Characterization Of Transcriptome Research Articles

TLR8 agonist selgantolimod regulates Kupffer cell differentiation status and impairs HBV entry into hepatocytes via an IL-6-dependent mechanism

ObjectiveAchieving HBV cure will require novel combination therapies of direct-acting antivirals and immunomodulatory agents. In this context, the toll-like receptor 8 (TLR8) agonist selgantolimod (SLGN) has been investigated in preclinical...

Abstract PO4-28-01: Molecular profiling revealed activation of cytokine signaling and suppression of lipid metabolism as the hallmarks of doxorubicin-resistant TNBC

Abstract Background: Chemotherapeutic resistance observed in triple-negative breast cancer (TNBC) poses a substantial clinical hurdle, emphasizing the imperative to enhance our comprehension of the underlying mechanisms with the aim of potentially mitigating or reversing this phenomenon. Methods: Doxorubicin-resistant (DoxR) TNBC models (MDA-MB-231 and BT-549) were established through continuous exposure to increasing concentrations of doxorubicin. RNA-Seq was conducted using the Illumina platform, while bioinformatics analyses were performed using CLC genomics workbench 20.2 and iDEP.91. Colony forming unit (CFU), flow cytometry and fluorescent microscopy were used to assess cell proliferation, cell cycle distribution, and cell death, respectively. Western blotting was used to confirm the expression and phosphorylation of protein targets. Ingenuity pathway analysis (IPA) and STRING database v 11.5 were used for network and pathway analyses, while Kaplan-Meier Plotter was used for survival analyses. Results: Herein, we provide a comprehensive functional and transcriptomic characterization of DoxR TNBC models, revealing multiple affected signaling networks and functional categories. The defense and immune response, response to stress, response to cytokine and external stimulus and cytokine-mediated signaling pathways were among the top activated, while suppression of cholesterol, sterol and lipid biosynthesis and metabolism were the hallmarks of DoxR cells. Upstream regulator analysis revealed IL-1B cytokine network activation in DoxR cells. Concordantly, disease and function analysis on the downregulated genes in DoxR TNBC cells revealed the most pronounced enrichment in pathways associated with cell invasion, colony formation, as well as lipid and carbohydrate metabolism. A number of upregulated genes were validated by qRT-PCR, which correlated with unfavorable overall survival (OS). Functionally, DoxR cells exhibited remarkable suppression of cell proliferation, as evidenced by diminished CFU potential, sphere formation and growth under 3D organoid culture, and cell migration. Although DoxR TNBC cells exhibited a slow cell cycling under normal culture conditions, wild-type TNBC cells exhibited remarkable arrest in the G2M phase when exposed to doxorubicin, which was less evident in DoxR TNBC models, suggesting DoxR cells undergo a quiescent state in response to chemotherapeutic challenge. In agreement with those data, increased phosphorylation of CHK2 and p53 proteins was remarkable in DoxR cells, thus promoting cellular dormancy. Conclusion: Our data revealed cellular dormancy and suppression of lipid metabolism as the hallmark associated with doxorubicin-resistant TNBC cells. On the other hand, cytokine signaling and stress response were the most enriched functional categories in DoxR TNBC cells. Therapeutic targeting to reverse the quiescent state or suppression of cytokine signaling networks could enhance the efficacy of doxorubicin-based therapeutics. Citation Format: Vishnubalaji Radhakrishnan, Nehad Alajez. Molecular profiling revealed activation of cytokine signaling and suppression of lipid metabolism as the hallmarks of doxorubicin-resistant TNBC [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 PO4-28-01.

