Resected Tumor Research Articles

Clinicopathological Analysis of Pediatric Posterior Fossa Tumors: Insights from a National Neurosurgical Center

BACKGROUNDː Pediatric posterior fossa tumors are the significant cause of morbidity and mortality in children and adolescents. This study aimed to investigate the characteristics of the patient population and report the experience in managing and treating children with these tumors, as well as their survival outcomes in Kazakhstan.<br /> METHODSː This retrospective study analysed data from the archives of the Pediatric Neurosurgery Department and included 214 pediatric patients with PFT in the period from January 2015 to December 2020.<br /> RESULTSː The study included 214 patients with a mean age of 7.29 ± 4.26 years. The most common tumor pathology observed in this study was medulloblastoma (33.18%). Grade I tumors showed a notable median survival of 56.64 months (95% CI, 53.93-59.35), surpassing Grade II tumors at 50.38 months (95% CI, 40.57-60.2). Grade III and IV tumors had median survivals of 38.64 months (95% CI, 31.11-46.17) and 38.76 months (95% CI, 33.96-43.56). Multivariate analysis using Cox regression model revealed significant predictors of overall survival. Grade III-IV tumors (RR = 0.577, 95% CI 0.462-0.720, p = 0.000), delayed resection (RR = 0.950, 95% CI 0.717-1.104, p = 0.000), and brainstem tumors (RR = 2.454, 95% CI 1.791-5.751, p = 0.000) had poorer survival. Tumor volume, age, and adjuvant chemotherapy were not significant predictors of 5-year survival (p > 0.05).<br /> CONCLUSIONSː The study found similar death rates in children with pilocytic astrocytoma compared to other population studies. Regrettably, the 5-year survival rate for medulloblastoma and ependymoma indicates a poorer outcome compared to previous reports.

Abstract 2405: Harnessing liquid biopsy and genetic barcoding in evaluating diversity within triple-negative breast cancer

Abstract Introduction: While liquid biopsy shows promise as a non-invasive precision medicine tool, its ability to comprehensively represent the complexity of a tumor or only a subset of its clones remains uncertain. This issue is particularly crucial in the context of triple-negative breast cancer (TNBC), a type of cancer known for its significant heterogeneity. The goal of this study is to examine the clonal diversity within Circulating Biomaterials (CBMs): namely circulating tumor cells (CTCs), extracellular vesicles RNA (evRNA), and circulating tumor DNA (ctDNA), employing genetic barcoding and patient-derived TNBC xenografts. Methodology: Cells from TNBC patients' resected tumors were tagged with a unique barcode sequence through vector transduction. These barcoded cells were subsequently introduced into immunodeficient mice to form xenografts. When these xenografts grew to a certain size (15mm in diameter), the mice were humanely euthanized, and the tumor tissues as well as CBMs from their blood and plasma were collected. CTCs were isolated through negative enrichment and DEPArray technology; evRNA was extracted using ultracentrifugation and TRIzol™ Plus RNA Purification method; ctDNA was retrieved using the QIAamp DNA Micro Kit. Tumor tissues were processed for RNA and DNA using RNeasy micro kit and Qiamp DNA micro kit, respectively. RNA sequencing of the tumor tissues was carried out using the Lexogen - CORALL Total RNA-Seq Kit and Illumina NextSeq high output reagents. Results: Analysis of xenografts from four patients showed that ctDNA was the predominant genetic material detected through liquid biopsy. Crucially, clonal analysis using Next Generation Sequencing (NGS) demonstrated that ctDNA provides an accurate reflection of the primary tumor's clonal heterogeneity. The method efficiently identified both main tumor clones and subclones, even those constituting as little as 1% of the tumor, with a 50% detection probability. Transcriptomic analysis of the tumor tissues uncovered a distinct mesenchymal and pro-metastatic signature, more pronounced in tumors with higher ctDNA release. Clonal analysis of CTCs and evRNA is still ongoing. Conclusions: This investigation affirms the effectiveness of ctDNA analysis in liquid biopsy for identifying subclonal diversity in TNBC. Our results suggest that liquid biopsy via ctDNA is capable of managing TNBC's extensive intra-tumoral heterogeneity, including the identification of smaller subclones. Furthermore, a link was identified between the release of ctDNA and a mesenchymal, prometastatic gene expression pattern in the tumors. Citation Format: Davide Ceresa, Barbara Cardinali, Antonio Daga, Roberta Tasso, Andrea Sciutto, Irene Appolloni, Daniela Marubbi, Franca Carli, Piero Fregatti, Paolo Malatesta, Lucia Del Mastro. Harnessing liquid biopsy and genetic barcoding in evaluating diversity within triple-negative breast 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 2405.

Abstract 3675: Design of high-performance tumor-informed minimal residual disease (MRD) panels from low FFPE tumor input

Abstract Background: Minimal residual disease (MRD) testing can detect cancer recurrence months to years earlier than the current standard of care, enabling earlier treatment of recurrence and improved patient outcomes. Tumor-informed MRD assays typically utilize formalin-fixed paraffin-embedded (FFPE) tumor tissue, which is available in limited quantities for some patients, for example, following core needle biopsy (CNB), after neoadjuvant treatment or when patients need multiple tests from the same tumor sample. To determine the lower limit of tissue input, we evaluated our MRD assay performance across a range of extracted tumor volumes. Methods: Resected tumors and CNBs were sectioned, H&E stained, and macro-dissected. Tumor gDNA was extracted, quantified, prepared into libraries and sequenced. Sequenced libraries were aligned and evaluated for depth of coverage, variation of coverage, and duplication rate. Somatic calling was performed on matched tumor and normal samples. Up to 1000 target sites were selected for high-depth targeted sequencing of the tumor and normal gDNA for confirmation of somatic variant calls. The positive predictive value (PPV) was computed as the percent of putative somatic variant sites that were present in the tumor capture library and absent in the normal capture library. Results: Extracted tumor volumes varied by almost two orders of magnitude, from 0.06mm3 (equivalent to needle core or fine needle aspirate biopsies) to 5mm3 (achievable with resected tumor). gDNA amount varied linearly (3.6ng to 1549ng) with tumor tissue input, indicating the low tissue to paraffin ratio did not have an adverse effect on yield. Tumor gDNA inputs into library prep ranged from 2.5ng to 100ng. DNA amounts above 100ng into library prep had no discernable benefit. Below 10 ng, depth of coverage and the coefficient of variation in coverage indicated poor-quality libraries. Samples with ~10 ng of gDNA input into library prep showed depth of coverage comparable to higher inputs and saturated the achievable library complexity. Additionally, PPV of somatic calling was consistent across the range of gDNA inputs from 10-100 ng, demonstrating equivalent assay performance. Conclusion: Tumor-informed MRD assays have immense potential for increasingly sensitive treatment response and recurrence monitoring that can inform better treatment decisions. FFPE tumor tissue is a critical input into MRD assays but is a limited resource. This study supports a minimum DNA input of 10 nanograms for a single attempt at extraction, corresponding to a tissue volume of 0.2mm3 or a single 10µm slide with a 20mm2 area, representing one of the lowest tissue input requirements for an MRD assay. Low FFPE tissue requirements expand the patient population that benefit from MRD testing by utilizing samples that have low tumor content, are post-neoadjuvant therapy or do not meet the tumor volume requirements of competing MRD offerings. Citation Format: Matt LaBella, Ashley Acevedo, Ravi Patel, Kiefer Haug, Sangita Ganesh, Elise Buser, Nafei Xu, Shalee Carlson, Kyle Trettin, Sarah Ratzel, Kieko Hara, Pavlos Msaouel, Kanishka Sircar, Chad Tang, Dale Muzzey, Genevieve Gould. Design of high-performance tumor-informed minimal residual disease (MRD) panels from low FFPE tumor input [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 3675.

