Colorectal Tumors Research Articles

Significance of Microsatellite Instability in Colorectal Carcinoma- A Complete Review

The microsatellite instability (MSI-H) or mismatch repair deficient (dMMR) colorectal tumors recently have been reported that can benefit from immunotherapy, and MSI can be used as a genetic instability of a tumor detection index. Many studies have shown that there are many heterogeneous phenomena in patients with MSI tumors in terms of immunotherapy, prognosis and chemotherapy sensitivity. Here we mainly review the research results of MSI detection methods, its mechanisms, occurrence and its relationship with related tumors, aiming in such a way for brief analysis of the micro satellite instability. Microsatellites (MS) are the repeated sequences of DNA that play an important role in maintaining the tissue morphology. Any mutation of the DNA or chromosomes, lead to the instability of the microsatellites, thereby causing the microsatellite instability. There are three types of microsatellite instability (MSI). High microsatellite instability (MSI-H), low microsatellite instability (MSI-L) and microsatellite stability (MSS). Recent clinical research tends to classify MSS-L and MSS as similar. Microstaellite instability plays an important role in colorectal carcinoma. Based on different molecular mechanisms, MSI in colorectal cancer can be divided into colorectal cancer (CRC) with no obvious family genetic history and Lynch syndrome with non-polyposis with family genetic history. Lynch syndrome is an autosomal dominant disorder and syndrome caused by mutations in MMR strains, and it can also cause tumors in other parts of the colon and rectum. With the recent development of MSI detection technology and immunosuppressant in tumor therapy, researchers found that MSI-H tumors respond well to immunotherapy. There are several methods to detect the microsatellite instability. 1. Next Generation sequencing (NGS), 2. Fluoresence multiplex PCR and capillary electrophoresis. 3. Immunohistochemistry. 4. Single molecule- molecular inversion probes (SmMIP). The main mechanism of MSI includes, Slipped strand mispairing, MMR deficient.

All-Trans-Retinoic Acid-Adjuvanted mRNA Vaccine Induces Mucosal Anti-Tumor Immune Responses for Treating Colorectal Cancer.

Messenger RNA (mRNA) cancer vaccines are a new class of immunotherapies that can activate the immune system to recognize and destroy cancer cells. However, their effectiveness in treating colorectal cancer located on the mucosal surface of the gut is limited due to the insufficient activation of mucosal immune response and inadequate infiltration of cytotoxic T cells into tumors. To address this issue, a new mRNA cancer vaccine is developed that can stimulate mucosal immune responses in the gut by co-delivering all-trans-retinoic acid (ATRA) and mRNA using lipid nanoparticle (LNP). The incorporation of ATRA has not only improved the mRNA transfection efficiency of LNP but also induced high expression of gut-homing receptors on vaccine-activated T cells. Additionally, the use of LNP improves the aqueous solubility of ATRA, eliminating the need for toxic solvents to administer ATRA. Upon intramuscular injections, ATRA-adjuvanted mRNA-LNP significantly increase the infiltration of antigen-specific, cytotoxic T cells in the lamina propria of the intestine, mesenteric lymph nodes, and orthotopic colorectal tumors, resulting in significantly improved tumor inhibition and prolonged animal survival compared to conventional mRNA-LNP without ATRA. Overall, this study provides a promising approach for improving the therapeutic efficacy of mRNA cancer vaccines against colorectal cancer.

Abstract 3439: Factors affecting the performance of existing epigenetic clocks to predict chronological age in colorectal tumor and normal tissues

Abstract Epigenetic age (EA) may serve as a risk stratification biomarker for early-onset colorectal cancer (EOCRC, <50 years old), which has been rising substantially in recent decades. We utilized publicly available data in a descriptive analysis to compare epigenetic clocks in colorectal tissue and to investigate differences between chronological age (CA) and biological age, as measured by EA, in relation to demographic and clinical features. We analyzed DNA methylation (DNAm) array data on 144 participants (96 CRC cases, 48 healthy controls) from the Colonomics Study (CLX; Barcelona, Spain) and 331 CRC cases (51 EOCRC, 316 average-onset (≥50) colorectal cancer (AOCRC)) from The Cancer Genome Atlas (TCGA) as well as corresponding demographic and clinical variables. Among CLX participants, the 96 CRC cases provided colon tumor and paired normal mucosa samples, while the 48 controls provided healthy colon mucosa samples. TCGA included primary tumor samples from 331 cases with colon or rectal adenocarcinoma (TCGA-COADREAD). The 2013 Horvath clock estimated EA based on CA, while epiTOC, estimated the relative stem cell division rate from tissue biospecimens. We examined the correlations between CA and EA stratified by case/control status, sample type, sex, and age of onset (TCGA only). Tissue from CLX controls demonstrated a strong, positive correlation (r>0.9) between CA and EA for both the 2013 Horvath and epiTOC clocks. Using the Horvath clock, CA and EA correlations in normal mucosa and tumor tissue samples from CLX varied, with r = 0.74 and r = 0.41, respectively, and were weaker using the epiTOC clock, with r = 0.26 (normal) and r = 0.10 (tumor). When CLX cases were stratified by sex, the CA and EA (Horvath) correlations among female cases were r = 0.80 (normal) and r = -0.12 (tumor), while the correlations for males were stronger at r = 0.58 (normal) and r = 0.31 (tumor). This is in comparison to the epiTOC clock with females showing correlations of r = -0.02 (normal) and r = 0.41 (tumor), while males had r = 0.06 (normal) and r = 0.11 (tumor). In TCGA, correlations for EOCRC were r = -0.20 (Horvath) and r = -0.08 (epiTOC) and for AOCRC were r = 0.29 and 0.20, respectively. By sex, correlations for females with EOCRC for Horvath and epiTOC were r = -0.09 and r = -0.07, respectively, while correlations for males with EOCRC were r = -0.02 and r = -0.08, respectively. For TCGA cases with AOCRC, the correlations between CA and EA were r = 0.35 and r = 0.22 for females, and r = 0.26 and r = 0.20 for males, respectively for Horvath and epiTOC. This study revealed substantial variability in the ability of existing epigenetic clocks to accurately predict chronological age, with tissue type and sex strongly influencing the resulting correlations. Our findings highlight the importance of considering these factors when choosing an epigenetic clock. Citation Format: Christopher L. Benson, Ferran Moratalla-Navarro, Anna Diez-Villanueva, Matthew A. Devall, Victor Moreno, Stephanie L. Schmit, Fredrick R. Schumacher. Factors affecting the performance of existing epigenetic clocks to predict chronological age in colorectal tumor and normal tissues [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 3439.

