Tumor Biomarkers Research Articles

Abstract 6143: Association of polygenic risk score and prostate tumor biomarkers with lethal prostate cancer

Abstract Prostate cancer (PCa) is a highly heritable cancer. While polygenic risk scores (PRS) stratify overall PCa risk among cancer-free men, they have not been reported to predict lethal outcomes in PCa patients. We aimed to examine to what extent PRS modifies associations between tumor biomarkers with cancer prognosis after diagnosis. We included men with primary, non-metastatic PCa in the Health Professionals Follow-up Study (HPFS) and Physicians’ Health Study (PHS). The PRS was constructed with 451 risk variants identified from prior PCa GWAS, measured on DNA from blood or buccal, standardized by adjusting for mean and standard deviation (SD) based on men without PCa with array-based genotyping data in HPFS/PHS. Prostate tumor biomarkers of molecular subtypes (TMPRSS2:ERG fusion, PTEN loss, and TP53 missense mutations from validated immunohistochemistry assays), insulin/lipid signaling pathways (FASN, IR, and IGF1-R), and cellular proliferation and tumor microenvironment (Ki-67, apoptosis rates, and angiogenesis) were measured on tumor tissue from radical prostatectomy or TURMP. Sample sizes varied by tumor biomarkers, ranging from 214 for angiogenesis markers to 598 for ERG protein expression. We first used either logistic or negative binomial regression to evaluate the association between the PRS and the protein expression (levels) of each individual biomarker, and then evaluated the addition of multiplicative interaction terms between PRS and biomarkers to logistic regression models for lethal PCa, defined as metastases or death from PCa. Lastly, we evaluated the predictive performance for lethal PCa by area under the curve (AUC). All models adjusted for age at diagnosis and Gleason score. Among all patients included in the analysis, the median age at diagnosis was 66 (interquartile range: 62-70) years, with 20% having a Gleason score≥8 and 10% having lethal PCa. PRS showed no association with lethal PCa (OR per SD increase PRS=0.95, 95%CI 0.85-1.06) or most tumor biomarkers, except for the apoptosis index (per SD in PRS corresponding to 0.22 units increase, 95%CI 0.02-0.42). Statistically significant interactions were found between PRS and p53 overexpression (p interaction = 1.6x10-5), PTEN loss (p=3.7x10-3), FASN (p=0.03), and Ki-67 (p=1.6x10-3), suggesting that compared to men with a PRS higher than the median, TP53 missense mutation, PTEN loss, higher FASN intensity, and higher Ki-67 indices were more strongly associated with lethal PCa in patients with lower PRS. Incorporating PRS with tumor biomarkers into predictive models enhanced the AUC beyond a model with tumor biomarker and age. The largest improvements were observed when combining the PRS with Ki-67 and apoptosis, showing absolute increases of 5% and 7% respectively. In conclusion, PRS integration with tumor biomarkers at diagnosis potentially improves the prediction of lethal PCa, thereby informing more targeted management strategies. Citation Format: Anqi Wang, Anna Plym, Konrad H. Stopsack, Lorelei A. Mucci, Kathryn L. Penney. Association of polygenic risk score and prostate tumor biomarkers with lethal prostate 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 6143.

Abstract 1066: Colocalization of ovarian cancer-associated biomarkers in tumors, cancer cells and extracellular vesicles

Abstract Introduction: We have previously shown that ovarian cancer can be detected with high specificity and sensitivity by interrogating colocalized membrane-associated cell-surface biomarkers on single tumor-associated extracellular vesicles (EVs). Our blood based Ovarian Cancer Test (OC Test) is composed of 5 cancer-associated biomarkers (BST-2, FOLR1, MUC-1, MUC-16, and sialylated Thomsen-nouveau antigen (sTn)) known to be overexpressed in ovarian cancer relative to healthy tissues. The test employs these 5 biomarkers in 3 combinations to capture and detect EVs from human plasma to distinguish high-grade serous ovarian carcinoma (HGSC) from both benign ovarian tumors and normal samples. Using super-resolution microscopy on ovarian cancer cell lines and EVs and multiplex immunohistochemistry of ovarian benign and tumor tissue, our study aimed to show that the 5 ovarian cancer biomarkers show 1) colocalization on ovarian cancer cells, 2) colocalization on the surface of EVs, and 3) colocalization on cancer cells within ovarian tumor biopsies. Methods: Super-resolution microscopy was employed to visualize stained biomarkers on the cell surface of a collection of ovarian cancer cell lines as well as on the surface of extracellular vesicles released by these cell lines. 58 HGSC (17 Stage I, 30 Stage II, and 10 Stage III) and 17 benign ovarian tumor K2EDTA plasma samples and paired FFPE tissue were sourced from the Ovarian Cancer Research Program (OVCARE, Vancouver BC, Canada). A tumor microarray from identical tissue samples was stained with an Opal multiplex-IHC (mIHC) assay comprised of antibodies to BST2, MUC1, sTn, and pan-cytokeratin and a DAPI counterstain. Machine learning based image analysis was utilized to determine colocalization of the biomarkers at the cellular level within benign and tumor tissue. RNA sequencing was carried out to assess expression levels of the biomarkers in each FFPE tissue sample. OC Tests were run on each plasma sample. Results: Super-resolution microscopy showed colocalization of OC Test combination biomarkers on ovarian cancer cells and EVs derived therefrom. Machine learning-based image analysis of tumor and benign tissue microarrays stained for BST2/MUC1/sTn using mIHC, showed strong evidence for colocalization of these biomarkers on single cells within ovarian tumor tissue, particularly in early-stage tumors, but not on benign tissue. RNA sequencing analysis showed good correlation of biomarker RNA expression levels and with the OC Test results. Conclusions: The results presented here demonstrate that the OC Test biomarkers are colocalized on tumor tissue, ovarian cancer cells, and EVs from ovarian cancer cell lines. RNA and protein expression levels show good correlation with OC Test results. These results provide further evidence that colocalized biomarkers on EVs can be utilized for early detection of cancer. Citation Format: Anthony D. Couvillon, Emily S. Winn-Deen, Shelby Thornton, Shuhong Liu, Michael DeRan, Maciej Pacula, Sanchari Banerjee, Daniel Gusenleitner, Laura T. Bortolin, Jonian Grosha, Timothy Santos-Heiman, Gabrielle Sangiuliano, Kelly M. Biette, Christopher R. Sedlak, Bilal Hamzeh, Delaney M. Byrne, Peter A. Duff, Julie Ho, Dongxia Gao, Amy Jamieson, Lauren T. Cuoco, MacKenzie S. King, Dawn R. Mattoon, Toumy Guettouche, Jessica N. McAlpine, David Huntsman. Colocalization of ovarian cancer-associated biomarkers in tumors, cancer cells and extracellular vesicles [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 1066.