The epidermal circadian clock integrates and subverts brain signals to guarantee skin homeostasis

In mammals, the circadian clock network drives daily rhythms of tissue-specific homeostasis. To dissect daily inter-tissue communication, we constructed a mouse minimal clock network comprising only two nodes: the peripheral epidermal clock and the central brain clock. By transcriptomic and functional characterization of this isolated connection, we identified a gatekeeping function of the peripheral tissue clock with respect to systemic inputs. The epidermal clock concurrently integrates and subverts brain signals to ensure timely execution of epidermal daily physiology. Timely cell-cycle termination in the epidermal stem cell compartment depends upon incorporation of clock-driven signals originating from the brain. In contrast, the epidermal clock corrects or outcompetes potentially disruptive feeding-related signals to ensure the optimal timing of DNA replication. Together, we present an approach for cataloging the systemic dependencies of daily temporal organization in a tissue and identify an essential gate-keeping function of peripheral circadian clocks that guarantees tissue homeostasis.

A pancreatic cancer organoid-in-matrix platform shows distinct sensitivities to T cell killing

Poor treatment responses of pancreatic ductal adenocarcinoma (PDAC) are in large part due to tumor heterogeneity and an immunosuppressive desmoplastic tumor stroma that impacts interactions with cells in the tumor microenvironment (TME). Thus, there is a pressing need for models to probe the contributions of cellular and noncellular crosstalk. Organoids are promising model systems with the potential to generate a plethora of data including phenotypic, transcriptomic and genomic characterization but still require improvements in culture conditions mimicking the TME. Here, we describe an INTERaction with Organoid-in-MatriX ("InterOMaX") model system, that presents a 3D co-culture-based platform for investigating matrix-dependent cellular crosstalk. We describe its potential to uncover new molecular mechanisms of T cell responses to murine KPC (LSL-KrasG12D/+27/Trp53tm1Tyj/J/p48Cre/+) PDAC cells as well as PDAC patient-derived organoids (PDOs). For this, a customizable matrix and homogenously sized organoid-in-matrix positioning of cancer cells were designed based on a standardized agarose microwell chip array system and established for co-culture with T cells and inclusion of stromal cells. We describe the detection and orthogonal analysis of murine and human PDAC cell populations with distinct sensitivity to T cell killing that is corroborated in vivo. By enabling both identification and validation of gene candidates for T cell resistance, this platform sets the stage for better mechanistic understanding of cancer cell-intrinsic resistance phenotypes in PDAC.

Establishment of Dual Fluorescent Labeled Human High Bone Metastasis Lung Adenocarcinoma Cell Line and Transcriptomic Characterization Analysis

Bone is a common site for metastasis in lung adenocarcinoma, but the mechanism behind lung adenocarcinoma bone metastasis is still unclear. And currently, there is a lack of easily traceable and stable lung adenocarcinoma bone metastasis cell models, which limits the research on the mechanism of lung adenocarcinoma bone metastasis. The establishment of human lung adenocarcinoma cell line that are highly metastatic to bone, labeled with green fluorescent proteins (GFP) and fireflies luciferase (LUC), along with transcriptomic characterization, would be beneficial for research on lung adenocarcinoma bone metastasis and provide new experimental methods. The human lung adenocarcinoma cell line A549-GFP-LUC was injected into nude mice via the left ventricle to construct a bone metastasis model, and was domesticated in vivo for three consecutive times to obtain the human high bone metastasis lung adenocarcinoma cell line A549-GFP-LUC-BM3; cell counting kit-8 (CCK-8), colony formation assay, scratch wound assays, Transwell assay and Western blot were used to compare the proliferation and invasion abilities of A549-GFP-LUC-BM3 with the parental cells. A549-GFP-LUC-BM3 cells and parental cells were further analyzed by transcriptomic sequencing. Human high-bone metastatic lung adenocarcinoma cells A549-GFP-LUC-BM3 was successfully established. Compared to parental cells, this cells exhibited a significantly higher incidence of bone metastasis and enhanced in vitro proliferation, migration, and invasion abilities. Transcriptomic sequencing results revealed that the A549-GFP-LUC-BM3 cell line had 2954 differentially expressed genes compared to the parental cells, with 1021 genes up-regulated and 1933 genes down-regulated. Gene Ontology (GO) functional enrichment analysis indicated that the differentially expressed genes were primarily localized in cellular components such as the cell periphery. The molecular functions identified as significantly enriched included signaling receptor activity, calcium ion binding, and extracellular matrix structural constituent. Additionally, the biological processes found to be enriched were cell adhesion and biological adhesion. The enrichment analysis conducted using the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that the differentially expressed genes were primarily involved in the metabolism of xenobiotics by cytochrome P450, retinol metabolism, drug metabolism-cytochrome P450, cell adhesion molecules, steroid hormone biosynthesis, and the nuclear factor kappa B (NF-κB) signaling pathway. The highly bone-metastatic human lung adenocarcinoma cell line with GFP and luciferase double labeling was successfully established. The biological behavior and transcriptome sequencing of the cell line suggest that it has a high bone-metastatic potential.

