Digital Spatial Profiling Research Articles

#1169 Class-specific gene expression profiling of glomerulus of lupus nephritis by spatial transcriptomics

Abstract Background and Aims Lupus nephritis exhibit various clinical features and subclassifications. Subclassification-specific alteration of transcriptomic profile of lupus nephritis needs additional study which may provide new insights regarding the subclass-specific pathophysiologic mechanism. Method Spatial transcriptomic profiling was conducted using GeoMx Digital Spatial Profiler on formalin-fixed paraffin-embedded kidney biopsy specimens obtained from control (n = 7), LN class I to V (n = 24). We also profiled native kidney primary glomerulonephritis (e.g. anti-PLA2R-associated MN) as additional disease control group. Subclass-specific transcriptomic alteration of glomerulus was compared between the subclasses and primary glomerulonephritis cases. Gene Ontology (GO) terms for DEGs were annotated using the ToppGene suite. Results We first focused on the glomerular transcriptomic alteration in class IV lupus nephritis, which was the most active form with high degree of proteinuria. We found 104 upregulated DEGs and 166 downregulated DEGs which were specifically different in the class IV lupus nephritis cases but not in other subclasses of the disease. The upregulated GO terms included interleukin 10 receptor activity, T cell activation, leukocyte activation, and vesicle membrane. On the other hand, the downregulated DEGs were mostly annotated with GO terms of double-stranded DNA binding domain. In our analysis regarding class V lupus nephritis, total of 128 DEGs were downregulated in class V LN compared to MN. These genes were also downregulated in class V LN when compared to control samples, while no significant expression differences were observed in other LN classes compared to controls. Eleven of 128 downregulated DEGs were annotated with biological process GO terms related to Golgi vesicle transport. Regarding cellular component GO terms, Golgi apparatus (30/128 DEGs), endoplasmic reticulum (ER) membrane (19/128 DEGs), and ER-Golgi intermediate compartment (6/128 DEGs) were among the annotated GO terms associated with the DEGs. DEGs in annotation included GOLGA3, TMED7, BET1L, and RAB10. Conclusion We profiled the class-specific transcriptomic changes in glomerulus of lupus nephritis. Class IV LN was associated upregulation of interleukin 10-mediated inflammatory pathway and downregulation of double stranded-DNA binding domain. The ER-Golgi network and related molecular pathway may be involved in the distinct pathogenesis and clinical features of class V LN. The findings provide novel view of the class-specific pathophysiologic mechanism of lupus nephritis.

HLA-A+ tertiary lymphoid structures with reactivated tumor infiltrating lymphocytes are associated with a positive immunotherapy response in esophageal squamous cell carcinoma.

Immune checkpoint blockade (ICB) therapy provides remarkable clinical benefits for multiple cancer types. However, the overall response rate to ICB therapy remains low in esophageal squamous cell carcinoma (ESCC). This study aimed to identify biomarkers of ICB therapy for ESCC and interrogate its potential clinical relevance. We investigated gene expression in 42 treatment-naïve ESCC tumor tissues and identified differentially expressed genes, tumor-infiltrating lymphocytes and immune-related genes signatures associated with differential immunotherapy responses. We systematically assessed the tumor microenvironment using the NanoString GeoMx digital spatial profiler, single-cell RNA-seq and multiplex immunohistochemistry in ESCC. Finally, we evaluated the associations between HLA-A-positive tertiary lymphoid structures (TLSs) and patients' responses to ICB in 60 ESCC patients. Tumor infiltrating B lymphocytes and several immune-related gene signatures, such as the antigen presenting machinery (APM) signature, are significantly elevated in ICB treatment responders. Multiplex immunohistochemistry identified the presence of HLA-A+ TLSs and showed that TLS-resident cells increasingly express HLA-A as TLSs mature. Most TLS-resident HLA-A+ cells are tumor-infiltrating T (TIL-T) or tumor-infiltrating B (TIL-B) lymphocytes. Digital spatial profiling of spatially distinct TIL-T lymphocytes and single-cell RNA-seq data from 60 ESCC tumor tissues revealed that CXCL13-expressing exhausted TIL-Ts inside TLSs are reactivated with elevated expression of the APM signature as TLSs mature. Finally, we demonstrated that HLA-A+ TLSs and their major cellular components, TIL-Ts and TIL-Bs, are associated with a clinical benefit from ICB treatment for ESCC. HLA-A+ TLSs are present in ESCC tumor tissues. TLS-resident TIL-Ts with elevated expression of the APM signature may be reactivated. HLA-A+ TLSs and their major cellular components, TIL-Ts and TIL-Bs, may serve as biomarkers for ICB-treated ESCC patients.

Topographic analysis of pancreatic cancer by TMA and digital spatial profiling reveals biological complexity with potential therapeutic implications

Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal human malignancies. Tissue microarrays (TMA) are an established method of high throughput biomarker interrogation in tissues but may not capture histological features of cancer with potential biological relevance. Topographic TMAs (T-TMAs) representing pathophysiological hallmarks of cancer were constructed from representative, retrospective PDAC diagnostic material, including 72 individual core tissue samples. The T-TMA was interrogated with tissue hybridization-based experiments to confirm the accuracy of the topographic sampling, expression of pro-tumourigenic and immune mediators of cancer, totalling more than 750 individual biomarker analyses. A custom designed Next Generation Sequencing (NGS) panel and a spatial distribution-specific transcriptomic evaluation were also employed. The morphological choice of the pathophysiological hallmarks of cancer was confirmed by protein-specific expression. Quantitative analysis identified topography-specific patterns of expression in the IDO/TGF-β axis; with a heterogeneous relationship of inflammation and desmoplasia across hallmark areas and a general but variable protein and gene expression of c-MET. NGS results highlighted underlying genetic heterogeneity within samples, which may have a confounding influence on the expression of a particular biomarker. T-TMAs, integrated with quantitative biomarker digital scoring, are useful tools to identify hallmark specific expression of biomarkers in pancreatic cancer.