Abstract 6396: Ex vivo 3D micro tumor testing to assess chemotherapy and immunotherapy responses for NSCLC patients

Abstract Background: Systemic treatment options for NSCLC patients consists of chemo-, targeted or immunotherapy. Although predictive biomarkers can guide treatment decisions, response prediction for chemo- and immunotherapy is still a challenge. Recent studies showed the potential of functional testing to assess patient sensitivity to drugs in various cancers, but NSCLC is lacking. This study reports the feasibility of ex vivo 3D micro lung tumor testing with native tumor microenvironment (TME) to enable treatment sensitivity profiling for all drug classes in parallel. Methods: Fresh NSCLC tumor tissue was collected from pleural fluid stage IVa/b (N=24) or resected primary tumor for stage I-III disease (N=11). Tumor clusters were isolated and exposed to drugs, while preserving the TME. Thirteen therapies were included, including cisplatin, pembrolizumab, osimertinib, and positive control for immune sensitivity (SEA). Morphological features were extracted from high-throughput 3D imaging data. Chemo- and targeted therapy sensitivity was based on AUC comparison of fitted dose-response curves. Immunotherapy sensitivity was classified on percentage and statistical significance of tumor killing, immune cell proliferation and cytokine profiling. Results: The overall assay success rate for solid samples was 64% (7/11), with 100% (4/4) success after protocol optimization. For pleural fluids, the overall success rate was 33% (8/24), caused by many samples arriving without tumor content (13/24, 54%). Excluding these samples, a technical success rate of 73% (8/11) was obtained. The assay was robust and reproducible (mean Z’ = 0.38, CV = 16.1%). Results were delivered in two weeks and on average, eight treatments were tested in parallel per sample. Patient-specific response profiles were observed for chemo-, targeted and immunotherapy. General immunotherapy sensitivity (SEA) was measured in 50% (6/12) of the tissues. Distinct responses were observed for the different immunotherapies: 33% (4/12), 17% (2/12) and 8% (1/12) of the patients responded to pembrolizumab, atezolizumab and/or ipilimumab, respectively. Strong response to osimertinib was observed in a patient with EGFR exon 19 mutation (AUC = 0.26) versus resistance in a WT patient (AUC=0.92). Conclusion: Ex vivo 3D micro tumor testing using liquid and solid tissues is feasible for NSCLC patients with resected primary tumor or pleuritis carcinomatosa. Distinct patient sensitivity profiles for chemo-, targeted and immunotherapies were measured. A preliminary correlation of targeted therapy response with mutation status was found. Discussion: The ex vivo 3D micro tumor testing platform is proven predictive for platinum-based therapy. The current study established the methods to accurately measure ex vivo NSCLC responses to all drug classes to correlate with clinical measures and further validate the platform for guiding treatment decisions. Citation Format: Esmee Koedoot, Timothy J. Sijsenaar, Lieke J. Ceton, Dieudonné J. van der Meer, Thomas J. van Brakel, Peter van Zwam, Erica Geraedts, Willemijn Vader, Egbert F. Smit, Laurie C. Steinbusch, Christi M. Steendam. Ex vivo 3D micro tumor testing to assess chemotherapy and immunotherapy responses for NSCLC patients [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 6396.

Abstract 20: KSQ-001EX: An engineered TIL therapy manufactured from a clinical-scale, feeder-free process for the treatment of solid tumor indications

Abstract Tumor Infiltrating Lymphocyte (TIL) therapy is an autologous adoptive cell therapy involving the isolation, ex vivo expansion and infusion of tumor infiltrating lymphocytes (TIL) into late-stage cancer patients for therapeutic benefit. While clinical responses to TIL therapy have been observed in metastatic melanoma, efficacy in other tumor types including non-small cell lung cancer (NSCLC), and head and neck squamous cell carcinoma (HNSCC) [SM1] is limited by the intrinsic functionality and persistence of transferred T cells and the immunosuppressive tumor microenvironment. To improve the clinical outcome of TIL therapy, we have developed KSQ-001EX, an engineered TIL therapy using CRISPR/Cas9 technology to knockout the SOCS1 gene, for the treatment of solid tumors. SOCS1 is a negative regulator of cytokine signaling in T cells that we previously identified as a top target restraining T cell anti-tumor function and persistence using genome-wide in vivo CRISPR screens. To streamline and shorten TIL manufacture, we established a next-generation manufacturing process with resected tumors or core biopsies as starting materials that eliminates the use of feeder cells and REP, shortening the length of manufacture to 22 days. We demonstrated robust manufacture of cryopreserved KSQ-001EX at clinical scale from NSCLC, HNSCC, checkpoint refractory melanoma, and heavily pre-treated colorectal carcinoma (CRC). KSQ-001EX manufactured from clinical-scale runs were highly viable (>90%) following cryopreservation and thaw, with > 90% SOCS1 on-target editing and complete knockdown of SOCS1 at the protein level. Importantly, KSQ-001EX across all indications assessed showed high frequency of CD8 (median ~80%), an attribute associated with TIL clinical responses. KSQ-001EX also retained high diversity of TCR repertoire. Consistent with the biology of SOCS1 editing, KSQ-001EX exhibited greater cytotoxicity and higher IFNγ production against tumor spheroids in comparison to TIL and enhanced induction of pSTAT4 upon IL-12 stimulation, demonstrating heightened sensitivity of KSQ-001EX to cytokines. In conclusion, KSQ-001EX, an engineered TIL therapy with CRISPR/Cas9 mediated inactivation of SOCS1, can be manufactured at clinical doses from surgical resections or core biopsies within 22 days using a simplified feeder-free manufacturing process from multiple indications. KSQ-001EX exhibits heightened anti-tumor activity in preclinical models, with therapeutic benefit to be evaluated in a planned clinical trial in patients with treatment-refractory melanoma, NSCLC, and HNSCC. [SM1]Spell out these at first instance? Citation Format: Sharon Lin, Gustavo Martinez, Marie-Andrée Forget, Katrina Adlerz, Mitali Ghose, Leila Williams, Paul Dunbar, Frank Thompson, Fiona Sharp, Hugh Gannon, Conor Calnan, Ashish Yeri, Dipen Sangurdekar, Donald Sakellariou-Thompson, Samantha Fix, Tamara Griffith, Ellie Jafari, Jane Zulovich, Priya Balasubramanian, Erin Willert, MIcah Benson, Chantale Bernatchez, Karrie Ka Wai Wong. KSQ-001EX: An engineered TIL therapy manufactured from a clinical-scale, feeder-free process for the treatment of solid tumor indications [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 20.