Transcriptomic and western blot characterisation of the human CLEFF4 clone, a new rapid cell line replacement for the Caco2 model

The CLEFF4 sub clone from stock late passage Caco2 cells has a unique property of being able to develop polarised cell monolayers with high P-gp expression and tight junctions much quicker than the original cell line. Instead of being useful for transport studies 21–24 days after initiating culture, the CLEFF4 cell line matures in 5–6 days with tight junctions surpassing that of 3 week old Caco2 cells in that time frame [1].This has enabled the CLEFF4 cell line to provide measures of apparent permeability for potential drug candidates, so important for pre-clinical drug development, 4 times faster than the original cell line. RNA samples were collected and analysed at days 4 and 7 of culture over a 3 year period and had full RNA transcriptome analysed by the ranaseq.eu open bioinformatics platform. Protein was also collected from day 4 to day 22 of culture. Differential expression data from the FASTQ files have shown significant differences in expression in multiple genes involved with drug efflux, tight junctions, phase 2 metabolism and growth factors, which have been confirmed from protein determination that may hold the key to understanding accelerated human cell maturation. These gene expression results may be significant for other tissues beyond the gastrointestinal tract, and potentially for accelerated cell growth for the new field of laboratory grown tissues for organ replacement. The data also confirms the different genetic expression in CLEFF4 cells compared to Caco2 and the stable nature of the different expression over many years.

ScRNAseq and High-Throughput Spatial Analysis of Tumor and Normal Microenvironment in Solid Tumors Reveal a Possible Origin of Circulating Tumor Hybrid Cells.

Metastatic cancer is a leading cause of death in cancer patients worldwide. While circulating hybrid cells (CHCs) are implicated in metastatic spread, studies documenting their tissue origin remain sparse, with limited candidate approaches using one-two markers. Utilizing high-throughput single-cell and spatial transcriptomics, we identified tumor hybrid cells (THCs) co-expressing epithelial and macrophage markers and expressing a distinct transcriptome. Rarely, normal tissue showed these cells (NHCs), but their transcriptome was easily distinguishable from THCs. THCs with unique transcriptomes were observed in breast and colon cancers, suggesting this to be a generalizable phenomenon across cancer types. This study establishes a framework for HC identification in large datasets, providing compelling evidence for their tissue residence and offering comprehensive transcriptomic characterization. Furthermore, it sheds light on their differential function and identifies pathways that could explain their newly acquired invasive capabilities. THCs should be considered as potential therapeutic targets.

Phylogenetic and transcriptomic characterization of insulin and growth factor receptor tyrosine kinases in crustaceans.

