immunosuppressive phenotypes of CRC. Functional study found that LOXL1 enhanced tumor cell proliferation, migration and invasion. Moreover, high LOXL1 levels corresponded to reduced CD8 + T cell infiltration and predicted poor clinical outcomes of immunotherapy. Similar trends were also observed at the pan-cancer level.ConclusionsOur findings underscore the critical role of LOXL1 in modulating both malignancy and immunosuppression in CRC. This positions LOXL1 as a promising biomarker for predicting prognosis and the response to immunotherapy in CRC patients.Graphical

LMTK3 gene expression and the molecular landscape of colorectal cancer (CRC).

172 Background: Lemur tail kinase 3 (LMTK3) plays a critical role in multiple cellular pathways such as Wnt signaling, KIT modulation, and the estrogen receptor pathway. We previously reported that LMTK3 gene polymorphisms are associated with clinical outcome in patients with CRC, and that LMTK3 and estrogen-mediated signaling play a crucial role in CRC tumorigenesis in vitro. Here, we aimed to characterize the molecular features associated with LMTK3 gene expression in CRC. Methods: 20,219 CRC were tested at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing on DNA (592 genes or WES) and RNA (WTS). Top quartile transcripts per million (TPM) for LMTK3 expression (Q4) were considered high while bottom quartile (Q1) low. Consensus molecular subtypes (CMS) were assessed using RNAseq. Cell infiltration (CI) in the tumor microenvironment (TME) was estimated by QuantiSEQ. X2 and Fisher-Exact tests were used, and significance was determined as p-value adjusted for multiple comparisons ( q < 0.05). Gene expression profiles were analyzed for transcriptional signatures predictive of response to immunotherapy (interferon gamma [IFNγ] score; T-cell inflamed signature [TIS] score). Results: LMTK3 expression was highest in left-sided (0.98 median TPM) followed by right-sided (0.96) and lowest in rectal tumors (0.92). No difference in patient sex distribution was observed between Q1 and Q4 cohorts. Overall, LMTK3 Q1 was associated with TMB-high (≥ 10 Mut/Mb, 11.4 vs 8.7%) and dMMR/MSI-H (8.1 vs 4.6%) ( q < 0.0001); however, these associations were no longer significant in pMMR/MSS tumors. In the pMMR/MSS cohort, LMTK3 expression was highest in CMS4 (1.09 median TPM) followed by CMS2 (0.98), CMS1 (0.88), and lowest in CMS3 (0.70, all intergroup q < 0.05). LMTK3 high showed differential rates of mutations and copy number alterations (CNA) in several genes, including higher mutation rates of APC, TP53, and CDX2 CNA, while lower mutation rates of KMT2A/D, ASXL1, ATM, SMAD4, RNF43 and AMER1 in the overall cohort ( q < 0.05). In the pMMR/MSS cohort, the associations with APC, TP53, SMAD4 and ATM mutations and CDX2 CNA still held true ( q < 0.05). High LMTK3 was associated with higher immune CI in the TME, including B cells, neutrophils, NK cells, CD4+ T cells, monocytes and dendritic cells, while macrophages and Tregs were lower regardless of tumor MSI status (fold change: 0.83-2.4, all q < 0.0001). The IFNγ score was significantly lower in LMTK3 Q4 while the TIS score was significantly higher in LMTK3 Q4 ( q < 0.0001). Conclusions: Our data show a strong association between LMTK3 gene expression and distinct molecular features and TME immune cell infiltration in CRC. These findings suggest that LMTK3 may be an important molecular factor that plays a role in determining the composition of the TME, thus targeting LMTK3 could represent a novel strategy in selected CRC subgroups.

Mitochondrial DNA copy number plays opposing roles in T-lymphocyte infiltration of colorectal cancer based on mismatch repair status: new directions for immunotherapy?