Abstract 5161: Integrating patient’s derived organoids and liquid biopsy: An exploratory study of early stage pancreatic cancer

Abstract Background: Pancreatic cancer (PC) has a 5-year survival of 12% despite recent therapeutic advancements. There is a desperate need to discover novel ways of treating PC since a large proportion of patients do not benefit from therapy and experience significant toxicity. A major cause of therapy failure is therapy resistance due to tumor heterogeneity. Nowadays, a deeper understanding of tumor heterogeneity could be assisted by the use of patients-derived organoids (PDOs). Furthermore, the use of liquid biopsy may allow for the investigation of circulating factors with predictive value and for disease monitoring over time. Methods: Patients were enrolled in the comprehensive, multiomic study of pancreatic cancer CONTAINER. Patients with early stage PC treated with preoperative chemotherapy or undergoing surgery first were selected for the present study. When possible, a surgical specimen was collected to obtain PDOs. Tissue from resected tumors was dissociated by GentleMACSTM dissociator (Miltenyi Biotec), fragments were embedded in MatrigelTMand cultured in PancreaCultTM human Organoid Media (stemcell technologies). PDO histological features were investigated by H&E staining and IHC. Blood samples were collected before and one month after surgery. From blood samples circulating tumor cells (CTCs) were enriched and isolated, extracellular vesicles (EVs) were isolated from plasma with size-exclusion chromatography and their concentration and size distribution was evaluated with NanoSight NS300. Then, EV surface antigens were characterized by flow cytometry. A panel of inflammatory cytokines was finally evaluated through Ella Automated Immunoassay System. Results: In CONTAINER study 113 patients were enrolled and 30 of them underwent surgery. 21 surgical specimens were received from which 18 PDOs were successfully established. EVs with diameter ≥ 70nm were isolated from plasma, EV mean size was similar before and after surgery whereas individual variations in particle concentration and in surface antigen exposure were observed. Correlation with clinical and pathological characteristics of patients will be performed once reached an adequate sample size for statistical analyses. A panel of inflammatory cytokines (IL1β-, IFNγ, TNFα, IL6, IL8, TGFβ1, CRP and Leptin) was assessed in plasma samples obtained before and after surgery. Except for IL1β, a significant individual variation of circulating cytokines before and after surgery was observed. Conclusions: This study will contribute to unveil mechanisms of disease progression and drug resistance in PC. Possible predictive factors and mechanisms of drug resistance will be investigated taking advantage of the information derived from both in vitro models and circulating tumor-related entities. Citation Format: Michela Cortesi, Tania Rossi, Michele Zanoni, Sara Bandini, Carlo Alberto Pacilio, Alessandro Cucchetti, Martina Valgiusti, Chiara Gallio, Alessandro Passardi, Giorgia Gurioli, Sara Bravaccini, Alessandra Dubini, Giovanni Luca Frassineti, Paola Ulivi, Giovanni Martinelli, Giorgio Ercolani, Ilario Giovanni Rapposelli. Integrating patient’s derived organoids and liquid biopsy: An exploratory study of early stage pancreatic 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 5161.

Abstract 2: T cells selected from lymph node acquisition for adoptive cell therapyin NSCLC

Abstract Background: A primary limitation of PD-1 inhibitors in non-small cell lung cancer (NSCLC) arises from their inability to act on 'cold' tumors without tumor-reactive T cells, necessitating alternative approaches. Adoptive cell therapy (ACT) using (CAR)-engineered cells, strives to enhance antitumor immunity but faces several challenges such as identifying safe antigens, tumor heterogeneity, antigen escape, cell trafficking, and T cell persistence. To address these issues, we explored a new source of T cells from the benign tumor draining lymph nodes (tdLNs) of NSCLC patients. Our initial results have shown that tdLNs is a reservoir for of tumor-relevant 'stem-like' T cells. We posit that employing these pluripotent T cells for ACT could achieve significant tumor rejection in NSCLC. Methods: Resected tumors, tdLN, non-draining (ndLN), and blood from NSCLC patients, as well as a syngeneic murine lung cancer model (344SQ), underwent analysis. T cells were profiled using flow cytometry, cytotoxicity and proliferation assays. TCR and single cell (sc)RNA sequencing assessed clonal expansion, diversity, and transcriptional profiles of tumor-relevant T cells. T cells were then transduced with an ICAM-1 targeting CAR, in vivo efficacy was evaluated in an A549 murine lung cancer model. Results: T cell subsets with stem-cell memory characteristics, as indicated by PD-1+, TCF1hi, CXCR5+, and CD8+ expression, which were not significantly found in the tumor or PB. These T cells exhibited progenitor-like transcriptional signatures, enhanced SELL and TCF-1 expression, fewer exhaustion markers, and superior in vitro proliferation compared to TILs from both a murine lung cancer model and patient-derived tissues. scRNA sequencing, coupled with TCR "tumor matching" (TM) techniques, exposed a rich clonal diversity of tumor-relevant clones within tdLNs, which showcased a broader transcriptional memory profile and distinct CD4+ and CD8+ phenotypes. Upon analyzing the top 100 expanded (n>3) TM clones, 47 featured the presence of tdLN-derived T cells, covering progenitor, stem cell-like, and central memory clusters. T cell subsets were then transduced with a CAR targeting ICAM-1—a cell surface protein frequently overexpressed in NSCLC tumors. Manufacturing protocol yielded high transduction efficiency and T cell expansion within two weeks in 6/6 patients, consistent with PB-derived CAR T cells and on par with the optimal dosing requirements of an ICAM-1 CAR Phase I trial (NCT04420754). tdLN-CAR T cells showed potent antitumor efficacy compared to the control in an aggressive NSCLC murine model (Median survival 103d vs 66d; respectively; p=0.006). Conclusions: This represents the first reported use of T cells from tdLN for genetically engineered ACT. The data indicate that modifying antigen-experienced, stem-like T cells from tdLN with CAR is a promising and efficient method in a NSCLC murine model, warranting further research. Citation Format: Tatiana Delgado Cruz, Yanping Yang, Rachel Honigsberg, Geoffrey Markowitz, Nasser K Altorki, Vivek Mittal, Moonsoo M. Jin, Jonathan Villena-Vargas. T cells selected from lymph node acquisition for adoptive cell therapyin NSCLC [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 2.

