Abstract 615: Spatially resolved expression of T cell receptors elucidates spatial relationships between T cells, immune infiltration, and cancer-associated pathways

Spatial distribution of T cells is key in understanding the escape of tumors from immune surveillance via the adaptive immune response, including interactions between immune cells and the surrounding tumor microenvironment. T cells are critical to the adaptive immune response to pathogens and cancers, mediating an antigen-specific response through both specificity and diversity of T cell receptor (TCR) clonotypes. Many methods exist to determine specific clonotypes and overall TCR diversity present from bulk tissues or sorted cell populations; however, nearly all fail to capture spatial orientation and arrangement of T cells engaging with their microenvironment, and most require large amounts of starting material from precious samples. Here, we present a TCR expression profiling panel for the GeoMx® Digital Spatial Profiler that can be combined with the GeoMx Cancer Transcriptome Atlas (CTA) or Human Whole Transcriptome Atlas (WTA) on archival formalin-fixed paraffin embedded (FFPE) tissue specimens. This represents the first commercial spatial expression profiling assay for the simultaneous quantification of TCR constant, variable, and joining segments in situ.

We show reliable sensitivity and specificity (>90%) with respect to orthogonal sequencing and robust detection of TCR chains with evidence of clonal expansion and CD8 infiltration across tumor regions in colorectal cancer tissue. These events also corresponded to increased signatures of exhaustion from the T cells and suggest that the T cells resident in or near the tumor are tumor-specific and poised for activation via checkpoint blockade. Signaling pathways and tumor-specific signatures were also evaluated to look for mechanisms through which tumor cells respond to T cell infiltration. We further validated the performance of the TCR probe pool in cell pellet arrays with orthogonal TCR sequencing, tonsil and colorectal cancer tissues.

Together, the combination of our TCR add-on panel with the CTA or WTA illuminates T cell phenotypes, signaling pathways, population dynamics, and transcriptomic changes, yielding an unparalleled view of the T cell response in any context.

FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.

Citation Format: Katrina van Raay, Michelle Kriner, Jason Reeves, Erin Piazza, Hargita Kaplan, John Vivian, Francis Fernandez, Margaret Hoang, Joseph Beechem. Spatially resolved expression of T cell receptors elucidates spatial relationships between T cells, immune infiltration, and cancer-associated pathways [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 615.

A herd immunity to rubella virus in selected geographical regions

Since 2017, the incidence rate of rubella in the Russian Federation has been below 1 case per million total population. In addition, no circulation of endemic strains of the rubella virus is recorded evidencing about achieving infection elimination phase. In modern conditions, it is important to constantly monitor the level of herd immunity to the rubella virus to identify epidemically significant population groups, especially in countries lacking rubella vaccination or featured with insufficient disease control. Purpose: to study herd immunity to the rubella virus in selected countries in Eurasia and Africa. Materials and methods. Between 2018 and 2021, 15,594 samples of blood sera were tested for IgG and IgM antibodies to the rubella virus from subjects of different ages obtained from regional measles and rubella surveillance centers in the Northwestern Federal District (NWFD) of the Russian Federation, the Republic of Serbia, South Vietnam, and the Republic of Guinea. The Anti-Rubella Virus ELISA (IgМ) and Anti-Rubella Virus ELISA (IgG) (Euroimmun, Germany) test kits were used. Statistical data processing was carried out using the MS Excel, Prizm 5.0 (GraphPad Software Inc.), and Statistica 8.0 (StatSoft Inc.) software package. Results. During the observation period (20182020) the population seroprevalence of the to the rubella virus in the NWFD of the Russian Federation was 96.697.7% and fluctuated slightly both in separate years and among individual age groups evidencing about high coverage of rubella vaccination. In the Republic of Serbia conducting two-fold immunization against rubella the overall seroprevalence rate was lower than in the Russian Federation and comprising 86.8%. The minimum number of IgG-positive sera was recorded in the 24-year-old age group pointing to the shortcomings of routine vaccination. In South Vietnam, children aged 13 years (41.9%) predominated among those recovering from rubella, i.e. the age cohort that should be protected by vaccination at the age of 18 months. No rubella vaccination is carried out in Guinea. The total proportion of seropositive individuals was 75%; herd immunity to the rubella virus was established mainly among children and adolescents, reaching 90% only in the older age group. 30% of unprotected subjects of the most active reproductive age were identified among the females surveyed in Guinea. Conclusion. Insufficient herd immunity to the rubella virus, identified in a number of countries, may contribute to the maintenance of the infectious process and the spread of infection. Globalization contributes to the virus importation into regions being at the stage of measles and rubella elimination. The results obtained suggest about a need to continue efforts aimed at maintaining epidemiological wellbeing regarding rubella in diverse countries of the world.