Researchers have previously reported that mitochondrial DNA copy number (mtDNA-CN) can play different roles in microsatellite instable/mismatch repair-deficient (MSI/dMMR) and microsatellite stable/mismatch repair-proficient (MSS/pMMR) colorectal cancer (CRC). To support malignancy, dMMR CRC relies on glycolysis, while pMMR CRC favors oxidative phosphorylation. However, it is unclear whether mtDNA-CN changes are related to T cell infiltration in CRC. The mtDNA-CN was detected by qRT-PCR in 532 patients, and the expression of CD3 and CD8 in 485 patients was detected by immunohistochemistry. The correlation between mtDNA-CN and the prognosis of CRC patients was further analyzed, and the correlation between mtDNA-CN and T lymphocyte infiltration was also analyzed. Biopsy specimens from the immune checkpoint inhibitors (ICIs) treatment cohort were obtained to verify the correlation between mtDNA-CN and the efficacy of ICIs. The effects of mtDNA-CN and MMR status on gene expression were analyzed by RNA-seq. Our results show that mtDNA-CN has inverse relationships to CRC prognosis in cases with different MMR statuses, potentially inducing the U-shaped association in CRC. The opposing correlations between mtDNA-CN and T lymphocyte infiltration in cases of dMMR CRC and pMMR CRC further suggest that mtDNA-CN might play an important role in CRC development. More importantly, cases of pMMR CRC with lower mtDNA-CN and of dMMR CRC with higher mtDNA-CN can benefit more dramatically from ICIs. Furthermore, RNA-seq revealed a link between the level of mtDNA-CN and T lymphocyte infiltration in CRC cases with different MMR statuses. Our study found a potential relationship between mtDNA-CN and CRC development that differs by MMR status, potentially providing a rationale for the use of mtDNA-CN as both a predictive biomarker and a therapeutic target for ICIs.

Colorectal cancer with low SLC35A3 is associated with immune infiltrates and poor prognosis

The expression level of SLC35A3 is associated with the prognosis of many cancers, but its role in colorectal cancer (CRC) is unclear. The purpose of our study was to elucidate the role of SLC35A3 in CRC. The expression levels of SLC35A3 in CRC were evaluated through tumor immune resource assessment (TIMER), The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), International Cancer Genome Consortium (ICGC), Human Protein Atlas (HPA), qRT-PCR, and immunohistochemical evaluation. TCGA, GEO, and ICGC databases were used to analyze the diagnostic and prognostic value of SLC35A3 in CRC. A overall survival (OS) model was constructed and validated based on the expression level of SLC35A3 and multivariable analysis results. The cBioPortal tool was used to analyze SLC35A3 mutation in CRC. The UALCAN tool was used to analyze the promoter methylation level of SLC35A3 in colorectal cancer. In addition, the role of SLC35A3 in CRC was determined through GO analysis, KEGG analysis, gene set enrichment analysis (GSEA), immune infiltration analysis, and immune checkpoint correlation analysis. In vitro experiments validated the function of SLC35A3 in colorectal cancer cells. Compared with adjacent normal tissues and colonic epithelial cells, the expression of SLC35A3 was decreased in CRC tissues and CRC cell lines. Low expression of SLC35A3 was associated with N stage, pathological stage, and lymphatic infiltration, and it was unfavorable for OS, disease-specific survival (DSS), recurrence-free survival (RFS), and post-progression survival (PPS). According to the Receiver Operating Characteristic (ROC) analysis, SLC35A3 is a potential important diagnostic biomarker for CRC patients. The nomograph based on the expression level of SLC35A3 showed a better predictive model for OS than single prognostic factors and TNM staging. SLC35A3 has multiple types of mutations in CRC, and its promoter methylation level is significantly decreased. GO and KEGG analysis indicated that SLC35A3 may be involved in transmembrane transport protein activity, cell communication, and interaction with neurotransmitter receptors. GSEA revealed that SLC35A3 may be involved in energy metabolism, DNA repair, and cancer pathways. In addition, SLC35A3 was closely related to immune cell infiltration and immune checkpoint expression. Immunohistochemistry confirmed the positive correlation between SLC35A3 and helper T cell infiltration. In vitro experiments showed that overexpression of SLC35A3 inhibited the proliferation and invasion capability of colorectal cancer cells and promoted apoptosis. The results of this study indicate that decreased expression of SLC35A3 is closely associated with poor prognosis and immune cell infiltration in colorectal cancer, and it can serve as a promising independent prognostic biomarker and potential therapeutic target.