Prognostic PET [11C]-acetate uptake is associated with hypoxia gene expression in patients with late-stage hepatocellular carcinoma – a bench to bed study

BackgroundPositron Emission Tomography (PET) with combined [18F]-FDG and [11C]-acetate (dual-tracer) is used for the management of hepatocellular carcinoma (HCC) patients, although its prognostic value and underlying molecular mechanism remain poorly understood. We hypothesized that radiotracer uptake might be associated with tumor hypoxia and validated our findings in public and local human HCC cohorts.MethodsTwelve orthotopic HCC xenografts were established using MHCC97L cells in female nude mice, with 5 having undergone hepatic artery ligation (HAL) to create tumor hypoxia in vivo. Tumors in both Control and HAL-treated xenografts were imaged with [11C]-acetate and [18F]-FDG PET-MR and RNA sequencing was performed on the resected tumors. Semiquantitative analysis of PET findings was then performed, and the findings were then validated on the Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) cohort and patients from our institution.ResultsHAL-treated mice showed lower [11C]-acetate (HAL-treated vs. Control, tumor-to-liver SUV ratio (SUVTLR): 2.14[2.05–2.21] vs 3.11[2.75–5.43], p = 0.02) but not [18F]-FDG (HAL-treated vs. Control, SUVTLR: 3.73[3.12–4.35] vs 3.86[3.7–5.29], p = 0.83) tumor uptakes. Gene expression analysis showed the PET phenotype is associated with upregulation of hallmark hypoxia signature. The prognostic value of the hypoxia gene signature was tested on the TCGA-LIHC cohort with upregulation of hypoxia gene signature associated with poorer overall survival (OS) in late-stage (stage III and IV) HCC patients (n = 66, OS 2.05 vs 1.67 years, p = 0.046). Using a local cohort of late-stage HCC patients who underwent dual-tracer PET-CT, tumors without [11C]-acetate uptake are associated with poorer prognosis (n = 51, OS 0.25 versus 1.21 years, p < 0.0001) and multivariable analyses showed [11C]-acetate tumor uptake as an independent predictor of OS (HR 0.17 95%C 0.06–0.42, p < 0.0001).Conclusions[11C]-acetate uptake is associated with alteration of tumor hypoxia gene expression and poorer prognosis in patients with advanced HCC.

Abstract 961: Detection of minimal residual disease in lymph predicts recurrence in HPV-negative head and neck cancer patients

Abstract Background: Locoregional cancer relapse remains a major cause of failure in head and neck squamous cell carcinoma (HNSCC), particularly for HPV-negative patients whose 2-year locoregional failure rate is up to 50%. There is unmet need for an accurate diagnostic test that predicts risk of recurrence prior to adjuvant therapy selection. We present a novel proximal assay for minimal residual disease (MRD) profiled in lymphatic exudate collected via surgical drains (“lymph”). Methods: Lymph, plasma, and blood were collected from 46 HPV-negative HNSCC patients postoperatively at 24 hours along with resected tumor. Cell-free DNA was extracted from lymph and plasma and sequenced using the TruSeq Oncology 500 panel to a depth of &amp;gt;100 million reads. Somatic mutations were identified by exome sequencing (200x) tumor and blood. Five patients had &amp;lt;2 mutations in tumor and were excluded. Two patients were censored due to lack of clinical data, yielding 18 patients with disease recurrence (REC) and 21 with no evidence of disease (NED) with &amp;gt;1 year of follow-up. Tumor-specific variants were force-called in lymph and plasma using a custom pipeline. Patients were considered MRD positive if the mean variant allele fraction (mVAF) was greater than 0.015% (the estimated limit of detection). The Kaplan-Meier (KM) estimator with log-rank test and Cox proportional-hazards model were used for survival analyses. Logistic regression model was performed with 5-fold cross-validation. Results: KM survival analyses showed lymph accurately predicts recurrence (sensitivity (SN) = 78%, specificity (SP) = 67%; p = 0.003, Hazard ratio (HR) = 4.7), while plasma was not significant (p = 0.92) at this postoperative timepoint. Performance was enhanced for locoregional relapse (SN = 92%, SP = 67%; p = 0.001, HR = 13.9. N=33). We also observed accurate recurrence prediction (SN = 83%, SP = 69%, p = 0.03, HR = 7.7) in the 19 N0 patients (node-negative by pathology). Lymph MRD outperformed individual pathology features (extranodal extension, perineural invasion, lymphovascular invasion, and nodal disease status) for recurrence prediction (HR = 3.4, 0.88, 2.5, 2.4, respectively). A logistic regression model combining lymph MRD with these 4 high-risk pathologic features showed superior performance over lymph alone or pathology alone (SN = 89%, SP = 67%; p = 0.0007, HR = 8.6). Conclusions: ctDNA analysis of lymph from surgical drains represents a novel proximal MRD approach in HPV-negative HNSCC. Postoperative lymph significantly outperforms plasma for prediction of recurrence, particularly in patients with locoregional relapse. Accurate MRD identification in patients with lower risk pathologic features suggests that lymph MRD testing has potential to augment traditional pathology and provide more personalized adjuvant treatment decision-making in patients with HPV-negative HNSCC. Citation Format: Wendy Winckler, Zhuosheng Gu, Damion Whitfield, Noah Earland, Adam Harmon, Megan Long, Peter Harris, Zhongping Xu, Ricardo Ramirez, Sophie Gerndt, Maciej Pacula, Marra S. Francis, Jose P. Zevallos, Aadel A. Chaudhuri. Detection of minimal residual disease in lymph predicts recurrence in HPV-negative head and neck cancer patients [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 961.

Abstract 7464: Tertiary lymphoid structures in pancreatic cancer: Biomarkers of immunogenic patients or direct contributors to anti-tumor immunity

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a cancer with low survival rates and currently no immunotherapy options. However, many tumors from PDAC patients can be heavily infiltrated with T and B cells associated with favorable survival outcomes indicating anti-tumor immunity is functional in certain patients. In some of these lymphocyte-inflamed PDAC tumors, spontaneous organization of tertiary lymphoid structures (TLS) is evident upon surgical resection and these patients have a clear survival advantage. TLS are predictive of immune checkpoint blockade response in some cancer types, yet PDAC patients, with or without TLS, are still insensitive to these strategies. To address this paradox, we evaluated surgically resected PDAC tumors from previously untreated patients and discovered that tumors with TLS (TLS+) recruited T and B cells with specific anti-tumor and memory phenotypes suggesting immunosurveillance of disease was enhanced. Furthermore, a subset of TLS+ patients contained germinal centers and improved humoral immune function corresponding to an increased neoantigen burden and long-term survival. When assessing gene expression differences between TLS+ and TLS- patients, operable inflammatory and immunosuppressive pathways emerged that could be therapeutically exploited to activate TLS neogenesis. To address these mechanistic questions, we have developed a method for inducing TLS formation in implantable mouse PDAC tumors in the orthotopic setting utilizing an antibody that agonizes the lymphotoxin beta receptor (LTBR) in mice bearing established PDAC tumors. These TLS are complexed with T cells, B cells, CXCL13+ cells, and PNAd+ HEV associated with reduced tumor growth, presence of lymphocyte-recruiting cancer associated fibroblasts and increases in anti-tumor T and B cell phenotypes. Interestingly, some mouse PDAC cell lines are resistant to TLS formation by LTBR agonism while others are susceptible offering a model to study patient heterogeneity. We will use this TLS+ PDAC mouse model to address how TLS may directly improve antigen-specific T cell and B cell immunity and elucidate the pathways that regulate TLS formation. These data will offer new strategies to overcome immunotherapy resistance in cancer patients. Citation Format: Shrijan Khanal, Olivia Harder, Elijah Kirschstein, Morgan Mack, Carl Ware, Michael Gough, Kristina Young, Andrew J. Gunderson. Tertiary lymphoid structures in pancreatic cancer: Biomarkers of immunogenic patients or direct contributors to anti-tumor immunity [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 7464.