Abstract 989: Spatial profiling of androgen receptor splice variant 7 transcriptional activity in prostate cancer metastases

Introduction: Androgen receptor splice variant 7 (AR-V7) is expressed in metastases from patients with castration resistant prostate cancer (CRPC) and shows a high level of inter- and intra-tumoral variability. However, the downstream activity generated by AR-V7 in tissue has not been shown. Whether AR-V7 is active in tissue or whether AR-V7 is a non-functioning biomarker with full-length AR is not known. To address this question, we constructed a tissue microarray (TMA) of 56 metastases from 27 patients with CRPC to analyze spatial gene expression using the GeoMx Digital Spatial Profiler. Immunostaining was performed to define epithelial, vascular, and stromal compartments. The stained tissues were then hybridized with barcoded tagged oligonucleotides targeting 2093 unique genes, which included those representing AR, AR-V cryptic exons, AR and neuroendocrine activity, and immune cell markers. One 500 um region of interest (ROI) was assessed per tissue core (approximately 1200 cells). A sequential section from the same TMA was then stained with AR-V7 and AR-C-terminal specific antibodies. ROIs for RNA and protein were selected to be similar between slides. In addition to DSP, each metastasis was assessed by RNA-seq on the bulk tissue.

Results: The most differentially expressed genes (FDR<0.05) based on association with AR-V7 staining were known downstream AR regulated genes including KLK2 and 3, FKBP5, NKX3.1, TMPRSS2, FASN, and TARP. Additionally, genes associated with proliferation and stemness, e.g., POLB, KRT1, SOX2, were significantly expressed. Since 93% of patients were on ADT at time of tissue collection and over 80% also had been treated with either abiraterone or enzalutamide, the increase in AR downstream genes would not be expected to occur from ligand activation of AR-FL. We also have previously shown that knock-down of AR-V7 in LNCaP95 cells results in loss of AR binding to AREs. In these metastases, then, activation of AR downstream genes would be a result of AR-V7 nuclear transport of AR-FL through AR-V7/AR-FL heterodimers or transcriptional activation by AR-V7 homodimers. Of further note, AR cryptic exons 1, 2, and 5 were also significantly expressed in AR-V7 positive ROIs (p< 0.0001). RNA-seq intron/exon junction reads were used to demonstrate that additional AR-Vs, most commonly AR-V9, were also expressed in tissues positive for AR-V7, suggesting that AR splicing is a common event in CRPC. Finally, expression of neuroendocrine (NE) genes INSM1 and TUBB2 were not expressed in AR-V7 positive ROIs (negatively correlated, p<0.001), indicating that AR-V7 and NE phenotypes cannot co-exist in the same cell.

Conclusion: AR-V7 continues to drive prostate cancer through activation of the AR-cistrome. Its expression is heterogenous in metastases along with NE cells, suggesting that in the presence of AR-V7 and NE markers, therapy needs to be directed at the N-terminus of AR and NE components.

Citation Format: Cynthia C. Sprenger, Ilsa Coleman, Michelle Kriner, Lauren Brady, Margaret Hoang, Martine Roudier, Mamatha Damodarasamy, Radhika Patel, Lawrence True, Peter Nelson, Michael Haffner, Stephen Plymate. Spatial profiling of androgen receptor splice variant 7 transcriptional activity in prostate cancer metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 989.

High-Plex Spatial RNA Profiling Reveals Cell Type‒Specific Biomarker Expression during Melanoma Development

Early diagnosis of melanoma is critical for improved survival. However, the biomarkers of early melanoma evolution and their origin within the tumor and its microenvironment, including the keratinocytes, are poorly defined. To address this, we used spatial transcript profiling that maintains the morphological tumor context to measure the expression of >1,000 RNAs in situ in patient-derived formalin-fixed, paraffin-embedded tissue sections in primary melanoma and melanocytic nevi. We profiled 134 regions of interest (each 200 μm in diameter) enriched in melanocytes, neighboring keratinocytes, or immune cells. This approach captured distinct expression patterns across cell types and tumor types during melanoma development. Unexpectedly, we discovered that S100A8 is expressed by keratinocytes within the tumor microenvironment during melanoma growth. Immunohistochemistry of 252 tumors showed prominent keratinocyte-derived S100A8 expression in melanoma but not in benign tumors and confirmed the same pattern for S100A8's binding partner S100A9, suggesting that injury to the epidermis may be an early and readily detectable indicator of melanoma development. Together, our results establish a framework for high-plex, spatial, and cell type‒specific resolution of gene expression in archival tissue applicable to the development of biomarkers and characterization of tumor microenvironment interactions in tumor evolution.

Spatial proteomic characterization of HER2-positive breast tumors through neoadjuvant therapy predicts response

The addition of HER2-targeted agents to neoadjuvant chemotherapy has dramatically improved pathological complete response (pCR) rates in early-stage, HER2-positive breast cancer. Nonetheless, up to 50% of patients have residual disease after treatment, while others are likely overtreated. Here, we performed multiplex spatial proteomic characterization of 122 samples from 57 HER2-positive breast tumors from the neoadjuvant TRIO-US B07 clinical trial sampled pre-treatment, after 14-21 d of HER2-targeted therapy and at surgery. We demonstrated that proteomic changes after a single cycle of HER2-targeted therapy aids the identification of tumors that ultimately undergo pCR, outperforming pre-treatment measures or transcriptomic changes. We further developed and validated a classifier that robustly predicted pCR using a single marker, CD45, measured on treatment, and showed that CD45-positive cell counts measured via conventional immunohistochemistry perform comparably. These results demonstrate robust biomarkers that can be used to enable the stratification of sensitive tumors early during neoadjuvant HER2-targeted therapy, with implications for tailoring subsequent therapy.

