Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy

The organization of immune cells in human tumors is not well understood. Immunogenic tumors harbor spatially localized multicellular 'immunity hubs' defined by expression of the T cell-attracting chemokines CXCL10/CXCL11 and abundant T cells. Here, we examined immunity hubs in human pre-immunotherapy lung cancer specimens and found an association with beneficial response to PD-1 blockade. Critically, we discovered the stem-immunity hub, a subtype of immunity hub strongly associated with favorable PD-1-blockade outcome. This hub is distinct from mature tertiary lymphoid structures and is enriched for stem-like TCF7+PD-1+CD8+ T cells, activated CCR7+LAMP3+ dendritic cells and CCL19+ fibroblasts as well as chemokines that organize these cells. Within the stem-immunity hub, we find preferential interactions between CXCL10+ macrophages and TCF7-CD8+ T cells as well as between mature regulatory dendritic cells and TCF7+CD4+ and regulatory T cells. These results provide a picture of the spatial organization of the human intratumoral immune response and its relevance to patient immunotherapy outcomes.

Therapy-associated remodeling of pancreatic cancer revealed by single-cell spatial transcriptomics and optimal transport analysis

In combination with cell intrinsic properties, interactions in the tumor microenvironment modulate therapeutic response. We leveraged high-plex single-cell spatial transcriptomics to dissect the remodeling of multicellular neighborhoods and cell-cell interactions in human pancreatic cancer associated with specific malignant subtypes and neoadjuvant chemotherapy/radiotherapy. We developed Spatially Constrained Optimal Transport Interaction Analysis (SCOTIA), an optimal transport model with a cost function that includes both spatial distance and ligand-receptor gene expression. Our results uncovered a marked change in ligand-receptor interactions between cancer-associated fibroblasts and malignant cells in response to treatment, which was supported by orthogonal datasets, including an ex vivo tumoroid co-culture system. Overall, this study demonstrates that characterization of the tumor microenvironment using high-plex single-cell spatial transcriptomics allows for identification of molecular interactions that may play a role in the emergence of chemoresistance and establishes a translational spatial biology paradigm that can be broadly applied to other malignancies, diseases, and treatments.

Spatial analysis of human lung cancer reveals organized immune hubs enriched for stem-like CD8 T cells and associated with immunotherapy response

The organization of immune cells in human tumors is not well understood. Immunogenic tumors harbor spatially-localized multicellular 'immunity hubs' defined by expression of the T cell-attracting chemokines CXCL10/CXCL11 and abundant T cells. Here, we examined immunity hubs in human pre-immunotherapy lung cancer specimens, and found that they were associated with beneficial responses to PD-1-blockade. Immunity hubs were enriched for many interferon-stimulated genes, T cells in multiple differentiation states, and CXCL9/10/11 + macrophages that preferentially interact with CD8 T cells. Critically, we discovered the stem-immunity hub, a subtype of immunity hub strongly associated with favorable PD-1-blockade outcomes, distinct from mature tertiary lymphoid structures, and enriched for stem-like TCF7+PD-1+ CD8 T cells and activated CCR7 + LAMP3 + dendritic cells, as well as chemokines that organize these cells. These results elucidate the spatial organization of the human intratumoral immune response and its relevance to patient immunotherapy outcomes.

Abstract 2513: Distinct cancer-intrinsic mechanisms mediate nerve recruitment/outgrowth versus perineural invasion

Pancreatic ductal adenocarcinoma (PDAC) features abundant perineural invasion (PNI). Intra-tumoral nerves play critical roles in cancer initiation, progression, recurrence, treatment-resistance, metastasis, and mortality for many malignancies but the diverse molecular mechanisms underlying tumor-nerve crosstalk remain largely unknown—hindering the development of therapies targeting this key pathological process. To address this gap, we performed whole transcriptome digital spatial profiling on twelve custom tissue microarrays (n=288 cores) derived from intratumorally-matched regions with and without PNI in primary PDAC specimens (n=31 patients) and independently measured gene expression from cancer cells, fibroblasts, and nerves. We undertook a differential gene expression analysis comparing malignant cells in PNI-present and -absent regions. We quantified the growth kinetics of dorsal root ganglia (DRG) sensory neurons cultured with exogenous candidate proteins, which validated that some candidates augment (e.g., Lgals1) and others inhibit (e.g., Sema3b) neurite outgrowth. Next, we mapped our previously discovered malignant cell programs onto the epithelial segments and observed a significant enrichment of the mesenchymal, basal-like, and neural-like progenitor (NRP) programs versus depletion of the classical program in PNI-present regions. To determine the effects of malignant subtype on nerve outgrowth, we engineered isogenic KrasG12D/+;Trp53FL/FL;Rosa26-dCas9-VPR (KP;dCas9-VPR) organoids to overexpress the master transcription factors (TFs) for each malignant subtype (e.g., Gata6 for classical, Glis3 for NRP). We then performed the DRG neuronal outgrowth assay using conditioned media from each subtype-specific organoid line versus an off-target control and observed that the classical line suppressed neurite outgrowth, the mesenchymal and basal-like lines were neutral, and the NRP line enhanced neurite outgrowth dynamics comparable to the Ngf positive control. Taken together, our findings suggest that the mechanisms underlying nerve recruitment/outgrowth and perineural invasion may be partly decoupled. To further test this hypothesis, we are performing transwell invasion assays comparing KP;dCas9-VPR cancer cell lines that overexpress each of the candidate PNI-associated genes and malignant subtype TFs. We anticipate that this study will transform our understanding of how cancer cells and the peripheral nervous system collaborate and guide prioritization for therapeutic intervention in the burgeoning cancer neuroscience field.

