Abstract 892: Single-cell RNA sequencing of patient-derived organoid reveals treatment-induced tumor resistance through cancer stem cells

The EGFR-MAPK signaling pathway is frequently activated in cancers, particularly due to KRAS gain-of-function mutations. Certain types, such as pancreatic ductal adenocarcinoma (PDAC) with KRAS mutations and cholangiocarcinoma with FGFR2 fusions, show dependency on EGFR. Recent studies demonstrate promising outcomes in metastatic colorectal cancer by combining an irreversible KRASG12C inhibitor with an EGFR inhibitor. To explore therapeutic benefits across tumor types, we analyzed the expression of EGFR and co-receptors (ERBB) in TCGA samples and CCLE models with different KRAS mutations. We also verified the reliance on ERBB receptors using DepMap data. Patient-derived organoid (PDO) models from PDAC, colorectal cancer (CRC), and CRC liver metastases were utilized to develop orthotopic tumor models. These PDO lines were characterized through mutational profiling, cell signaling analysis, RNA-sequencing, and whole exome sequencing, providing insights into their molecular features. Higher EGFR expression levels at both protein and RNA levels were observed in specific CRC PDO models, consistent in in-vitro PDO models and in-vivo PDO-derived Xenograft (PDOX) tissues from subcutaneous implantation in immunocompromised mice. Additionally, the PDO models were evaluated for sensitivity to standard of care (SOC) drugs and EGFR inhibitors, revealing EGFR expression-independent and tumor type-dependent sensitivities (e.g., Afatinib IC50: PDAC (128nM+/-123) vs CRC (2776nM+/-3099)). Surface expression levels of ERBBs were measured in in-vivo PDOX tissues to assess the comparative use case for targeting the EGFR pathway via inhibition or antibody-drug conjugate (ADC) molecules. Furthermore, we generated and validated stable tumoroid models expressing firefly luciferase in PDOs derived from primary CRC, CRC metastasis to the liver, and primary PDAC. To further validate the potential for in-vivo models, orthotopic tumor models were established in immunocompromised mice for each PDO line, monitoring tumor burden using bioluminescence imaging. Correlation with MRI and ultrasound imaging was conducted for PDAC and liver tumor burden, respectively, with significant correlation observed. Overall, this study aims to enhance understanding of tumor biology and response to treatment through the development and validation of PDO-based orthotopic models, with future work involving validation of EGFR inhibitors targeting the pathway and ADCs based on ERBBs targeting tumor cells expressing these proteins. In vivo luciferase reactivation in our models will allow us to dissect the mechanisms of resistance to these agents using physiologically relevant tumor models and single-cell RNA-sequencing analysis. Citation Format: Krishna S. Tummala, Milind Chalishazar, Minilik Angagaw, Ali Savadipour, Qingyun Yan, Cui Long, Mark Buchanan, Panagiotis N. Lalagkas, Eric Muise, Lan Chen, Kuoyuan Cheng, Eunsil Park, Jennifer Piesvaux, Erica Leccese, Brian Long, Nicolas Solban. Orthotopic tumor models using luciferized patient-derived organoids for investigating EGFR-MAPK pathway inhibition in colorectal and pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 27.