Receptor tyrosine kinases (RTKs) mediate the actions of growth factors in metazoans. In decapod crustaceans, RTKs are implicated in various physiological processes, such molting and growth, limb regeneration, reproduction and sexual differentiation, and innate immunity. RTKs are organized into two main types: insulin receptors (InsRs) and growth factor receptors, which include epidermal growth factor receptor (EGFR), fibroblast growth factor receptor (FGFR), vascular endothelial growth factor receptor (VEGFR), and platelet-derived growth factor receptor (PDGFR). The identities of crustacean RTK genes are incomplete. A phylogenetic analysis of the CrusTome transcriptome database, which included all major crustacean taxa, showed that RTK sequences segregated into receptor clades representing InsR (72 sequences), EGFR (228 sequences), FGFR (129 sequences), and PDGFR/VEGFR (PVR; 235 sequences). These four receptor families were distinguished by the domain organization of the extracellular N-terminal region and motif sequences in the protein kinase catalytic domain in the C-terminus or the ligand-binding domain in the N-terminus. EGFR1 formed a single monophyletic group, while the other RTK sequences were divided into subclades, designated InsR1-3, FGFR1-3, and PVR1-2. In decapods, isoforms within the RTK subclades were common. InsRs were characterized by leucine-rich repeat, furin-like cysteine-rich, and fibronectin type 3 domains in the N-terminus. EGFRs had leucine-rich repeat, furin-like cysteine-rich, and growth factor IV domains. N-terminal regions of FGFR1 had one to three immunoglobulin-like domains, whereas FGFR2 had a cadherin tandem repeat domain. PVRs had between two and five immunoglobulin-like domains. A classification nomenclature of the four RTK classes, based on phylogenetic analysis and multiple sequence alignments, is proposed.

Characterization of the malignant cells and microenvironment of infantile fibrosarcoma via single-cell RNA sequencing.

Infantile fibrosarcoma (IFS) is the most prevalent soft tissue sarcoma in children under 1 year old and is known for its rapid growth. The tumor lacks specific immunohistochemical tumor marker and a general view of tumor microenvironment (TME). Its primary therapeutic intervention places patients at a risk of disability or mutilation. This study aimed to elucidate the universal transcriptional characteristics of IFS and explore novel targets for diagnosis and therapy using single-cell RNA sequencing (scRNA-seq). Fresh tissue samples of IFS for scRNA-seq were collected from four patients before other treatments were administered. We conducted cell clustering, inferring copy number variation from scRNA-seq (InferCNV) analysis, gene differential expression analysis, cell function evaluation, Pearson correlation analysis, and cell-cell and ligand-receptor interaction analysis to investigate the distinct ecosystem of IFS. According to the single-cell resolution data, we depicted the cell atlas of IFS, which comprised 14 cell populations. Through comparison with normal cells, the malignant cells were distinguished, and potential novel markers (POSTN, IGFBP2 and CTHRC1) were identified. We also found four various functional malignant cell subtypes, three of which exhibited cancer stem cells (CSCs) phenotypes, and investigated the interplay between these subtypes and nonmalignant cells in the TME of IFS. Endothelial cells and macrophages were found to dominate the cell-cell communication landscape within the microenvironment, promoting tumorigenesis via multiple receptor-ligand interactions. This study provides a comprehensive characterization of the tumor transcriptome and TME of IFS at the cellular level, offering valuable insights for clinically significant advancements in the immunohistochemical diagnosis and treatment of IFS.

Identification of cells of leukemic stem cell origin with non-canonical regenerative properties

Despite most acute myeloid leukemia (AML) patients entering remission following chemotherapy, outcomes remain poor due to surviving leukemic cells that contribute to relapse. The nature of these enduring cells ispoorly understood. Here, through temporal single-cell transcriptomic characterization of AML hierarchical regeneration in response to chemotherapy, we reveal a cell population: AML regeneration enriched cells(RECs). RECs are defined by CD74/CD68 expression, and although derived from leukemic stem cells (LSCs), are devoid of stem/progenitor capacity. Based on REC in situ proximity to CD34-expressing cells identified using spatial transcriptomics on AML patient bone marrow samples, RECs demonstrate the ability to augment or reduce leukemic regeneration invivo based on transfusion or depletion, respectively. Furthermore, RECs are prognostic for patient survival as well as predictive of treatment failure in AML cohorts. Our study reveals RECs as a previously unknown functional catalyst of LSC-driven regeneration contributing to the non-canonical framework of AML regeneration.