Citation Format: William L. Hwang, Jennifer Su, Carina Shiau, Peter L. Wang, Jimmy A. Guo, Nicole A. Lester, Jaimie L. Barth, Hannah I. Hoffman, Prajan Divakar, Jason W. Reeves, Eric Miller, Joseph M. Beechem, Andrew J. Aguirre, Lei Zheng, David T. Ting, Mari Mino-Kenudson, Tyler Jacks. Distinct cancer-intrinsic mechanisms mediate nerve recruitment/outgrowth versus perineural invasion [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 2513.

Abstract 5637: Path to the holy grail of spatial biology: Spatial single-cell whole transcriptomes using 6000-plex spatial molecular imaging on FFPE tissue

Cancer research across drug development, molecular biomarkers, and patient response depends on understanding biology that is dependent on complex interactions between malignant, immune, and stromal cells. To survive clearance mechanisms, a tumor can rely on a myriad of escape strategies, and the microenvironment is architected around the current path of escape. To enable a more comprehensive picture of tumor biology, we have developed the CosMx™ Spatial Molecular Imager (SMI) technology to capture a snapshot of thousands of RNA species resolved subcellularly from a single, standard histopathology slide. Building upon the previously released panels, this study tests a new 6,000-plex panel, the highest RNA plex measured in situ within human tissue, allowing the imputation of a spatial whole transcriptome in the tissue. We performed an ultra-high-plex RNA assay to detect 6,000 targets simultaneously in situ on an FFPE human liver cancer tissue (~1 cm2 area) using the CosMx SMI. This RNA panel covers broad biological areas with special emphasis on oncology, immunology, and signal transduction, such that all cancer researchers can benefit from the direct detection of targets of interest (sans imputation) in intact tissue. Analysis algorithms were developed to allow robust assessments of cell types, cell states, cell-cell interactions, and pathway activation. Imputation based on reference profiles from HCA, TCGA, and other public repositories allows estimation of non-measured transcripts at a ratio of approximately 1:3, compared to the approximate 1:20-1:70 imputations performed previously for spatial data.Thousands of transcripts were simultaneously detected with high sensitivity and specificity on the FFPE liver cancer tissue section at single-cell subcellular resolution. We were able to accurately map known reference profiles from scRNA-seq into this sample while identifying cancer-specific malignant, immune, and stromal cells in this tissue sample using this ultra-high plex RNA panel. In addition, we constructed sample-specific spatial neighborhoods, defined by cell types, cell states, and nearly unlimited sets of biological pathways through the imputed whole transcriptome. Finally, we measured >1,000 ligand-receptor interactions between key cell types of adjacent cells in the tissue, identifying mechanisms for tumor-mediated escape as well as reactive re-architecting of the native stroma which defines the trajectory of cancer’s evolution. Single-cell spatial measurements of gene expression at 6,000 plex from a single FFPE slide has the potential to transform our understanding of tumor biology and facilitate the next advances in cancer research by extracting the highest data density possible from rare specimens collected during patient treatment.

Citation Format: Shanshan He, Michael Patrick, Jason W. Reeves, Patrick Danaher, Julian Preciado, Joseph Phan, Erin Piazza, Zachary Reitz, Lidan Wu, Rustem Khafizov, Haiyan Zhai, Michael Rhodes, David Ruff, Joseph Beechem. Path to the holy grail of spatial biology: Spatial single-cell whole transcriptomes using 6000-plex spatial molecular imaging on FFPE tissue. [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 5637.