Abstract 6901: Paired colorectal and pancreatic cancer patient-derived tumor and organoids biobank

Abstract Patient-derived xenograft (PDX) models constitute a crucial tool in precision cancer medicine owing to their high accuracy in predicting the response to therapeutic drugs among patients in clinical settings. Our center has established a biobank that collects more than 80 colorectal cancer and 25 pancreatic cancer PDX tissues, along with essential information about patients’ tumors and PDX models. However, cost-intensive and time-consuming limit the usage of PDX model in high throughput screening during drug development. To overcome this hurdle, we are generating a PDX-match paired organoid (PDXO) biobank by using emerging three-dimensional culture techniques. Before large-scaled expansion, the concordance between PDX tissues and PDXOs of partial specimens was evaluated firstly using short-tandem repeat (STR) analysis, immunohistochemistry (IHC) and H&E staining. Data of STR analysis performed by using AmpFLSTR Identifiler PLUS PCR Amplification Kit demonstrated that PDX tissues and PDXOs have identical DNA fingerprinting. IHC and H&E staining revealed PDX tissues and PDXOs have highly similar organ-specific markers expression (e.g., Cytokeratin 20, Caudal Type Homeobox 2, and Pan Cytokeratin) and histological morphology. Even after passing to at least five generations, passed PDXOs maintained high fidelity to their original state, as confirmed by whole-exome sequencing (WES) and STR analysis across passages. The WES analysis for passage 0 (P0) and passage 5 (P5) of PDXOs from different PDX tissues revealed there is more than 95% intersection between P0 and P5 PDXOs with the same missense mutation gene. The results of STR analysis showed that P0 and P5 PDXOs have identical STR profile. To evaluate the capability of PDXOs in clinical response prediction, several effective and ineffective drugs (e.g., oxapliplatin, 5-FU, gemcitabine) were tested. The results of drug testing indicated that PDXOs can be used to accurately predict the response to therapeutic drugs as PDX model but more efficient than PDX model. Therefore, PDXO biobank can serve as a valuable resource for high throughput in vitro drug screening prior in vivo efficacy confirmation using PDX models. Citation Format: Juiling Wang, Wen-Hui Ma, Yun-Chi Lo, Hsiao-Chun Hsieh, Li-Ju Hsiao, Yu-Pin Bau, Nai-Chieh Yang, Shaw-Jenq Tsai, Yan-Shen Shan, Tzu-Yu Chen, Yu-Ling Chen, Pei-Ju Chiang, Tzu-Ling Chen, Hsiu-Ping Chang, Hsian-Jean Chin. Paired colorectal and pancreatic cancer patient-derived tumor and organoids biobank [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 6901.

Abstract 1017: Characterizing immune cell infiltration in colorectal cancer tumor microenvironment among Native Hawaiians

Abstract Background Colorectal cancer (CRC) is recognized as a heterogeneous disease, ranking third in new cancer diagnoses and second in cancer-related deaths globally and nationally. CRC incidence is higher in the state of Hawaii compared to the U.S. overall. This study focuses on profiling immune cell infiltration in Native Hawaiian(NH)-specific CRC tumor microenvironments. Identifying the race-specific tumor infiltrating microenvironment may uncover potential mechanisms for CRC development in the NH population. Methods Deidentified, archival formalin-fixed paraffin-embedded tumor samples from Native Hawaiian patients diagnosed with primary CRC between 1990 and 2006 were obtained from the Hawaii Tumor Registry. RNA was extracted from tumor and adjacent normal tissues. RNA-seq data from Caucasian American (CA) CRC samples were obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO). Differentially expressed genes for each cohort were identified via DESeq2 with Benjamini-Hochberg multiple testing q-value<0.05 and a cutoff of 2-fold change. From the gene expression profiles, we applied the ESTIMATE algorithm to calculate the overall immune cell infiltration score for each sample. Based on a deconvolution algorithm, known as CIBERSORT to estimate the abundance of 22 immune cell types, we profiled the tumor-infiltrating immune cells present in each cohort’s paired samples, respectively. To improve the accuracy, p-value and root mean squared error were counted for each sample. Data with p<0.05 were filtered and selected for the next analysis. The fraction of immune cell subpopulations was evaluated and compared between paired tumor and adjacent normal tissues in NH and CA cohorts. Results In the NH cohort, we found the overall immune cell infiltration score was significantly lower in cancer tissues than the adjacent normal tissues (p<0.05), and there were significantly higher fractions of activated dendritic cells, resting natural killer (NK), and follicular helper T cells in tumor tissues compared to adjacent non-tumor tissues (p<0.05). Furthermore, the fractions of activated NK cells and plasma cells were significantly lower in tumor tissues than in adjacent non-tumor tissues in NH (p<0.05). Resting NK cells are upregulated in both the NH and the CA cohorts, while plasma cells are the only immune cell type downregulated in either cohort. In the NH cohort, activated dendritic cells and follicular helper T cells are exclusively upregulated, while activated NK cells are downregulated relative to the CA cohort. Conclusion This study demonstrates that the NH cohort displays distinctive immunological variances between tumor and adjacent non-tumor tissues which distinguishes them from the CA cohort. This emphasizes the significance of acknowledging population-specific genetic variations which may help understand race specific difference in CRC. Citation Format: Yuanyuan Fu, Gino Quintal, Masaki Nasu, Mayumi Jijiwa, Sudhir K. Rai, Isam Mohd-Ibrahim, Yu Chen, Hua Yang, Zhanwei Wang, Christina Wai, Owen Chan, Brenda Y. Hernandez, Youping Deng. Characterizing immune cell infiltration in colorectal cancer tumor microenvironment among Native Hawaiians [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 1017.