Backgrounds: Hematogenous dissemination is a prevalent route of colorectal cancer (CRC) metastasis, whereas the underlying mechanism is unclear. Tumor pericytes (TPCs) are important components of tumor vessels, which are attached to the endothelial cells and embedded within the walls of capillaries. However, as the gatekeeper of vessels, the role of TPCs in hematogenous metastasis remains largely unknown. Here, we aimed to investigate the heterogeneity of TPCs and their effects on CRC metastasis. Methods: TPCs were first isolated from the primary CRC tissues using microdissection combined with pericyte medium-based approach. Then, TPCs derived from CRC liver-metastatic (CRCLM) and CRC non-metastatic (CRCNM) patients were analyzed by single-cell RNA sequencing (scRNA-seq). Clinical CRC specimens were collected to analyze the association between the molecular profiling of TPCs and CRC metastasis. The mechanisms by which TCF21 regulated perivascular matrix remodeling and integrin α5 modulated TCF21 DNA hypermethylation were investigated using RNA-sequencing, chromatin immunoprecipitation-sequencing and bisulfite-sequencing. Pericyte-conditional Tcf21-knockout mice were constructed to investigate the effects of TCF21 in TPCs on CRC metastasis. Masson staining, atomic force microscopy, second-harmonic generation and two-photon fluorescence microscopy were employed to observe perivascular extracellular matrix (ECM) remodeling. Pericyte TCF21-targeting peptide was designed by AlphaFold and its mechanisms were examined by microscale thermophoresis. Results: Thirteen TPC subpopulations were identified by scRNA-seq. A novel subpopulation of TCF21high TPCs was found to bed associated with liver metastasis in CRC patients. Genes highly-expressed in TCF21high TPCs were enriched in ECM and ECM remodeling, thus termed as matrix pericytes. TCF21 in TPCs increased perivascular ECM stiffness, collagen rearrangement and basement membrane degradation, establishing a perivascular metastatic microenvironment to instigate CRC liver metastasis. Mechanistic studies indicated that loss of integrin α5 inhibited the FAK/PI3K/AKT/DNMT1 axis to impair TCF21 DNA hypermethylation in TCF21high TPCs. Conditional deletion of Tcf21 in TPCs or pharmacological blocking the transcriptional activity of TCF21 in TPCs could mitigate perivascular ECM remodeling and CRC liver metastasis. Conclusions: This study first uncovers the heterogeneity of TPCs during CRC liver metastasis and reveals a novel mechanism that TPCs drive CRC liver metastasis through remodeling perivascular matrix, which provides a potential diagnostic marker and therapeutic target for CRC metastasis. Citation Format: Xiaobo Li, Jinghua Pan, Qun Miao, Xiaoyu Wu, Zhan Zhao, Yihai Cao, Minfeng Chen, Dongmei Zhang, Wencai Ye. Pericytes promote colorectal cancer metastasis by remodeling perivascular matrix [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1307.

This study aimed to explore the role of plasma methylated SEPT9 (mSEPT9) in predicting liver metastasis (LM) in colorectal cancer (CRC) patients. The clinicopathological information of 115 consecutive CRC patients were collected. The differences of clinical characteristics and several biomarkers between CRC patients with LM and those with non-liver metastasis (NM) were analyzed. Multivariate logistic regression analysis was used to identify the risk factors for predicting LM in CRC patients. Receiver operating characteristic curve (ROC) analysis was applied to investigate the sensitivity and specificity of potential biomarkers in indicating the presence of LM in CRC. Compared with the CRC without LM, the levels of plasma mSEPT9 and carcinoembryonic antigen (CEA) were significantly increased in CRC with LM. Multivariate logistic regression analysis showed that plasma mSEPT9 was an independent risk factor for predicting LM in CRC. ROC curves showed that mSEPT9 and CEA could efficiently distinguish LM from NM in CRC. The area under the curve (AUC) of mSEPT9 was 0.850, which was slightly higher than that of CEA (0.842). The optimal cut-off value of mSEPT9 was 35.09 with a sensitivity of 81.82% and a specificity of 73.33%, both similar with that of CEA (sensitivity 87.27% and specificity 75.00%). In addition, the combination of mSEPT9 and CEA had a higher specificity than CEA alone (81.70% Vs 75.00%). Our findings suggest, for the first time, that plasma mSEPT9 might serve as a potential biomarker to predict LM in CRC, which deserves further in-depth study.