Abstract PR004: Spatial proteomics and transcriptomics reveal an altered immune cell landscape in bladder cancer patients unresponsive to BCG treatment

Abstract Introduction: Patients with high-risk non-muscle invasive bladder cancer (NMIBC) are recommended treatment with Bacillus Calmette-Guérin (BCG). The therapeutic effect of BCG is highly dependent on the host immune system and the tumor microenvironment (TME). The cellular composition and the functional status of the TME have been shown to play crucial roles for treatment efficacy. However, much is still unknown regarding the cellular interactions and mechanisms of BCG. Using spatial proteomics and transcriptomics, we investigated the immune cell landscape in a cohort of BCG treated patients. Materials and methods: A total of 183 tumors from 111 patients with NMIBC treated with BCG were included on a tissue microarray (TMA). The TMA included paired pre- and post-BCG tumors. We analyzed the tumor tissue using Imaging Mass Cytometry (IMC; StandardBioTools) for simultaneous detection of 35 immune and tumor-related proteins at single cell resolution. Ilastik was used to generate probability maps and DeepCell Mesmer was used for cell segmentation. Markers were quantified for the mean intensity per cell. GeoMX Digital Spatial Profiling (DSP) was used for spatial proteomics and transcriptomics profiling of tumor and stromal areas, targeting 63 protein targets and whole transcriptome amplification, respectively. Results: We identified a total of 364,504 cells in the tumor tissue using IMC. After computing a neighborhood graph using the log normalised and z-scaled signal and embedding it using UMAP, leiden clustering was performed to detect communities of unique cell types by interrogating the presence of phenotypic markers. We identified major lineages such as macrophages, CD8 T cells, dendritic cells (DCs), NK cells and neutrophils in the TME of analyzed tumors. Specifically, we observed more CD8 T cells after BCG (p=0.015), especially in females (p=0.048). Females also had higher levels of DCs and macrophages after treatment compared to males (p=0.024 and p=0.048). Patients who progressed to MIBC after BCG had higher numbers of CD8 T cells and NK cells prior to BCG (p=0.039 and p=0.021). Prolonged exposure to interferons has been associated with immune evasion and tumor cell proliferation. In concordance, we found high pretreatment protein expression of IFNα and IFNγ in tumor regions from patients with a pronounced signature of CD8 T cell exhaustion after BCG treatment using GeoMX DSP proteomic analysis. Data analysis is currently ongoing, and additional results will be presented at the conference. Conclusion: The composition and functional status of the TME is associated with clinical and biological features such as immune cell abundance, CD8 T cell exhaustion, sex and progression. A greater understanding of the TME may help identify patients unresponsive to BCG earlier and improve the understanding of biological differences in tumor development and aggressiveness. This may ultimately improve patient outcomes. Citation Format: Trine Strandgaard, Tine Ginnerup Andreasen, Tessa Jane Divita, Liina Salminen, Sean Houghton, Kasper Thorsen, Iver Nordentoft, Iyinyeoluwa Okulate, Alexander Schmitz, Søren Riis Paludan, John Sfakianos, Amir Horowitz, Jørgen Bjerggaard Jensen, Lars Dyrskjøt. Spatial proteomics and transcriptomics reveal an altered immune cell landscape in bladder cancer patients unresponsive to BCG treatment [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr PR004.

Abstract PO3-14-01: Heterogeneity of tumor immune microenvironment to predict everolimus efficacy in premenopausal women with hormone receptor-positive/human epidermal growth factor receptor 2-negative adavanced breast cancer

Abstract Objective Everolimus (EVE), a mammalian target of rapamycin (mTOR) inhibitor, has been shown to prolong survival of patients with hormone receptor-positive/human epidermal growth factor receptor 2-negative (HR+/HER2-), advanced breast cancer (ABC) with endocrine resistance. Preclinical studies have suggested that mTOR is closely associated with the tumor immune microenvironment (TME). We aimed to explore the tumor heterogeneity of TME between patients with different response to everolimus (EVE), and identify potential markers to predict efficacy of EVE in premenopausal patients with HR+/HER2−, advanced breast cancer (ABC) suffering endocrine resistance. Methods Patients were divided into two groups according to the best response to EVE: the responsive subgroup (RS) and the non-responsive subgroup (NRS). Postoperative tumor tissue from patients who received EVE was collected for whole exome sequencing. Transcript abundance of 126 distinct tumor regions of interest (ROIs) were quantitated using digital spatial profiling, including 42 tumor cell zones (TCZs), 42 immune cell zones (ICZs), and 42 stroma cell zones (SCZs). Based on investigation in multiple discrete areas, differences in cell components, function and pathway, gene expression and immune cell infiltration between RS and NRS were investigated. Results Totally, 93 differentially expressed genes (DEGs) were identified in the ICZs, 174 DEGs in the TCZs, and 197 DEGs in the SCZs, using p< 0.05 and |log2FC >1| as the screening criterion. Among all the subgroup analyses on different ROIs, the statistical significance of PIP gene was the highest (ICZs: p=2.6E-12, TCZs: p=1.25E-20, SCZs: p=2.0E-18) in the comparison of RS and NRS. Moreover, we found that PIP was highly expressed in NRS and patients with a progression-free survival < 1 year. The receptor-legend analysis showed that, the intra-and inter-cellular communication in RS was mainly mediated by interaction between CCL-CCR family, while NRS mainly by COL family complex. Comparing all cell components extracted from each ROI, no statistical differences were found between RS and NRS, only a statistical trend in the SCZs (p=0.098). Further cell classification analysis showed fibroblasts highest in TCZs and SCZs, macrophages in ICZs. Compared to NRS, in TCZs, fibroblasts were significantly increased (p=0.01), and plasma cells (p=0.02) and neutrophils (p=0.03) were decreased in RS. In SCZs, the downregulated fibroblasts (p=0.04) and enhanced plasma cells (p=0.01) were observed in NRS. In ICZs, pDCs (p=0.048) and neutrophils (p=0.006) were significantly elevated in NRS compared with RS. Conclusion The utility of digital spatial gene expression profiling might provide some references to predict the efficacy of EVE in premenopausal patients with HR+/HER2- ABC with endocrine resistance. Citation Format: Yujing Tan, Fei Ma, Jiayu Wang, Pin Zhang, Binghe Xu, Liyan Xue, Ying Fan. Heterogeneity of tumor immune microenvironment to predict everolimus efficacy in premenopausal women with hormone receptor-positive/human epidermal growth factor receptor 2-negative adavanced breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-14-01.