Abstract 6782: 3D-EXpress - an ex vivo platform using viably cryopreserved tumoroids for rapid assessment of targeted therapeutic outcomes

Abstract Background: it has been a significant challenge to select, combine, and sequence the multiple FDA-approved IO therapies and pharmaceutical agents, highlighting the need to develop a precision oncology platform to explore novel combination treatments. 3D-EXpress is a unique ex vivo therapeutics testing platform using a biorepository of fresh patient tumoroids that were never dissociated, propagated, or reassembled to retain an intact microenvironment. Therefore, these specimens provide an excellent ex vivo platform to investigate the efficacy of therapeutics targeting the tumor microenvironment. Here, we employed the 3D-EXpress platform to compare the efficacy of different therapeutic modalities targeting tumor antigens and immune checkpoint ex vivo. Methods: Tumoroids measuring 150 μm in size retaining tumor cell heterogeneity, tumor-resident immune cells, stromal components, and extracellular matrix interaction were prepared from human endometrial and colorectal tumors. Tumoroids were cryopreserved and were selected based on tumor antigen status. Samples were treated for 72 hours ex vivo with antibody-drug conjugates, chimeric antigen receptor (CAR)T cells, or bispecific antibodies alone and in combinations. Treatment-mediated changes in tumor cell killing and tumor immune microenvironment were investigated. Results: 3D high throughput confocal imaging and Nilogen Oncosystem’s proprietary algorithm were used to detect and analyze treatment-induced tumor cell killing activity in tumoroids. The impact of ex vivo treatment by different modalities in combination with chemotherapeutic agents upon tumor resident immune cell populations was monitored by deep immune phenotyping and multiplex cytokine release assay. Based on the ex vivo responses tumors were assigned to treatment sensitive and resistant groups. Correlative analysis was performed and compared with detailed clinicopathologic data that is readily available for Biorepository tumors. Conclusions: The 3D-EXpress platform using cryopreserved 3D tumoroids with intact tumor microenvironment is an effective tool for the pre-clinical assessment of rational drug combinations for treatment of solid tumors. Furthermore, the 3D-EXpress platform provides unique insight into the microenvironment of both treatment responsive and non-responsive tumors and can aid in the development of patient-centered therapeutic regimens. Citation Format: Vanessa Garrido, Michelle Ataya, Nisha R. Dhanushkodi, Seth Currlin, Alliyah Humphrey, Jared Ehrhart, Rikhia Chakraborty. 3D-EXpress - an ex vivo platform using viably cryopreserved tumoroids for rapid assessment of targeted therapeutic outcomes [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 6782.

Abstract 5099: Prevalence of fibroblast growth factor receptor (FGFR) alterations (alts) and programmed death-ligand 1 (PD-L1) expression (exp) in Chinese solid tumor patients (pts)

Abstract Background: PD-L1 expression drives anti-PD(L)-1 treatment decisions across many cancer indications. FGFR inhibitors have been approved for the treatment of metastatic urothelial cancer (UC) and cholangiocarcinoma with FGFR alts. BALVERSA (erdafitinib), a selective pan-FGFR kinase inhibitor, has shown clinical activity against FGFR altered solid tumors in pts who exhausted standard treatment options. It is important to understand the prevalence of FGFR alts and relationship between FGFR alts and PD-L1 expression levels in different cancer types. Methods: In this real-world study, 9937 Chinese solid tumor pts with the PD-L1 (22C3) immunohistochemistry and OrigiMed 450-gene next-generation sequencing panel results were selected. Chi-square test and Fisher test were used to explore the association between the FGFR alts and PD-L1 expression. Results: FGFR1-4 somatic alts were found in 9.0% of Chinese cancer pts evaluated. FGFR1 amplification (amp) was the most prevalent alts identified (1.9%). There were no significant differences in frequency of FGFR alts between the Chinese cohort and MSK-IMPACT cohort in each cancer type tested. Up to 40.6% of pts evaluated were PD-L1 positive (CPS ≥1 or TPS ≥1%). The PD-L1 positive rate (TPS ≥1%) in SCLC (12.4%, n=121) and NSCLC adenocarcinoma tumors (LUAD) (26.1%, n=2902) was relatively low. In few tumor types, higher expression of PD-L1 in FGFR altered samples was observed compared with FGFR unaltered samples in pan-tumor (mean TPS 14.8% vs.8.6%, P=6.0*E-9; mean CPS 6.3 vs. 6.1, P=3*E-4). Those includes LUAD (mean TPS 14.2% vs. 7.4%, P = 1.7*E-16), colorectal tumor (mean CPS 4.6 vs. 3.9, P = 4.6*E-8), and uterine tumor (mean CPS 8.1 vs. 6.5, P = 9.6*E-5). While PD-L1 expression is lower in FGFR altered samples than FGFR unaltered samples in UC (n=154; mean CPS 3.9 vs. 6.8, P = 0.004). No relationship was observed between FGFR alts and PD-L1 expression in cholangiocarcinoma (n=610). Specific FGFR alts eligible for erdafitinib UC treatment were further investigated in UC and observed with rate 10.4%, including FGFR3 short variants (9.7%) as main alts. Specific FGFR altered tumors showed similar trend with lower PD-L1 expression than FGFR unaltered tumors in UC. The inverse relationship between FGFR alts and PD-L1 expression in UC compared to other solid tumors may explain variable role of FGFRs since the predominant FGFR alt types vary among different cancer types (FGFR3 short variants enriched in UC vs no such predominant FGFR alt types in other cancer types). Conclusion: The large Chinese solid tumor cohort analysis showed comparable FGFR alts prevalence between Chinese and Western population. Differences in relationship between FGFR alts and PD-L1 expression across tumor types reflect the differential role of predominant FGFR types in each tumor type. Citation Format: Min Qing, Fei Yang, Xiaowei Chen, Xuesong Lyu, Aodi Wang, Yanfei Yu, Shibu Thomas, Longen Zhou. Prevalence of fibroblast growth factor receptor (FGFR) alterations (alts) and programmed death-ligand 1 (PD-L1) expression (exp) in Chinese solid tumor patients (pts) [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 5099.

Abstract 6741: Targeting glutamine metabolism potentiates antigen presentation in colorectal cancer

Abstract Colorectal cancer (CRC) ranks among the most prevalent cancers worldwide, causing substantial mortality. The urgent need for effective treatments has driven research into immune checkpoint blockade (ICB) therapies, which have demonstrated significant clinical benefits across various cancer types. Despite the success of ICB therapies, a significant proportion of CRC patients exhibit resistance to treatment, prompting the identification of mechanisms that hinder therapy resistance or enhance treatment response. CRC cells display remarkable adaptability, orchestrating metabolic changes that confer growth advantages, pro-tumor microenvironment, and therapeutic resistance. One such metabolic change occurs in glutamine metabolism. In this study, we found that colorectal tumors with high glutaminase (GLS) expression exhibit reduced T-cell infiltration and cytotoxicity, leading to poor clinical outcomes. To validate these findings, we applied the ovalbumin (OVA)/OT-I T cell-based cytotoxicity assay and the CRC patient-derived organoids (PDOs)/autologous T cell killing assay. Our results indicated that inhibition of GLS significantly enhanced T-cell cytotoxicity in vitro and ex vivo. Mechanistically, we elucidated that inhibition of GLS activated reactive oxygen species-related signaling pathways in tumor cells, thereby potentially increasing tumor immunogenicity by promoting antigen presentation. The combinational therapy of GLS inhibitor and ICB exhibited a superior tumor growth inhibitory effect in comparison with either of the monotherapies. These findings shed new light on clinical therapeutic strategies for CRC patients, offering a promising approach to enhance the efficacy of ICB therapy. Citation Format: Tao Yu, Kevin Van der Jeught, Haiqi Zhu, Zhuolong Zhou, Samantha Sharma, Sheng Liu, Ka Man So, Haniyeh Eyvani, Xiyu Wang, George E. Sandusky, Yunlong Liu, Mateusz Opyrchal, Sha Cao, Jun Wan, Chi Zhang, Xinna Zhang. Targeting glutamine metabolism potentiates antigen presentation in 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 6741.