Inter- and intra-tumor heterogeneity of metastatic prostate cancer determined by digital spatial gene expression profiling

Metastatic prostate cancer (mPC) comprises a spectrum of diverse phenotypes. However, the extent of inter- and intra-tumor heterogeneity is not established. Here we use digital spatial profiling (DSP) technology to quantitate transcript and protein abundance in spatially-distinct regions of mPCs. By assessing multiple discrete areas across multiple metastases, we find a high level of intra-patient homogeneity with respect to tumor phenotype. However, there are notable exceptions including tumors comprised of regions with high and low androgen receptor (AR) and neuroendocrine activity. While the vast majority of metastases examined are devoid of significant inflammatory infiltrates and lack PD1, PD-L1 and CTLA4, the B7-H3/CD276 immune checkpoint protein is highly expressed, particularly in mPCs with high AR activity. Our results demonstrate the utility of DSP for accurately classifying tumor phenotype, assessing tumor heterogeneity, and identifying aspects of tumor biology involving the immunological composition of metastases.

The inter- and intra-tumor heterogeneity of metastatic prostate cancer (mPC) is underexplored. Here the authors use Digital Spatial Profiling to study gene and protein expression heterogeneity in 27 mPC patients, finding variation in associated pathways and potential immunotherapy targets.

The role of α-ketoglutarate and the hypoxia sensing pathway in the regulation of pancreatic β-cell function

Anaplerosis and the associated mitochondrial metabolite transporters generate unique cytosolic metabolic signaling molecules that can regulate insulin release from pancreatic β-cells. It has been shown that mitochondrial metabolites, transported by the citrate carrier (CIC), dicarboxylate carrier (DIC), oxoglutarate carrier (OGC), and mitochondrial pyruvate carrier (MPC) play a vital role in the regulation of glucose-stimulated insulin secretion (GSIS). Metabolomic studies on static and biphasic insulin secretion, suggests that several anaplerotic derived metabolites, including α-ketoglutarate (αKG), are strongly associated with nutrient regulated insulin secretion. Support for a role of αKG in the regulation of insulin secretion comes from studies looking at αKG dependent enzymes, including hypoxia-inducible factor-prolyl hydroxylases (PHDs) in clonal β-cells, and rodent and human islets. This review will focus on the possible link between defective anaplerotic-derived αKG, PHDs, and the development of type 2 diabetes (T2D).

Abstract 1688: High-throughput immune cell phenotyping using GeoMx DSP reveals Non-Small Cell Lung Cancers (NSCLC) are divided into distinct immunological subtypes

GeoMx DSP reveals NSCLCs are divided into distinct immunological subtypes, and local immune signatures of tumor sub-regions differentially affect neighboring tumor biology. Although cancer immunotherapy is considered an effective cancer-treatment option, means to measure its effect on sub-tumor regions are on demands. Despite its popularity, scRNA-seq only reveals cell populations found within a tissue but is mute on roles in tumor microenvironment (TME) like the impact of one cell type on another's behavior. To gain insights inaccessible to single-cell methods, we demonstrate a harmonized analysis of scRNA-seq and NanoString GeoMx™ data in lung tumors. This approach reveals the spatial distribution of cell populations defined via scRNA-seq, enabling rich descriptions of cells' responses to each other and to their locations within the tumor. GeoMx Digital Spatial Profiler (GeoMx DSP) is based on barcoding technology that enables spatially resolved, digital characterization of proteins or mRNA in a highly multiplexed (over 1,500-plex) assay. The oligonucleotide tags cleaved from discrete regions are quantitated by NGS, and counts are mapped back to tissue location, yielding a spatially-resolved digital profile of analyte abundance. To measure immune infiltrates in tumors, we employed machine learning techniques to classify gene sets of immune cell phenotypes and built an immune cell phenotyping panel for GeoMx DSP. Gene expression data from subregions of a tumor tissue were analyzed through this immune cell phenotyping pipeline to quantify immune infiltrates. We applied scRNA-seq to predefine the cell populations present in NSCLC tumors, and we applied the GeoMx platform to measure these populations across dozens of FFPE tumor sections. We found that there were three immunological subtypes; cold, myeloid enriched and lymphoid enriched groups. This finding was validated using traditional methods, such as FACS or immunohistochemistry analysis. In addition, we also profiled immune infiltrates of sub-tumor regions within a tumor tissue and found that spatial profiling of subregions and their neighboring environment (TME) enabled us to measure how TME differentially affects tumor biology. These measurements enable us to describe the distribution of immune populations across spatial variables like tumor interior vs. margin, to catalog the degree to which immune populations traffic together within the tumor, and to correlate gene expression in tumor cells with neighboring immune populations. These analyses demonstrate the ability of spatial RNA profiling to reach conclusions inaccessible to single-cell data alone. “FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.”