Abstract PS03-03: The spatially resolved single-cell atlas of the tumor immune architecture revealed the central role of IFN-alpha and plasmacytoid dendritic cells in triple-negative breast cancer in the Mayo Clinic cohort and FinXX trial

Abstract Background: Multiple studies have confirmed the central role of preexisting immune response measured by stromal tumor-infiltrating lymphocytes (sTILs) in triple-negative breast cancer (TNBC). Emerging studies showed that not only the number of TILs but also the location of TILs is important. There are 3 distinct immune architectures described based on the amount and locations of TILs, namely immune enriched (IN), immune excluded (IE), and immune desert (ID). Here we evaluated outcomes and characteristics associated with each immune landscape. Methods: NanoString Digital Spatial Profiling (DSP) and CosMx, a spatial multi-omics single-cell imaging platform, were performed in 75 samples from the Mayo Clinic (MC) TNBC cohort (Leon-Ferre BCRT 2018). NanoString IO360 was performed in 114 samples from the FinXX trial ( NCT00114816) . Firstly, tumors with sTIL quantified by H&E ≤ 30% were classified as ID. The rest of the tumors with high sTIL > 30% were categorized according to the intratumoral CD8 protein expression by DSP, with IE having intratumoral CD8 in the lower median and IN having intratumoral CD8 in the upper median. Chi-square test, gene set enrichment, Cox regression, and Kaplan-Meier analysis were used. Differential expression listed as log 2-fold change (FC) was estimated from the linear mixed model with significance defined as two-sided p< 0.05. Results: ID is associated with low Ki67 < 5% (23.3% vs. 9.6% ID, p 0.02) as well as apocrine (11/13, 84.6%) and metaplastic histology (10/12, 83%). In both univariate and multivariate analysis, patients with IN had significantly improved recurrence-free survival (RFS) compared to those with ID (HR 0.37, 95%CI 0.18-0.74, p 0.005). Despite having high sTILs, IE had poor outcomes similar to ID (HR 0.84, 95%CI 0.36-1.98). Strikingly, we identified that IE patients had significantly lower plasmacytoid dendritic cells (pDCs) compared to IN (mean 0 vs. 0.26/100 tumor cells, 95%CI 0.08-0.43 , p 0.01). Using Gene Set Enrichment Analysis to evaluate differential hallmarks between IN and IE, we identified IF Nɑ and IFNγ (FDR < 0.001) responses as significantly enriched in IN group, consistent wi th the function of pDCs, which are a subset of dendritic cells specialized in secreting high levels of type I interferon. To validate this finding, we further evaluated the 11 leading edge gene IFNɑ signature in the FinXX trial. A high IFNɑ signature score was associated with significantly improved outcomes in the FinXX trial (HR 0.21, 95%CI 0.09-0.51 , p < 0.001). Similar findings were observed using Kaplan-Meier analysis in the FinXX trial with significantly improved RFS (p 0.0006) and overall survival (p 0.0001) in patients with high IFNɑ signature scores. Furthermore, we evaluated the differential gene expression unique to IN tumors in the Mayo cohort. Expressions of MHC class I and class II in tumor cells, including HLA-A, HLA-B, HLA-C, HLA-DRA, HLA-DRB1, HLA-DPA1, and HLA-E, were associated with IN and significantly improved outcomes (p < 0.05) compared to ID and IE. Conclusions: Highlighting the importance of spatial context, we identified that patients with IE tumors had poor outcomes despite having high TILs. Moreover, u sing an in-depth analysis with spatially defined context, we identified the central role of pDC and the significance of IF Nɑ in TNBC. Support: Breast Cancer Research Foundation, Mayo Clinic Breast Cancer SPORE (P50CA116201-17) W81XWH-15-1-0292, P50CA015083, R35CA253187 Citation Format: Saranya Chumsri, Yi Liu, Yaohua Ma, Jodi Carter, Mark Gregory, Sarah Church, Jason Reeves, Heather Ann Brauer, Sarah Warren, Heikki Joensuu, Edith Perez, Roberto Leon-Ferre, David Hillman, Judy Boughey, James Ingle, Krishna Kalari, Fergus Couch, Matthew Goetz, Keith Knutson, E. Thompson. The spatially resolved single-cell atlas of the tumor immune architecture revealed the central role of IFN-alpha and plasmacytoid dendritic cells in triple-negative breast cancer in the Mayo Clinic cohort and FinXX trial [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS03-03.

Abstract PO1-29-04: Spatial tumor microenvironment profiling identifies immune features that correlate with response to T-DXd treatment in patients with metastatic breast cancer

Abstract Objective: It is unclear which patients with metastatic breast cancer respond to the new antibody drug conjugate T-DXd treatment. Methods: We profiled 22 pre-T-DXd treatment metastatic tissue samples from patients using Nanostring GeoMX digital spatial profiler of tumor infiltrating immune cells and stroma components. Among the 22 metastatic samples, 10 were bone metastases 7 of the patients were defined as responder (R) and 3 were defined as non-responder (NR) to T-DXd treatment; 4 brain metastases with 2 R and 2 NR; 4 lymph node metastases with 2 R and 2 NR, and 3 liver metastases with all patients were NR to T-DXd. In each metastatic tissue section, 6-8 circular regions of interest (ROI) with 300µm diameter were selected by tumor epithepial marker (pan CK) and immune cells marker (CD45) throughout different areas of the tumor. The spatial quantification of 22 immune markers and 3 stroma elements (fibronectin, fibroblast activation protein, and smooth muscle actin) in each ROI was analyzed. Results: Based on the segmented CD45-positive cell numbers, a total of 144 ROIs were classified into high tumor-infiltrating immune ROIs (high-TIL, n=47) and low-TIL ROIs (n=97). Within the high-TIL ROIs, none immune markers showed significant difference in either the R or NR group across all metastasis sites (P >0.05, Figure 1). Within the low-TIL ROIs, several immune markers, including PD-L1, PD-1, CD3, CD56, CD20, CD14, CD11c, CTLA-4, CD45, and B2M (Beta-2-microglobulin, an antigen presentation marker) showed significant elevation in the R group than those in the NR group (P < 0.05, Figure 2). Other immune markers including CD4 and CD8 were not significantly different in the R vs. NR groups in the low-TIL ROIs. High Ki-67 was correlated with R in both high and low-TIL ROIs. None of the three stroma markers was associated to treatment response to T-DXd. Conclusions: Enrichment of PD-L1, PD-1, CD3, CD56, CD20, CD14, CD11c, CTLA-4, CD45, and B2M in the metastatic tumor sites favors the treatment response to T-DXd in patients with metastatic breast cancer. Our study provides novel evidence that immune-suppression is associated with patients’ response to T-DXd treatment, which may due to the unique mechanism of action of T-DXd. Citation Format: Hong Zhao, Matthew Vasquez, Jeffrey Zhang, Glori Das, Ji-Hoon Lee, Yuan Gao, Jilun Zhang, Xiaoxian Li, Jenny Chang, Stephen Wong. Spatial tumor microenvironment profiling identifies immune features that correlate with response to T-DXd treatment in patients with metastatic breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-29-04.