Abstract 3627: Volrustomig a novel PD-1/CTLA-4 bispecific antibody leads to robust increase in peripheral and intra-tumoral pharmacodynamic biomarkers in solid tumors from FTiH study

Abstract Background: Volrustomig (MEDI5752) is designed to fully inhibit PD-1 while preferentially inhibiting CTLA-4 on activated PD-1+ T cells. In a FTiH trial, volrustomig demonstrated meaningful clinical activity in patients with solid tumors (including 1L RCC and NSCLC), acceptable safety profile, sustained PD-1 receptor occupancy, and T cell proliferation at levels greater than seen with clinically tolerable doses of CTLA-4 inhibitors with co-administration of anti-PD(L)-1. We sought to further characterize volrustomig pharmacodynamic effect in the periphery and tumor to demonstrate its biological activity and inform dose optimization. Methods: Pre- and on-treatment blood samples from 86 patients enrolled in dose exploration were collected. Peripheral T cell profiling was assayed by flow cytometry, RNAseq, TCRSeq and serum proteomics. Paired tumor biopsies (N=17), pre- and at week 6 on-treatment, were analyzed for T cell infiltration and function using RNAseq and computational image analysis of immune cell marker density detected by histochemistry and multiplex immune fluorescence assays. Results: Volrustomig achieved dose-dependent peripheral pharmacodynamic changes of biomarkers specific to CTLA-4 blockade at ≥ 225mg. At C1D8 with doses ≥ 500mg, increases in CD4 T cell proliferation (ki67), activation (ICOS), and memory T cells (1516%, 321% and 88%, respectively) were seen, each greater than observed with historical controls of patients treated with tremelimumab 3mg/kg (T3) in combination with durvalumab. Similarly, CD8 proliferation and activation were also higher than T3 at C1D8 with 300% and 161% increase respectively. Additional CD4 and CD8 T cell proliferation and activation was observed at C2D8 supporting the benefit of repeat dosing. Higher peripheral T cell clonal expansion at doses ≥ 500mg was seen and associated with PFS and OS benefit. In patients with paired biopsies, volrustomig achieved robust T cell mediated anti-tumor activity including increases in T cell infiltration (CD8+, 2.3 fold, p=0.04), proliferation (CD8+ Ki67+, 2.1 fold, p=0.04) and, T cell cytotoxicity and activation (GrB+, 2.2 fold, p=0.01; T cell effector and IFNg gene signatures, > 2-fold, p< 0.01). Additionally, volrustomig increased CD8 proliferation in tumor compared to historical control durvalumab alone (>2-fold increase in 70% vs 50% patients). Conclusion: Voltrustomig demonstrated robust peripheral and intra-tumoral T cell activation and proliferation, broadening the pool of antigen experienced T cells, at levels greater than seen with dual checkpoint blockade currently used in the clinic. Citation Format: Ikbel Achour, Michael Kuziora, Florian Song, Steven Eck, Lina Meinecke, Jorge Blando, Jennifer Pearson, Megha Saraiya, Christian Eisen, Felix Segerer, Markus Schick, Nicolas Triltsch, Michael Surace, Gisele Silva Boos, Harald Hessel, Mai Bui, Katrin Pratsch, Alma Andoni, Shelby Denise Gainer, Dan Freeman, Deepa Subramaniam, Ben Tran. Volrustomig a novel PD-1/CTLA-4 bispecific antibody leads to robust increase in peripheral and intra-tumoral pharmacodynamic biomarkers in solid tumors from FTiH study [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 3627.

Abstract 581: Identification of potential biomarkers of response to RASMULTI(ON) plus anti-PD-1 combination in preclinical PDAC models

Abstract Mutant KRAS is present in more than 80% pancreatic cancer, promotes cancer cell survival, and protects cancer cells from immune recognition and attack. We have shown that inhibitors of the active state of RAS (RAS(ON)) promote cancer neoantigen recognition and synergize with immunotherapy in preclinical immunogenic models. 1 We evaluated the impact of RMC-6236, an investigational RASMULTI(ON) inhibitor on anti-tumor activity and tumor microenvironment (TME) remodeling in two congenic KRASG12D/+ GEMM-derived PDAC models resistant to anti-PD-1 therapy - KPCY clone 2 (6694c2) and clone 3 (2838c3), developed by Ben Stanger at UPenn. 2 Daily oral administration of RMC-6236 drove tumor regressions in KPCY clone 3, leading to 10% durable complete responses (CRs). In combination with anti-PD-1, 40% of durable CRs were achieved. However, RMC-6236 only drove tumor growth inhibition in KPCY clone 2, and no combination benefit with anti-PD-1. We conducted preclinical biomarker analyses in the TME and periphery to explore differences in response to RMC-6236 alone and in combination with anti-PD-1 in these models. Assessment of baseline predictive biomarkers in tumors elucidated that the KPCY clone 3 cells developed tumors with lower suppressive myeloid cells (gMDSCs) and higher CD8+ T cell infiltration compared to those derived from KPCY clone 2 cells. IHC analyses showed that T cells in clone 3 were in the tumor core, while CD8+ T cells in clone 2 were at the tumor border (the latter frequently observed in PDAC patients). RMC-6236 induced transformation of the TME in favor of anti-tumor immunity in only the KPCY clone 3 - with decreased immunosuppressive gMDSCs, and increased T cells. Limited modulation of the TME was observed in the KPCY clone 2 cells-derived tumors, and gMDSC levels significantly higher than those in baseline tumors of KPCY clone 3. Peripheral immunophenotyping analyses revealed that baseline peripheral suppressive myeloid cells (mMDSCs) were significantly higher in mice harboring tumors originated from KPCY clone 2 cells, suggestive of a more systemic immunosuppressive status. Studies are ongoing to assess additional peripheral immune signatures of preclinical activity of RMC-6236 in combination with anti-PD-1. Taken together, baseline tumor levels of suppressive myeloid cells (gMDSCs) were shown to be a negative predictive biomarker for treatment outcome to RMC-6236 +/- anti-PD-1 in KRAS mutant preclinical PDAC models. Peripheral mMDSCs were shown to be higher in the mice with tumors from the PDAC model not sensitive to the combination of RMC-6236 with anti-PD-1, suggesting that it could be predictive of poor outcome for this combination. These studies in immune-competent models of RAS mutant PDAC allow us to generate tumor and blood-based biomarkers that may predict outcomes to RAS(ON) inhibitor combinations in the clinic. 1 Menard et al. AACR 2023 2 Li et al. Immunity 2018 Citation Format: Lillian Seu, Marie Menard, Jasmine Lee, Christopher Chow, Cristina Blaj, Mariela Moreno Ayala, Nataliya Shifrin, Avery Salmon, Swetha Ganesh, Philip Wig, Alice Kumamoto, Paola Soto-Perez, Tippy Taavili, Vivian Morton, James W. Evans, Jacqueline A. Smith, Elsa Quintana. Identification of potential biomarkers of response to RASMULTI(ON) plus anti-PD-1 combination in preclinical PDAC 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 581.

Abstract 3763: Comparative spatial analyses of the tumor immune landscape in different mouse models of glioblastoma