Abstract 62: Intra-tumor persistence of activated anti-mesothelin hYP218 CAR T cells is associated with increased efficacy in gastric and colorectal cancers

Abstract Purpose: Patients with gastric and colorectal cancers that have progressed after standard therapies have poor prognosis. Given the high expression of mesothelin in these tumor types, we examined the potential utility of the anti-mesothelin hYP218 CAR T cells to treat these cancers. Experimental Design: Cell surface mesothelin expression in a panel of gastric and colorectal cancer cell-lines was analyzed using flow cytometry. In vitro efficacy of hYP218 CAR T cells against these cell lines was evaluated using cytotoxicity and cytokine release assays. In vivo efficacy of hYP218 CAR T cells was studied using gastric (HGC27) and colorectal (SW48) tumor xenografts in NSG mice. NSG mice were injected with 1 × 106 cancer cells and the tumors were allowed to grow until they reached a volume of 80-100mm³, after which the mice were treated with either 5 × 106 hYP218 CAR T cells, 5 × 106 untransduced T cells, or saline and monitored over time. Persistence of CAR T cells in the tumor was evaluated over time and expression of activation and exhaustion markers were studied. Results: hYP218 CAR T cells demonstrated strong cytotoxic activity against mesothelin positive gastric and colorectal cancer cell lines and exhibited increased pro-inflammatory cytokine production. In both the HGC27 and SW48 tumor models hYP218 CAR T cells demonstrated significant reduction in tumor volume and overall survival compared to mice treated with untransduced T cells or saline. CAR T cells isolated from tumors of both the xenograft models, at day 40 after treatment, displayed higher expression levels of activation markers CD39 and CD69 when compared to the infused product. Furthermore, a concomitant elevation in the levels of effector cytokines, TNF-α and IFN-γ, was detected in the blood of treated mice demonstrating the functional capacity of the CAR T cells to not only persist but also to maintain an activated state. Conclusions: hYP218 CAR T cells show anti-tumor efficacy against gastric and colorectal tumor xenografts due to increased accumulation of activated CAR T cells in the tumor and warrants further investigation for treatment of patients with these cancers. Citation Format: Sameer A. Mir, Abhilash Venugopalan, Jingli Zhang, Mana Kamana Khanal, Chaido Stathopoulou, Manjistha Sengupta, Qun Jiang, Raffit Hassan. Intra-tumor persistence of activated anti-mesothelin hYP218 CAR T cells is associated with increased efficacy in gastric and colorectal cancers [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 62.

Abstract 3519: Reconstructing a latent representation of gene expression from genomic alterations to improve clinical utility of real-world clinicogenomics data

Abstract Background: Molecularly and clinically well-annotated patient datasets are ideal for studying tumor biology and developing robust machine learning (ML) models for predicting outcome and treatment response. These data however rarely exist in real-world settings or in sufficient quantities within research contexts. Large publicly available datasets like The Cancer Genome Atlas (TCGA) which provid multi-omic profiles for diverse cancer types, have profoundly advanced cancer research and facilitated development of novel therapies and personalized medicines. However, the absence of patient outcome data tied to treatment limits the applicability of these data for understanding and modeling treatment response. Real-world clinicogenomics cohorts, such as the AACR Project GENIE, on the other hand are typically very rich in clinical annotations, including treatment regimens and outcomes measures. These data are however sparsely annotated for patient tumor molecular profiles, rarely exceeding ~100’s of genes profiled. We hypothesized that it would be possible to reconstruct latent tumor mRNA representations from limited genomic and clinical data available in real-world clinicogenomic cohorts, and that these reconstructed expression profiles would be useful for a variety of clinically meaningful downstream applications. Methods: We developed an ML model, called Mut2Ex, to reconstruct tumor gene expression profiles using genetic information available on commercial next generation sequencing panels using a Principle Label Space Transformation (PLST) we adapted to regression problem, along with embeddings from clinical information (OncoTree code, sex and stage) generated by a language model. Mut2Ex was trained on ~1200 cell lines from DepMap representing 26 cancer types, to generate ~2000 reconstructed mRNA gene profiles that were applied to a variety of clinical tasks. We used Mut2Ex to reconstruct mRNA profiles for ~10,000 tumors from TCGA and ~180,000 tumors from AACR Project GENIE. Results: Reconstructed mRNA expression by Mut2Ex was highly correlated with true expression in cell lines (rho = 0.926, [0.924-0.928 95% CI, N = 1184]). Compared to true expression, reconstructed profiles recapitulate sub-clusters within cancer types, PAM50 subtyping in breast tumors, survival signatures in colorectal tumors and multiple oncogenic signatures in a pan-cancer manner. Analysis of reconstructed expression for AACR Project GENIE tumors revealed expected enrichment of known driver genes within expression subtypes and enrichment of oncogenic signatures associated with distinct clinical outcomes in a cancer type specific manner. Conclusions: Our flexible analytic framework for reconstructing gene expression profiles from clinicogenomics data substantially augments the clinical utility and value of data acquired in real-world settings. Citation Format: Maayan Baron, Sunil Kumar, Felicia Kuperwaser, Dillon Tracy, Emily Vucic, Jeff Sherman. Reconstructing a latent representation of gene expression from genomic alterations to improve clinical utility of real-world clinicogenomics data [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 3519.