Abstract PS03-04: Tumor immune microenvironment modulates resistance to estrogen suppression in ER+ breast cancer

Abstract Despite major advances in the treatment of estrogen receptor positive (ER+) breast cancer (BC), advanced disease continues to be the main cause of death from this disease. The role of the tumor immune microenvironment (TIME) in the progression of ER+ BC and its response to treatment is not completely understood. The aim of this study was to elucidate the role the TIME in the response of ER+ tumors to estrogen deprivation (ED). We collected samples from 215 postmenopausal patients with stage I-III ER+ BC, treated with letrozole for 2-4 weeks, to induce ED. We used AQUA on pre-treatment biopsies and on-treatment surgical biopsies to assess ER, PR, HER2, and Ki67. Then, we categorized the patients’ response to ED based on the Ki67 score in on-treatment samples: ED-sensitive (ED-S) if natural log (ln) of the Ki67 score ≤1.0 or ≤2.7% Ki67+ cells vs. ED-resistant (ED-R) if ln ≥2.0 or ≥7.4% Ki67+ cells. Firstly, we assessed TIME composition by investigating stromal tumor-infiltrating lymphocytes (sTILs) in H&E-stained FFPE of on-treatment tumor sections. ED-R tumors exhibited a significantly higher stromal TILs score (p=0.0001) relative to ED-S tumors. We next prepared tissue microarrays from 227 (on-treatment) surgical sections and subjected them to cyclic immunofluorescence (CycIF) with 38 antibodies to examine their intra-tumoral immune cell infiltration. From each tumor core, we segmented single cells and labeled them as immune, cancer, or stromal cells based on expression of a set of markers. Briefly, cells that stained strongly for CD45 (leukocyte marker), and/or CD4 (T lymphocyte marker), or CD68 (macrophage marker) were labeled immune cells. CD45/CD4/CD68-negative cells were categorized as tumor if E-cadherin and/or cytokeratin-positive, or stromal cells if -negative. Next, we assessed cell specific spatial enrichment by quantifying the expression of immune markers in the area immediately adjacent to each tumor cell. Immune-suppressive T-reg (FOXP3+) cells were enriched in the ED-S tumors (p=0.0004), as well as PD1+ (exhausted) T cells (p=0.0004), and CD68+ cells (p < 0.0001) compared to ED-R tumors. ED-R tumors exhibited higher CD20+ B cells (p < 0.0001), higher CD8+ T cells (p=0.0329), in addition to higher CD45+ cells (p < 0.0001), compared to ED-S tumors. RNA-sequencing of the same surgical samples showed a higher T cells cytolytic score in ED-R relative to ED-S (p=0.0058), suggesting enhanced CD8+ T cells activity, in addition to their higher infiltration. We are currently analyzing letrozole-induced changes in TIME composition using Geomix digital spatial profiler in paired pre- and on-treatment biopsies from ED-R and ED-S tumors and will be presented at the meeting. Consistent with the CycIF findings, GSEA of hallmark gene signatures from bulk RNA-sequencing of treated tumors revealed that immune-related gene sets, such as “IFN α response”, “IFNɣ response”, and “allograft rejection” were upregulated in ED-R vs. ED-S cancers. ED-R tumors showed enrichment of CXCL9, CXCL10, and CXCL11 chemokines and their receptor, CXCR3. Publicly available datasets of patients with ER+ breast cancers showed that higher expression CXCL9 (HR 1.36; p=0.016), CXCL10 (HR 1.71; p< 0.0001), and CXCL11 (HR 1.5; p=0.0016) are predictive of shorter relapse-free survival on antiestrogen therapy. We are currently investigating whether these chemokines play a causal role in resistance to ED, and if this is phenocopied by co-cultures of ER+ BC cells and CD8+ T-cells. Conclusions ED-resistant tumors are enriched with stromal TILs and exhibit higher immune cell intra-tumoral infiltration and CD8+T cells cytolytic activity compared to ER+ tumors sensitive to estrogen suppression. In contrast, ED-S tumors showed a more immunosuppressed milieu. The role of CXCL9, CXCL10 and CXCL11 in inducing resistance to ED warrants further investigation. Citation Format: Fabiana Napolitano, Yunguan Wang, Dhivya Sudhan, Paula Gonzalez-Ericsson, Luigi Formisano, Lei Guo, M Rosario Chica-Parrado, Chang-Ching Lin, Kyung-Min Lee, Hongli Ma, Nathaniel Evans, Alberto Servetto, Saurabh Mendiratta, Spencer Barnes, Yisheng Fang, Lin Xu, Justin Balko, Gordon Mills, Marilyne Labrie, Ariella Hanker, Carlos Arteaga. Tumor immune microenvironment modulates resistance to estrogen suppression in ER+ breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS03-04.

Activin A signaling stimulates neutrophil activation and macrophage migration in pancreatitis

Acute Pancreatitis (AP) is associated with high mortality and current treatment options are limited to supportive care. We found that blockade of activin A (activin) in mice improves outcomes in two murine models of AP. To test the hypothesis that activin is produced early in response to pancreatitis and is maintained throughout disease progression to stimulate immune cells, we first performed digital spatial profiling (DSP) of human chronic pancreatitis (CP) patient tissue. Then, transwell migration assays using RAW264.7 mouse macrophages and qPCR analysis of “neutrophil-like” HL-60 cells were used for functional correlation. Immunofluorescence and western blots on cerulein-induced pancreatitis samples from pancreatic acinar cell-specific Kras knock-in (Ptf1aCreER™; LSL-KrasG12D) and functional WT Ptf1aCreER™ mouse lines mimicking AP and CP to allow for in vivo confirmation. Our data suggest activin promotes neutrophil and macrophage activation both in situ and in vitro, while pancreatic activin production is increased as early as 1 h in response to pancreatitis and is maintained throughout CP in vivo. Taken together, activin is produced early in response to pancreatitis and is maintained throughout disease progression to promote neutrophil and macrophage activation.