Identification of a novel lymphangiogenesis signature associated with immune cell infiltration in colorectal cancer based on bioinformatics analysis

BackgroundLymphangiogenesis plays an important role in tumor progression and is significantly associated with tumor immune infiltration. However, the role and mechanisms of lymphangiogenesis in colorectal cancer (CRC) are still unknown. Thus, the objective is to identify the lymphangiogenesis-related genes associated with immune infiltration and investigation of their prognosis value.MethodsmRNA expression profiles and corresponding clinical information of CRC samples were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The lymphangiogenesis-related genes (LymRGs) were collected from the Molecular Signatures database (MSigDB). Lymphangiogenesis score (LymScore) and immune cell infiltrating levels were quantified using ssGSEA. LymScore) and immune cell infiltrating levels-related hub genes were identified using weighted gene co-expression network analysis (WGCNA). Univariate Cox and LASSO regression analyses were performed to identify the prognostic gene signature and construct a risk model. Furthermore, a predictive nomogram was constructed based on the independent risk factor generated from a multivariate Cox model.ResultsA total of 1076 LymScore and immune cell infiltrating levels-related hub genes from three key modules were identified by WGCNA. Lymscore is positively associated with natural killer cells as well as regulator T cells infiltrating. These modular genes were enriched in extracellular matrix and structure, collagen fibril organization, cell-substrate adhesion, etc. NUMBL, TSPAN11, PHF21A, PDGFRA, ZNF385A, and RIMKLB were eventually identified as the prognostic gene signature in CRC. And patients were divided into high-risk and low-risk groups based on the median risk score, the patients in the high-risk group indicated poor survival and were predisposed to metastasis and advanced stages. NUMBL and PHF21A were upregulated but PDGFRA was downregulated in tumor samples compared with normal samples in the Human Protein Atlas (HPA) database.ConclusionOur finding highlights the critical role of lymphangiogenesis in CRC progression and metastasis and provides a novel gene signature for CRC and novel therapeutic strategies for anti-lymphangiogenic therapies in CRC.

Opposing roles by KRAS and BRAF mutation on immune cell infiltration in colorectal cancer – possible implications for immunotherapy

BackgroundThe immune response has important clinical value in colorectal cancer (CRC) in both prognosis and response to immunotherapy. This study aims to explore tumour immune cell infiltration in relation to clinically well-established molecular markers of CRC.MethodsMultiplex immunohistochemistry and multispectral imaging was used to evaluate tumour infiltration of cytotoxic T cells (CD8+), Th1 cells (T-bet+), T regulatory cells (FoxP3+), B cells (CD20+), and macrophages (CD68+) in a cohort of 257 CRC patients.ResultsWe found the expected association between higher immune-cell infiltration and microsatellite instability. Also, whereas BRAF-mutated tumours displayed increased immune-cell infiltration compared to BRAF wild-type tumours, the opposite was seen for KRAS-mutated tumours, differences that were most prominent for cytotoxic T cells and Th1 cells. The opposing relationships of BRAF and KRAS mutations with tumour infiltration of cytotoxic T cells was validated in an independent cohort of 608 CRC patients. A positive prognostic importance of cytotoxic T cells was found in wild-type as well as KRAS and BRAF-mutated CRCs in both cohorts.ConclusionA combined evaluation of MSI status, KRAS and BRAF mutational status, and immune infiltration (cytotoxic T cells) may provide important insights to prognosis and response to immunotherapy in CRC.

ID1 expressing macrophages support cancer cell stemness and limit CD8+ T cell infiltration in colorectal cancer

Elimination of cancer stem cells (CSCs) and reinvigoration of antitumor immunity remain unmet challenges for cancer therapy. Tumor-associated macrophages (TAMs) constitute the prominant population of immune cells in tumor tissues, contributing to the formation of CSC niches and a suppressive immune microenvironment. Here, we report that high expression of inhibitor of differentiation 1 (ID1) in TAMs correlates with poor outcome in patients with colorectal cancer (CRC). ID1 expressing macrophages maintain cancer stemness and impede CD8+ T cell infiltration. Mechanistically, ID1 interacts with STAT1 to induce its cytoplasmic distribution and inhibits STAT1-mediated SerpinB2 and CCL4 transcription, two secretory factors responsible for cancer stemness inhibition and CD8+ T cell recruitment. Reducing ID1 expression ameliorates CRC progression and enhances tumor sensitivity to immunotherapy and chemotherapy. Collectively, our study highlights the pivotal role of ID1 in controlling the protumor phenotype of TAMs and paves the way for therapeutic targeting of ID1 in CRC.