Abstract 3323: Novel Pan-RAS inhibitor ADT-007: A unique mechanism of antitumor selectivity in pancreatic and colorectal carcinoma models

Abstract Multiple types of RAS mutations activate RAS isoforms, HRAS, NRAS, or KRAS, that drive oncogenic signaling leading to uncontrolled cell proliferation and tumor development. RAS mutations occur de novo in approximately one-third of all human cancers, and are especially prevalent in pancreatic, colorectal, and lung tumors. Where RAS mutations are less frequent in other cancers, such as breast cancer, RAS can be pathologically activated by growth factor receptors that engage numerous downstream effectors. The currently FDA-approved KRAS-targeted drugs are designed to covalently inactivate only G12C KRAS mutants, however, this mutation is only prevalent in lung cancer. The most common mutations in pancreatic ductal adenocarcinoma (PDAC) are KRAS-G12D, KRAS-G12V, and KRAS-G12R. Our novel class of pan-RAS inhibitors, exemplified by ADT-007, addresses the urgent need for pan-RAS inhibitors with antitumor activity in cancers harboring these common mutations. These pan-RAS inhibitors have unique pharmacological properties that allow for selective killing of cancer cells harboring RAS mutations. ADT-007 inhibited growth of an array of carcinoma tumor cell lines in vitro with single digit nM IC50 values regardless of RAS mutant allele, and inhibited RAS activation and MAPK/AKT signaling. Because it is a pan-RAS inhibitor, ADT-007 may not be susceptible to commonly reported mechanisms of resistance to covalent KRAS inhibitors, such as activation of wild type (WT) alleles or secondary RAS mutations. Differentiated normal epithelial or hepatic cells, and tumor cells with WT RAS were insensitive to ADT-007 due to enzymatic detoxification of ADT-007 via glucuronidation, representing a novel mechanism of tumor selectivity. An orally bioavailable prodrug of ADT-007 (ADT-1004) is well tolerated in vivo, and produced sustained concentrations of ADT-007 well above IC50 values in plasma and even higher levels in tumors. Daily oral administration of ADT-1004 significantly inhibited RAS signaling and tumor growth in orthotopic and PDX mouse models of pancreatic cancer. Citation Format: Junwei Wang, Adam B. Keeton, Sindhu Ramesh, Peyton Johnson, Yulia Y. Maxuitenko, Jeremy B. Foote, Chung-Hui Huang, Kristy L. Berry, Khalda Fadlalla, Bandi D. Reddy, Ganji P. Nagaraju, Elmar Nurmemmedov, Ivan Babic, Vadim Gaponenko, Xi Chen, Bassel F. El-Rayes, Donald J. Buchsbaum, Gary A. Piazza. Novel Pan-RAS inhibitor ADT-007: A unique mechanism of antitumor selectivity in pancreatic and colorectal carcinoma models [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 3323.

Abstract 4256: Autologous organoids and T cell co-cultures as a powerful personalized platform for immunotherapy development

Abstract Recent advances in cancer immunotherapy have had a positive impact on the life expectancy of patients for an extensive range of clinical indications. With new treatment strategies and druggable targets being identified at an increasing pace, the number of patients eligible for cancer immunotherapy is expected to expand steadily. However, promising therapeutic developments face hurdles in translating preclinical findings into therapy since conventional 2D cancer models hold low clinical predictive value. We developed an innovative alternative, building on the discovery that adult stem cells proliferate and organize into three-dimensional organotypic structures when they are embedded into extracellular matrix. Patient-derived organoids are generated from normal and malignant tissues and stored as high-quality biobanks that yield highly reproducible results. HUB Organoids® recapitulate complex characteristics of the parental tissue, including molecular heterogeneity, as well as morphological and functional traits. Since cancer progression and response to immunotherapy are governed by immune cell interactions in the tumor microenvironment, we developed an assay in which colorectal (CRC) and non-small cell lung cancer (NSCLC) tumor organoids are co-cultured with paired tumor infiltrating lymphocytes (TIL) that are simultaneously expanded as a source of tumor reactive cells. Paired resources allow for the screening of immune-modulatory therapies under physiologic conditions, not depending on peptide-pulsing and alloreactivity. We quantify tumor organoid killing and TILs reactivity by combining imaging-based analysis of apoptotic cells with flow cytometry to measure cytokine release by cytotoxic TILs. Here, we show that our system is robust and reproducible with an establishment rate of 75%, allowing for expansion of TILs that preserve T cell receptor repertoires. First line expansion of both PDO and TIL components can be used to effectively build coculture models and probe the tumor and immune components, respectively. Our system offers a powerful tool for the development and validation of cancer immunotherapy and can help to stratify cancer patients for susceptibility to various types of immunotherapies. We certify that the research use of each of the HBS marked above was conducted according to the expectations of each institution. Citation Format: Claudia Beaurivage, BanuPriya Sridharan, Sumeyra Mucuk, Kimberly Nadwodny, Derek Poore, Anna Schepers, Farzin Pourfarzad, Sylvia F. Boj. Autologous organoids and T cell co-cultures as a powerful personalized platform for immunotherapy development [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 4256.

Abstract 1615: Balanced molecular feature selection unveils universally tumor-lineage informative methylation sites in colorectal cancer

Abstract In the era of precision medicine, performing comparative analysis over diverse patient populations is a fundamental step toward tailoring healthcare interventions. However, the critical aspect of equitably selecting molecular features across multiple patients is often overlooked. To address this challenge, we introduce FALAFL (FAir muLti-sAmple Feature seLection), a novel algorithmic approach based on integer linear programming. FALAFL is designed to bridge the gap between molecular feature selection and algorithmic fairness, ensuring a balanced selection of molecular features across different patient samples. We have applied FALAFL to the problem of selecting lineage-informative CpG sites within a cohort of 9 colorectal cancer patients subjected to low-coverage single-cell methylation sequencing. Our results demonstrate that FALAFL excels at rapidly determining the optimal set of CpG sites, which are well covered by cells across the vast majority of the patients, while ensuring that each patient contributes a similar number of sites to the final selection. An analysis of the FALAFL-selected CpG sites reveals that their lineage informativeness exhibits a strong association across diverse patient profiles, suggesting the non-stochasticity and universality of methylation changes in tumor evolution. Furthermore, these universally lineage-informative sites exhibit subclonal level alterations in the colorectal cancer primary tumors and are strongly associated with lineage-specific gene expression patterns. By integrating equity considerations into the molecular feature selection process, FALAFL is poised to propel equitable healthcare data science practices and advance our understanding of cancer and other complex diseases. Citation Format: Xuan Cindy Li, Yuelin Liu, Alejandro A. Schäffer, Stephen M. Mount, Süleyman C. Sahinalp. Balanced molecular feature selection unveils universally tumor-lineage informative methylation sites in 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 1615.