Multiplex Digital Spatial Profiling in Breast Cancer Research: State-of-the-Art Technologies and Applications across the Translational Science Spectrum.

While RNA sequencing and multi-omic approaches have significantly advanced cancer diagnosis and treatment, their limitation in preserving critical spatial information has been a notable drawback. This spatial context is essential for understanding cellular interactions and tissue dynamics. Multiplex digital spatial profiling (MDSP) technologies overcome this limitation by enabling the simultaneous analysis of transcriptome and proteome data within the intact spatial architecture of tissues. In breast cancer research, MDSP has emerged as a promising tool, revealing complex biological questions related to disease evolution, identifying biomarkers, and discovering drug targets. This review highlights the potential of MDSP to revolutionize clinical applications, ranging from risk assessment and diagnostics to prognostics, patient monitoring, and the customization of treatment strategies, including clinical trial guidance. We discuss the major MDSP techniques, their applications in breast cancer research, and their integration in clinical practice, addressing both their potential and current limitations. Emphasizing the strategic use of MDSP in risk stratification for women with benign breast disease, we also highlight its transformative potential in reshaping the landscape of breast cancer research and treatment.

Spatially Preserved Multi-Region Transcriptomic Subtyping and Biomarkers of Chemoimmunotherapy Outcome in Extensive-Stage Small Cell Lung Cancer.

Transcriptomic subtyping holds promise for personalized therapy in extensive-stage small cell lung cancer (ES-SCLC). In this study, we aimed to assess intratumoral transcriptomic subtype diversity and to identify biomarkers of long-term chemoimmunotherapy benefit in human ES-SCLC. We analyzed tumor samples from 58 patients with ES-SCLC enrolled in two multicenter single-arm phase IIIb studies evaluating frontline chemoimmunotherapy in Spain: n = 32 from the IMfirst trial and n = 26 from the CANTABRICO trial. We used the GeoMx Digital Spatial Profiler system to perform multi-region transcriptomic analysis. For subtype classification, we performed hierarchical clustering using the relative expression of ASCL1 (SCLC-A), NEUROD1 (SCLC-N), POU2F3 (SCLC-P), and YAP1 (SCLC-Y). Subtype distribution was found to be similar between bothcohorts, except for SCLC-P, which was not identified in the CANTABRICO_DSP cohort. A total of 44% of the patients in both cohorts had tumors with multiple coexisting transcriptional subtypes. Transcriptional subtypes or subtype heterogeneity was not associated with outcomes. Most potential targets did not show subtype-specific expression. Consistently in both cohorts, tumors from patients with long-term benefit (time to progression ≥12 months) contained an IFNγ-dominated mRNA profile, including enhanced capacity for antigen presentation. Hypoxia and glycolytic pathways were associated with resistance to chemoimmunotherapy. This work suggests that intratumoral heterogeneity, inconsistent association with outcome, and unclear subtype-specific target expression might be significant challenges for subtype-based precision oncology in SCLC. Preexisting IFNγ-driven immunity and mitochondrial metabolism seem to be correlates of long-term efficacy in this study, although the absence of a chemotherapy control arm precludes concluding that these are predictive features specific for immunotherapy.

Abstract P21: Single Cell Resolution Spatial Modeling Uncovers Survival-associated Phenotypes in Diffuse Large B Cell Lymphoma

Abstract Diffuse large B-cell lymphoma (DLBCL) is the most common aggressive lymphoma and overexpression of the oncogenes MYC, BCL2 and BCL6 impacts patient outcomes. We demonstrated using single-cell resolved analysis that cells with unique co-expression of high MYC and BCL2 but lacking BCL6 (M+2+6-) were consistently correlated with poor survival compared to other combinations. Here we present a follow-up study evaluating M+2+6- spatial patterns and their relationship to survival, tumour processes, and the immune microenvironment. We measured oncogene co-expression at single-cell resolution through multiplexed fluorescent immunohistochemistry (mfIHC) in four cohorts of DLBCL (n=449). Spatial point patterns were derived from multispectral images, upon which Gibbs modeling was applied. This analysis uncovered a ‘dispersed’ spatial phenotype exhibited by M+2+6- cells, which stratified DLBCL cohorts for survival. Bulk/single-cell transcriptomic analyses of DLBCL samples enriched with the ‘dispersed’ phenotype identified several genes, such as LAG3 and IFI27, that are implicated in migration, cell adhesion, and invasion- suggesting that this spatial phenotype is associated with tumour invasiveness. Single cell analysis revealed unique communication pathways IL10 and SEMA3 between this phenotype and immune cells. IL10 promotes aggressiveness and proliferation in DLBCL and SEMA3 and is a regulator of RAC1 that influences cell migration. Digital Spatial Profiling (DSP) analyses were also performed, applying the protein-based nCounter method (29 immune markers) to 110 DLBCL samples, and the Whole Transcriptome Atlas (WTA) panel (18,000 genes) to CD3+ enriched regions of 47 DLBCL samples. Analysis of patients enriched in the ‘dispersed’ phenotype revealed an immune cold microenvironment, enriched in Tregs and exhausted CD4+ and CD8+ T cells. Taken together, we postulate that the M+2+6- associated ‘dispersed’ spatial phenotype is associated with tumor cell invasiveness and an immune cold microenvironment composition, all contributing towards the poor prognosis associated with this spatial phenotype. Citation Format: Shruti Sridhar, Michal Marek Hoppe, Min Liu, Patrick Jaynes, Yanfen Peng, Sanjay De Mel, Limei Poon, Esther Hian Li Chan, Joanne Lee, Chandramouli Nagarajan, Nicholas F. Grigoropoulos, Soo-Yong Tan, Susan Swee-Shan Hue, Shaoying Li, Joseph D. Khoury, Pedro Farinha, Anja Mottok, David W. Scott, Gayatri Kumar, Kasthuri Kannan, Wee Joo Chng, Yen Lin Chee, Siok-Bian Ng, Claudio Tripodo, Anand D. Jeyasekharan. Single Cell Resolution Spatial Modeling Uncovers Survival-associated Phenotypes in Diffuse Large B Cell Lymphoma [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P21.