EphA2 as a phase separation protein associated with ferroptosis and immune cell infiltration in colorectal cancer.

Colorectal cancer is one of the most common malignant tumors in the digestive system, and its high incidence and metastasis rate make it a terrible killer that threatens human health. In-depth exploration of the targets affecting the progression of colorectal cancer cells and the development of specific targeted drugs for them are of great significance for the prognosis of colorectal cancer patients. Erythropoietin-producing hepatocellular A2 (EphA2) is a member of the Eph subfamily with tyrosine kinase activity, plays a key role in the regulation of signaling pathways related to the malignant phenotype of various tumor cells, but its specific regulatory mechanism in colorectal cancer needs to be further clarified. Here, we found that EphA2 was abnormally highly expressed in colorectal cancer and that patients with colorectal cancer with high EphA2 expression had a worse prognosis. We also found that EphA2 can form liquid-liquid phase separation condensates on cell membrane, which can be disrupted by ALW-II-41-27, an inhibitor of EphA2. In addition, we found that EphA2 expression in colorectal cancer was positively correlated with the expression of ferroptosis-related genes and the infiltration of multiple immune cells. These findings suggest that EphA2 is a novel membrane protein with phase separation ability and is associated with ferroptosis and immune cell infiltration, which further suggests that malignant progression of colorectal cancer may be inhibited by suppressing the phase separation ability of EphA2.

BRAF D594A mutation defines a unique biological and immuno-modulatory subgroup associated with functional CD8+ T cell infiltration in colorectal cancer

BackgroundBRAF non-V600 mutation occupies a relatively small but critical subset in colorectal cancer (CRC). However, little is known about the biological functions and impacts of BRAF class III mutation in CRC. Here, we aim to explore how D594A mutation impacts on biological behaviors and immune related signatures in murine CRC cells.MethodsBRAF V600E (class I), G469V (class II) and D594A (class III) mutant cell lines were established based on MC38 cells. The biological behaviors of cells were evaluated in respect of cell growth, cell proliferation, cell apoptosis, cell migration and invasion by the methods of colony-forming assay, CCK-8 assay, Annexin V/PI staining and transwell assay. The concentrations of soluble cytokines were detected by ELISA. The membrane expression of immuno-modulatory molecules and the pattern of tumor infiltrating lymphocyte were evaluated by flow cytometry. The molecular mechanism was explored by RNA sequencing. Immunohistochemistry (IHC) staining was used for the detection of CD8α in tumor tissues. qRT-PCR and western blot were performed to assess the mRNA and protein expression. Anti-PD-L1 treatment and cytokines neutralization experiments were conducted in in vivo models.ResultsD594A mutant cells displayed lower grade malignancy characteristics than V600E (class I) and G469V (class II) mutant cells. Meanwhile, D594A mutation led to evident immuno-modulatory features including upregulation of MHC Class I and PD-L1. In vivo experiments displayed that the frequency of infiltrated CD8+ T cells was significantly high within D594A mutant tumors, which may provide potential response to anti-PD-L1 therapy. RNA sequencing analysis showed that D594A mutation led to enhanced expression of ATF3 and THBS1, which thus facilitated CXCL9 and CXCL10 production upon IFN-γ treatment. In addition, CXCL9 or CXCL10 neutralization reduced the infiltration of CD8+ T cells into THBS1-overexpressing tumors.ConclusionsD594A mutant CRC exhibited lower aggressiveness and immune-activated phenotype. ATF3-THBS1-CXCL9/CXCL10 axis mediated functional CD8+ T cells infiltration into the microenvironment of D594A mutant CRC. Our present study is helpful to define this mutation in CRC and provide important insights in designing effective immunotherapeutic strategies in clinic.