Abstract 5154: Bacterium LF-3: A dual player in colorectal cancer, shaping prognosis and immune responses

Abstract Background: Colorectal cancer is distinctive for its heightened intra-tumor bacterial presence. While previous studies concentrated on the genus level, the impact of unclassified bacteria, identified through extensive genome sequencing, has been underexplored. Methods: Utilizing samples from colorectal cancer patients in the Cancer Microbiome Atlas project (TCMA), we applied phyloseq for a nuanced analysis of microbial abundance disparities between tumor and paracancer tissues. Prognostic implications of microbial enrichment were explored through survival analysis, with mechanistic insights gleaned from Gene Set Enrichment Analysis (GSEA). Results: We meticulously examined 151 colorectal cancer tumors and 22 corresponding para-cancer tissues, scrutinizing a total of 1217 microbial species. We observed that 240 species exhibited a statistically significant enrichment in tumor samples. A focused investigation involving 22 tumor and para-cancer tissue pairs unveiled 35 species with notable enrichment specifically within tumors. A subset of 25 species, including well-documented entities like Fusobacterium sp. oral taxon 370 and Streptococcus oralis, emerged consistently across both comprehensive and paired analyses. We then delved into the prognostic implications of these enriched bacteria. Strikingly, patients with bacterium LF-3 positivity exhibited significantly improved prognoses compared to those without (HR 0.40, 95% CI 0.18-0.91, log-rank p = 0.024). Considering the pivotal role of Microsatellite Instability (MSI) status in the context of Tumor Immuno-Microenvironment (TIME) and prognosis, our analysis of bacterium LF-3 encompassed both MSI-H and MSS CRC cases, with proportions of 12/28 (43%) and 55/102 (54%), respectively. Even after meticulous adjustments for MSI status, bacterium LF-3 maintained a robust correlation with prognosis (HR 0.42, 95% CI 0.18-0.99, p = 0.048), highlighting its independent prognostic significance. Further exploration among MSS patients (N = 112) unearthed intricate details about the impact of bacterium LF-3 on tumor signaling pathways. TNF-α and IFN-γ pathways were significantly up-regulated in bacterium LF-3-positive cases, while the MYC pathway, PI3K pathway, and various cell cycle-related pathways (G2M checkpoint, The E2 factor [E2F] targets, and mitotic spindle assembly) were down-regulated. As for TIME, bacterium LF-3 positivity correlated with the significant enrichment of CD4+ Th2 cells, suggesting a potential role in modulating immune responses. Conclusion: Bacterium LF-3 in colorectal cancer reveals a dual role, instigating inflammation and tumorigenesis, yet simultaneously activating the innate immune system and promoting cellular immunity. This dual functionality contributes to improved patient prognosis, highlighting the intricate interplay between microbes, immune responses, and colorectal cancer outcomes. Citation Format: Kunli Du, Feilong Zhao, Fan Feng. Bacterium LF-3: A dual player in colorectal cancer, shaping prognosis and immune responses [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 5154.

Abstract 738: MBRC-101: a novel antibody-drug conjugate (ADC) targeting the tyrosine kinase receptor EphA5

Abstract Introduction: The receptor tyrosine kinase EphA5 has the classical receptor kinase topology with an extracellular-binding domain, a single-pass transmembrane domain, and a cytoplasmic kinase domain. Previously, EphA5 has been shown to contribute to DNA-damage repair and radiation therapy resistance in lung cancer. We investigated EphA5 expression in lung cancer as well as breast, pancreatic, gastric, and colorectal cancer and assessed its potential as a therapeutic target using a novel ADC, MBRC-101. Methods: MBRC-101 is composed of a humanized anti-EphA5 IgG1 monoclonal antibody conjugated to monomethyl auristatin E (MMAE) via a cleavable valine-citrulline linker using site-specific ThioBridge™ technology. The specificity profile of the anti-EphA5 antibody was characterized using a membrane proteome array. Receptor-mediated antibody internalization was determined by real-time live-cell analysis, and cell killing assays were performed using analysis of cell confluence and luminescent-based viability. Expression of EphA5 in archival human tissue sections was evaluated by immunohistochemistry (IHC) using a commercial antibody. Efficacy studies used patient-derived xenograft (PDX) models of lung adenocarcinoma, squamous cell carcinoma of both lung and head and neck, and breast cancer. Results: IHC demonstrated selective EphA5 membrane expression in 78% (18/23) of triple negative and 88% (23/26) of hormone receptor-positive breast cancer tumors tested. EphA5 membrane expression was also detected in 85% (29/34), 73% (16/22), 70% (7/10), 70% (15/22), and 50% (6/12) of lung squamous cell carcinoma, lung adenocarcinoma, gastric, colorectal, and pancreatic patient tumors tested, respectively. EphA5 expression was not detected in adjacent, non-malignant tissue in any of the tumors examined. The anti-EphA5 antibody bound exclusively to EphA5 and did not cross-react with other members of the Eph receptor/ephrin ligand family. Binding of the anti-EphA5 antibody on the cell surface triggered rapid internalization and processing through the endosomal-lysosomal system. MBRC-101 was cytotoxic to EphA5-expressing cells and its activity was concentration-dependent and commensurate to levels of EphA5 on the cell surface. In PDX models, once weekly administrations of intravenous MBRC-101 showed dose-dependent, robust, and reproducible anti-tumor activity. Partial tumor responses were observed at doses of 2.5 mg/Kg and complete tumor responses starting at 5 mg/Kg. Toxicologic findings in Sprague-Dawley rats and cynomolgus monkeys were attributed to the MMAE payload and not target-related. Based on an HNSTD of 10 mg/kg in monkeys, the starting human dose was 0.5 mg/kg with ~15-fold safety margin. Conclusions: EphA5 is a new and promising molecular target for the development of ADC-based therapies against many human cancers. A Phase 1/1b study of MBRC-101 is currently recruiting (NCT06014658). Citation Format: Fernanda I. Staquicini, Fenny H. Tang, Vanessa de Oliveira, Daniela I. Staquicini, Yongjian Wu, Kirstin F. Barnhart, J Kellogg Parsons, Wadih Arap, Isan Chen, Renata Pasqualini. MBRC-101: a novel antibody-drug conjugate (ADC) targeting the tyrosine kinase receptor EphA5 [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 738.