Aberrant expression of musashi2 (MSI‐2) has been detected in several malignancies. However, its role in the progression of colorectal cancer (CRC) remains unknown. Our study was designed to investigate the expression and prognostic significance of MSI‐2 protein in patients with colorectal cancer. The expression of MSI‐2 was detected in 164 patients’ colorectal cancer and control specimens by the tissue microarray technique and immunohistochemical staining. The correlations between MSI‐2 expression and clinicopathological variables including overall survival were analyzed. The prognostic value of liver metastasis is evaluated by logistic regression and receiver operating characteristic (ROC) analysis. MSI‐2 was highly expressed in 32.9% (54/164) of the colorectal cancer. Overexpression of MSI‐2 was associated with depth of invasion, lymph node metastasis, distant metastasis, liver metastasis, Tumor Node Metastasis (TNM) clinical stage, and Carcinoembryonicantigen (CEA) level (P = 0.040, 0.014, <0.001, <0.001, 0.003, and 0.002, respectively). In the Cox multivariate test, MSI‐2 overexpression, lymph node metastasis, and distant metastasis were found to be the independent prognostic factors (P = 0.027, 0.010, and 0.001, respectively). Further logistic regression suggested that TNM stage and MSI‐2 high expression were related to liver metastasis in colorectal cancer patients. Conclusively, our study indicates that MSI‐2 overexpression is associated with an unfavorable prognosis and may be a potential biomarker for liver metastasis in colorectal cancer patients.

目的 探讨结直肠癌肝转移患者血清中 CD44和 CD54含量与结直肠癌肝转移发生发展的关系,寻找一个稳定的早期诊断结直肠癌肝转移的生物学指标.方法应用酶联免疫吸附测定方法( ELISA)检测 38例结直肠癌和 21例结直肠癌肝转移患者以及 40例健康成人(正常对照组)的血清 CD44和 CD54含量, 并比较血清中 CD44和 CD54含量在治疗前后的变化.结果结直肠癌肝转移组和结直肠癌组血清中 CD44和 CD54含量明显高于正常对照组,且结直肠癌肝转移组较结直肠癌组含量也明显增高.结直肠癌肝转移组和结直肠癌组治疗后的血清 CD44和 CD54含量比治疗前下降.结论 CD44和 CD54可以作为临床早期诊断结直肠癌肝转移的生物学指标,同时也可以作为监测结直肠癌和结直肠癌肝转移预后的客观指标.

The tumor-derived factors involved in the expansion and accumulation of myeloid-derived suppressor cells (MDSCs) in metastatic dissemination of colorectal cancer (CRC) to the liver has not been studied. Immunohistochemistry was used to detect sphingosine-1-phosphate receptor 1 (S1PR1) and signal transducer and activator of transcription-3 (STAT3) in human colorectal tumors. IL-6 and interferon-γ were detected by enzyme-linked immunosorbent assay (ELISA). Tumor growth, invasion, and migration were evaluated by MTT, transwell, and wound healing assays, respectively. Subcutaneous tumor-bearing and CRC liver metastasis (CRLM) nude mouse models were constructed. The percentage of MDSCs was measured using multicolor flow cytometry. Western blot assay was used to evaluate S1PR1 and p-STAT3 expression in MDSCs after separation from the liver and tumor by magnetic antibody. T-cell suppression assay was detected by carboxyfluorescein succinimidyl ester (CFSE). Aberrant co-expressed S1PR1 and p-STAT3 was correlated with metachronous liver metastasis and poor prognosis in CRC. A mutual activation loop between S1PR1 and STAT3 can enhance CRC cell proliferation, migration, and invasion in vitro and in vivo. The expression of p-STAT3 and its downstream proteins can be regulated by S1PR1. p-STAT3 was the dependent signaling pathway of S1PR1 in the promotion of cell growth and liver metastasis in CRC. The level of IL-6 and the associated MDSCs stimulated by the S1PR1–STAT3 correlated with the number of liver metastatic nodes in the CRLM mouse models and patients. Increased CD14+HLA-DR−/low MDSCs from CRLM patients inhibited autologous T-cell proliferation and predict poor prognosis. The S1PR1–STAT3–IL-6–MDSCs axis operates in both tumor cells and MDSCs involved in the promotion of growth and liver metastasis in CRC. MDSCs induced by S1PR1–STAT3 in CRC cells formed the premetastatic niche in the liver can promote organ-specific metastasis.