Citation Format: Youngmi Kim, Patrick Danaher, Brenn Nelson, Maddy Griswold, Margaret Hoang, McGarry A. Houghton, Joseph M. Beechem. High-throughput immune cell phenotyping using GeoMx DSP reveals Non-Small Cell Lung Cancers (NSCLC) are divided into distinct immunological subtypes [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1688.

Abstract 840: Pathway enrichment analysis of gene expression data from formalin-fixed paraffin embedded (FFPE) samples using the GeoMx™ DSP Platform

The GeoMx Digital Spatial Profiling (DSP) Platform enables robust detection of high-plex protein and RNA expression from user-defined sections within FFPE samples. As the number of targets detected within such tissues increases, it becomes important to apply systems biology strategies in order to better interpret the complex biology of the tumor microenvironment.

In this study, we investigated the expression profiles of more than 1600 genes by utilizing more than 10,000 DSP-specific in situ hybridized (ISH) probes on FFPE samples. The bioinformatics tools we have development are enabling us to move beyond single-gene profiling to a better understanding of pathway-based expression. Our study includes colorectal cancer patient samples from which we have matching bulk RNA sequencing and NanoString analysis to compare. The panel of genes profiled have a strong focus around capturing biological signaling along canonical signaling pathways and cell-intrinsic signaling from immune cells and other cell types. We demonstrate the ability to leverage foundational pathway interrogation tools, including Reactome, with the data to capture spatially-resolved pathway interactions and signaling within FFPE tissues.

As we look towards the future of the GeoMx platform and high-plex RNA profiling of tissue samples, these experiments highlight not only the need but the capacity for this platform to derive deep understanding of the biology within and across a single slide of tissue. These experiments are being used to drive development of the software features within the GeoMx ecosystem, which will provide further support for pathway-level exploration of expression when working with highly multiplexed reagents in future platform offerings.

GeoMx™ DSP technology is for Research Use Only and not for use in diagnostic procedures.

Citation Format: Tressa R. Hood, Jason Reeves, Zach Norgaard, Margaret Hoang, Sarah Warren, Erin Piazza, Rich Boykin, Joseph Beechem. Pathway enrichment analysis of gene expression data from formalin-fixed paraffin embedded (FFPE) samples using the GeoMx™ DSP Platform [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 840.

Abstract 2825: High-plex, spatial RNA profiling of tumor infiltrating leukocytes and the tumor microenvironment of microsatellite instable colorectal cancer using GeoMx™ Digital Spatial Profiler

Immunotherapeutic intervention has revolutionized cancer treatment but improved understanding of immunomodulation in tumors is still necessary to expand the reach of these therapies and identify rational combination approaches. An important aspect of this process will be characterizing the molecular differences between tumor-infiltrating leukocytes (TILs) and stromal leukocytes (non-TILs) surrounding the same tissues. Most studies to date have focused on dissociated tissues, which means identifying the origin of the profiled leukocytes is only possible with post-hoc inference. High-plex profiling that retains spatial orientation has proven difficult in fixed tissues, preventing direct understanding of TIL localization beyond a handful of pre-selected targets. To explore the transcriptional profile of TILs in situ, we leveraged a high-plex (1,400+ gene) mRNA panel for the GeoMxTM Digital Spatial Profiler (DSP) to profile microsatellite instable (MSI) colorectal cancer (CRC) samples noted to have a high abundance of CD3+ TILs by 4-color immunofluorescence (IF).

In this study, more than 5,000 unique probes (3 to 10 probes per target mRNA) with coupled photocleavable oligonucleotide tags were hybridized to formalin-fixed paraffin-embedded (FFPE) tissue sections from these CRC samples. Regions of interest were selected inside (n = 6, per tumor) and outside (n = 6, per tumor) the tumor invasive margin focusing on tumor or stromal regions with high numbers of CD3+ cells. Within each region of interest, we created a custom segmentation strategy to specifically illuminate CD3+ cells, and then sequentially illuminate regions neighboring those cells. These additional custom masks (n = 47) were defined by extending multiple contours around the initially selected TILs and non-TILs to determine differences in the local environment of each population.