Abstract C052: Identifying mediators of perineural invasion in pancreatic cancer using spatial transcriptomics

Intratumoral nerves play important and versatile roles in cancer initiation, progression, recurrence, treatment-resistance, metastasis, morbidity, and mortality for many malignancies but the diverse molecular mechanisms underlying tumor-nerve crosstalk remain largely unknown. One of the differentiating hallmarks of pancreatic ductal adenocarcinoma (PDAC) is an exceptionally high frequency of perineural invasion (PNI), a histopathologic manifestation of tumor-nerve crosstalk whereby cancer cells recruit, migrate towards, and envelop or invade peripheral nerves. Evidence for some neurochemicals/neurotrophins involved in PNI have been uncovered, but most of the underlying work was limited by a lack of cell-type specificity, spatial context, and fragmented focus on individual pathways. To address these shortcomings, we set out to comprehensively identify cell-type specific genes spatially linked to PNI in patient tumors and then dissect the functional roles of these genes through live imaging of dorsal root ganglia (DRG) sensory neurons incubated in conditioned media from cancer cell organoids overexpressing candidate genes via CRISPR activation (CRISPRa). First, we performed whole transcriptome digital spatial profiling (NanoString GeoMx) on twelve custom tissue microarrays (n=288 cores) derived from intratumorally-matched malignant regions with and without PNI in primary resected PDAC specimens (n=31 patients). Differential gene expression (DE) analysis (FDR < 0.001) for PNI demonstrated that for malignant cells there were 271 enriched and 65 depleted genes, and for fibroblasts there were 16 enriched and 27 depleted genes. We further evaluated associations between PNI and expression of malignant subtypes previously identified from single-nucleus RNA-seq applied to 43 primary resected PDAC specimens. We found that malignant cells engaged in PNI were enriched in the mesenchymal, basaloid and neural-like progenitor (NRP) subtypes and depleted in the classical subtype. To test these associations functionally, we generated isogenic murine organoid lines (KrasG12D/+;Trp53FL/FL;R26-dCas9-VPR) overexpressing subtype-driving transcription factors and collected conditioned media. DRG sensory neurons demonstrate enhanced and suppressed growth kinetics when grown in NRP and classical conditioned media, respectively; mesenchymal and basal-like conditioned media do not appear to influence growth kinetics. These results suggest that while mesenchymal, basaloid, and NRP cells likely all play a role in cancer cell invasion of nerves, NRP cells may have an additional role in tumor-nerve tropism. Additional experiments exploring the functional effects of the top enriched and depleted genes from the DE analysis are ongoing. We anticipate that this study will provide a high-resolution understanding of critical intercellular interactions in the PDAC tumor microenvironment that facilitate PNI and tumor-nerve crosstalk more broadly to guide novel therapeutic strategies.

Citation Format: William L. Hwang, Jennifer Su, Jimmy A. Guo, Carina Shiau, Jaimie L. Barth, Hannah I. Hoffman, Prajan Divakar, Jason W. Reeves, Eric Miller, Grissel Cervantes-Jaramillo, William Freed-Pastor, Vanessa Funes, Jennifer Y. Wo, Theodore S. Hong, Carlos Fernandez-del Castillo, Lei Zheng, Andrew J. Aguirre, David T. Ting, Mari Mino-Kenudson, Tyler Jacks. Identifying mediators of perineural invasion in pancreatic cancer using spatial transcriptomics [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C052.

Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet inform clinical management or therapeutic development. Here, we construct a high-resolution molecular landscape of the cellular subtypes and spatial communities that compose PDAC using single-nucleus RNA sequencing and whole-transcriptome digital spatial profiling (DSP) of 43 primary PDAC tumor specimens that either received neoadjuvant therapy or were treatment naive. We uncovered recurrent expression programs across malignant cells and fibroblasts, including a newly identified neural-like progenitor malignant cell program that was enriched after chemotherapy and radiotherapy and associated with poor prognosis in independent cohorts. Integrating spatial and cellular profiles revealed three multicellular communities with distinct contributions from malignant, fibroblast and immune subtypes: classical, squamoid-basaloid and treatment enriched. Our refined molecular and cellular taxonomy can provide a framework for stratification in clinical trials and serve as a roadmap for therapeutic targeting of specific cellular phenotypes and multicellular interactions.