Introduction: Colorectal cancer is the second cause of cancer related deaths worldwide, with the poor survival outcomes attributable to the presence of metastases. To tackle this problem, (phospho)proteomics analysis enables valuable insights into changes of protein expression and signalling in cancer that can be perturbed by drugs. To study mechanisms driving metastasis and perform subsequent drug testing, patient derived organoids (PDOs) are in development as preclinical models. PDOs are obtained by 3D culture of tumour tissue ex-vivo, which enables them to retain the heterogeneity and architecture of the tumor source. To identify putative drug targets for colon cancer metastasis, we performed comparative (phospho)proteomics analysis of metastatic colon tissues and their matched PDOs. Methods: (Phospho)proteomics profiling was performed on PDOs generated from 10 patients with colon metastases to the liver, 10 matched tumour tissues and 4 normal colon mucosa. Unsupervised analysis of the (phospho)proteomic landscape was used to identify differentially expressed genes and pathways in colon metastases and their matched PDOs, compared to normal colon mucosa. We focused on phosphosites, proteins and pathways showing consistently altered expression in tumour tissues and PDOs. Kinase-substrate enrichment analysis was used to identify aberrantly activated kinases, based on the abundance of phosphorylation on the substrates. Putative drugs were selected using the consensus expression response to multiple small molecule drugs across cell lines and conditions from the Library of Integrated Network-Based Cellular Signatures (LINCS) database. Drug treatment of drug candidates was performed using the MTT Cell Proliferation Assay. Results: Using the approach described above we identified 103 differentially expressed proteins and 236 phosphosites between tumour tissues and normals, which were also detected in PDOs, with overall high correlation of t statistics (0.6 Spearman’s rho) between tumor tissues and PDOs. MYC-targets, G2M checkpoints and E2F-targets were amongst the top positively enriched pathways in common, and the LINCS analysis identified multi-kinase inhibitor Nintedanib and NFKB pathway-targeting KIN0-260 as putative drugs for upregulated proteins. The kinase CSNK2A1 was overactivated in both groups, pointing towards the use of CK2 inhibitors for drug testing. Treatment at 5 days with Nintedanib and KIN001-260 on the PDOs resulted in significant reduction of cell viability compared with 5-FU. Conclusion: Our study provides evidence that PDOs recapitulate relevant tumor features at the proteomic and phosphoproteomic levels, supporting the utility of this ex-vivo model as a tool for drug sensitivity testing for metastatic colon cancer. Citation Format: Gina Faye Boot, Federica Panebianco, John Gallon, Charlotte Kiu Yan Ng, Salvatore Piscuoglio. (Phospho)proteomics profiling of patient-derived colon cancer organoids for the discovery of putative drug targets [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3074.