Abstract 409: Deciphering chromosomal instability in consensus molecular subtypes (CMS) in CRC: Insights from an integrative multi-omics approach

Abstract CRC is a heterogeneous disease with different molecular subtypes, which can have a profound impact on treatment response and patient outcomes. CMS classification based on gene expression profiles has been shown to differentiate patients into clinically relevant sub-groups. However, deep multi-omics characterization of the CMS classes based on high quality patient data is lacking. Through the integration of multi-omics data, we aim to enhance our understanding of CRC’s molecular heterogeneity and thereby facilitate the development of personalized therapeutic strategies. We performed a multi-omics analysis of CRC patients to identify potential new features of CMS groups. 890 fresh-frozen, surgically resected CRC tumor and adjacent normal samples were used to analyze whole genome and RNA sequencing data. DNA and RNA was prepared using Qiagen AllPrep Universal and KAPA Hyper Prep kit (DNA), as well as TruSeq Stranded Total mRNA kits and sequenced on a NovaSeq6000 system. We identified CMS subtypes based on RNA-Seq data and performed all statistical analyses using R. Our analysis revealed distinct molecular characteristics across the four CMS subtypes, including unique driver mutations, signaling cascades, and immune cell infiltration profiles. The poor prognosis associated with CMS4 patients was corroborated by our clinical data. Notably, we observed high global chromosomal instability (CIN) profiles for both CMS2 and CMS4 and identified recurrent global aneuploidy patterns within these subtypes that link alterations of known cancer genes to these large-scale structural events. We found higher levels of CIN in CMS2 compared to CMS4, which appears to be predominantly driven by numerical, rather than structural CIN. Specifically, in CMS2, SMAD2/4 is commonly impacted by deletion on chromosome arm 18q, while PLCG1 is more influenced by amplifications on 20q respectively, suggesting potential values as CRC CMS biomarkers. In conclusion, our integrative multi-omics analysis offers a comprehensive understanding of CRC molecular subtypes, which can inform personalized treatment strategies. Our findings underscore the importance of considering not only specific driver mutations but also large-scale structural rearrangements in the context of CMS subtypes. Citation Format: Julia Bischof, Jonathan Woodsmith, David Church. Deciphering chromosomal instability in consensus molecular subtypes (CMS) in CRC: Insights from an integrative multi-omics approach [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 409.

Abstract 900: Development and validation of an artificial-intelligence-based pathomics biomarker to predict resistance to first-line treatment in metastatic colorectal cancer

Abstract Background: The backbone chemotherapy of first-line standard of care (SOC) for microsatellite stable (MSS) metastatic colorectal cancer (mCRC) combines 5-Fluorouracil to oxaliplatin and/or irinotecan. There are no biomarkers to predict response, which is complete or long-lasting (CR/LLR) in 20-25% of patients, while 10-15% are primary refractory. The aim of this work is to develop a predictive biomarker, based on digital pathology images, that can help stratify patients according to their risk of resistance. Methods: We trained a supervised bag-of-words artificial intelligence (AI)-based model on a cohort of response outliers mCRC patients classified as “really sensitive” (RS) if they achieved CR or LLR &amp;gt;10 months to any SOC, or “really resistant” (RR) if progression occurred at first disease reassessment. Whole-slide Imaging (WSI) of the resected primary tumors were tiled into patches of 224 × 224 pixel (0.5μm/pixel). First-order and texture features were subsequently extracted from all tumoral tiles and grouped into homogenous clusters through a k-means algorithm (k=6). For each patient, the percentage of tiles belonging to each tiles’ cluster was computed to represent new features (called bag of words) with whom different machine learning classifiers were trained. Main clinicopathological features were matched to treatment response by Fisher’s exact test. Results: To date, we analyzed 82 response outlier patients, of whom 35 were classified as RS and 46 RR. Of them, patients identified at Italian centers were used as construction cohort (N=47; 27 RR and 20 RS) and those identified at Spanish centers were used a validation cohort (N=35; 19 RR and 16 RS). The best result was obtained using a stepwise logistic regression, reaching a negative predictive value (NPV) of 90% (18/20; 95% CI=70-97%) and 71% (10/14; 95% CI=49-87%), in the construction and validation sets. No standard clinicopathological features (including stage, RAS/BRAF status, histology and sidedness) was associated with the chance of being RR. Conclusions: We demonstrated that a pathomics signature has the potential to predict resistance to SOC in MSS mCRC. Further validation of these preliminary findings on a larger cohort of response outlier patients is ongoing. Citation Format: Luca Lazzari, Gianluca Mauri, Valentina Giannini, Debora Cafaro, Giulia Nicoletti, Caterina Marchiò, Andrea Sartore-Bianchi, Federica Marmorino, Maria Nieva Munoz, Nadia Saoudi Gonzalez, Alberto Puccini, Chiara Cremolini, Clara Montagut, Elena Elez, Stefania Sciallero, Enrico Berrino, Martina Carullo, Pietro Paolo Vitiello, Maria Costanza Aquilano, Martina Di Como, Emanuela Bonoldi, Salvatore Siena, Alberto Bardelli, Daniele Regge, Silvia Marsoni. Development and validation of an artificial-intelligence-based pathomics biomarker to predict resistance to first-line treatment in metastatic 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 900.