Abstract 7414: Claire: a search engine leveraging deep databases for reliable detection of peptides, with a special focus on proteogenomic applications

Abstract As the field of cancer diagnostics and treatment evolves, the significance of peptides characterized by post-translational modifications and amino acid substitutions is becoming increasingly prominent. These molecular alterations frequently offer critical insights into tumor biology, aiding the development of targeted therapies and methods for personalized medicine. However, despite ongoing advances in shotgun proteomics, the field still faces multiple challenges for the reliable detection of rare peptide forms, for instance, amino acid substitutions when the corresponding DNA or RNA sequencing is unavailable. As a response to these challenges, our group has developed Claire—a probabilistic search engine employing large peptide databases for detection. These databases, often on the terabyte scale, further incorporate the estimates of peptides' prior probabilities to improve detection accuracy and utilize several optimizations to allow fast interpretation of tandem mass spectra. Claire outperformed state-of-the-art software, such as MSFragger and TagGraph when evaluated on the protein-level detection of single nucleotide variants in the public NCI60 proteome dataset. Further, Claire's analysis of a range of NCI60 datasets revealed high protein-level mutational burdens in genomically unstable cancer cell lines and detected mislabeling and contamination across several omics datasets. In a clinical domain, Claire discerned the hypermutation status of colorectal cancer patients' tumors, identifying candidates suitable for immunotherapy. Protein-level variation in peripheral blood mononuclear cells also recognized individuals, monozygotic twins aside, revealing the pseudonymous nature of germline proteome datasets, and raising the need for their protection. From a computational perspective, Claire can be run as a standalone software in the Linux operating system, or its capabilities accessed remotely using an interface on our cloud computing infrastructure. Claire has thus shown remarkable potential in enhancing peptide detection, offers substantial advancements for both clinical and research applications, and allows direct incorporation of its capabilities into various computational workflows. Citation Format: Miroslav Hruska, Petr Dzubak, Marian Hajduch. Claire: a search engine leveraging deep databases for reliable detection of peptides, with a special focus on proteogenomic applications [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 7414.

Abstract 3496: EpigenPlot: A tool for the gene-level methylation analysis of colorectal tumors

Abstract Introduction. Aberrant DNA methylation patterns are frequent in colorectal adenocarcinoma (CRC) tissues. The investigation of this layer of epigenetic regulation holds the promise of a better understanding of tumour progression and the identification of novel biomarker candidates. Purpose. Our goal was to collect and analyse publicly available DNA methylation data of colorectal samples and create a user-friendly tool for exploring and visualizing the CRC methylome. Methods. We used Illumina Infinium Methylation Arrays, which is a popular platform for genome-wide methylation analysis of large cohorts. Gene Expression Omnibus database (GEO) and TCGA-COAD (The Cancer Genome Atlas Colon Adenocarcinoma) datasets including normal colorectal mucosa, adenoma, and adenocarcinoma samples were systematically collected and filtered. Differentially methylated regions were identified using the Kruskal-Wallis test. Genes with significant methylation changes were further analysed using ROC (Receiver Operator Characteristic) analysis. Finally, we established a web application using the shiny R package. Results. We assembled a database including methylation data of 2,586 samples. Adenoma and adenocarcinoma samples were globally hypomethylated. Hypermethylation (p < 0.05, Δβ >= 0.2) in adenocarcinoma samples was predominantly present in regions near proximal promoters. Out of the 74 previously proposed biomarkers examined, 50 had a cross-validated AUC of over 0.8. FDA-approved biomarkers BMP3, NDRG4, and SEPT9 have shown the highest performance in the TSS200 region (cvAUC = 0.8, 0.83, and 0.76, respectively). Genes with the highest performance were ITGA4 (5’UTR, first exon: cvAUC = 0.9), MDFI (5’UTR: cvAUC = 0.9), CNRIP1 (5’UTR, first exon: cvAUC = 0.89). The established web application can visualize methylation at CpG sites and gene regions, and KEGG pathway genes. The platform is available at https://epigenplot.com. Conclusion. We collected and analysed a sizeable database of colorectal tissue data. Gene regions with the best performance include previously proposed and novel diagnostic biomarker candidates. The web platform provides an tool for the efficient exploration of the assembled data. Citation Format: Dalma Müller, Balazs Gyorffy. EpigenPlot: A tool for the gene-level methylation analysis of colorectal tumors [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 3496.

Abstract 7363: Clinical, genomic, transcriptomic and immunologic profile of BRAF mutant colorectal tumors

Abstract Background: Colorectal cancer (CRC) is the second leading cause of cancer-related death worldwide. BRAF, a protein kinase of the Mitogen-Activated Protein Kinase (MAPK) pathway, is mutated in 12% of colorectal cancers and is a poor prognostic factor for patients. BRAF mutations at the V600 codon are most studied but non-V600 BRAF mutations also exist and behave differently. BRAF V600 CRC treated with BRAF+MEK inhibitors show 12% response rates while we observe 65% response rates in BRAF V600 Melanoma. Additionally, no approved targeted therapies exist for non-V600 BRAF mutant cancers and retrospective studies show poorer PFS with BRAF+MEK inhibitors vs BRAF V600 cancers. We interrogated publicly available data of BRAF mutant CRC to uncover differences in the tumor microenvironment and signalling pathways of BRAF V600 and non-V600 tumors in hopes of uncovering better treatments. Methods: We analyzed the clinical and genomic profile of BRAF mutant CRC tumors from the GENIE v12 data. Gene Set Enrichment Analysis was performed on RNAseq from the TCGA data (discovery cohort) and the combined data from CPTAC and Sidra-LUMC data (validation cohort). We investigated the composition of tumor infiltrating immune cells using CIBERSORTx (deconvolution algorithm for bulk RNAseq). Results: Non-V600 mutations (n=219/1061) were most represented in patients of Asian or Black race compared to White patients (p<0.0001) and importantly, were found in younger patients (p<0.0001). We identified n=67 and n=74 BRAF mutant RNAseq samples in the discovery and validation cohorts, respectively. In the discovery cohort: BRAF V600 CRC were enriched for Interferon Gamma Signaling, Complement pathway, and IL6 JAK STAT3 Signaling (p<0.05) while the non-V600 BRAF mutant CRC showed an enrichment for Wnt-beta Catenin, Notch, and Hedgehog Signaling pathways (p<0.05). In the validation cohorts these same pathways were enriched in V600 and non-V600 BRAF mutant tumors. Interestingly, enrichment of genes co-mutated (GENIE data) in non-V600 BRAF mutant CRC also revealed the Wnt pathway. Non-V600 CRC tumors have a higher proportion of M0 macrophages (p=0.0035) and CD4 memory resting T cells (p<0.0001) while patients with V600 CRC have higher proportions of CD8 T cells (p=0.006) and activated mast cells (p=0.0341). Conclusion: No optimal therapeutic strategies have been defined for these potentially actionable non-V600 BRAF mutant CRCs. By exploring the multi-omic landscape of these tumors we have identified unique characteristics of non-V600 BRAF mutant CRC that could be therapeutically exploited. Citation Format: Emmanuelle Rousselle, Suzanne Kazandjian, April Rose. Clinical, genomic, transcriptomic and immunologic profile of BRAF mutant colorectal tumors [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 7363.