Abstract 1364: Spatially resolved T-cell receptor profiling elucidates relationships between TCR diversity, immune infiltration, and cancer-associated pathways

As T-cells mature, genes encoding T-cell receptor (TCR) segments are somatically recombined to generate a diverse repertoire of receptors specific to unique antigens. The resultant TCR diversity, and subsequent clonal expansion events, are critical in understanding the adaptive immune response to pathogens and cancers. While many methods have been developed to determine specific clonotypes and overall TCR diversity present in various tissues, these methods to date have failed to capture spatial orientation and arrangement of T-cells engaging with their microenvironment. Tracking T-cell migration and infiltration into the tumor has thus been limited to post-hoc low-plex profiling methods. To better understand T-cell localization during tumor development, we have developed a TCR 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). This novel spatial assay enables simultaneous quantification of all functional TCR constant, variable and joining segments in situ along with transcriptome-wide gene expression profiling in spatially defined regions of a tissue. We validated the performance of the TCR probe pool in inflamed tonsil and cell pellet arrays, demonstrating comparable sensitivity and specificity relative to orthogonal methods. We next used the GeoMx TCR spike-in panel to characterize intra- and inter-patient TCR heterogeneity in a cohort of 68 T-cell lymphomas to track clonal interactions between the malignant and non-malignant immune microenvironment. We demonstrate the ability to link the spatial context of TCR segment expression to activation of malignant signaling cascades as well as non-cancerous T-cell response to the presence of other immune cells and cancer-associated signaling. Together, the combination of our TCR spike-in panel with the CTA or WTA illuminates spatial distribution of T-cell clones paving the way for studies to comprehensively link TCR clonality changes to the tumor microenvironment.

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

Citation Format: Michelle A. Kriner, Katrina van Raay, Jason W. Reeves, Kit A. Fuhrman, Andrew Klock, Alecksandr Kutchma, Erin Piazza, Joseph Beechem. Spatially resolved T-cell receptor profiling elucidates relationships between TCR diversity, immune infiltration, and cancer-associated pathways [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 1364.

Abstract SY12-04: Multicellular spatial community featuring a novel neuronal-like malignant phenotype is enriched in pancreatic cancer after neoadjuvant chemotherapy and radiotherapy

Pancreatic ductal adenocarcinoma (PDAC) is projected to be the second leading cause of cancer mortality in the United States by 2030. Given that resistance to cytotoxic therapy is pervasive, there is a critical need to elucidate salient gene expression programs and spatial relationships among malignant and stromal cells in the tumor microenvironment (TME), particularly in residual disease. We developed and applied a single-nucleus RNA-seq (snRNA-seq) technique to 43 banked frozen primary PDAC specimens that either received neoadjuvant therapy (n=25) or were treatment-naïve (n=18). We discovered expression programs across malignant cell and fibroblast profiles that formed the basis for a refined molecular taxonomy, including a novel neural-like progenitor (NRP) malignant program enriched with neoadjuvant treatment in tumors and organoids, and associated with the worst prognosis in bulk profiles from independent cohorts.

To elucidate how neoadjuvant treatment and cancer cell- and fibroblast-intrinsic programs modulate the composition of multicellular neighborhoods, we performed spatial profiling with the GeoMx[1] platform (NanoString) on 21 formalin-fixed paraffin-embedded sections using the human whole transcriptome atlas (WTA). Each tumor showed intra-tumoral heterogeneity in tissue architecture and regions of interest (ROIs) with diverse patterns of neoplastic cells, cancer-associated fibroblasts (CAFs), and immune cells were selected for profiling. We deconvolved the WTA data with our snRNA-seq cell type signatures and mapped expression programs onto the tumor architecture to reveal three distinct multicellular neighborhoods, which we annotated as classical, squamoid-basaloid, and treatment-enriched. The observed enrichment in post-treatment residual disease of multiple spatially-defined receptor-ligand interactions and a neighborhood featuring the NRP program, neurotropic CAF program, and CD8+ T cells may open new therapeutic opportunities.

Next, we mapped malignant/CAF programs and immune cell subsets at single-cell spatial resolution by performing spatial molecular imaging (SMI[2]; NanoString CosMx) using a panel of 960 RNA targets on a subset of seven tumors (2 untreated, 5 treated) and captured over 200,000 cells with an average of more than 450 transcripts detected per cell. Correlating ROIs from whole-transcriptome DSP to matched fields of view in kiloplex SMI enabled further dissection of PDAC architecture and treatment-associated remodeling of cell type distributions and receptor-ligand interactions.