Patients with metastatic colorectal cancer (CRC) have few targeted treatment options compared with other major malignancies, and both over- and undertreatment with cytostatic drugs remain a challenge. Recent studies show that patient-derived organoids (PDOs) can predict clinical responses to systemic therapies in a personalized manner, but tumor heterogeneity may limit the clinical benefit of anticancer therapies, as well as the accuracy of preclinical predictions. PDO lineage establishment from multiple distinct lesions per patient presents a novel opportunity for preclinical investigation of intrapatient pharmacotranscriptomic heterogeneity. From September 2017 until November 2019, we have established a living biobank of 107 PDOs from 53 patients who underwent resection of CRC liver metastases at Oslo University Hospital, Norway, 31 of whom had multiple (2-5) metastases. All PDOs were screened for sensitivity to 40 anticancer agents, including clinically relevant targeted drugs and conventional chemotherapies. Molecular profiling by gene expression and mutation analyses is ongoing and currently completed for 27 PDOs. Recapitulation of known pharmacogenomic/transcriptomic associations was confirmed in PDOs for EGFR inhibition and RAS/BRAFV600E mutation status, as well as TP53-MDM2 inhibition and TP53 mutation status and TP53 transcriptional activity. Antimetabolites such as gemcitabine and methotrexate, or small-molecule inhibitors in late-stage clinical development targeting Aurora A, PLK1, and HSP90, showed strong differential activities, enabling identification of sensitive subgroups. Strong sensitivity to HSP90 inhibition was associated with low protein expression of Heat Shock Transcription Factor 1, which had a homogenous intrapatient intermetastatic expression pattern. Principal component analyses revealed a clear patient-wise separation of PDOs based on both their pharmacologic and transcriptomic profiles separately, indicating only modest intrapatient heterogeneity among distinct metastatic lesions. Accurate prediction of clinical responses to 5-FU and oxaliplatin was shown in PDOs from one patient treated for recurrent liver metastases. Additionally, PDOs from recurrent liver metastases showed an increased sensitivity to off-label drugs compared to PDOs from the first liver resection, supporting therapy repurposing in later lines of treatment. In summary, patient-derived models of CRC liver metastases reveal modest intrapatient pharmacotranscriptomic heterogeneity—an encouraging result for further efforts to develop personalized drug repurposing strategies for this poor-prognosis patient group. Citation Format: Kushtrim Kryeziu, Jarle Bruun, Peter W. Eide, Seyed H. Moosavi, Ina A. Eilertsen, Jonas Langerud, Bård Røsok, Tuva H. Brunsell, Marianne G. Guren, Andreas Abildgaard, Arild Nesbakken, Bjørn Atle Bjørnbeth, Anita Sveen, Ragnhild A. Lothe. Modeling intrapatient pharmacotranscriptomic heterogeneity with organoids derived from colorectal cancer liver metastases [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr A19.

Methylation of circulating free DNA (CfDNA) has emerged as an efficient marker of tumor screening and prognostics. However, no efficient methylation marker has been developed for monitoring liver metastasis (LM) in colorectal cancer (CRC). Utilizing methylome profiling and bisulfite sequencing polymerase chain reaction of paired primary and LM sites, significantly increased methylation of TCHH was identified in the process of LM in CRC in the present study. Methylight analysis of TCHH methylation in CfDNA displayed a promisingly discriminative power between CRC with and without LM. Besides, significant coefficient of TCHH methylation and LM tumor volume was also validated. Together, these results indicated the potential of TCHH methylation in CfDNA as a monitoring marker of LM in CRC.

The advances in the development of preclinical models for various cancers have tremendously helped study of the biology and genetics of human cancers as well as for development of therapeutics. Recently, patient-derived organoids (PDOs) have emerged as a robust preclinical platform that can provide insight into the patient specific genetic mechanisms, cancer progression and drug susceptibility. We have developed a novel PDO platform by embedding patient-derived organoids in a 3D hydrogel suspension culture. Our previous studies have shown that, when cultured in hydrogel, spheroids derived from cancer cell lines demonstrated upregulated gene expression signatures in relation to migration and angiogenesis compared to cultures in media, suggesting a more hypoxic, nutrient deficient environment. Given that hypoxia and nutrient deficiency are important feathers of solid tumors, the hydrogel environment could provide a good platform for in vitro study of tumor development and resistance to treatment. In the current study, we embedded PDOs derived from liver metastasis of colorectal cancer into the 3D suspension hydrogel culture. The PDOs adapted well in the hydrogel gel environment. We assessed the response of PDOs in hydrogel to anticancer agents, and compared that to those cultured in media. The PDOs cultured in hydrogel showed significantly elevated resistance to the treatments. The IC50s of chemotherapeutic drugs 5-fluorouracil and oxaliplatin are increased by ~5-10 fold when cultured in hydrogel compared to those in media. Further studies through RNAseq analysis revealed differentially activated signaling pathways. In particular, the levels of the CXC ligand family chemokines are significantly up-regulated in the PDOs cultured in the hydrogel. The CXC ligand family chemokines are important immune stimulants that are known to play key role in the chemotaxis and tumor recruitment of immune cells including neutrophil, T-cell and B-cells. Interestingly, the elevated levels of CXC-ligands have been shown to relate to resistance of colorectal cancer against drug treatment such as 5-fluorouracil. Our hydrogel model could help elucidate the mechanisms behind such resistance. Future study will focus on evaluating how well the hydrogel PDO platform can recapitulate tumor microenvironment and its potential in screening for personalized medicine. Citation Format: He Wei, Eveliina Karelehto, Karen Dubbin, Aimy Sebastian, Robert Warren, Monica Moya, Gaby Loots, Elizabeth Wheeler, Matthew Coleman. Developing 3d hydrogel model for patient-derived organoids of metastatic colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2638.