Abstract Background: Despite advances in treatment, glioblastoma (GBM) remains one of the most difficult types of cancer to treat, and the prognosis is poor. The current median survival time for patients with GBM is about 12-15 months, and the five-year survival rate is less than 10%. There is an unmet need for better GBM treatment options, leveraged from relevant experimental models. To develop new therapies, preclinical animal models are important for analyzing the biology of GBM and evaluating the efficacy of novel therapeutic strategies. While a variety of experimental models are used to study GBM, most preclinical investigations involve mice. In this study we utilize a spatial phenotyping application that permits comprehensive characterization and comparison of key proteins in the brain tumor immune microenvironment (TiME), and detailed comparison the TiME between different immune-competent GBM mouse models. Methods: The Phenocycler-Fusion is a fast spatial biology solution that affords ultrahigh-plex single-cell spatial readouts. We used this solution for the whole slide imaging of mouse FFPE tissues and deep immune phenotyping of >40 proteins, comprising immune cell lineages, activation states and checkpoints, as well as biomarkers for tumor, vascular and neural landscapes of various GBM mouse models. Results: Via single cell spatial phenotyping, we isolated spatial signatures within the mouse GBM tissue immune microenvironment. We focused on multiple immune biomarkers, including microglia/myeloid cells that were identified via the combinatorial expression of the key markers CD68, Iba-1, F4/80, Tmem119 and CD11b. The macrophages and their biomarker expression profiles exhibited significant inter- and intra-tumoral heterogeneity within different mouse GBM models, indicative of the heterogeneous and complex biology of GBM. Conclusions: Our work encompasses the development of a custom antibody panel, an imaging workflow, as well as a novel bioinformatic analysis method. Deployment of this workflow on different mouse GBM models allowed us to study cell populations, according to biomarker profiles and spatial distribution. This study provides a deeper characterization of the diverse mouse GBM models to determine the optimal model that most accurately recapitulates the complex TiME of human GBM, including key features such as invasive tumor margins, high vascularity, blood-brain barrier, etc. We anticipate that this approach has enormous potential for a broad range of applications for which biomolecules’ spatial information is important and will deepen our understanding of the GBM TiME. Citation Format: Dmytro Klymyshyn, Niyati Jhaveri, Aditya Pratapa, Nadezhda Nikulina, Tsz H. Tam, Nadine Nelson, Riccardo Dolcetti, Davide Moi, Roberta Mazzieri, Theo Mantamadiotis. Comparative spatial analyses of the tumor immune landscape in different mouse models of glioblastoma [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 3763.

Abstract 5718: TGN-1062, a dual CDK7 and FLT3 Inhibitor, shows potent anti-AML activity and synergizes with Venetoclax

Abstract Purpose: Acute Myeloid leukemia (AML) is an aggressive malignancy of the hematopoietic system with poor survival rates. The best responses to treatment are achieved for young and fit patients who can tolerate chemotherapy followed by stem cell transplantation compared to older patients unfit to take intense chemotherapy. Since its approval venetoclax, a BCL2 inhibitor, has been the standard treatment for older patients in combination with a hypomethylating agent (HMA), such as azacitidine or decitabine, with a 76% complete response (CR). Despite this success as a frontline treatment, there is limited response for patients with relapse and refractory (r/r) and development of novel agents is required to improve overall therapeutic response. MYC has been shown to be frequently activated in AML and plays an important role in the induction of leukemogenesis and leukemic progression. While BCL2 inhibition via venetoclax has, in part, been shown to control c-MYC activation, the addition of another inhibitor which controls MYC may prove beneficial. CDK7 plays a dual role in tumor progression by regulating the cell cycle and transcription. CDK7 has also been shown to be associated with the overexpression of oncogenic driver genes such as BCL2 and MYC. Previously, we have presented the development of a potent and reversible CDK7 inhibitor, TGN-1062. Here, we have generated data supporting the potential benefit of CDK7 inhibition in combination with standard of care therapy for AML. Methods: AML lines were co-treated with TGN-1062, venetoclax, and/or an HMA, assessed for viabilities with CellTiter-Glo, and analyzed with the Bliss synergy model. AML CDX or PDX cells were implanted subcutaneously or transplanted via tail vein, respectively, and treated with TGN-1062 and/or venetoclax. Subcutaneous tumors were measured to determine tumor growth inhibition (TGI) and correlating drug accumulation levels were measured in tumors and plasma using mass spectrometry. Leukemic burden and survival were evaluated at the end of treatment for transplanted models. Immunohistochemistry (IHC), Western blotting, and RT-PCR were performed to determine changes in relevant biomarkers in tumors and/or AML cell lines. Results: Previously we have reported that TGN-1062 was effective in suppressing the growth of MV4-11 AML model. We extend these studies and show that TGN-1062 has activity at lower doses in both in vitro and in vivo AML models. In addition, we show synergy between TGN-1062 and other agents for AML treatment, including venetoclax or an HMA. Western blotting demonstrated significant changes in apoptotic markers. Survival of mice bearing AML was significantly increased with TGN-1062 treatment and combination treatment with venetoclax produced the longest survival. Conclusion: Targeting CDK7 with TGN-1062 in combination with venetoclax or an HMA is a promising therapeutic approach for treatment of AML and needs further investigation. Citation Format: Trason Thode, Le Xuan Truong Nguyen, Brian Durbin, Alexis Weston, Serina Ng, Tithi Ghosh Halder, Taylor Bargenquast, Raffaella Soldi, Srinivas Kasibhatla, Vincent Chung, Victoria Villaflor, Mohan Kaadige, Guido Marcucci, Sunil Sharma. TGN-1062, a dual CDK7 and FLT3 Inhibitor, shows potent anti-AML activity and synergizes with Venetoclax [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 5718.

Abstract 76: Correlated multi-scale 3D optical microscopy of tumor tissues

Abstract Three-dimensional (3D) optical microscopy in combination with advanced tissue clearing methods permits the interrogation of intact large-sized tumor tissues. There are many optical microscopy methods (e.g. light-sheet and confocal microscopy) offering 3D tumor images at varying levels of spatial resolution (e.g. organ, tissue, cell, and molecule level). However, it is a challenge to correlatively integrate various resolution 3D images obtained by different optical microscopy of tumor tissue. In this project, we developed a correlated multi-scale 3D optical microscopy method that enables the acquisition of macroscopic to microscopic spatial information from a single tumor tissue in 3D. Firstly, we used light sheet microscopy to image a whole large-sized, cleared tumor tissue and analyzed the results to identify regions of interests (ROIs). After defining ROIs in the 3D whole tumor image, we added a UV-activatable visible dye, spiropyran, in the agarose gel surrounding the cleared tumor and exposed the sample to a UV light sheet horizontally at the height (z-axis) of the tumor where the ROIs present. The activated dye showed ‘purple’ colored lines in the agarose gel and we physically marked the gel along the visible colored lines. We further sectioned the tumor at the ROI positions using a vibratome after reversing tissue clearing process. After immunofluorescence staining and aqueous-based tissue clearing, confocal microscopy allowed the localization of various cell types in the ROIs of tumor macrosections. To validate the method for multi-scale evaluation of cancer immunotherapy, we tested it with control and DMXAA-treated mouse mammary tumor tissues. We successfully acquired the 3D images of whole tumors by capturing autofluorescence signals with a 633 nm excitation laser and its matched emission filter. Based on the autofluorescence tumor images, we defined two ROIs for each control and treated tumor and performed optical marking and physical sectioning of the tumors as described above. Next, we stained the macrosections (400 µm thick) with DAPI, CK8-DL488, CD45-DL550, and ER-TR7-DL680 to visualize cancer, immune, and stromal cells in the ROIs at cellular resolution. We quantitatively analyzed the correlated multi-scale 3D image data for assessment of the effects of DMXAA treatment on the tumor microenvironment including eradiation of cancer cells, immune infiltration, and remodeling of tumor stroma. In summary, this new microscopy method will provide comprehensive spatial information of tumor tissues and benefit a broad cancer research field such as the discovery of new tumor biomarkers and the development of effective cancer therapies. Citation Format: Jingtian Zheng, Steve Seung-Young Lee. Correlated multi-scale 3D optical microscopy of tumor 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 76.