Transcriptomic characterization of the histopathological growth patterns in breast cancer liver metastases.

Metastatic breast cancer (mBC) remains incurable and liver metastases (LM) are observed in approximately 50% of all patients with mBC. In some cases, surgical resection of breast cancer liver metastases (BCLM) is associated with prolonged survival. However, there are currently no validated marker to identify these patients. The interactions between the metastatic cancer cells and the liver microenvironment result in two main histopathological growth patterns (HGP): replacement (r-HGP), characterized by a direct contact between the cancer cells and the hepatocytes, and desmoplastic (d-HGP), in which a fibrous rim surrounds the tumor cells. In patients who underwent resection of BCLM, the r-HGP is associated with a worse postoperative prognosis than the d-HGP. Here, we aim at unraveling the biological differences between these HGP within ten patients presenting both HGP within the same metastasis. The transcriptomic analyses reveal overexpression of genes involved in cell cycle, DNA repair, vessel co-option and cell motility in r-HGP while angiogenesis, wound healing, and several immune processes were found overexpressed in d-HGP LM. Understanding the biology of the LM could open avenues to refine treatment of BC patients with LM.

Abstract 5072: Multi-omic, multi-scale characterisation of colorectal cancer defines spatiotemporal patterns of recurrence

Abstract Aim: Patients who undergo intended curative resection of colorectal cancer (CRC) have a 20-25% chance of metachronous recurrence, the site and timing of which are unpredictable and resistant to current treatment. The biological basis for such heterogeneous disease behavior remains to be elucidated. Bulk transcriptomic profiling and subsequently single-cell RNAseq have provided insight in the epithelial subtypes and immune microenvironment. Recently spatially resolved transcriptomic assessment allow molecular profiling of tissue while preserving tissue architecture. Utilizing ST technology we sought to perform deep characterization of a large cohort of patients with primary CRC with the intention to decipher the biological determinants of spatio-temporal patterns of recurrence. Methods: 750 patients who underwent resection of CRC with mature follow up were studied. Bulk transcriptomic, genomic and multiplex immune characterization was performed using a TMA format. Of these, 28 patients were assessed using single cell spatial transcriptomics (Nanostring CosMx Spatial Molecular Imager (SMI, 1000plex gene panel)), 120 tumors underwent regional whole transcriptome profiling of epithelium and TME (Nanostring GeoMx Digital Spatial Profiler using FFPE tissue). We used image analysis and bioinformatics to integrate these complex datasets in over 120000 single-cells in the context of their spatial tissue architecture and clinicopatholgical outcome and recurrence data. Results: Using the CosMx SMI we characterized cells with complete topographic detail and defined 2 unique epithelial cell states defined. Each epithelial state had distinct spatial properties including cell size and morphology, average distance to nearest lymphocyte, neighboring cell types and stromal neighborhood. This epithelial signature was integrated in GeoMx samples and were found to predict recurrence (p<0.05). The Epithelial, Fibroblast and Immune GeoMx transcriptomic compartments were expanded and grouped using unsupervised clustering. Each compartment demonstrated groups of patients where specific spatially derived signatures could predict site and time of recurrence (p<0.05). Conclusions: By maintaining the tissue structure, we have directly measured cellular interactions and captured cells commonly missed during dissociative studies whilst defining novel molecular subtypes of CRC with clinical relevance. Novel platforms such as CosMx allow deeper characterization of unique cell types and cellular interactions that may pave the way for novel therapeutics and precision medicine for patients with CRC. Citation Format: Colin Stuart Wood, Joao Da Silva Filho, Andrew Cameron, Assya Legrini, Holly Leslie, Tengyu Zhang, Yoana Doncheva, Claire Kennedy-Dietrich, Matthias Marti, Joanne Edwards, Paul Horgan, Campbell Roxburgh, Colin Steele, Nigel Jamieson. Multi-omic, multi-scale characterisation of colorectal cancer defines spatiotemporal patterns of recurrence [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 5072.