Abstract CT203: Multi-omic analysis of serial biopsies to inform biomarkers of sensitivity to olaparib and durvalumab in patients with metastatic BRCA-wildtype triple negative breast cancer (mTNBC)

Abstract Background: The phase 2 Adaptive Multi-Drug Treatment of Evolving Cancers (AMTEC) trial (NCT03801369) evaluated the efficacy of the combination of the PARP inhibitor Olaparib (Ola) and the PD-L1 inhibitor Durvalumab (Durva) in participants with BRCA-wildtype mTNBC. The combination was found to be effective with a median progression free survival (mPFS) of 5.5 months (AACR 2022). Here we report on updated biomarker analyses from paired biopsies (Bx) pre- and on-Ola therapy from 14 AMTEC participants. Methods: AMTEC participants undergo a pre-Ola Bx (Bx1), then one (28-day) cycle of Ola monotherapy with a repeat on-Ola Bx (Bx2) before adding Durva to Ola. Multi-omic profiling of DNA, RNA, and protein signals in Bx1 and Bx2 using Deep candidate gene sequencing, RNAseq, Nanostring Digital Spatial Profiling (DSP), and multiplex immunohistochemistry (mIHC) was correlated with clinical outcomes to identify predictors of Ola + Durva sensitivity, and adaptive resistance to PARPi therapy. Results: We identified over 30 biomarkers, with the optimal predictive value arising from Bx2. Key potential biomarkers were confirmed in an independent test set. Markers of good prognosis: • Basal Immune Activated (BLIA)/Basal Immune Suppressed (BLIS subtype) - A BLIA subtype on Bx2 was associated with a mPFS of 7.36 months compared to 1.71 months for BLIS/Luminal androgen receptor subtypes (p=0.001) • Multi-omic immune composite - A positive immune consensus signature (RNA, DSP, mIHC) on Bx2 was associated with a mPFS of 7.36 months compared to 2.29 months (p=0.005) • B cell activation signature - We developed a novel B-cell RNA activation signature that was highly predictive of response in Bx2, with mPFS of 8.54 and 1.04 months in signature-positive and signature-negative tumors, respectively (p=0.0004) Markers of poor prognosis: • AKT/MAPK pathway - AKT pathway gene mutations in Bx2 with concomitant protein phosphorylation of pathway members correlated with a shorter mPFS of 2.4 months compared to 7.13 months for no pathway mutation/activation (p=0.03). MAPK pathway protein phosphorylation in Bx2 was a negative prognostic factor, with mPFS of 2.17 months (p=0.004) • Angiogenesis - An upregulated Hallmark of Cancer angiogenesis RNA signature on Bx2 was associated with a shorter mPFS of 1.94 months compared to 7.95 months with no angiogenesis upregulation (p=0.0009) The following markers did not show significant association with survival outcomes on AMTEC: • PD-L1 positivity by IHC (defined as >1% Tumor Proportion Score, 22C3 antibody) • Tumor mutational burden • HRD, as measured by Rad51 foci or by mutations in HR pathway members Conclusions: Findings highlight the value of paired Bxs to identify predictive biomarkers of PARPi + immune checkpoint inhibitor sensitivity. The striking predictive value of the BLIA/BLIS signature warrants evaluation in a larger trial. Emerging resistance mechanisms justify AMTEC trial expansion to include PARPi + MEKi or PARPi + AKTi in biomarker selected patients, which is now in progress. Citation Format: Zahi I. Mitri, Allison L. Creason, Jayne M. Stommel, Daniel Bottomly, Jeong Youn Lim, SMMART Clinical Trials Program, Christopher L. Corless, Shannon McWeeney, Gordon B. Mills. Multi-omic analysis of serial biopsies to inform biomarkers of sensitivity to olaparib and durvalumab in patients with metastatic BRCA-wildtype triple negative breast cancer (mTNBC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr CT203.

Disease and brain region specific immune response profiles in neurodegenerative diseases with pure and mixed protein pathologies

The disease-specific accumulation of pathological proteins has long been the major focus of research in neurodegenerative diseases (ND), including Alzheimer’s disease (AD) and related dementias (RD), but the recent identification of a multitude of genetic risk factors for ND in immune-associated genes highlights the importance of immune processes in disease pathogenesis and progression. Studies in animal models have characterized the local immune response to disease-specific proteins in AD and ADRD, but due to the complexity of disease processes and the co-existence of multiple protein pathologies in human donor brains, the precise role of immune processes in ND is far from understood. To better characterize the interplay between different extracellular and intracellular protein pathologies and the brain’s intrinsic immune system in ND, we set out to comprehensively profile the local immune response in postmortem brain samples of individuals with “pure” beta-Amyloid and tau pathology (AD), “pure” α-Synuclein pathology in Lewy body diseases (LBD), as well as cases with Alzheimer’s disease neuropathological changes (ADNC) and Lewy body pathology (MIX). Combining immunohistochemical profiling of microglia and digital image analysis, along with deep immunophenotyping using gene expression profiling on the NanoString nCounter® platform and digital spatial profiling on the NanoString GeoMx® platform we identified a robust immune activation signature in AD brain samples. This signature is maintained in persons with mixed pathologies, irrespective of co-existence of AD pathology and Lewy body (LB) pathology, while LBD brain samples with “pure” LB pathology exhibit an attenuated and distinct immune signature. Our studies highlight disease- and brain region-specific immune response profiles to intracellular and extracellular protein pathologies and further underscore the complexity of neuroimmune interactions in ND.

Predictive and Prognostic Biomarkers in Patients With Mycosis Fungoides and Sézary Syndrome (BIO-MUSE): Protocol for a Translational Study.