ObjectiveHaematogenous dissemination is a prevalent route of colorectal cancer (CRC) metastasis. However, as the gatekeeper of vessels, the role of tumour pericytes (TPCs) in haematogenous metastasis remains largely unknown. Here,...

BackgroundMore than 50% of patients with colorectal cancer (CRC) present with liver metastases and there are few effective medications for treating CRC liver metastases (CRLM). Innate immunity plays an important...

This study aimed to investigate the prevalence, risk, and prognostic factors for synchronous liver metastasis (LM) in colorectal cancer (CRC) and to construct nomogram for predicting occurrence and prognosis of synchronous LM. A total of 203,998 CRC patients who were registered in the SEER database between 2010 and 2016 were included. Logistic regression was used to analyze risk factors and Kaplan-Meier was used to estimate the overall survival of CRC patients with LM. Potential prognostic factors were identified by multivariable Cox regression. For predicting the risk for development and prognosis in CRC patients with LM, we constructed nomogram and the predictive performance was estimated by the receiver operating characteristics cure, the concordance index, and calibration curve. In total, 15.3% of the CRC patients (N = 31,288) had synchronous LM. Male gender, black, uninsured status, left colon, T4/T1, and bone and lung metastases were positively associated with synchronous LM risk. The 1-year, 3-year, and 5-year overall survival rate was 49.1%, 18.4%, and 9.2%, respectively. Older age, male gender, black, uninsured status, poor histological differentiation, lymphatic metastasis, T4/T1, positive carcinoembryonic antigen, and lung, bone, and brain metastases were associated with the overall survival. Nomogram was constructed to predict the development and prognosis of synchronous LM and both of them were proved to have good calibration and discrimination. LM is highly prevalent in CRC patients. Nomogram basing on the risk and prognostic factors for synchronous LM was proved to have good performance for predicting the probability of LM occurrence and prognosis.

Liver metastasis is a critical factor influencing the 5-year survival rate in colorectal cancer (CRC). However, the biological function of most circRNAs in liver metastasis of CRC is still unknown. In this study, we identified differentially expressed circRNAs associated with liver metastasis (LM-DE-circRNAs). A total of 247 LM-DE-circRNAs were identified, and crucial signaling pathways, including the regulation of actin cytoskeleton, were significantly enriched, featuring six LM-DE-circRNAs. Notably, circDIAPH1 (hsa_circ_0074323), with the highest AUC value, emerged as a potential biomarker for CRC liver metastasis (CRLM). Functional assays following circDIAPH1 knockdown demonstrated induced apoptosis, suppressed proliferation, reduced metastasis, and invasion in CRC cell lines in vitro. The circDIAPH1 knockdown attenuated tumor growth in a cell-derived xenograft model. Furthermore, circDIAPH1 knockdown lessened the liver metastasis. Transcriptome profiling revealed that CEACAM6 was the most downregulated gene while circDIAPH1 was knocked down, and possesses high expression value in CRC. Most importantly, we found that circDIAPH1 recruited transcription factor FOXA1 to bind in the promoter region of CEACAM6 and initiated CEACAM6 expression. Additionally, the study identified the transcription factor BRD4 as a regulator of circDIAPH1 expression in CRC. In conclusion, this study reveals that circDIAPH1 recruits FOXA1 to initiate CEACAM6 expression, promoting liver metastasis and development of CRC.

Ubiquitin-specific peptidase 15 regulates the TFAP4/PCGF1 axis facilitating liver metastasis of colorectal cancer and cell stemness