Abstract 6982: The roles of NDRG1 in HCC progression and its clinical significance

Abstract Background: Hepatocellular carcinoma (HCC) is prevalent globally and the third leading cause of cancer-related mortality. N-myc downstream regulated 1 (NDRG1) was found to be tumor promoting in some cancers while suppressive in others. The expression of NDRG1 is induced by stress signals such as DNA damage and hypoxia. In HCC, it has been found to promote proliferation and metastasis. Contradictory results, however, were also suggested on the functions of NDRG1. Methods: Our own HCC cohort and multiple publicly available databases were examined for NDRG1 expression and clinicopathologic correlation. NDRG1 expression under hypoxic conditions was investigated. Various functional assays were performed for NDRG1-knockdown HCC cell lines Huh-7 and PLC/PRF/5. Results: With RT-qPCR analysis on our 102 pairs of patients’ HCC tumor and corresponding non-tumorous liver samples, we found NDRG1 to be upregulated in HCC tumors. Similarly, RNA-sequencing analysis comparing 41 pairs of samples confirmed NDRG1 enrichment in HCC tumors. The upregulation was significantly and positively correlated with the absence of tumor encapsulation and cellular differentiation. These were further supported by TCGA and ICGC databases, in which upregulation of NDRG1 was significantly correlated with poor HCC patient overall survival. Interestingly, in the TCGA database, only 17% of the HCC cases were inferred to have copy number amplification of NDRG1 gene while NDRG1 mutations were rarely found. As hypoxia is a major tumor microenvironmental factor in HCC, we investigated NDRG1’s expression level in HCC cells under hypoxic or normoxic conditions and found significant increase in NDRG1 expression under hypoxic environment. We further found that NDRG1 knockdown inhibited cell proliferation, self-renewal ability, and migration. RT-qPCR analysis found lower LGR5 and SOX2 expression upon NDRG1 knockdown. This is in line with the positive correlation between NDRG1 and various cancer stemness-related gene expression, including LGR5, CD24, MYC, SOX2, and NOTCH1, in TCGA database. Lastly, in the resected HCC tumors on which spatial transcriptomics using Visium 10X and single-cell RNA-sequencing using Chromium 10X were performed, we found NDRG1 enrichment in both tumors cells and cancer associated fibroblasts (CAFs). Conclusion: NDRG1 was found to be significantly upregulated in HCC cells in our in-house cohort and publicly available databases. NDRG1 consistently promotes various oncogenic features of HCC cells, including proliferation, self-renewal ability, and migration. In addition, NDRG1 was found to be enriched in both the HCC cells and CAFs. Citation Format: Jingyi Lu, Lu Tian, Yu-Man Tsui, Xia Wong, Qingyang Zhang, Daniel Wai-Hung Ho, Irene Oi-Lin Ng. The roles of NDRG1 in HCC progression and its clinical significance [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 6982.

Abstract 4140: Enhanced microglial phagocytosis of metastatic brain tumor cells with Cd24a/Cd47 depletion

Abstract Despite the robust homeostasis of the brain, its high prevalence of tumor metastasis is intriguing and the underlying mechanism may contribute to the development of novel therapies. Microglia have emerged as promising therapeutic targets due to their role in brain parenchymal homeostasis. However, with evidence for both pro- and anti-tumorigenic functions, their role in brain metastasis (BrM) remains unclear. Here, we show that the microglial response to tumor cells within a single host is heterogeneous and can alter tumor fate. Single-cell RNA sequencing was performed on five surgically resected metastatic brain tumors, and the transcriptome of tumor-associated microglia was extracted by single-cell variational inference (scVI). Evidence for the coexistence of cytokine-secreting and angiogenesis-supporting subsets, as well as subsets associated with phagocytosis and antigen presentation, within each tumor sample was determined. To demonstrate the intra-tumoral functional heterogeneity of tumor-associated microglia, we established a metastatic brain tumor model that allows us to visualize the metastatic process and the dynamic microglial response in vivo by injecting mCherry-tagged allogeneic cancer cells into the internal carotid artery of CX3CR1-EGFP mice. Metastasis formation was suppressed in microglia-depleted mice, identifying a dominant microglial response that promotes tumor growth. However, continuous in vivo imaging of the BrM model revealed tumor-eradicating anti-tumor microglia coexisting with pro-tumor microglia in the same host. The transcriptome of anti-tumor microglia supported that they are enriched for phagocytosis, antigen processing and antigen presentation genes. The subset was identified in microglia extracted from human samples. We then examined the immune checkpoint of microglial phagocytosis in the tumor transcriptome and identified Cd24a and Cd47. Simultaneous deletion of both genes in cancer cells enhanced microglial phagocytosis, reduced tumor volume and improved survival, and rescue of both genes reversed these anti-tumor effects. The microglial dependency was addressed by microglial depletion experiments, and the anti-tumor effects were reproducible in nude mice lacking mature T cells. These results suggest that there are distinct immune cell subtypes that respond to lung tumor metastases in the brain and either promote tumor growth or inhibit metastasis through phagocytosis. Furthermore, anti-tumor activity in mouse models can be enhanced by genetic deletion of Cd24a and Cd47 in tumor cells, which regulate phagocytosis by microglia. Citation Format: Takahiro Tsuji, Haruka Hirose, Mariko Shindo, Rahadian Yudo Hartantyo, Yutaro Saito, Kazutaka Hosoya, Hiroshi Yoshida, Daisuke Kato, Akihiko Yoshizawa, Yoshiki Arakawa, Hiroaki Ozasa, Toyohiro Hirai, Hiroaki Wake. Enhanced microglial phagocytosis of metastatic brain tumor cells with Cd24a/Cd47 depletion [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 4140.

Abstract 5533: The difference of immune microenvironment betweende novometastatic and non-metastatic microsatellite instability-high colorectal cancer

Abstract Introduction: Microsatellite instability-high (MSI-H) colorectal cancer (CRC) consists of 15% of all CRC but only 2-4% of metastatic CRC. The favorable prognosis of non-metastatic (early-stage) MSI-H CRC may be related to vigorous immune reaction in tumor microenvironment. However, the mechanisms of immune evasion in metastatic (late stage) MSI-H CRC are largely unknown. Materials and Methods: We retrospectively collected patients with MSI-H CRC from National Taiwan University Hospital and Kaohsiung Chang Gung Memorial Hospital. The archival tumor specimens were used for immune cells analysis by Nanostring PanCancer Immune Panel, and spatial immune characterization by multiplex immunofluorescence stains. Only surgical resected primary tumors and metastatic tumors were included. Gene expression and immune cells composition were compared between non-metastatic and de novo metastatic tumors. Results: We enrolled 59 and 27 patients with early-stage and late-stage MSI-H CRC, respectively. Twelve metastatic site tumors were also collected. The clinicopathologic characteristics between patients who have early- and late-stage MSI-H CRC were not significantly different. There are heterogeneous immune cell compositions in these 98 MSI-H tumors. Compared to early-stage MSI-H tumors, there are significantly fewer cytotoxic (difference -0.497, p = 0.001) and dendritic cells (difference -0.528, p = 0.021) in late-stage MSI-H tumors. Gene set enrichment analysis disclosed significantly decrease in the expression of JAK-STAT-IFN-γ- and antigen processing-related pathways in late-stage MSI-H tumors. The top 5 genes with significantly differential expression between late-stage and early-stage tumors are C7, TNFRSF12A, MFGE8(up-regulated) and CXCL5, IFNL1, GZMH, HMGB1 and CXCR1 (down-regulated). Conclusions: There are significantly fewer cytotoxic and dendritic cells in late-stage MSI-H CRC, compared to early-stage MSI-H CRC, which is associated with decrease expression in JAK-STAT-IFN-γ- and antigen processing-related pathways. Citation Format: Kuo-Hsing Chen, Chia-Lang u Hs, Yu-Li Su, Chang-Tsu Yuan, Jia-Huei Tsai, Yi-Hsin Liang, Ann-Lii Cheng, Kun-Huei Yeh. The difference of immune microenvironment betweende novometastatic and non-metastatic microsatellite instability-high 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 5533.