Collected photocleaved oligonucleotide tags were sequenced using the GeoMxTM NGS workflow. Targets included in the 1,400+ gene panel represent immune cell markers, checkpoint molecules, cytokines and chemokines, canonical cancer pathways, and biological signatures. We found that regions neighboring TILs express higher levels of known oncogenic pathways and stromal regions neighboring non-TILs were noted to have higher expression of ECM genes, confirming the specificity of the profiling approach. Furthermore, we found that TILs specifically up-regulate expression of cytolytic pathway genes, as well as several coinhibitory and costimulatory checkpoint genes. We also observe dysregulation of members of the adenosine metabolism pathway within the tumor regions profiled and TILs, but not in regions adjacent to the tumor itself. Together, our results demonstrate the feasibility of profiling specific cell populations with a high plex mRNA panel in situ in FFPE tissue, thus enabling pathway level differential expression analyses and exploration of key interactions between neighboring cell types while retaining their spatial context. For research use only. Not for use in diagnostic procedures.

Citation Format: Zachary Norgaard, Dan Zollinger, Jason Reeves, Zoey Zhou, Michelle Kriner, Jill McKay-Fleisch, Arya Bahrami, Sarah Warren, Sarah Church, Chris Merritt, Margaret Hoang, Joseph Beechem. High-plex, spatial RNA profiling of tumor infiltrating leukocytes and the tumor microenvironment of microsatellite instable colorectal cancer using GeoMx™ Digital Spatial Profiler [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2825.

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

Digital Spatial Profiling (DSP) is a method for highly multiplex spatial profiling of proteins or RNAs suitable for use on formalin-fixed, paraffin-embedded (FFPE) samples. The approach relies on (1) multiplexed readout of proteins or RNAs using oligonucleotide tags; (2) oligonucleotide tags attached to affinity reagents (antibodies or RNA probes) through a photocleavable (PC) linker; and (3) photocleaving light projected onto the tissue sample to release PC oligonucleotides in any spatial pattern across a region of interest (ROI) covering 1 to ~5,000 cells. DSP is capable of single-cell sensitivity within an ROI using the antibody readout, with RNA detection feasible down to ~600 individual mRNA transcripts. We show spatial profiling of up to 44 proteins and 96 genes (928 RNA probes) in lymphoid, colorectal tumor and autoimmune tissues by using the nCounter system and 1,412 genes (4,998 RNA probes) by using next-generation sequencing (NGS). DSP may be used to profile not only proteins and RNAs in biobanked samples but also immune markers in patient samples, with potential prognostic and predictive potential for clinical decision-making.

Abstract P4-10-12: Characterizing the tumor and immune microenvironment through treatment to predict response to neoadjuvant HER2-targeted therapy using the Digital Spatial Profiler

Background: While introduction of HER2-targeted therapies has dramatically improved outcomes for patients with HER2-positive disease, even with the addition of HER2-targeted agents, 40-50% of patients do not achieve a pCR (pathologic complete response) following neoadjuvant therapy implying that clinical or molecular differences may be present in responders versus non-responders. While recent bulk expression studies have identified several biomarkers associated with response to HER2-targeted therapies in the neoadjuvant setting, these studies are limited in their ability to assign observed changes to specific geographic or phenotypic cell populations, such as the malignant tumor core or the surrounding microenvironment.

Methods: Here we used the Digital Spatial Profiler (DSP, NanoString Technologies, Inc.) to profile regions-of-interest containing pancytokeratin (panCK)+ tumor cells and infiltrated immune cells that are co-localized with the tumor cells. Using this technology, we assayed archival tissue from 28 patients with HER2-positive breast cancer from the TRIO-B07 (NCT00769470) clinical trial, who were treated with trastuzumab, lapatinib, or both, followed by standard chemotherapy plus HER2-targeted therapy. Tissue specimens were collected from the pre-treatment diagnostic biopsy (Baseline) and after one cycle of targeted therapy (Runin). To study regional heterogeneity, we selected an average of four panCK-enriched tissue regions from each sample. Using DSP, we performed multiplexed quantification of 38 tumor and immune protein markers and 96 RNA markers on the selected tissue regions and compared our findings to bulk mRNA expression data from the same cohort.

Results: Within the panCK-enriched regions, DSP revealed significant treatment-associated decreases in HER2 protein levels and the downstream PI3K-Akt signaling pathway in Runin compared to Baseline samples. In tandem, we observed a significant increase in infiltrating leukocytes, with CD45, a pan-leukocyte marker, and CD8, a marker for T cells that mediate tumor cell killing, showing the most dramatic changes. These changes in Runin compared to Baseline were more significant in the subset of cases that achieved a pCR versus those that do not, independent of ER status. Comparison of Runin samples to matched Baseline samples from the same patient enabled improved prediction of patient outcome (pCR) compared with analysis of a single timepoint alone. We also found that the DSP panCK enrichment strategy captures additional signal not observed in bulk expression data. For instance, using bulk expression, a decrease in HER2 RNA levels between Baseline and Runin was evident but there was no difference in the degree of decrease in HER2 mRNA between pCR and no pCR cases. Using DSP, we observed that the significant decrease in HER2 levels at Runin is more pronounced in cases that achieved a pCR. Across both tumor and immune markers, regional heterogeneity increased at Runin compared to Baseline.