Abstract 822: A retrospective study on the disparities of hepatocellular carcinoma

Abstract Background: Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer in adults and the third leading cause of cancer-related deaths worldwide. Studies report that the incidence of, and mortality from HCC vary significantly by age, sex, and race/ethnicity; however, disparities in the expression level of tumor biomarkers, liver functions, lipid profiles, and comorbidities have not been thoroughly investigated among subpopulations of patient with HCC. Methods: A retrospective study was conducted to review 247 serial HCC cases enrolled in the University of Mississippi Medical Center during June 2000 to May 2023. The entire HCC population was stratified into subpopulations by race, gender, age and BMI. Then comparisons were performed between two corresponding subpopulations in the expression level of HCC-related biomarkers including Alpha-FP, liver functions including albumin, ALT, AST, and ALP, plasma lipid profiles including cholesterol, and comorbidity conditions including cirrhosis in benign liver tissues, smoking, alcohol using, and illness with viral hepatitis. Two-tailed Student’s T-test was used to calculate the difference in mean values, and Chi-Square Test was used to compare the difference in rates or percentages. The significant p value was set at p<0.05. Results: In total 247 HCC cases, males were 178 (72.1%) and females were 69 (27.9%) with a male to female ratio of 2.6:1; black patients were 108 (43.7%), white patients were 127 (51.4%), and others were 4.9%. The mean age was 59.6 years and mean BMI was 27.04. AFP was the only one of detected tumor biomarkers showing disparities: it was significantly higher in patients of male (p=0.026), younger age (p<0.0001), lower BMI (p=0.039), smokers (p=0.0325) and illness with viral hepatitis (p=0.0007). Disparities in liver functions included: 1) AST was significantly higher in Black HCC patients (p=0.027); 2) no statistical difference of liver functions in gender; 3) younger HCC patients had significantly lower level of Albumin (p=0.006), and higher levels of ALT (p=0.014) and AST (p=0.0032); 4) HCC patients with lower BMI also had lower level of Albumin (p=0.015), and higher levels of AST (p=0.0480 and ALP (p=0.0057). There was no statistical difference of plasma lipid profiles between subpopulations, Black HCC patients except that Black HCC patients had significantly higher levels of cholesterol (p=0.0006) and HDL (p=0.048). In comorbidity, Black HCC patients had higher rates of alcohol using and existence of cirrhosis; and male HCC patients had higher rates of smoking, alcohol usage and viral hepatitis. Conclusions: HCC patients are greatly disparate in the expression level of tumor biomarkers, liver functions, plasma lipid profiles and comorbidity conditions between subpopulations stratified by race, gender, age and BMI. These results could provide useful information for clinical management and prognosis of patients with HCC. Citation Format: Xinchun Zhou, Barrett Aldridge, Nazar Rahmanov, Zhirong Liu, Jinghe Mao, Neha Varshney. A retrospective study on the disparities of hepatocellular carcinoma [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 822.

Abstract 3690: Monitoring prostate specific membrane antigen or androgen receptor expression on circulating stromal cells in advanced prostate cancer patients and their correlation with patient response

Abstract Background: Metastatic Prostate cancer (mPCa) mortality rates are high despite numerous treatment options against various mechanisms of action, including targeted therapies, i.e. prostate specific membrane antigen (PSMA)-targeted therapy (Pluvicto) or anti-androgen receptor (AR) (Enzulamide, Biculamide). Further, tumor biomarkers (i.e. PSMA and AR) can change over time and with resistance mechanisms that develop after treatments. This suggests that primary biopsies may not represent later PCa tumors necessitating a way to identify patients that may respond to later line therapies. Blood based biopsies can be used to monitor PCa treatment, which can include circulating tumor cells (CTCs) and the newly discovered cancer associated macrophage like cells (CAMLs), a cancer specific circulating phagocytic stromal cells. Interestingly, while PSMA & AR have been identified in CTCs, they have not been evaluated in CAMLs, nor have PSMA & AR expressions in CTCs & CAMLs been evaluated in anti-AR therapy settings. We measured CAMLs & CTCs in mPCa to evaluate their PSMA & AR expression, including in patients treated with anti-AR therapy. Methods: We evaluated CAMLs & CTCs in a multi-institutional prospective pilot study using n=30 mPCa patients with progressive disease, prior to starting a new line of therapy (T0). Whole peripheral blood (7.5mL) was filtered for CAMLs & CTCs and stained for PSMA (n=15) & AR (n=15). In addition, 15 patients were treated with anti-AR therapy as standard of care and responses by PET/CT were compared against AR expression. When possible, follow up samples (T1) were also procured. Results: CTCs were identified in 16% (n=5/30) of patients and CAMLs were identified in 96% (n=29/30), with 53% of patients having hyperengorged CAMLs ≥50 μm (n=16/30). CTCs in patients were not statistically significant for worse outcomes PFS HR= 0.1748, p=0.546 nor OS (HR= 1.303, p=0.865), nor were CAMLs prognostic for PFS or OS. However, patients with ≥50 μm CAMLs did have significantly worse PFS (HR= 5.9, CI95% 2.2-16.3, p=0.001) and worse OS (HR= 3.1, CI95% 1.3-7.1, p=0.016). Further, PSMA CAML/CTC expression was high in 60% (n=9/15) of patients and AR CAML/CTC expression was high in 53% (n=8/15). Of the n=15 patients who received anti-AR therapy after T0, high AR expressing CAMLs/CTCs (n=8/15) had a ~250% better mPFS of 10.3 months (mons) (progressing at 2.2-32.6 mons) vs low AR CAMLs/CTCs mPFS of 4 mons (progressing at 0.2-7.2 mons). Additional mOS analysis from T1 samples and 2-year survival is ongoing. Conclusion: We utilized liquid biopsies to monitor the expression of two common cell surface receptors (PSMA & AR) in CAMLs and CTCs in mPCa. Further, in a small subset of patients treated with AR therapy, high AR CTC/CAML expression appeared to correlate with better response rates, though larger prospective studies are needed. Citation Format: Dimpal M. Kasabwala, Raymond C. Bergan, R. Katherine Alpaugh, Daniel C. Danila, Tuan L. Chuang, Brenda Y. Hurtado, Daniel L. Adams. Monitoring prostate specific membrane antigen or androgen receptor expression on circulating stromal cells in advanced prostate cancer patients and their correlation with patient response [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 3690.

Abstract 3755: Impact of antigen retrieval and other parameters on detection of FGFR2b in various solid tumors on a BenchMark ULTRA automated staining platform: Development of a new IHC assay for FGFR2b

Abstract Background: Fibroblast growth factor receptor 2b (FGFR2b) is part of the FGFR transmembrane tyrosine kinase receptor family. This protein has gained more attention in recent years as a tumor progression biomarker in numerous solid tumors. The detection of FGFR2b by immunohistochemistry (IHC) has been used recently in immunotherapy clinical trials with multiple tumor types. During IHC assay development on formalin-fixed paraffin embedded tissue, a thorough study of antigen retrieval through cell conditioning or enzyme incubation, primary antibody incubation, and detection parameters is critical to evaluate staining performance. Design: A study of an investigational anti-FGFR2b (FPR2-D) assay developed on a BenchMark ULTRA automated staining platform explored the effect of antigen retrieval and detection parameters on staining performance. VENTANA System Software was used to modify steps in the IHC staining protocol resulting in 42 permutations. Ten different solid tumors were stained with these modifications to the assay and subsequently evaluated for FGFR2b expression. Result:s The results demonstrate that the staining clarity, intensity, and dynamic range within tissue cases of FGFR2b staining can vary widely between different solid tumor types. While most permutations of the initial assay parameters had minimal impact on the staining performance and readability by a pathologist, the order of the enzyme treatment and the cell conditioning steps (in addition to increased incubation time of primary antibody) had a significant impact when comparing across different solid tumors. Detection of FGFR2b seemed to have a greater susceptibility by tumor type to the antigen retrieval process than has traditionally been observed in other biomarkers. Conclusion: The overall results of this investigation show the importance of an extensive parameter screening approach when evaluating new antibody targets and indication combinations in IHC to ensure optimal staining performance. This is critical to downstream testing and the potential use of new assays in the context of in vitro diagnostics. Citation Format: Autumn Sky Watson, Catherine Le, Anne M. Wertheimer, Spencer Escobedo, Lisa So, Bhavani Bagevalu Siddegowda, John D. Palting, Susan Marion, Steven P. Stratton, Birte Aggeler. Impact of antigen retrieval and other parameters on detection of FGFR2b in various solid tumors on a BenchMark ULTRA automated staining platform: Development of a new IHC assay for FGFR2b [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 3755.