A Multiomics Analysis of the Close Connection between Intratumoral Microbiota and Immune Cell Infiltration in Colorectal Cancer

The colorectal intratumoral microbiome and its association with the expression of the tumor genome and immune cell infiltration remain poorly characterized. Our study aims to investigate the relationship between intratumoral microbiota with tumor immune infiltration, patient prognosis, and potential downstream signaling pathways. We collected biopsy samples of tumor tissue and paracancerous tissue from 92 patients with colorectal cancer, and acquired microbiota profiling in these samples using 16s rRNA sequencing. Meanwhile, the immune markers including CD8, FOXP3, CD163, PD-1 and PD-L1 were stained by immunohistochemistry (IHC) to identify the immune infiltration in tumors. Furthermore, we used The Cancer Genome Atlas and The Cancer Microbiome Atlas databases to conduct multiomics analysis on tumor flora and patient survival, tumor gene expression profile and potential downstream pathways. There was a significant difference in α-diversity (p = 0.00051) and β-diversity (p = 0.004) between tumor and paracancerous tissues. The β-diversity of intratumoral bacterial differed by colorectal cancer tumor stage (early vs. late stage, p = 0.049) and location (left vs. right colon, p = 0.04). Stage-related flora cluster (Porphyromonas, Lachnoclostridium, Bacteroides, Aggregatibacter, and Hungatella) were identified and found to be associated with poor prognosis in colorectal cancer patients (HR = 1.79, p = 0.015). By IHC staining, we found that expression of PD-1 and FOXP3 was significantly reduced at low abundance of stage-related bacterial cluster (p<0.05). Among of them, Hungatella was negatively associated with CD8+T cell infiltration (p<0.05) in tumor. Besides, tumor-location related flora cluster (Bacteroides and Blautia) were identified and found to be associated with good prognosis in colorectal cancer patients (HR = 0.52, p = 0.011). Expression of CD163 was decreased at high abundance of location-related bacterial cluster (p<0.05). Among of them, Blautia was negatively correlated with tumor-associated macrophage infiltration(p<0.05). Furthermore, we found that the stage-related flora cluster was positively connected with the pathway of bile acid metabolism, whereas the location-dependent cluster was negatively correlated with this pathway. We found specific intratumoral bacterial clusters that were related to tumor stage and location, and the clusters were strongly associated with tumor immune infiltration and patient prognosis. Our findings may provide new viewpoint for future research between intratumoral microbiota, metabolism pathway and tumor microenvironment.

Relationship Between Infiltration of CD163+ TAMs, FoxP3+ Tregs, or CD66b+ TANs and Cell Differentiation in Colorectal Cancer Tissues.

There are many studies on immune cell infiltration in colorectal cancer, including FoxP3+-regulatory T cells, CD66b+ tumorassociated neutrophils, and CD163+ tumor-associated macrophages. These studies mainly focus on the relationship between cell infiltration and tumor progression, prognosis, and so on, while the relationship between tumor cell differentiation and cell infiltration is poorly understood. We aimed to explore the relationship between cell infiltration and tumor cell differentiation. The tissue microarray and immunohistochemistry were used to determine the infiltration of FoxP3+-regulatory T cells, CD66b+ tumor-associated neutrophils, and CD163+ tumor-associated macrophages in 673 colorectal cancer samples from the Second Affiliated Hospital, Wenzhou Medical University (2001-2009). Kruskal-Wallis test was used to assess the positive cell infiltration in colorectal cancer tissues with tumor cells of varying degrees of differentiation. The number of CD163+ tumor-associated macrophages, FoxP3+-regulatory T cells, and CD66b+ tumor-associated neutrophils in colorectal cancer tissues was different, and the level of CD163+ tumor-associated macrophages was the highest while the level of FoxP3+-regulatory T cells was the least. There were significant differences in the cell infiltration of colorectal cancer tissue cells with different levels of differentiation (P < .05). The highest infiltration of CD163+ tumor-associated macrophages (154.07 ± 6.95) and FoxP3+-regulatory T cells (20.14 ± 2.07) were in the poorly differentiated colorectal cancer tissues, while the higher infiltration of CD66b+ tumor-associated neutrophils was in the moderately or well-differentiated colorectal cancer tissues (36.70 ± 1.10 and 36.09 ± 1.06, respectively). Infiltration of CD163+ tumor-associated macrophages, FoxP3+-regulatory T cells, and CD66b+ tumor-associated neutrophils in colorectal cancer tissues may be related to the differentiation of tumor cells.