Conclusions: In this study, we used DSP and a panCK enrichment strategy to retrospectively delineate the changes that occurred in tumor cells and co-localized immune cells during HER2-targeted therapy. In comparison to traditional or multiplexed IHC, DSP allows for simultaneous profiling of a large number of markers, enabling the characterization of multiple cancer signaling pathways and immune markers on a single tissue specimen. This study demonstrates the utility of pancytokeratin-enriched spatial proteomic profiling to characterize treatment-associated changes and identify predictive biomarkers.

NanoString’s Digital Spatial Profiler is for Research Use Only. Not to be used for diagnostic procedures.

Citation Format: Katherine Lee McNamara, Jennifer L. Caswell-Jin, Zhicheng Ma, Jason J. Zoeller, Michelle Kriner, Zoey Zhou, Jason Reeves, Margaret Hoang, Joseph Beechem, Dennis J. Slamon, Michael F. Press, Joan Brugge, Sara A. Hurvitz, Christina Curtis. Characterizing the tumor and immune microenvironment through treatment to predict response to neoadjuvant HER2-targeted therapy using the Digital Spatial Profiler [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-10-12.

Abstract 498: Integrating bulk and spatial profiling technologies for the discovery of RNA and protein biomarkers in muscle invasive bladder cancer

Muscle-invasive bladder cancer (MIBC) is an aggressive disease with limited therapeutic options. Although immunotherapies are approved for MIBC, the majority of patients fail to respond, suggesting the existence of complementary immune evasion mechanisms underscoring the need for comprehensive immune profiling of patient tumor samples. The PPARγ pathway constitutes a tumor-intrinsic mechanism underlying immune evasion in MIBC. Immune cell-infiltration is controlled by activated PPARγ, which in turn inhibits expression/secretion of inflammatory cytokines. Clinical data sets indicate that PPARγHigh impairs CD8+ T-cell infiltration and confers partial resistance to immunotherapies.

Here, we report a comprehensive biomarker study aimed at identifying a single, highly multiplexed platform for profiling the tumor microenvironment in clinical-type specimens as formalin-fixed, paraffin-embedded (FFPE) samples. A cohort of PPARγHigh and PPARγLow muscle invasive bladder cancer samples were used for the technology assessments. Gene expression patterns were measured using a combination of research use only genomics and spatial genomic technologies to determine concordance including RNA-seq, spatial in situ hybridization (GeoMx™ Digital Spatial Profiler) and IO360. We determined that multiple RNA and protein-based technologies were able to accurately characterize the immune phenotypes of PPARγHigh tumors. However, the GeoMx™ technology was ideal for precious samples since it digitally quantifies target abundance while maintaining spatial resolution in only two FFPE slides.

GeoMxTM DSP technology is for Research Use Only and not for use in diagnostic procedures.

Citation Format: Zhaojie Zhang, Subhasree Das, Manav Korpal, Pavan Kumar, Jingjing Gong, Yan Liang, Margaret Hoang, Joseph Beecham, Victoria Rimkunas. Integrating bulk and spatial profiling technologies for the discovery of RNA and protein biomarkers in muscle invasive bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 498.

Abstract 753: In situ RNA expression profiling of 1600+ immuno-oncology targets in FFPE tissue using NanoString GeoMx™Digital Spatial Profiler

Clinical specimens including formalin-fixed, paraffin embedded (FFPE) tumor sections preserve spatial and molecular information of tumor cells and their surrounding microenvironment. This valuable spatial information is loss with bulk RNA-seq, the most prevalent method for gene expression profiling of archival FFPE samples. In contrast, the NanoString GeoMx™ Digital Spatial Profiler (DSP) is a high multiplexing assay that can profile thousands of RNAs from user selectable regions of interest (ROIs) in FFPE sections. Here we introduce a 1600+ gene panel of tumor, stroma, and immune cell-specific content derived from NanoString nCounter® PanCancer series. We compare RNA profiling using our 1600+ immune-oncology panel to the RNA-seq methodology in FFPE samples. DSP RNA in situ probes are photocleavable oligonucleotides tags coupled to hybridization sequences that bind to mRNA transcripts in the FFPE tissue section. We gridded 96 ROIs upon the FFPE section, photocleaved oligonucleotide tags from each ROI were collected and prepared into sequencing libraries with our NGS readout workflow. After sequencing, reads were charted back to each ROI in the tissue section, generating a map of transcript activity within the tissue. We found high concordance between “bulk” DSP RNA (counts from all 96 gridded ROIs) and RNA-seq from the same FFPE block. Individually, however, each ROI showed different expression patterns than bulk and ROI expression patterns clustered based on similar tissue morphology. We further profiled the tumor and microenvironment compartments from multiple FFPE cancer tissues, comparing our 1600+ RNA expression profile to RNA-seq. DSP was able to detect a higher number of genes with low expression within each spatial compartment compared to bulk RNA-seq. These data demonstrate that DSP offers unparalleled sensitivity for large-scale gene expression while preserving critical information about tissue architecture. GeoMx™ DSP technology is for Research Use Only and not for use in diagnostic procedures.