Abstract 2420: Evaluating circulating tumor DNA (ctDNA) as a prognostic biomarker utilizing a tissue-free epigenomic assay in early-stage triple negative breast cancer (TNBC)

Abstract Background: ctDNA has shown promise as a prognostic biomarker in early-stage solid tumors. Current breast cancer clinical guidelines do not recommend routine screening for metastatic disease outside of clinical features suggestive of disease recurrence. The detection of ctDNA may be a useful biomarker for the management of early-stage cancer patients to identify patients who are at high risk of recurrence. Methods: Patients with stage II or III TNBC undergoing neoadjuvant docetaxel and carboplatin chemotherapy on a clinical trial (NCT02124902) followed by surgery were included in this study. Blood samples were prospectively collected prior to, during, and after completion of neoadjuvant chemotherapy, post-surgery, and throughout pre-specified surveillance time points (every 6 months for 5 years). Plasma samples were analyzed using Guardant Reveal powered by Infinity, a tissue-free, multiomic assay that interrogates differentially methylated regions of DNA using an applied bioinformatics filter optimized to detect breast cancer DNA from non-cancerous cell-free DNA and estimate quantitative tumor fraction. Samples were sequenced and resulted blinded to the patients’ clinical data. Results: A total of 120 patients with evaluable plasma samples were included in this study. At baseline prior to chemotherapy, ctDNA was detected in 75% (54/72) of patients. Baseline ctDNA detection was higher in node-positive cancers (100%; 29/29) versus node-negative cancers (58%; 25/43; p<0.0001). ctDNA quantity was higher in node-positive cancers (p<0.0001), and in stage III versus stage II disease (p=0.0179). During surveillance follow-up, the sensitivity for detecting any distant metastatic recurrence was 71% (5/7). Among patients with samples drawn within one year of recurrence, the sensitivity for detecting distant recurrence was 83% (5/6) with a sample-level specificity of 98% (186/190) and a patient-level specificity of 94% (63/67). ctDNA detection prior to recurrence had a median lead time of 5.0 months (range, 4.6-5.6). Notably, the detection of ctDNA during follow-up was associated with worse recurrence-free (HR 23.3, 95% CI 2.70-201, p<0.0001) and distant-recurrence free survival (HR 29.3, 95% CI 1.86-461, p<0.0001). Conclusions: ctDNA is detected with a tissue-free MRD assay with high sensitivity and specificity for distant recurrence in early-stage TNBC. Furthermore, the presence of ctDNA during follow-up is a prognostic indicator. Additional prospective studies are needed to assess the clinical utility of ctDNA monitoring in early-stage TNBC. Citation Format: Foluso O. Ademuyiwa, Cynthia X. Ma, Katherine Weilbaecher, Rama Suresh, Lindsay Peterson, Ron Bose, Nusayba Bagegni, Caron E. Rigden, Ashley Frith, Katherine Clifton, Andrew Davis, Derek Dustin, Mingyang Cai. Evaluating circulating tumor DNA (ctDNA) as a prognostic biomarker utilizing a tissue-free epigenomic assay in early-stage triple negative breast cancer (TNBC) [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 2420.

Abstract 6120: Genomic profiling of KRAS and EGFR-altered non-squamous non-small cell lung cancer reveal ancestry-specific co-alterations with therapeutic implications

Abstract Background: Racial and ethnic disparities are highly prevalent in cancer care and impact treatment outcomes, with an underrepresentation of minority populations in clinical studies. The impact of genetic ancestry on the genomic landscape of tumors remains understudied. To address this, we sought to comprehensively characterize the ancestry-based genomic co-alteration landscape and immunotherapy-related biomarkers in KRAS and EGFR-altered tumors, two major driver populations in non-squamous non-small cell lung cancer (non-Sq NSCLC). Methods: Our study consisted of 68,197 adult patients with non-Sq NSCLC who underwent comprehensive genomic profiling using FoundationOne® or FoundationOne®CDx during routine clinical care in the United States. Genetic ancestry was inferred using a SNP-based approach. Tumor mutational burden (TMB) was calculated across 0.8-1.2 megabases. PD-L1 expression was determined by immunohistochemistry using the Dako 22C3 PD-L1 antibody. Results: Overall, 81% of the patients were of European (EUR; n= 55,430), 10% of African (AFR; n=7,062), 5% of East Asian (EAS; n=3,297), 3% of Admixed American (AMR; n=2,011) and less than 1% of South Asian ancestry (SAS; n=497). KRAS was the most frequently altered oncogene in EUR (39%) and AFR (33%), whereas EGFR was most frequently altered in EAS (53%), SAS (36%), and AMR (30%) ancestry groups. While STK11 and KEAP1 alterations co-occurred with KRAS across all ancestry groups, they were significantly (FDR p <= 0.05) less frequent in EAS (16%) and AMR (15%) compared to EUR (28%). Additional ancestry-specific co-alteration patterns in KRAS-altered tumors included co-occurrence with GNAS alterations in AMR (Odds ratio, OR: 3.5, p < 10-5), co-occurrence with ARID1A alterations in SAS (OR: 4.7, p = 0.02), and mutual exclusivity with NF1 alterations in EUR (OR: 0.4, p < 10-5) and AFR (OR: 0.4, p < 10-5). In contrast, EGFR-altered tumors had a more conserved co-alteration landscape across all ancestry groups. Despite the known mutual exclusivity of KRAS and EGFR alterations, 13% of patients of EAS ancestry (compared to 2-4% of other ancestry groups) with KRAS alterations had co-occurring EGFR alterations; notably, a majority of these patients had an amplification in KRAS and/or EGFR, potentially representing treatment resistance mechanisms. Among immunotherapy-associated biomarkers, PD-L1 expression was similar across ancestries. Of note, patients of AFR ancestry with KRAS or EGFR alterations had higher TMB and the SAS ancestry group had the lowest TMB. Conclusion: Our study provides a comprehensive landscape of ancestry-specific patterns in KRAS and EGFR-altered non-Sq NSCLC. These findings can help better understand cancer disparities, aid in the development of new therapeutic strategies and inform more inclusive clinical trials and treatment decisions. Citation Format: Saumya D. Sisoudiya, Armande A. Houle, Tharu M. Fernando, Timothy R. Wilson, Jennifer L. Schutzman, Jessica K. Lee, Alexa B. Schrock, Ethan S. Sokol, Smruthy Sivakumar, Zhen Shi, Gaurav Pathria. Genomic profiling of KRAS and EGFR-altered non-squamous non-small cell lung cancer reveal ancestry-specific co-alterations with therapeutic implications [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 6120.