Abstract 2496: Molecular characterization of stage III colon cancer patients with recurrence after adjuvant chemotherapy

Abstract Introduction: Patients with stage III colon cancer are routinely treated with resection followed by adjuvant chemotherapy (ACT) with a fluoropyrimidine and oxaliplatin. This one-size-fits-all approach does not account for heterogeneity in tumor biology and fails to cure ~30% of patients, highlighting the urgency for biomarkers to better understand and predict resistance to ACT or to offer alternative targeted treatment. Aim: To identify molecular characteristics predictive of resistance to standard ACT in stage III colon cancer. Methods: Patients with resected stage III colon cancer who received ACT (93% CAPOX, 7% CAP) were selected from the Prospective Dutch Colorectal Cancer cohort (PLCRC). RNA exome capture sequencing was performed on resected FFPE tumor tissue to compare differential gene expression, hallmark pathway enrichment, immune cell deconvolution and consensus molecular subtypes (CMS) between patients with versus without recurrence after surgery and ACT. Postsurgery circulating tumor DNA (ctDNA) detected in PLCRC-PROVENC3 (separate abstract) was used to select a subgroup with minimal residual disease (MRD) postsurgery, as sensitivity analysis of patients with recurrence despite ACT (chemoresistant) versus curation by ACT (chemosensitive). Results: For 264 out of 278 patients (95%), tumor-derived RNA sequencing libraries were of sufficient quality. 67 patients (25%) with recurrence (median after 13 months [IQR 7-23]) were compared to 178 patients with at least 2 year recurrence-free follow-up (median 42 months [IQR 30-53]). A total of 320 genes were differentially expressed between patients with versus without recurrence. Genesets defining epithelial-mesenchymal transition (p = 0.002) and angiogenesis (p &amp;lt; 0.001) were enriched in the primary tumor of patients with recurrence, in part explained by the estimated larger fraction of stroma (Wilcoxon effect size r 0.18, p &amp;lt; 0.001) and cancer-associated fibroblasts (CAFs) (r 0.19, p = 0.003). In contrast, the fraction of CD4+ T cells was lower (r 0.14, p = 0.001). Consistently, CMS4 was found more frequently in tumors from patients with versus without recurrence (57% versus 34%, p &amp;lt; 0.001). Of the subgroup with ctDNA-based MRD postsurgery (26 out of 171 assessed patients), 19 patients (73%) with recurrence (median after 12 months [IQR 7-17]) were compared to 7 patients without recurrence (minimum follow-up 32 months). This sensitivity analysis showed similar trends in pathways, immune cells and CMS as the main analysis, with a more pronounced effect size for CAFs (r 0.27). Conclusion: Stage III colon tumors of patients who experience recurrence after resection and ACT are enriched for stroma and CAFs, while displaying less CD4+ T cells. The observed trends are sustained in the patients with MRD postsurgery. These findings may help to better predict resistance to standard ACT and elucidate targets for alternative personalized treatment. Citation Format: Ingrid Franken, Steven Ketelaars, Carmen Rubio-Alarcón, Sietske van Nassau, Suzanna Schraa, Gerrit Meijer, Mark Sausen, Miriam Koopman, Geraldine Vink, Sanne Abeln, Remond Fijneman, Jeanine Roodhart, on behalf of the PLCRC-MEDOCC group. Molecular characterization of stage III colon cancer patients with recurrence after adjuvant chemotherapy [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 2496.

Abstract 6903: Treatment efficacy of transcatheter hepatic arterial infusion chemotherapy with cisplatin in a severe immunodeficient rat model with patient-derived primary pancreatic ductal adenocarcinoma xenografted into the liver

Abstract Purpose: Liver metastases of pancreatic ductal adenocarcinoma (PDAC) is a highly fatal disease; most patients die within 5 years. There is a critical need to identify appropriate anticancer treatments for these patients. A patient-derived tumor xenograft (PDX) model in severe immunodeficient rat with primary PDAC xenografted into the liver is suitable for evaluating transcatheter hepatic arterial infusion chemotherapy. Materials and Methods: The purpose of this study was to develop a severe immunodeficient rat model with patient-derived primary PDAC xenografted into the liver, and to assess the treatment efficacy of hepatic arterial infusion chemotherapy with cisplatin in this model. Three patient-derived tumors of PDAC were transplanted into the liver of 21 rats each, totaling 63 rats. Four weeks after transplantation, the 21 rats were randomly assigned into three treatment groups of seven rats each: hepatic arterial infusion, systemic venous infusion, and control group. Tumor volumes were evaluated on CT twice at pre-treatment and 4-weeks post-treatment. Following euthanasia of the rats, resected tumor specimens were pathologically analyzed. Results: The liver-implanted PDAC PDX rat model was established in all 63 rats. hepatic arterial infusion chemotherapy and systemic venous infusion chemotherapy with cisplatin were able to be performed in the assigned rats. The hepatic arterial infusion group significantly inhibited tumor growth and reduced Ki67 expression, indicating lower cell proliferation, compared to the control group in three PDX tumors. Conclusion: A rat-based preclinical platform was established by liver-implanted PDAC PDX rat model. Arterial cisplatin infusion chemotherapy would be one of potential therapies for PDAC liver metastases. Citation Format: Ken Kageyama, Akira Yamamoto, Masanori Ozaki, Kenjiro Kimura, Shinpei Eguchi, Ryota Tanaka, Mizue Terai, Takami Sato, Yukio Miki. Treatment efficacy of transcatheter hepatic arterial infusion chemotherapy with cisplatin in a severe immunodeficient rat model with patient-derived primary pancreatic ductal adenocarcinoma xenografted into the liver [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 6903.