Citation Format: Margaret Hoang, Zoey Zhou, Michelle Kriner, Kristina Sorg, Zach Norgaard, Erin Piazza, Chris Merritt, Dae Kim, Joseph Beechem. In situ RNA expression profiling of 1600+ immuno-oncology targets in FFPE tissue using NanoString GeoMx™Digital Spatial Profiler [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 753.

Single- and double-stranded viral RNA generate distinct cytokine and antiviral responses in human fetal membranes

There has been growing interest in the role of viral infections and their association with adverse pregnancy outcomes. However, little is known about the impact viral infections have on the fetal membranes (FM). Toll-like receptors (TLR) are thought to play a role in infection-associated inflammation at the maternal-fetal interface. Therefore, the objective of this study was to characterize the cytokine profile and antiviral response in human FMs exposed to viral dsRNA, which activates TLR3, and viral ssRNA, which activates TLR8; and to determine the mechanisms involved. The viral dsRNA analog, Poly(I:C), induced up-regulated secretion of MIP-1α, MIP-1β, RANTES and TNF-α, and down-regulated interleukin (IL)-2 and VEGF secretion. In contrast, viral ssRNA induced a broader panel of cytokines in the FMs by up-regulating the secretion of IL-1β, IL-2, IL-6, G-CSF, MCP-1, MIP-1α, MIP-1β, RANTES, TNF-α and GRO-α. Using inhibitory peptides against TLR adapter proteins, FM secretion of MIP-1β and RANTES in response to Poly(I:C) was MyD88 dependent; MIP-1α secretion was dependent on MyD88 and TRIF; and TNF-α production was independent of MyD88 and TRIF. Viral ssRNA-induced FM secretion of IL-1β, IL-2, IL-6, G-CSF, MIP-1α, RANTES and GRO-α was dependent on MyD88 and TRIF; MIP-1β was dependent upon TRIF, but not MyD88; and TNF-α and MCP-1 secretion was dependent on neither. Poly(I:C), but not ssRNA, induced an FM antiviral response by up-regulating the expression of IFNβ, myxovirus-resistance A, 2',5'-oligoadenylate synthetase and apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G. These findings demonstrate that human FMs respond to two viral signatures by generating distinct inflammatory cytokine/chemokine profiles and antiviral responses through different mechanisms.

An albumin leader sequence coupled with a cleavage site modification enhances the yield of recombinant C-terminal Mullerian Inhibiting Substance

Mullerian Inhibiting Substance (MIS) has been shown to inhibit ovarian cancer cells both in-vitro and in-vivo. Furthermore, recent evidence suggests that MIS may effectively target a putative ovarian cancer progenitor cell population enriched by a panel of CD44+, CD24+, Ep-CAM+, and E-cadherin-cell surface markers. In order to accommodate clinical testing of MIS in ovarian cancer patients, the production of recombinant human MIS must be optimized to increase yield and purity. Here we show that, compared to wild type, the substitution of the MIS leader sequence to that of human serum albumin, combined with a modification of the endogenous cleavage site from RAQR/S to a furin/kex2 RARR/S consensus site results in high expression, increased C-terminus cleavage and a reduction in unwanted cryptic internal cleavage products when produced in CHO cells. Purified MIS containing these alterations retains its capacity to induce regression of the Mullerian duct in fetal rat embryonic urogenital ridge assays.

Abstract 20: Whole exome sequencing of aristolochic acid induced upper urothelial carcinomas

Aristolochic acid (AA), a human carcinogen and nephrotoxin, produced by Aristolochia plants and used extensively in traditional herbal medicines, was shown to be responsible for the clinical syndromes known as Chinese herb nephropathy and endemic (Balkan) nephropathy (EN), and to contribute to the high rate of upper urinary tract carcinoma (UUC) observed in certain Asian countries such as Taiwan. After bio-activation, AA gives rise to long-lived, pro-mutagenic aristolactam-DNA (AL-DNA) adducts that serve as specific biomarkers of exposure. Our studies of the TP53 gene in AA-induced UUC tumors detected a mutation spectrum that was dominated by A>T transversions located almost exclusively on the non-transcribed DNA strand, reflecting a failure to excise AL-DNA adducts by global genomic nucleotide excision repair. In the present study we undertook the whole exome sequencing of a set of AAN/UUC tumors from Taiwanese patients, and matching normal DNAs, to establish the genome wide consequence of AA-exposure. To establish that AA was critical in tumor formation we selected patients who had: 1) detectable AL-DNA adducts in kidney cortex DNA, and 2) the TP53 gene in tumor DNA contained an A>T mutation on the non-transcribed strand. The results indicate that these tumors indeed harbor a very high number of single base substitutions (SBS) in their coding exons (median of 545 SBS per tumor). Of these, 70% were A>T mutations with the majority of the mutated adenines on the non-transcribed strand. We are currently completing whole exome sequencing of an additional set of AA-induced UUC tumors, and ten smoking-induced UUC tumors for comparison. We will present an analysis of the driver mutations found in these tumors and the pathways harboring oncogenic mutations. Our goal is to define a panel of AA-specific mutations useful for developing biomarker screens for early detection of UUC in at risk populations.