Abstract 3419: Demographic, health history, and lifestyle factors in association with biomarkers of colorectal cancer prognosis: A pilot study

Abstract Background/Objectives: Multiple demographic, health history, and lifestyle factors have been associated with prognosis of colorectal cancer (CRC), but the mechanisms underlying these associations remain poorly understood. Knowledge of these mechanisms could reveal new strategies to improve outcomes among CRC patients. The primary objective of this project was to explore the association of these factors, which were assessed pre-diagnostically, with expression of two biomarkers in CRC tumors, SPARC and PD-L1, for which lower and higher levels of expression, respectively, have been previously associated with poorer CRC prognosis. Methods: Participants were drawn from the British Columbia Generations Project (BCGP). At the time of recruitment, they completed a detailed questionnaire that ascertained demographic factors (e.g., biological sex and household income), health history (e.g., personal history of CRC screening), and lifestyle factors (daily fruit and vegetable consumption and alcohol consumption). Formalin-fixed paraffin-embedded blocks (FFPE) with adequate volumes of tumor were obtained for 49 incident CRC cases diagnosed within the BCGP. Cores were extracted from the blocks to create tumor tissue microarrays (TMAs). Slides created from thin sections of the TMAs were stained with SPARC and PD-L1 antibodies and then imaged and analyzed to calculate H-scores as measures of expression in both epithelial and non-epithelial tissues. Linear regression analyses were conducted to evaluate associations between the various factors and ln-transformed H-scores. Results: Compared to non-smokers, smokers, on average, had 47% lower SPARC H-scores (p=0.05) in the epithelial tissues of their CRC tumors. Individuals with incomes higher than $74,999/year had 33% higher SPARC H-scores (p=0.04) in their CRC tumor non-epithelial tissues than those who earned less than $74 999/year. Females had 2.8-fold greater PD-L1 H-scores (p=0.005) in their CRC tumor epithelial tissues than males. Compared to those without a history of CRC screening, those with a history of CRC screening had 2.2 and 2.0-fold greater PD-L1 H-scores in their epithelial and non-epithelial CRC tumor tissues, respectively. Conclusion: Larger-scale studies with prognostic data are needed to confirm our findings, but our results suggest that differences in the expression of SPARC and PDL-1 may contribute to the previously observed impacts of some demographic, healthy history, and lifestyle factors on CRC prognosis. Citation Format: Umaimah Zanif, Isabella Tai, Stephen Yip, Sindy Babinszky, Katy Milne, Peter Watson, Rachel Murphy, Parveen Bhatti. Demographic, health history, and lifestyle factors in association with biomarkers of colorectal cancer prognosis: A pilot study [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 3419.

Abstract 6562: Comprehensive liquid biopsy: Multi-analyte evaluation of cellular and plasma components of blood in prostate cancer from a single blood collection tube

Abstract Background Liquid biopsy samples offer a non-invasive method for investigating drug targets and biomarkers in solid tumors. In this study, we describe a comprehensive liquid biopsy analysis of whole blood to identify circulating tumor cells (CTCs), large extracellular vesicles and CTC fragments, and CTC-white blood cell hybrids; quantify protein biomarker expression on CTCs; perform targeted mutation profiling on CTCs and cell-free DNA (cfDNA) from plasma; and analyze protein expression on white blood cells (WBCs) from a single 7.5 mL blood sample. This array of tests was applied to blood samples from patients with Stage IV prostate cancer to demonstrate clinical feasibility. Methods A novel dual biomarker CTC assay was developed to measure protein expression of PSMA and ARv7 on CTCs from stage IV prostate cancer patients. Nucleated cells from clinical samples were processed to microscope slides using AccuCyte®, an unbiased, density-based separation method that also allows for plasma collection for downstream analysis. Slides were fixed and stained with antibodies to cytokeratin, EpCAM, and CD45 to detect CTCs and exclude WBCs, and with PSMA and ARv7 to evaluate protein biomarker expression on identified CTCs. The slides were imaged with the CyteFinder® automated immunofluorescence scanning microscope that identifies CTCs for confirmation by trained reviewers and quantitatively measures protein mean fluorescence intensity (MFI) on any cells detected on the slides (CTCs, CTC-WBC hybrids, large extracellular vesicles and CTC fragments and WBCs). Individual CTCs and control pools of WBCs from clinical samples with at least 4 CTCs were picked using CytePicker®, a needle-based system used to isolate single cells. cfDNA was isolated from plasma removed during the AccuCyte® process using a QIAamp MinElute ccfDNA kit. Picked CTCs, WBC pools, and isolated ctDNA were sequenced using the OncoZoom Cancer HotSpot panel from Paragon Genomics. Results Nine progressing Stage IV prostate cancer patient blood samples were stained with a novel PSMA/ARv7 dual biomarker assay. CTCs were identified in all clinical samples (median 4, range 1 - 384). PSMA positivity in clinical samples ranged from 0% to 75%, and ARv7 positivity ranged from 33% to 100%, and. Additional analysis using QuPath was performed to determine PSMA/ARv7 protein expression on WBCs and CTC fragments. ctDNA analysis from 5 individual samples was compared to sequencing results from individual CTCs from the same samples. Conclusions Using a single 7.5 mL blood liquid biopsy, we can measure protein expression on enumerated CTCs and quantify these same protein biomarkers on WBCs and CTC fragments/oncosomes, determine the genetic makeup of the tumor through the sequencing of cfDNA, and monitor genetic mutations in intact CTCs in circulation. Citation Format: Jon Ladd, Erin Bayer, Brock Bartels, Arista Tischner, Rachel Ponting, Eric Kaldjian, Arturo Ramirez. Comprehensive liquid biopsy: Multi-analyte evaluation of cellular and plasma components of blood in prostate cancer from a single blood collection tube [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 6562.

Abstract 7001: Profiling the CpG methylation patterns of Epstein-Barr virus DNA in lymphoma patients from Ethiopia

Abstract Introduction: Epstein-Barr virus (EBV) is a tumor virus associated with various malignancies, driven by genetic mutations and epigenetic alterations, including DNA methylation. Abnormal CpG methylation holds promise as a diagnostic and therapeutic biomarker for EBV-associated tumors. However, the understanding of EBV's epigenetic mechanisms remain limited. Determining the methylation profile of EBV is crucial for gaining insights into the pathogenesis of EBV-associated tumors, developing diagnostic biomarkers, and exploring potential therapeutic strategies. Therefore, our study aimed to assess the CpG methylation profile of EBV DNA in lymphoma patients from Ethiopia. Methods: This study enrolled 115 lymphoma patients from Tikur Anbessa Specialized Hospital in Addis Ababa, Ethiopia. Plasma and formalin-fixed paraffin-embedded blocks were collected from the participants, and isolation of DNA was performed from these samples. The methylation analysis was performed using the methylation-iPLEX assay. iPLEX capture and extension primers were designed to amplify and target EBV CpGs from bisulfite-converted DNA sequences. Ethical approval was also obtained from respected institutions. Results: Among the 115 participants, 65.2% (n = 75) were male patients. The largest proportion (n = 35, 30.4%) fell within the 41-60 age group. Non-Hodgkin lymphoma (NHL) was diagnosed in 96 patients, while 19 had Hodgkin lymphoma (HL). In the NHL group, the majority (n = 27, 28.1%) were classified as diffuse large cell lymphoma, followed by follicular lymphoma (n = 24, 25%). Out of the different EBV genome methylation sites, we have identified 24 EBV genes to assess the methylation status of the EBV genome. Average methylation levels of these genes were ranged from 45% to 50%. Notably, the HL group exhibited significant heterogeneity in methylation levels, while the CpG methylation status of EBV genes in NHL subtypes demonstrated a consistent pattern. A significant proportion of our samples exhibited methylation loss in the lytic gene BZLF1 and at the origin of replication associated with lytic replication. Conclusions: This study presents the first data from East Africa, shedding light on the EBV DNA methylation status in a diverse group of lymphoma patients. Further investigations in different locations are necessary to elucidate the impact of EBV DNA methylation on tumor progression. Citation Format: Seifegebriel T. Feleke, Kidist Z. Shita, Abdulaziz A. Sherif, Fisihatsion T. Woldegebriel, Christoph Weigel, Elshafa H. Ahmed, Tamrat A. Zeleke, Robert A. Baiocchi. Profiling the CpG methylation patterns of Epstein-Barr virus DNA in lymphoma patients from Ethiopia [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 7001.