RNA demethylase ALKBH5 suppresses tumorigenesis via inhibiting proliferation and invasion and promoting CD8+ T cell infiltration in colorectal cancer

ALKBH5 belongs to the ALKB family consists of a Fe (II) and a-ketoglutarate-dependent dioxygenase. ALKBH5 directly catalyzes the oxidative demethylation of m6A-methylated adenosine. ALKBH5 involves in tumorigenesis and tumor progression, and is often dysregulated in a wide range of cancers, including colorectal cancer. Emerging evidence indicates that the expression of ALKBH5 is associated with the abundance of infiltrating immune cells in the microenvironment. However, how ALKBH5 affects immune cell infiltration in the microenvironment in colorectal cancer (CRC) has not been reported. The aim of this study was to identify how the expression of ALKBH5 affects the biological behaviors of CRC cell lines and regulates the effects on infiltrating CD8+ T cells in CRC microenvironment with its specific mechanism. Firstly, the transcriptional expression profiles of CRC were downloaded from TCGA database and integrated via R software (4.1.2). Between CRC and normal colorectal tissues, ALKBH5 mRNA expressions were compared (Wilcoxon rank-sum). We further identified the expression levels of ALKBH5 in CRC tissues and cell lines through quantitative PCR, western blot, and immunohistochemistry. Then, how ALKBH5 affects the biological behaviors of CRC cells were confirmed by gain- and loss-of-function analysis. Furthermore, the relationship between ALKBH5 level and 22 tumor-infiltrating immune cells was examined through CIBERSORT in R software. Furthermore, we explored the correlation between ALKBH5 expression and tumor-infiltrated CD8+, CD4+ and regulatory T cells by utilizing the TIMER database. Finally, the association between chemokines and CD8+ T cells infiltration in CRC was analyzed using GEPIA online database. qRT-PCR, WB and IHC were used to further determine the effect of ALKBH5 on NF-κB-CCL5 signaling axis and CD8+ T cells infiltration. Clinically, ALKBH5 expression was downregulated in CRC and low levels of ALKBH5 expression were correlated with poor overall survival (OS). Functionally, overexpression of ALKBH5 reduced the proliferation, migration and invasion of CRC cells, and vice versa. Overexpression of ALKBH5 suppresses NF-κB pathway, thus reduces CCL5 expression and promotes CD8+ T cells infiltration in CRC microenvironment. ALKBH5 is poorly expressed in CRC, and overexpression of ALKBH5 attenuates CRC malignant progression by inhibiting CRC cell proliferation, migration, invasion and promoting CD8+ T cells infiltration in the tumor microenvironment through NF-κB-CCL5 axis.

Correlation between SMADs and Colorectal Cancer Expression, Prognosis, and Immune Infiltrates.

In recent years, the incidence and mortality of colorectal cancer (CRC) are increasing, and the 5-year survival rate of advanced metastatic CRC is poor. Small mothers against decapentaplegic (SMAD) superfamily are intracellular signal transduction proteins associated with the development and prognosis of a variety of tumors. At present, no study has systematically analysed the relationship between SMADs and CRC. Here, R3.6.3 was used to analyse the expression of SMADs in pan-cancer and CRC. Protein expression of SMADs were analysed by Human Protein Atlas (HPA). Gene expression profiling interactive analysis (GEPIA) was used to evaluate the correlation between SMADs and tumor stage in CRC. The effect of R language and GEPIA on prognosis was analysed. Mutation rates of SMADs in CRC were determined by cBioPortal, and potentially related genes were predicted using GeneMANIA. R analysis was used to correlate immune cell infiltration in CRC. Both SMAD1 and SMAD2 were found to be weakly expressed in CRC and correlated with the immune invasion level. SMAD1 was correlated with patient prognosis, and SMAD2 was correlated with tumor stage. SMAD3, SMAD4, and SMAD7 were all expressed at low levels in CRC and associated with a variety of immune cells. SMAD3 and SMAD4 proteins were also expressed at low levels, and SMAD4 had the highest mutation rate. SMAD5 and SMAD6 were overexpressed in CRC, and SMAD6 was also associated with patient overall survival (OS) and CD8+ T cells, macrophages, and neutrophils. Our results reveal innovative and strong evidence that SMADs can be used as biomarkers for the treatment and prognosis of CRC.