Citation Format: Thomas A. Rosenquist, Margaret Hoang, Maasaki Moriya, Victoriya S. Sidorenko, Kathleen Dickman, Chung-Hsin Chen, Lin Wu, Nickolas Papadopoulos, Yeong-Shiau Pu, Kenneth W. Kinzler, Bert Vogelstein, Arthur P. Grollman. Whole exome sequencing of aristolochic acid induced upper urothelial carcinomas. [abstract]. In: Proceedings of the AACR Special Conference on Post-GWAS Horizons in Molecular Epidemiology: Digging Deeper into the Environment; 2012 Nov 11-14; Hollywood, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(11 Suppl):Abstract nr 20.

Mapping tobacco industry strategies in South East Asia for action planning and surveillance

Objective:

To develop a comprehensive conceptual framework of tobacco industry tactics in four countries in South East Asia for the purpose of: (1) generating consensus on key areas of importance and feasibility for regional and cross country tobacco industry monitoring and surveillance; (2) developing measures to track and monitor the effects of the tobacco industry and to design counterstrategies; and (3) building capacity to improve tobacco control planning in the participating countries.

Design:

A structured conceptualisation methodology known as concept mapping was used. The process included brainstorming, sorting and rating of statements describing industry activities. Statistical analyses used multidimensional scaling and cluster analysis. Interpretation of the maps was participatory, using regional tobacco control researchers, practitioners, and policy makers during a face to face meeting.

Participants:

31 participants in this study come from the four countries represented in the project along with six people from the Johns Hopkins Blomberg School of Public Health.

Conclusions:

The map shows eight clusters of industry activities within the four countries. These were arranged into four general sectors: economics, politics, public relations and deception. For project design purposes, the map indicates areas of importance and feasibility for monitoring tobacco industry activities and serves as a basis for an initial discussion about action planning. Furthermore, the development of the map used a consensus building process across different stakeholders or stakeholder agencies and is critical when developing regional, cross border strategies for tracking and surveillance.

In vitro activities of RWJ-54428 (MC-02,479) against multiresistant gram-positive bacteria

RWJ-54428 (MC-02,479) is a new cephalosporin with a high level of activity against gram-positive bacteria. In a broth microdilution susceptibility test against methicillin-resistant Staphylococcus aureus (MRSA), RWJ-54428 was as active as vancomycin, with an MIC at which 90% of isolates are inhibited (MIC(90)) of 2 microg/ml. For coagulase-negative staphylococci, RWJ-54428 was 32 times more active than imipenem, with an MIC(90) of 2 microg/ml. RWJ-54428 was active against S. aureus, Staphylococcus epidermidis, and Staphylococcus haemolyticus isolates with reduced susceptibility to glycopeptides (RWJ-54428 MIC range, < or = 0.0625 to 1 microg/ml). RWJ-54428 was eight times more potent than methicillin and cefotaxime against methicillin-susceptible S. aureus (MIC(90), 0.5 microg/ml). For ampicillin-susceptible Enterococcus faecalis (including vancomycin-resistant and high-level aminoglycoside-resistant strains), RWJ-54428 had an MIC(90) of 0.125 microg/ml. RWJ-54428 was also active against Enterococcus faecium, including vancomycin-, gentamicin-, and ciprofloxacin-resistant strains. The potency against enterococci correlated with ampicillin susceptibility; RWJ-54428 MICs ranged between < or = 0.0625 and 1 microg/ml for ampicillin-susceptible strains and 0.125 and 8 microg/ml for ampicillin-resistant strains. RWJ-54428 was more active than penicillin G and cefotaxime against penicillin-resistant, -intermediate, and -susceptible strains of Streptococcus pneumoniae (MIC(90)s, 0.25, 0.125, and < or = 0.0625 microg/ml, respectively). RWJ-54428 was only marginally active against most gram-negative bacteria; however, significant activity was observed against Haemophilus influenzae and Moraxella catarrhalis (MIC(90)s, 0.25 and 0.5 microg/ml, respectively). This survey of the susceptibilities of more than 1,000 multidrug-resistant gram-positive isolates to RWJ-54428 indicates that this new cephalosporin has the potential to be useful in the treatment of infections due to gram-positive bacteria, including strains resistant to currently available antimicrobials.

Morphology and Pore Structure of Rare Earth Oxides

The morphology observed by transmission electron microscopy of rare earth oxides, prepared by two different routes, has been related to adsorption characteristics for nitrogen at 77 K. The most common morphology was that of thin sheets, then small equiaxed particles, and, more rarely, rod-like particles. The presence of small equiaxed particles was found to be a prerequisite for adsorption hysteresis. Evaluation of linear 't' plots indicated freedom from micropores in all samples, but positive deviations in the presence of sheet morphology at high relative pressures left open the possibility of wedge-like pores in these samples.