Abstract 1525: Integration of high-plex tumor-Immune phenotyping and checkpoint interactions for deeper spatial characterization of human cancer tissues

Abstract Background: Immune evasion is a key cancer hallmark, and one of the primary mechanisms is the PD-1/PD-L1 checkpoint axis. While immunotherapies that target these interactions have reshaped cancer treatment, the variable efficacy in patients is not fully understood. Due to the weak correlation between PD-1/PD-L1 expression measured by single-plex assays and observed clinical outcomes, there is a need to understand protein interactions at the cellular and subcellular level. Proximity Ligation Assays, detecting spatial interactions between ligand-receptor targets, provide insights into the activation of signaling pathways. Coupled with high-plex spatial phenotyping with tumor and immune profiling biomarkers, the integration of cellular and functional information will be beneficial for a deeper characterization of the tumor microenvironment (TME), understanding immune responses, and identifying spatial signatures for patient stratification and targeted treatment strategies. Methods: In this study, we phenotyped biopsies from head and neck cancer patients enrolled in immune checkpoint inhibitor therapies. We integrated Naveni® PD-1/PD-L1 proximity ligation assays and a customizable high-plex PhenoCode™ Signature Panel (CD3ε/CD8/CD20/CD68/PanCK) for high-throughput profiling of the TME utilizing the PhenoImager® HT 2.0 platform. Comprehensive bioinformatic analyses were conducted for whole-slide segmentation, identifying cellular phenotypes, spatial neighborhoods, functional interactions, and distinct spatial signatures via the open-source image analysis software QuPath. Results: Our analyses revealed key differences in the localization of the PD-1/PD-L1 interactions within the TME of head and neck cancers. Areas of PD-1/PD-L1 interactions are associated with immune cell types on the periphery of the tumor and some within the tumor-infiltrating lymphocytes. The PhenoCode Signature panels helped resolve the localization of PD-1/PD-L1 interactions to immune cell types within the TME and provided a dual workflow for spatial co-localization of interacting receptor/ligand interactions and cell phenotypes within the TME. Conclusions: By combining spatial immune profiling with Akoya’s PhenoCode Signature panels and protein-protein interaction data from Navinci’s Naveni® PD-1/PD-L1 assay, deep correlative insights of the TME can be applied to improve predictions of clinical outcomes. This innovative approach enriches our comprehension of underlying mechanisms and stands as a promising tool for refining patient selection and optimizing treatment outcomes in immunotherapy. Citation Format: Sara Bodbin, Ning Ma, Aditya Pratapa, Nadya Nikulina, James Monkman, Niyati Jhaveri, Hampus Elofsson, Subham Basu, Agata Zieba-Wicher, Arutha Kulasinghe. Integration of high-plex tumor-Immune phenotyping and checkpoint interactions for deeper spatial characterization of human cancer 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 1525.

Abstract 7493: Real-time monitoring of CTC number, biomarker expression, and kinetics as prognostic and predictive markers in patients with GI malignancies

Abstract Background: Most of the utility in the clinic regarding liquid biopsies has been around circulating tumor DNA (ctDNA). ctDNA analysis provides valuable insight into mutational burden and therapeutic targets, but the speed and cost of analysis are prohibitive especially when it comes to serial testing. Using a cohort of patients with advanced or metastatic gastrointestinal (GI) cancers, we herein show the feasibility of using circulating tumor cell (CTC) enumeration, biomarker analysis, and kinetics as complementary to or as an alternative to ctDNA testing. Methods: Using the RareCyte platform, nucleated cells from blood were collected, spread on slides, stained, and imaged with CyteFinder® for CTC identification (CK/EpCAM+, CD45-) and quantification of biomarkers (PD-L1/HER2 or Ki67/EGFR). CTC enumeration (CLIA-accredited CTC test) and biomarker status for each patient were tracked over time and compared with ctDNA mutational analysis and tumor burden. Results: CTCs were detected in 60/70 samples (86%) and in 36/38 unique patients (95%). On average, more CTCs were detected in baseline samples from colorectal cancer patients compared to other subtypes (Table 1). Moreover, multiple patients showed pronounced changes in CTC number that correlated with treatment response, as well as strong correlation between CTC and tissue biomarker expression e.g. HER2. Rapid decline and/or CTC clearance was seen as early as a few days into starting effective systemic therapy. The average turnaround time for CTC testing was 5-7 days. Table 1. CTC values in initial baseline blood draw sample Gastrointestinal cancer subtype # of patients Average # of CTCs per 7.5mL blood Median # of CTCs per 7.5mL blood Minimum # of CTCs per 7.5mL blood Maximum # of CTCs per 7.5mL blood Colorectal carcinoma 27 84 3 0 1378 Cholangiocarcinoma 3 8 3 1 23 Pancreatic cancer 3 2 2 0 3 Hepatocellular carcinoma 2 4 5 0 10 Gallbladder cancer 1 6 6 3 8 Appendix cancer 1 2 2 1 3 Anal cancer 1 0 0 0 0 Conclusions: Our study emphasizes that real-time monitoring of CTCs is complementary to traditional tumor burden monitoring via imaging and ctDNA analysis. CTCs offer multiple unique advantages vs ctDNA including early response assessment within days of initiating therapy, a substantial decrease in cost of serial testing, and the ability to assess clinically relevant cell surface protein biomarkers e.g. HER2 and PD-L1. Citation Format: Erin G. Bayer, Brock M. Bartels, Rachel N. Ponting, Areeb Lutfi, Maaz K. Afghan, Arturo B. Ramirez, Pashtoon M. Kasi. Real-time monitoring of CTC number, biomarker expression, and kinetics as prognostic and predictive markers in patients with GI malignancies [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 7493.