Abstract 2695: A higher percentage of M2 macrophages in non-tumor part predict the tumor recurrence in patients with hepatocellular carcinoma after surgical resection

Abstract The primary hurdle in improving outcomes for hepatocellular carcinoma (HCC) patients after curative treatment is the high early recurrence rate. The existing literature indicates the presence of type 2 macrophages (M2), renowned for their immunosuppressive capabilities, has been implicated in creating a microenvironment conducive to tumor growth and recurrence. However, the intricate interplay involving M2 macrophages and the recurrence of HCC is underexplored. Therefore, we conducted an analysis involving HCC patients who underwent hepatectomy at our hospital between 2013 and 2017. We collected samples from both the tumor and non-tumor regions and subjected them to bulk RNA sequencing for comprehensive molecular profiling. The proportion of immune cells was calculated by CIBERSORTx.In our study, we enrolled fifty patients, with sixty percent presenting with cirrhosis and seventy-three percent having viral hepatitis. Twenty-three patients experienced tumor recurrence, with a median time to recurrence of 12.6 months. First, we found no correlation between five TIMR subtypes defined by TIMELASER (Xue R, Nature, 2022) and recurrence. However, as for the proportions of immune cell, a significantly lower NK/Treg ratio (p= 0.0163) and high within the resected tumor section in recurrent group was found. On the other hand, the ratio of M2 macrophages to total macrophages (M2/M) was significantly higher within the non-tumor region in patients experiencing tumor recurrence after hepatectomy (p=0.0357). Furthermore, the expression of the ACGT2 gene in non-tumor part, which strongly correlates with Treg function, was significantly higher (p=0.0056) in recurrent group. In addition, the innate T cells score was increased in non-tumor pat in recurrent group but with borderline significance (p=0.0628). However, in multivariable analysis, only a higher M2/M ratio within the non-tumor region (HR 3.756, p=0.0072) were identified as independent risk factors for tumor recurrence. We also found that patients with a higher M2/M ratio had a lower percentage of cirrhotic patients (p=0.0049) and less association with TIME-IA (immune activation) subtype of HCC by TIMELASER classification (p=0.0030). In conclusion, a higher M2/M ratio within the non-tumor region predict the tumor recurrence in patients with hepatocellular carcinoma. Citation Format: Po-Ting Lin, Wei-Ting Ku, Tsung-Han Wu, Cheng-Heng Wu, Chan-Keng Yang, Wei Teng, Yung-Chang Lin, Chun-Yen Lin. A higher percentage of M2 macrophages in non-tumor part predict the tumor recurrence in patients with hepatocellular carcinoma after surgical resection [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 2695.

Abstract 7364: Comprehensive multi-omics analysis for resectable hepatocellular carcinoma uncovers biomarkers to predict microvascular invasion

Abstract Introduction: Microvascular invasion (MVI) is a well-known prognostic factor in predicting cancer relapse after curative resection of resectable hepatocellular carcinoma (HCC).Therefore, there is a clear unmet need for a precision strategy based on cancer-specific multi-omics features to predict the MVI feature at the initial diagnosis of HCC. Methods: Using gene expression profiling for resected human HCC (Discovery cohort, n=240), we identified the transcriptomic signature predicting the MVI feature. Comprehensive analyses were performed using the dataset from the cancer dependency map (DepMap) project, including cancer-specific molecular characterization with multi-omics data, and drug sensitivity with compound screening, and integrative in-silico prediction methods to uncover MVI. The transcriptomic signature predicting the MVI feature were validated in independent translational cohorts (TCGA-LIHC; n=373, KOREA; n=188, TOKYO; n=183, MODENA; n=78, ZHONGSHAN; n=159). Results: The MVI signature with 1028 genes was identified from robust statistical testing from the discovery cohort, and robust validation for the prediction performance of the MVI signature showed significant accuracy in the validation cohort (AUC=0.865, p&amp;lt;0.01). Multi-omics analysis revealed aggressive tumor biology associated with the MVI signature and specified biomarkers. Conclusions: Integrative multi-omics profiling for resectable HCC uncovers biomarkers to predict MVI. A novel combination of biomarkers performs in sorting out the tumor with aggressive tumor biology. A precision strategy to discover resectable tumors beneficial from surgical resection can be established from consecutive clinical trials based on this translational study. Citation Format: Incheon Kang, Woo Young Kwon, Sung Hwan Lee. Comprehensive multi-omics analysis for resectable hepatocellular carcinoma uncovers biomarkers to predict microvascular invasion [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 7364.

Abstract 1923: Cytoplasmic localization of KRAS in Her2-amplified colorectal cancer induces an altered dependency of the oncogenic signaling pathway from RAS/MAPK to PI3K/AKT

Abstract Nowadays, KRAS-G12C specific inhibitor has been used for the treatment of patients with KRAS mutated non-small cell lung cancer, but not for colorectal cancer (CRC) patients. Recent clinical trials have shown that the efficacy of a single KRAS inhibitor treatment was limited for CRC due to multiple primary/adaptive resistance mechanisms. In the CRC, clinical trial with dual inhibition of KRAS-G12C and EGFR has demonstrated that combination therapy had improved partial response rate, suggesting that primary resistance to KRAS inhibitor is mainly caused by EGFR-mediated adaptation. Meanwhile, more than half of the primary resistance mechanisms are still unknown. To understand the intrinsic resistance mechanisms to KRAS inhibitors in CRC, KRAS G12C- or G12D-positive CRC patient-derived cells (PDCs) were established from surgically resected tumor specimens. Analysis of cell proliferation under KRAS inhibitor treatment or KRAS knockdown revealed these PDCs were not solely dependent on KRAS mediated growth signaling. To clarify the compensatory activated pathways in KRAS inhibitor, inhibitor library screening and sequencing analysis were performed among 8 KRAS-mutated PDCs. As a result, PDCs were categorized into EGFR inhibitor with KRAS inhibitor sensitive group and PI3K pathway activating group harboring PIK3CA mutation or/and ERBB2 amplification with KRAS mutation. To explore the novel intrinsic resistance mechanisms, we deeply analyzed one of the PDC named JC261, harboring PIK3CA, ERBB2, and KRAS alterations. We observed that PI3K pathway was highly activated in JC261 cells, and cell proliferation was mainly dependent on PI3K/AKT/mTOR pathway regardless the existence of KRAS-G12C mutation. To examine whether Her2 amplification contributes to the PI3K pathway dependency, we established Her2 knockout JC261 cells. Notably, Her2 knockout suppressed Her2-Her3-PI3K signaling and restored KRAS-MAPK dependency. To analyze the mechanism of how KRAS-MAPK pathway was activated in Her2 knockout cells, we focused on KRAS localization, since the MAPK activation is known to initiate from plasma membrane localization of KRAS after appropriate modifications. Remarkably, immunofluorescence staining of KRAS revealed that KRAS was aberrantly localized in the cytoplasm in JC261, while KRAS localization was changed to the plasm membrane in Her2 knockout JC261 cells. In addition, the cytoplasmic KRAS localization was also observed in Her2-amplified, KRAS-WT PDC (JC69). These results suggest that Her2 amplification may induce aberrant KRAS localization, resulting in low dependence on the KRAS-MAPK pathway. Thus, KRAS localization may regulate the balance between MAPK and PI3K signaling intensity. Citation Format: Kohei Maruyama, Satoshi Nagayama, Ryohei Katayama. Cytoplasmic localization of KRAS in Her2-amplified colorectal cancer induces an altered dependency of the oncogenic signaling pathway from RAS/MAPK to PI3K/AKT [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 1923.