Ongoing functional studies have begun to elucidate the key regulatory elements underlying the distinct treatment-associated NRP malignant program and its interactions with the TME. Overall, the complementary combination of snRNA-seq, whole-transcriptome DSP, and kiloplex SMI provides a high-resolution molecular framework that can be harnessed to augment precision oncology efforts in pancreatic cancer.

[1] GeoMx DSP is for Research Use Only and not for use in diagnostic procedures. [2] CosMx SMI is for Research Use Only and not for use in diagnostic procedures.

Citation Format: William L. Hwang, Karthik A. Jagadeesh, Jimmy A. Guo, Hannah I. Hoffman, Carina Shiau, Jennifer Su, Payman Yadollahpour, Jason W. Reeves, Youngmi Kim, Sean Kim, Mark Gregory, Prajan Divakar, Eric Miller, Michael Rhodes, Sarah Warren, Erroll Rueckert, Kit Fuhrman, Daniel R. Zollinger, Robin Fropf, Joseph M. Beechem, Arnav Mehta, Toni Delorey, Cristin McCabe, Jaimie L. Barth, Piotr Zelga, Cristina R. Ferrone, Motaz Qadan, Keith D. Lillemoe, Rakesh K. Jain, Jennifer Y. Wo, Theodore S. Hong, Ramnik Xavier, Orit Rozenblatt-Rosen, Andrew J. Aguirre, Carlos Fernandez-Del Castillo, Andrew S. Liss, Mari Mino-Kenudson, David T. Ting, Tyler Jacks, Aviv Regev. Multicellular spatial community featuring a novel neuronal-like malignant phenotype is enriched in pancreatic cancer after neoadjuvant chemotherapy and radiotherapy [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 SY12-04.

Visualizing in deceased COVID-19 patients how SARS-CoV-2 attacks the respiratory and olfactory mucosae but spares the olfactory bulb

Anosmia, the loss of smell, is a common and often the sole symptom of COVID-19. The onset of the sequence of pathobiological events leading to olfactory dysfunction remains obscure. Here, we have developed a postmortem bedside surgical procedure to harvest endoscopically samples of respiratory and olfactory mucosae and whole olfactory bulbs. Our cohort of 85 cases included COVID-19 patients who died a few days after infection with SARS-CoV-2, enabling us to catch the virus while it was still replicating. We found that sustentacular cells are the major target cell type in the olfactory mucosa. We failed to find evidence for infection of olfactory sensory neurons, and the parenchyma of the olfactory bulb is spared as well. Thus, SARS-CoV-2 does not appear to be a neurotropic virus. We postulate that transient insufficient support from sustentacular cells triggers transient olfactory dysfunction in COVID-19. Olfactory sensory neurons would become affected without getting infected.

The CD155/TIGIT axis promotes and maintains immune evasion in neoantigen-expressing pancreatic cancer

The CD155/TIGIT axis can be co-opted during immune evasion in chronic viral infections and cancer. Pancreatic adenocarcinoma (PDAC) is a highly lethal malignancy, and immune-based strategies to combat this disease have been largely unsuccessful to date. We corroborate prior reports that a substantial portion of PDAC harbors predicted high-affinity MHC class I-restricted neoepitopes and extend these findings to advanced/metastatic disease. Using multiple preclinical models of neoantigen-expressing PDAC, we demonstrate that intratumoral neoantigen-specific CD8+ T cells adopt multiple states of dysfunction, resembling those in tumor-infiltrating lymphocytes of PDAC patients. Mechanistically, genetic and/or pharmacologic modulation of the CD155/TIGIT axis was sufficient to promote immune evasion in autochthonous neoantigen-expressing PDAC. Finally, we demonstrate that the CD155/TIGIT axis is critical in maintaining immune evasion in PDAC and uncover a combination immunotherapy (TIGIT/PD-1 co-blockade plus CD40 agonism) that elicits profound anti-tumor responses in preclinical models, now poised for clinical evaluation.

Best Practices for Spatial Profiling for Breast Cancer Research with the GeoMx® Digital Spatial Profiler

Breast cancer is a heterogenous disease with variability in tumor cells and in the surrounding tumor microenvironment (TME). Understanding the molecular diversity in breast cancer is critical for improving prediction of therapeutic response and prognostication. High-plex spatial profiling of tumors enables characterization of heterogeneity in the breast TME, which can holistically illuminate the biology of tumor growth, dissemination and, ultimately, response to therapy. The GeoMx Digital Spatial Profiler (DSP) enables researchers to spatially resolve and quantify proteins and RNA transcripts from tissue sections. The platform is compatible with both formalin-fixed paraffin-embedded and frozen tissues. RNA profiling was developed at the whole transcriptome level for human and mouse samples and protein profiling of 100-plex for human samples. Tissue can be optically segmented for analysis of regions of interest or cell populations to study biology-directed tissue characterization. The GeoMx Breast Cancer Consortium (GBCC) is composed of breast cancer researchers who are developing innovative approaches for spatial profiling to accelerate biomarker discovery. Here, the GBCC presents best practices for GeoMx profiling to promote the collection of high-quality data, optimization of data analysis and integration of datasets to advance collaboration and meta-analyses. Although the capabilities of the platform are presented in the context of breast cancer research, they can be generalized to a variety of other tumor types that are characterized by high heterogeneity.