Abstract 2551: Harness the power of real-world-data for oncology target and biomarker research: A case study by applying clinic-genomics data for 2,659 lung cancer patients and beyond

Abstract Randomized controlled trials (RCTs) are the gold standard for evaluating drug safety and efficacy in controlled settings, but they have limited generalizability due to their focus on selective and homogeneous populations. Real-world-data (RWD), collected from larger and more varied patient populations, can address inherent limitations of RCTs and aid in clinical trial design and drug approval. However, with the challenges of RWD, unlocking its full potential for tumor target and biomarker identification and validation demands innovative analytical approaches. Here we present RWD analyses of ConcertAI® electronic health records (EHR) linked with Caris Lab data for 2,659 lung cancer patients. Comprehensive genomics analyses incorporate WES and RNA-seq data, coupled with rich clinical EHR data. By integrating clinical and genomics data, we showcase the potential of harnessing RWD as follows: (1) we investigated genomic alterations across five histology groups (adenocarcinoma, squamous, large cell, small cell lung cancer [SCLC], neuroendocrine [NE] lung cancer). Notably, TP53 and LRP1B mutations were prevalent across all groups. LRP1B mutations correlated with higher tumor mutation burden, indicative of a favorable response to immunotherapy. Biallelic TP53 and RB1 inactivation was predominant in SCLC and NE lung tumors. The five histological groups exhibit distinct expression profiles, reflecting tumor intrinsic characteristics. Most immune gene signature scores were significantly lower in SCLC and NE tumors, aligned with that they are cold tumors with immune resistance, except CD56-centered NK and neuroendocrine gene signatures; (2) we analyzed patient treatment patterns and persistence by line of therapy. Among the 206 NSCLC patients with clinically actionable EGFR mutations, 143 received targeted therapy during their treatment courses (69.4%). Time to treatment discontinuation (TTD) was used as a surrogate clinical outcome endpoint. TTD was significantly longer when TKI was the first line treatment compared to later lines (p = 0.01), while the trend is opposite for ICI where TTD is significantly shorter in the 1st line setting (p = 0.025); (3) we highlight the unique potential of leveraging H&E imaging modality in such RWD. In summary, we successfully identified unique molecular signatures among various lung cancer histological groups, pinpointed distinct subpopulations within lung adenocarcinoma and squamous tumors linked to their immune phenotypes, and investigated the different patient treatment patterns and outcomes, facilitating personalized medicine. In the broader context of our work, we have developed a framework for harnessing various data modalities (clinical, multi-omics, imaging) within AbbVie's oncology RWD realm, enhancing the discovery and validation of new oncology targets and biomarkers. Citation Format: Si Wu, Weilong Zhao, Christy Choi, Mona Cai, Peter Ansell, Alexander Liede, Rong Chen, Xi Zhao, Josue Samayoa. Harness the power of real-world-data for oncology target and biomarker research: A case study by applying clinic-genomics data for 2,659 lung cancer patients and beyond [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 2551.

Abstract 176: Stearic acid induces pro-inflammatory macrophage response important for lung cancer development

Abstract Background Survival is improved with early detection and treatment initiation in patients with lung cancer (LC) emphasizing the importance of tumor initiation and biomarker development in individuals at high risk for developing LC and those with early-stage LC. Recent studies suggest that immunologic and metabolic changes within the microenvironment are pivotal for tumor formation. We recently demonstrated that in patients with resectable, early-stage LC, elevated levels of stearic acid (SA), a long chain fatty acid, and macrophage inflammatory protein 1β (MIP-1β/CCL4) were predictive of tumor affected lung lobes. Therefore, we hypothesize that SA promotes LC initiation through the activation of macrophages (MΦ) and production of proinflammatory cytokines like CCL4. Methods and Results: We performed untargeted metabolomics utilizing LC-MS from the plasma of patients with various stages of LC and found elevated levels of SA in patients with early-stage LC. To further study the mechanistic role of SA in tumorigenesis, cell lines including immortalized lung epithelial, LC cells, and immune (MΦ and T) cells were treated with SA. We found that physiological concentrations of SA did not affect cellular viability. However, in MΦ, SA induced expression of inflammatory (IL6, iNOS), and immunomodulatory (Arg1, CD206) genes suggesting a role for SA in promoting a pro-tumorigenic immunologic state. Additionally, analysis of the secretome from SA stimulated MΦ using single cell proteomic analysis (Isolight, Bruker Cellular Analysis, Inc), indicated a significant enrichment of polyfunctional MΦs with enhanced secretion of enriched effector and stimulatory cytokines. Furthermore, conditioned media derived from SA stimulated MΦ led to increased proliferation, as well as anchorage independent growth, of BEAS2B immortalized lung epithelial cells. Conclusion: Our data demonstrates plasma levels of SA are increased in early-stage compared to late-stage patients with LC. This observation corresponds to our prior data demonstrating enrichment of SA in the tumor affected lobes of patients with early-stage LC. Recent studies demonstrating the induction of inflammatory responses through MΦ activation in obese patients by circulating SA in blood corroborates our observations as well. Our data suggests that the SA effect on MΦ, is critical in LC initiation not only increasing proliferation but also induction of neoplastic transformation of immortalized lung epithelial cells. Furthermore, our data indicates that blood plasma levels of SA, a fatty acid understudied in tumor biology, could also be exploited as a potential biomarker for LC development in individuals at high-risk for LC development as well as those patients with early-stage disease. Citation Format: Amrita Roy, Martin Davis, Samuel Weinberg, Apurva Mallisetty, Alicia Hulbert, Frank D. Weinberg. Stearic acid induces pro-inflammatory macrophage response important for lung cancer 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 176.

Abstract 5943: Development of a SMART theranostic agent for precision pancreatic cancer therapeutics

Abstract Pancreatic cancer is predicted to emerge as the second leading cause of cancer-related deaths in the United States by 2030. Pancreatic ductal adenocarcinoma (PDAC) - the most common form of pancreatic cancer - is often diagnosed as metastatic disease and has demonstrated the least improvement in overall survival over the last three decades with incidence rising by 0.5% to 1.0% per year due in part to lack of effective and tumor-selective treatment strategies. One approach to reduce host toxicity is the development of novel molecules and innovative therapeutic approaches that are nontoxic to normal cells but can be activated only under tumor-specific conditions for lethality, which we coined as SMART (Selective Method of Activation for Response in Tumors) therapeutic agents. We utilized explicit properties and biomarkers present in PDAC tumors but not in normal tissues to develop a SMART DNA-damaging anti-cancer agent with both therapeutic and diagnostic (theranostic) activities. We evaluated the tumoricidal effect of our SMART agent using long-term survival assays in PDAC cell lines and 3D co-culture spheroids, as well as in tumor xenograft model studies in mice. We also tested the ability of our SMART agent to treat, detect/diagnose (via click chemistry), and identify critical resistance mechanisms (via proteomics) as a single agent or as a chemosensitizer with predictive tumor biomarkers for tumor-selective therapeutic response. We found that our SMART small molecule induces tumor-selective lethal effects as a monotherapy or in combination with DNA repair inhibitors or small molecules known to generate hydrogen peroxide (H2O2) in a tumor-selective manner for activation. Using “click” chemistry, we detected and quantified the incorporation of our SMART small molecule as a DNA-damaging agent via flow cytometry that correlated with therapeutic response, which is a feature that could facilitate the stratification, treatment monitoring, and management of patients with pancreatic cancers. We also found that our SMART agent is less toxic and more effective as a monotherapy than cisplatin in PDAC cell line-derived xenograft studies in mice. Overall, our novel SMART theranostic agent could provide a significant advancement as they are preferentially activated under tumor-specific conditions to induce tumor-selective therapeutic response. Furthermore, the diagnostic component our SMART agent could provide oncologists with essential information to make rapid clinical decisions on treatment strategies. Our SMART agent is also remarkably versatile as it can be utilized as a chemosensitizer or as a chemical probe to identify targetable vulnerabilities to potentiate its therapeutic effects at lower doses. Citation Format: Edward A. Motea, Jarrett J. Smith, Oluwasijibomi Ketiku. Development of a SMART theranostic agent for precision pancreatic cancer therapeutics [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 5943.