USP20 is a predictor of poor prognosis in colorectal cancer and associated with lymph node metastasis, immune infiltration and chemotherapy resistance.

Colorectal cancer (CRC) is a highly prevalent malignancy with a poor prognosis. USP20 can support progression of variety of tumors. USP20 was shown to promote breast tumor metastasis, and proliferation of oral squamous carcinoma cells. However, the role of USP20 in CRC remains unclear. We used bioinformatics to analyze the expression and prognosis of USP20 in pan-cancer and explore the relationship between USP20 expression and immune infiltration, immune checkpoints, and chemotherapy resistance in CRC. The differential expression and prognostic role of USP20 in CRC was validated by qRT-PCR and immunohistochemistry. Cox univariate and multivariate analyses were performed to assess risk factors for poor prognosis of CRC, and new prognostic prediction models were constructed and evaluated by decision curve analysis (ROC) and receiver operating characteristic (DCA). USP20 was overexpressed in CRC cell lines to explore the effect of USP20 on the functionalities of CRC cells. Enrichment analyses were used to explore the possible mechanism of USP20 in CRC. The expression of USP20 was lower in CRC tissues than adjacent normal tissues. Compared with low USP20 expression patients, CRC patients with high USP20 expression level had shorter OS. Correlation analysis showed that USP20 expression was associated with lymph node metastasis. Cox regression analysis revealed USP20 as an independent risk factor for poor prognosis in CRC patients. ROC and DCA analyses showed that the performance of the newly constructed prediction model was better than the traditional TNM model. Immune infiltration analysis shown that USP20 expression is closely associated with T cell infiltration in CRC. A co-expression analysis showed that USP20 expression was positively correlated with several immune checkpoint genes including ADORA2A, CD160, CD27 and TNFRSF25 genes and positively associated with multiple multi-drug resistance genes such as MRP1, MRP3, and MRP5 genes. USP20 expression positively correlated with the sensitivity of cells to multiple anticancer drugs. Overexpression of USP20 enhanced the migration and invasive ability of CRC cells. Enrichment pathway analyses showed the USP20 may play a role via the Notch pathway, Hedgehog pathway and beta-catenin pathway. USP20 is downregulated in CRC and associated with prognosis in CRC. USP20 enhances CRC cells metastasis and is associated with immune infiltration, immune checkpoints, and chemotherapy resistance.

MXRA8 is an immune-relative prognostic biomarker associated with metastasis and CD8+ T cell infiltration in colorectal cancer.

Colorectal cancer (CRC) is the second most common cause of cancer-related deaths worldwide. Tumor metastasis and CD8+ T cell infiltration play a crucial role in CRC patient survival. It is important to determine the etiology and mechanism of the malignant progression of CRC to develop more effective treatment strategies. We conducted weighted gene co-expression network analysis (WGCNA) to explore vital modules of tumor metastasis and CD8+ T cell infiltration, then with hub gene selection and survival analysis. Multi-omics analysis is used to explore the expression pattern, immunity, and prognostic effect of MXRA8. The molecular and immune characteristics of MXRA8 are analyzed in independent cohorts, clinical specimens, and in vitro. MXRA8 expression was strongly correlated with tumor malignancy, metastasis, recurrence, and immunosuppressive microenvironment. Furthermore, MXRA8 expression predicts poor prognosis and is an independent prognostic factor for OS in CRC. MXRA8 may be a potential immunotherapeutic and prognostic biomarker for CRC.