Cutaneous T-cell lymphoma (CTCL) is a rare group of lymphomas that primarily affects the skin. Mycosis fungoides (MF) is the most common form of CTCL and Sézary syndrome (SS) is more infrequent. Early stages (IA-IIA) have a favorable prognosis, while advanced stages (IIB-IVB) have a worse prognosis. Around 25% of patients with early stages of the disease will progress to advanced stages. Malignant skin-infiltrating T-cells in CTCL are accompanied by infiltrates of nonmalignant T-cells and other immune cells that produce cytokines that modulate the inflammation. Skin infection, often with Staphylococcus aureus, is frequent in advanced stages and can lead to sepsis and death. S. aureus has also been reported to contribute to the progression of the disease. Previous reports indicate a shift from Th1 to Th2 cytokine production and dysfunction of the skin barrier in CTCL. Treatment response is highly variable and often unpredictable, and there is a need for new predictive and prognostic biomarkers. This prospective translational study aims to identify prognostic biomarkers in the blood and skin of patients with MF and SS. The Predictive and Prognostic Biomarkers in Patients With MF and SS (BIO-MUSE) study aims to recruit 120 adult patients with MF or SS and a control group of 20 healthy volunteers. The treatments will be given according to clinical routine. The sampling of each patient will be performed every 3 months for 3 years. The blood samples will be analyzed for lactate dehydrogenase, immunoglobulin E, interleukins, thymus and activation-regulated chemokine, and lymphocyte subpopulations. The lymphoma microenvironment will be investigated through digital spatial profiling and single-cell RNA sequencing. Microbiological sampling and analysis of skin barrier function will be performed. The life quality parameters will be evaluated. The results will be evaluated by the stage of the disease. Patient inclusion started in 2021 and is still ongoing in 2023, with 18 patients and 20 healthy controls enrolled. The publication of selected translational findings before the publication of the main results of the trial is accepted. This study aims to investigate blood and skin with a focus on immune cells and the microbiological environment to identify potential new prognostic biomarkers in MF and SS. ClinicalTrials.gov NCT04904146; https://www.clinicaltrials.gov/study/NCT04904146. DERR1-10.2196/55723.

Digital Spatial Profiling Identifies Distinct Molecular Signatures of Vascular Lesions in Pulmonary Arterial Hypertension.

Rationale: Idiopathic pulmonary arterial hypertension (IPAH) is characterized by extensive pulmonary vascular remodeling caused by plexiform and obliterative lesions, media hypertrophy, inflammatory cell infiltration, and alterations of the adventitia. Objective: We sought to test the hypothesis that microscopic IPAH vascular lesions express unique molecular profiles, which collectively are different from control pulmonary arteries. Methods: We used digital spatial transcriptomics to profile the genomewide differential transcriptomic signature of key pathological lesions (plexiform, obliterative, intima+media hypertrophy, and adventitia) in IPAH lungs (n = 11) and compared these data with the intima+media hypertrophy and adventitia of control pulmonary artery (n = 5). Measurements and Main Results: We detected 8,273 transcripts in the IPAH lesions and control lung pulmonary arteries. Plexiform lesions and IPAH adventitia exhibited the greatest number of differentially expressed genes when compared with intima+media hypertrophy and obliterative lesions. Plexiform lesions in IPAH showed enrichment for 1) genes associated with transforming growth factor β signaling and 2) mutated genes affecting the extracellular matrix and endothelial-mesenchymal transformation. Plexiform lesions and IPAH adventitia showed upregulation of genes involved in immune and IFN signaling, coagulation, and complement pathways. Cellular deconvolution indicated variability in the number of vascular and inflammatory cells between IPAH lesions, which underlies the differential transcript profiling. Conclusions: IPAH lesions express unique molecular transcript profiles enriched for pathways involving pathogenetic pathways, including genetic disease drivers, innate and acquired immunity, hypoxia sensing, and angiogenesis signaling. These data provide a rich molecular-structural framework in IPAH vascular lesions that inform novel biomarkers and therapeutic targets in this highly morbid disease.

270 Inducing Neural Maturation and Increasing Survival in SHH Medulloblastoma Using EZH2 Inhibition in a Mouse Model

INTRODUCTION: Medulloblastoma (MB) is the most common malignant pediatric brain tumor. Genetically, MB can be divided into four subgroups of which the SHH subtype histologically shows nodular architecture. Within this nodular architecture, there are islands of mature cells, with more abundant neuropil and a low proliferation rate, scattered among sheets of primitive cells. METHODS: We performed laser capture microdissection followed by whole transcriptome analysis, spatial transcriptomics using Digital Spatial Profiling, whole genome DNA methylation and ChIP-Seq analysis of mature and primitive areas from 8 medulloblastomas. We developed a genetically-engineered mouse model of SHH MB showing spontaneous maturation and lack of maturation with a conditional EZH2 genetic ablation or EZH2 overactivation respectively. Finally, we developed a fucoidan-based nanoparticle drug delivery across the blood brain barrier (BBB) for targeted molecular inhibition. RESULTS: Using whole transcriptome and DNA methylation analysis, we identified ∼120 differentially expressed genes between primitive and mature regions with enrichment for genes regulated by H3K4me3 and H3K27me3. ChIP-Seq analysis showed striking differences in H3K27me3 enrichment between primitive and mature medulloblastoma cells including at the EZH2 locus. Medulloblastoma specific EZH2 genetic ablation resulted in diffuse tumor cell differentiation and prolonged survival in mice (n = 10 per group, log-rank p = 0.01). Conversely, conditional EZH2 (Y641F) activation prevented medulloblastoma differentiation. A fucoidan-based nanoparticle successfully delivered the EZH2 inhibitor (EPZ-6438) across the murine BBB to achieve significant extension of mouse survival (median 70 days compared to 21 days in control mice; *p = 0.01, Mantel-Cox). CONCLUSIONS: Spontaneous maturation of medulloblastoma cells can be induced by inhibition of EZH2. Fucoidan-based nanoparticle delivery systems allows tumor specific targeted delivery across the BBB extending survival in mice.