Abstract 636: Coculture model for investigating cellular interactions between colorectal tumor organoids and cancer-associated fibroblasts

Abstract The tumor microenvironment (TME) is well recognized for its role in tumor progression, chemoresistance, and recurrence. The TME consists of various components, such as extracellular matrix (ECM), chemical and mechanical cues, as well as stromal cells and their interactions. As the most abundant cells in tumor stroma, cancer-associated fibroblasts (CAFs) have drawn a lot of attention. It has been reported that CAFs not only directly interact with cancer cells via surface proteins and cytokines, but also influence their behaviors by remodeling the ECM. However, due to their heterogenous characteristics and diverse functions, the influence of tumor-CAF interactions on drug response is not fully understood. Here, we present a coculture model for investigating CAF effects on patient-derived colorectal tumor organoids (CTOs) growth, differentiation, and drug response. It consists of normal colon fibroblasts, CCD18-Co, or patient-derived CAFs seeded with CTOs in a mixed hydrogel containing 90% basement membrane extract (BME) and 10% collagen type I. Media conditions were optimized (1:1 mix of CTO culture media plus reduced media excluding growth factors and inhibitors) to achieve similar organoid sizes in the monoculture and coculture conditions at the onset of drug testing. To support higher throughput investigations, our workflow incorporates a liquid handler for automated CTO seeding, media and drug exchange, and an automated microscope with a robotic arm for multi-plate imaging. Briefly, single cell CTOs and fibroblasts were seeded at a 1:1 ratio (3000 total cells/well) in 96-well plates. After 4 days in culture, anti-cancer drugs were administrated in reduced media to the samples. Brightfield images were acquired on days 0, 3, and 5 after drug administration. The collected images were analyzed with a neural network (NN) to dynamically monitor the growth and viability of individual organoids. The CellTiter-Glo assay was performed on day 5 to quantify the total CTO cell viability. The normalized drug response (NDR) was calculated from the NN processed images to determine the drug response. An immunostaining panel, which includes protein markers such as CK20, Ki67, α-SMA, Vimentin, and FAP, was used to evaluate the fibroblast phenotypes and CTO differentiation. Additionally, the cultures were subjected to fluorescent lifetime imaging microscopy (FLIM), a label-free imaging technique, to measure the metabolic adaptations of each cell population. Preliminary studies revealed a CAF-dependent increase in CTO growth and glycolytic signatures in the co-culture setting; however, minimal effects on drug response to common chemotherapy agents such as 5-fluorouracil and irinotecan were observed. In the future, we will use this integrated pipeline as a screening method to identify new treatment strategies aimed at targeting the stromal microenvironment in colorectal cancer. Citation Format: Yuyuan Zhou, Yu-Kai Huang, Emma J. Fong, Elizabeth Elton, Erin McManus, Brandon Choi, Seungil Kim, Shannon M. Mumenthaler. Coculture model for investigating cellular interactions between colorectal tumor organoids and cancer-associated fibroblasts [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 636.

Abstract 1375: Abundance of KLRB1+ (CD161) T cells in anti-PD1 non responders coupled with enhanced tumor cytotoxicity of anti-CD161 (IMT-009) with anti-PD1 makes it a rational target for combination with anti-PD-(L)1 immunotherapy

Abstract Background: Intra-tumoral CD4+ and CD8+ T cells expressing inhibitory receptor CD161 have an effector memory phenotype with high cytotoxic potential. CD161 inhibits T and NK cell function in the presence of its ligand, CLEC2D. This suppression can be recovered by treatment with IMT-009, a first in class anti-CD161 antibody. Single cell transcriptomic analysis of anti-PD1 refractory microsatellite stable colorectal tumors identified presence of CD161+ CD4+ cytotoxic T cells and CD161+ PD1+ exhausted CD8 T cells suggesting that anti-CD161 treatment may provide benefit in these tumors both as a monotherapy and in combination with anti-PD1. It was also observed that CD161+ CD4/CD8T cells are more abundant in anti-PD1/L1 non responders compared with responders in hepatocellular carcinoma, cutaneous squamous cell carcinoma, clear cell renal carcinoma and breast cancer, providing a rationale for targeting CD161. Using engineered ex-vivo tumor models and dissociated human tumors, we have demonstrated that IMT-009 reverses CLEC2D mediated inhibition and restores primary T cell function. Additionally, co-treatment of IMT-009 with anti-PD1 further enhanced T cell mediated cytotoxicity, providing rationale for studies combining IMT-009 and anti PD1 in the clinic. Methods: Using the Snakemake pipeline developed in house, we processed publicly available scRNAseq data. Cells were clustered by Louvian method followed by cell type annotation by Seurat, and gene expression and gene signature levels per cluster were plotted. For ex-vivo assays, antigen specific CD8 T cells expanded from HLA-A2:01 donors were co-cultured with HLA-A2:01 expressing MDA-MB 231 triple negative breast cancer cell line or Raji Burkitt Lymphoma model with HLA-A2:01 allelic overexpression. Target tumor cells were engineered to express the ligands CLEC2D or PDL1. These cell lines were made to overexpress luciferase for monitoring target cell death using a luminescence readout. Additionally, dissociated tumor cells (DTCs) were cultured in presence of the treatment molecules. Intracellular staining of cytotoxic T cells along with detection of IFNγ, IL-2, TNFα and Granzyme B levels in culture supernatants by MSD/ELISA were used to assess activation profile of tumor infiltrated T cells. Results: Combining anti-PD1 and IMT-009 significantly enhanced cytotoxic benefit compared to individual monotherapy in both Raji and MDA-MB-231 target cell line models. IFNγ levels in supernatants of DTCs treated with this combination were elevated as compared to individual monotherapy. Together with scRNAseq data of increased abundance of KLRB1 (CD161) expressing T cells in anti PD1 non-responder patients, our data provide rationale for testing combination of IMT-009 with anti-PD1 in patients that may not respond to anti PD1 alone. Citation Format: Adwitiya Kar, Tim Nieuwenhuis, Meixue Duan, Siamak Tabrizi, Matthew Huggins, Elizabeth Scanlon, Cynthia Hession, Matthew Bernstein, Michael Ross, Ming Tang, Shruti Malu. Abundance of KLRB1+ (CD161) T cells in anti-PD1 non responders coupled with enhanced tumor cytotoxicity of anti-CD161 (IMT-009) with anti-PD1 makes it a rational target for combination with anti-PD-(L)1 immunotherapy [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 1375.