Spatially organized multicellular immune hubs in human colorectal cancer

Immune responses to cancer are highly variable, with mismatch repair-deficient (MMRd) tumors exhibiting more anti-tumor immunity than mismatch repair-proficient (MMRp) tumors. To understand the rules governing these varied responses, we transcriptionally profiled 371,223 cells from colorectal tumors and adjacent normal tissues of 28 MMRp and 34 MMRd individuals. Analysis of 88 cell subsets and their 204 associated gene expression programs revealed extensive transcriptional and spatial remodeling across tumors. To discover hubs of interacting malignant and immune cells, we identified expression programs in different cell types that co-varied across tumors from affected individuals and used spatial profiling to localize coordinated programs. We discovered a myeloid cell-attracting hub at the tumor-luminal interface associated with tissue damage and an MMRd-enriched immune hub within the tumor, with activated T cells together with malignant and myeloid cells expressing T cell-attracting chemokines. By identifying interacting cellular programs, we reveal the logic underlying spatially organized immune-malignant cell networks.

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.

Comprehensive analysis of cutaneous and uveal melanoma liver metastases

BACKGROUND

The profound disparity in response to immune checkpoint blockade (ICB) by cutaneous melanoma (CM) and uveal melanoma (UM) patients is not well understood. Therefore, we characterized metastases of CM and UM from the same metastatic site (liver), in order to dissect the potential underlying mechanism in differential response on ICB.

METHODS

Tumor liver samples from CM (n=38) and UM (n=28) patients were analyzed at the genomic (whole exome sequencing), transcriptional (RNA sequencing) and protein (immunohistochemistry and GeoMx Digital Spatial Profiling) level.

RESULTS

Comparison of CM and UM metastases from the same metastatic site revealed that, although originating from the same melanocyte lineage, CM and UM differed in somatic mutation profile, copy number profile, tumor mutational burden (TMB) and consequently predicted neoantigens. A higher melanin content and higher expression of the melanoma differentiation antigen MelanA was observed in liver metastases of UM patients. No difference in B2M and human leukocyte antigen-DR (HLA-DR) expression was observed. A higher expression of programmed cell death ligand 1 (PD-L1) was found in CM compared with UM liver metastases, although the majority of CM and UM liver metastases lacked PD-L1 expression. There was no difference in the extent of immune infiltration observed between CM and UM metastases, with the exception of a higher expression of CD163 (p<0.0001) in CM liver samples. While the extent of immune infiltration was similar for CM and UM metastases, the ratio of exhausted CD8 T cells to cytotoxic T cells, to total CD8 T cells and to Th1 cells, was significantly higher in UM metastases.

CONCLUSIONS

While TMB was different between CM and UM metastases, tumor immune infiltration was similar. The greater dependency on PD-L1 as an immune checkpoint in CM and the identification of higher exhaustion ratios in UM may both serve as explanations for the difference in response to ICB. Consequently, in order to improve current treatment for metastatic UM, reversal of T cell exhaustion beyond programmed cell death 1 blockade should be considered.

Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection

The relationship of SARS-CoV-2 lung infection and severity of pulmonary disease is not fully understood. We analyzed autopsy specimens from 24 patients who succumbed to SARS-CoV-2 infection using a combination of different RNA and protein analytical platforms to characterize inter- and intra- patient heterogeneity of pulmonary virus infection. There was a spectrum of high and low virus cases that was associated with duration of disease and activation of interferon pathway genes. Using a digital spatial profiling platform, the virus corresponded to distinct spatial expression of interferon response genes and immune checkpoint genes demonstrating the intra-pulmonary heterogeneity of SARS-CoV-2 infection.

Perspectives on genetic and genomic technologies in an academic medical center: the duke experience

In this age of personalized medicine, genetic and genomic testing is expected to become instrumental in health care delivery, but little is known about its actual implementation in clinical practice.