Chronic villitis as a distinctive feature of placental injury in maternal SARS-CoV-2 infection

BackgroundSARS-CoV-2 infection during pregnancy is associated with increased risk of stillbirth, preeclampsia and preterm birth. However, this does not appear to be due to intrauterine fetal infection, as vertical transmission is rarely reported. There is a paucity of data regarding associated placental SARS-CoV-2 histopathology and their relationship to timing and severity of infection. ObjectiveTo determine if maternal SARS-CoV-2 infection is associated with specific patterns of placental injury and whether these findings differ by gestational age at time of infection or disease severity. Study DesignA retrospective cohort study was performed at University of California San Diego between 03/2020 to 02/2021. Placentas from pregnancies with a positive SARS-CoV-2 test were matched to two sets of controls: one set was time-matched by delivery date and sent to pathology for routine clinical indications, and the other was chosen from a cohort of placentas previously collected for research purposes without clinical indications for pathologic examination prior to the SARS-CoV-2 outbreak. Placental pathologic lesions were defined based on standard criteria and included maternal and fetal vascular malperfusion, and acute and chronic inflammatory lesions. Bivariate analysis was performed with independent Student’s T test and Pearson’s chi-square. Logistic regression was used to control for relevant covariates. Regions of SARS-CoV-2-associated villitis were further investigated using protein-based digital spatial profiling (DSP) assays on the GeoMx platform, validated by immunohistochemistry, and compared to cases of infectious villitis and villitis of unknown etiology. Differential expression analysis was performed to identify protein expression differences between these groups of villitis. ResultsWe included 272 SARS-CoV-2 positive cases, 272 time-matched controls, and 272 historical controls. The mean age of SARS-CoV-2 affected subjects was 30.1 ± 5.5 years and the majority were Hispanic (53.7%) and parous (65.7%). SARS-CoV-2 placentas demonstrated a higher frequency of the four major patterns of placental injury (all p<.001), compared to historical controls. SARS-CoV-2 placentas also showed a higher frequency of chronic villitis (CV) and severe CV (p=.03 for both) compared to time-matched controls, which remained significant after controlling for gestational age at delivery (aOR 1.52, 95% CI 1.01-2.28; aOR 2.12, 95% CI 1.16-3.88, respectively). DSP revealed programmed death-ligand 1 (PD-L1) to be increased in villitis-positive regions of the SARS-CoV-2 (logFC 0.47, adj p-value=0.002) and VUE (logFC 0.58, adj p-value=0.003) cases, but conversely decreased in villitis-positive regions of the infectious villitis group (log FC -1.40, adj p-value<0.001). ConclusionsCV appears to the most specific histopathological finding associated with SARS-CoV-2 maternal infection. CV involves damage to the vasculosyncytial membrane of the chorionic villi, involved in gas/nutrient exchange, suggesting potential mechanisms of placental (and perhaps neonatal) injury, even in the absence of vertical transmission. Surprisingly, changes in protein expression in SARS-CoV-2-associated villitis appear to be more similar to VUE rather than infectious villitis.

Human Plasma-Like Medium Activates Immune Elements in Glioma

INTRODUCTION: Glioma Surgically eXplanted Organoids (SXOs) are ex vivo three-dimensional models demonstrated to recapitulate the parental tumor microenvironment (TME). Human plasma-like medium (HPLM), a culture medium that mirrors physiologic nutrient conditions, has been found in other cancer subtypes to induce transcriptional differences in T-lymphocyte activation. We hypothesized that SXO culture in HPLM would maintain immune cell populations and induce physiologically relevant immune-modulatory pathways. METHODS: SXOs were established and cultured in conventional Glioma Organoid Complete medium (GOC) and transitioned to HPLM for 24 or 120 hours. Formalin-fixed paraffin-embedded samples were stained for tumor cells (GFAP), immune cells (CD45), and nucleic acid (SYTO-13) and analyzed using the Nanostring GeoMx™ Digital Spatial Profiler for spatial transcriptomics. Gene expression clustering profiles were conducted using GSEA and CIBERSORT. The gene expression differences of SXOs cultured in HPLM for 24 and 120 hours compared to those in GOC were analyzed by unpaired t-tests. RESULTS: Glioma SXOs retain diverse cell populations, with 20-30% of cells belonging to the TME. CD4+ T-cells were the most common (9.7 ± 1.0), followed by CD8+ T-cells (4.4 ± 0.6) and macrophages (3.1 ± 1.2). Following the transition to HPLM for 24 or 120 hours, there were no significant differences in tumor, immune, and stromal cell fractions. HPLM culture upregulated the immune response in SXOs, encompassing enhanced cytokine secretion, as well as improved adaptive and innate immune pathways. We particularly highlighted CD4+ T-cell activation (CD69+), Treg, and TGF-β signaling pathways as significantly increased. CONCLUSIONS: Here, we present that the culture of SXOs in physiologically similar media retains the heterogeneous TME and activates innate and adaptive immune signaling pathways. Culture in HPLM enables investigation of the glioma immune microenvironment, expanding the biological relevance of experimental results from in vitro SXO models.

Abstract 3770: Comparative analysis of single cell expression and digital spatial profiling in FFPE tumor tissues

Abstract Formalin Fixed Paraffin Embedded (FFPE) tissues are a staple in clinical diagnostics associated with solid tumor. Next Generation Sequencing (NGS) approaches characterize genomes, epigenomes, transcriptomes, and proteomes from a single sample source. FFPE blocks from several different tumor tissue types were serially sliced into FFPE slides. Individual slides were then utilized to explore the genome, epigenome, single cell RNA-Seq (scRNA-Seq), and Digital Spatial Profiling (DSP). Here we present a comparative analysis of two transcriptomic modalities within one FFPE tissue sample: fixed-cell scRNA-Seq of the transcriptome and digital spatial profiling of the whole transcriptome. Independent analysis of scRNA-Seq and DSP identified common trends as well as distinct differences within the same sample. Comparative analysis within sample between modalities identified statistically significant differences, driven by local tumor microenvironment, but also highlighted commonalities between methods. Cross sample comparisons showed striking differences, as indicated by tumor type. These studies highlight the strengths of each assay individually, as well as the power of a dual-assay approach for comprehensive analysis of the tumor and its microenvironment. Conclusions from this standalone analysis were further aggregated into downstream multiomics analyses, including proteomics analysis, illustrating the expanding landscape of information that can be extracted from FFPE derived tissue and the potential for novel discovery and diagnostic power integrating these complex data types holds. Citation Format: Anthony Moore, Andrea O'Hara, Pranay Vishwanath, Laure Turner, Haythem Latif, Chris Mozdzierz, Ginger Zhou. Comparative analysis of single cell expression and digital spatial profiling in FFPE 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 3770.