METHODS

We surveyed Duke faculty and healthcare providers to examine the extent of genetic and genomic testing adoption. We assessed providers' use of genetic and genomic testing options and indications in clinical practice, providers' awareness of pharmacogenetic applications, and providers' opinions on returning research-generated genetic test results to participants. Most clinician respondents currently use family history routinely in their clinical practice, but only 18 percent of clinicians use pharmacogenetics. Only two respondents correctly identified the number of drug package inserts with pharmacogenetic indications. We also found strong support for the return of genetic research results to participants. Our results demonstrate that while Duke healthcare providers are enthusiastic about genomic technologies, use of genomic tools outside of research has been limited. Respondents favor return of research-based genetic results to participants, but clinicians lack knowledge about pharmacogenetic applications. We identified challenges faced by this institution when implementing genetic and genomic testing into patient care that should inform a policy and education agenda to improve provider support and clinician-researcher partnerships.

Perceptions of Personalized Medicine in an Academic Health System: Educational Findings

OBJECTIVE

Prior reports demonstrate that personalized medicine implementation in clinical care is lacking. Given the program focus at Duke University on personalized medicine, we assessed health care providers' perspectives on their preparation and educational needs to effectively integrate personalized medicine tools and applications into their clinical practices.

METHODS

Data from 78 health care providers who participated in a larger study of personalized and precision medicine at Duke University were analyzed using Qualtrics (descriptive statistics). Individuals age 18 years and older were recruited for the larger study through broad email contacts across the university and health system. All participants completed an online 35-question survey that was developed, pilot-tested, and administered by a team of interdisciplinary researchers and clinicians at the Center for Applied Genomics and Precision Medicine.

RESULTS

Overall, providers reported being ill-equipped to implement personalized medicine in clinical practice. Many respondents identified educational resources as critical for strengthening personalized medicine implementation in both research and clinical practice. Responses did not differ significantly between specialists and primary providers or by years since completion of the medical degree.

CONCLUSIONS

Survey findings support prior calls for provider and patient education in personalized medicine. Respondents identified focus areas in training, education, and research for improving personalized medicine uptake. Given respondents' emphasis on educational needs, now may be an ideal time to address these needs in clinical training and public education programs.

Histone modifications within the human X centromere region

Human centromeres are multi-megabase regions of highly ordered arrays of alpha satellite DNA that are separated from chromosome arms by unordered alpha satellite monomers and other repetitive elements. Complexities in assembling such large repetitive regions have limited detailed studies of centromeric chromatin organization. However, a genomic map of the human X centromere has provided new opportunities to explore genomic architecture of a complex locus. We used ChIP to examine the distribution of modified histones within centromere regions of multiple X chromosomes. Methylation of H3 at lysine 4 coincided with DXZ1 higher order alpha satellite, the site of CENP-A localization. Heterochromatic histone modifications were distributed across the 400–500 kb pericentromeric regions. The large arrays of alpha satellite and gamma satellite DNA were enriched for both euchromatic and heterochromatic modifications, implying that some pericentromeric repeats have multiple chromatin characteristics. Partial truncation of the X centromere resulted in reduction in the size of the CENP-A/Cenp-A domain and increased heterochromatic modifications in the flanking pericentromere. Although the deletion removed ∼1/3 of centromeric DNA, the ratio of CENP-A to alpha satellite array size was maintained in the same proportion, suggesting that a limited, but defined linear region of the centromeric DNA is necessary for kinetochore assembly. Our results indicate that the human X centromere contains multiple types of chromatin, is organized similarly to smaller eukaryotic centromeres, and responds to structural changes by expanding or contracting domains.

Oligonucleotide transformation of yeast reveals mismatch repair complexes to be differentially active on DNA replication strands

Transformation of both prokaryotes and eukaryotes with single-stranded oligonucleotides can transfer sequence information from the oligonucleotide to the chromosome. We have studied this process using oligonucleotides that correct a -1 frameshift mutation in the LYS2 gene of Saccharomyces cerevisiae. We demonstrate that transformation by oligonucleotides occurs preferentially on the lagging strand of replication and is strongly inhibited by the mismatch-repair system. These results are consistent with a mechanism in which oligonucleotides anneal to single-stranded regions of DNA at a replication fork and serve as primers for DNA synthesis. Because the mispairs the primers create are efficiently removed by the mismatch-repair system, single-stranded oligonucleotides can be used to probe mismatch-repair function in a chromosomal context. Removal of mispairs created by annealing of the single-stranded oligonucleotides to the chromosomal DNA is as expected, with 7-nt loops being recognized solely by MutS beta and 1-nt loops being recognized by both MutS alpha and MutS beta. We also find evidence for Mlh1-independent repair of 7-nt, but not 1-nt, loops. Unexpectedly, we find a strand asymmetry of mismatch-repair function; transformation is blocked more efficiently by MutS alpha on the lagging strand of replication, whereas MutS beta does not show a significant strand bias. These results suggest an inherent strand-related difference in how the yeast MutS alpha and MutS beta complexes access and/or repair mismatches that arise in the context of DNA replication.

The effects of mismatch repair and RAD1 genes on interchromosomal crossover recombination in Saccharomyces cerevisiae

We have previously shown that recombination between 400-bp substrates containing only 4-bp differences, when present in an inverted repeat orientation, is suppressed by >20-fold in wild-type strains of S. cerevisiae. Among the genes involved in this suppression were three genes involved in mismatch repair--MSH2, MSH3, and MSH6--and one in nucleotide excision repair, RAD1. We now report the involvement of these genes in interchromosomal recombination occurring via crossovers using these same short substrates. In these experiments, recombination was stimulated by a double-strand break generated by the HO endonuclease and can occur between completely identical (homologous) substrates or between nonidentical (homeologous) substrates. In addition, a unique feature of this system is that recombining DNA strands can be given a choice of either type of substrate. We find that interchromosomal crossover recombination with these short substrates is severely inhibited in the absence of MSH2, MSH3, or RAD1 and is relatively insensitive to the presence of mismatches. We propose that crossover recombination with these short substrates requires the products of MSH2, MSH3, and RAD1 and that these proteins have functions in recombination in addition to the removal of terminal nonhomology. We further propose that the observed insensitivity to homeology is a result of the difference in recombinational mechanism and/or the timing of the observed recombination events. These results are in contrast with those obtained using longer substrates and may be particularly relevant to recombination events between the abundant short repeated sequences that characterize the genomes of higher eukaryotes.

Preliminary findings from tests of a microwave applicator designed to treat Barrett's oesophagus

Barrett's oesophagus is considered to increase the risk of cancer 30-fold. Helical microwave antennas have been developed for ablative treatment of Barrett's. A microwave balloon applicator was tested in an initial animal study using adult white pigs. For treatment, a balloon filled with tissue-equivalent material encapsulated the antenna. A range of different treatment temperatures and durations was used to investigate a range of thermal ablations of the oesophageal epithelium. Eight animals were investigated, five non-survival and three with a 1-week survival period. The balloon was fitted with an array of temperature sensors, which gave an indication of the treatment in situ and allowed modifications to be performed in real time. Temperature data were recorded from all four quadrants of the balloon throughout and test sites were collected and analysed histologically. All experiments were successfully completed without perforation, serious adverse effects or death. Sites of discrete ulceration were induced in the survival tests, whereas the non-survival tests yielded little reproducible tissue modification. Results suggested that an activation temperature of approximately 55 degrees C needed to be reached during the treatment for tissue damage to be induced. Once damage had been triggered the severity was related to the mean temperature attained during the treatment period. A mean temperature of 52 degrees C or more resulted in substantial damage, whilst a mean temperature of approximately 50 degrees C resulted in the desired surface damage with sparing of subjacent tissues.

Effect of insertion depth on helical antenna performance in a muscle-equivalent phantom

Barrett's oesophagus is considered to increase the risk of cancer 30 fold. A set of helical microwave antennas was designed to investigate their potential use in the thermal therapy of Barrett's oesophagus. For treatment, a balloon filled with muscle-equivalent material encapsulates the antenna. The effects of insertion depth and coil-spacing on the thermal distribution produced by the antennas (20-35 mm) were characterized. The 35 mm helical antenna, with a coil-spacing of 3.6 mm resulted in uniform heating for an insertion depth of 40 mm. It was observed that the resultant temperature distribution produced, by the antennas, was dependent on the insertion depth within the phantom. For all antennas studied, deeper insertion resulted in two high intensity regions, approximately 1/4 and 3/4 along the antenna length. In contrast, shallow insertion resulted in predominant tip heating with undesirable heating at the phantom entry point. However, by manipulating the coil-spacing of the helix, uniform temperature profiles were achieved for a range of insertion depths.

A new reversion assay for measuring all possible base pair substitutions in Saccharomyces cerevisiae

A TRP5-based reversion system that allows the rates of all possible base pair substitutions to be measured when the TRP5 locus is in both orientations relative to a defined origin of replication has been developed. This system should be useful for a wide variety of mutation and repair studies in yeast.