Abstract 4187: Transcriptome profiling and characterization of peritoneal metastasis ovarian cancer xenografts in humanized mice

Abstract Background: Although immunotherapy has not yet been as successful in ovarian cancer (OC), it remains a potential therapeutic strategy. Preclinical models of OC are necessary to evaluate the efficacy of immuno-oncology (IO) drugs targeting human cancer and immune components but have been underutilized. Developing mouse models with a humanized (Hu) immune system can help understand the human immune response to IO drugs, including immune checkpoint inhibitors (ICIs), which have demonstrated limited effectiveness in OC patients. Methods: We established OC xenograft Hu-mouse models by intraperitoneally injecting luciferase-expressing SKOV-3 Luc and OVCAR-3 Luc OC cells into CD34+ Hu-mice. Tumor growth was monitored through bioluminescence imaging (BLI). We assessed the efficacy of PD-1 blockade with pembrolizumab in the SKOV-3 Luc Hu-mouse model. The immune profiles of the tumors were characterized using colorimetric immunostaining and flow cytometry. Additionally, we analyzed RNA-seq data to investigate the gene expression signature of pembrolizumab refractory tumors. Results: We confirmed tumor development in both OC cell lines within CD34+ Hu-mice. In these models, human lymphocyte and myeloid cell subsets were present in the tumors, draining lymph nodes, blood, and spleens. The SKOV-3 Luc tumor-bearing Hu-mice did not respond to pembrolizumab monotherapy. These tumors exhibited a high presence of tumor-infiltrating macrophages. Tumors in Hu-mice unresponsive to pembrolizumab showed a lower abundance of CD8+ T-cells, memory B cells, plasma cells, and a higher proportion of naïve M0 macrophages and mast cells compared to the PBS control. Furthermore, we identified 43 significantly enriched gene sets in these tumors. The differentially expressed genes (DEGs) were predominantly enriched in HDAC class I, RB1, KLF1/3, TCF21, MYD88, SMARCE1 target genes, and genes associated with epithelial-mesenchymal transition (EMT) and fibroblasts. Conclusion: Our xenograft Hu-mouse model of OC provides a valuable tool for investigating the efficacy of IO drugs. The insights gained from this model offer potential avenues to explore mechanisms of resistance to PD-1/PD-L1 blockade in OC. Citation Format: Sung Wan Kang, Ji-young Lee, Ok-Ju Kang, Yong-Man Kim, Eun Kyung Choi, Shin-Wha Lee. Transcriptome profiling and characterization of peritoneal metastasis ovarian cancer xenografts in humanized mice [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 4187.

Abstract 1143: Dissection of melanoma and cutaneous lymphoma spatial molecular architecture by multimodal single-cell and spatial transcriptomics with generative AI

Abstract Advances in single-cell multiomic technologies have revolutionized our understanding of how heterogeneous cell types and cell states shape the tumor microenvironment (TME). However, dissociated single cell profiling lacks spatial context. To resolve the organization, cell-cell communication, and granular structures in the TME, new single-cell spatial transcriptomic (ST) characterizations are needed. Here, we dissected the spatial molecular architecture of the melanoma (30 tumors, 30 patients) and transformed cutaneous T-cell lymphoma (tCTCL, 12 tumors, 6 patients) TMEs by Multiplexed Error-Robust FISH (305 gene MERFISH), with benchmarking scRNAseq data from matched tissues (6 melanoma scFFPEseq, 6 tCTCL scVDJ/RNAseq) for cross-platform validation. We profiled 565,122 cells in melanoma and 92584 cells in tCTCL by MERFISH. We interrogated both datasets using a novel computational framework that includes cell typing by Leiden clustering and marker genes, spatial neighborhood and receptor-ligand (R-L) analyses, and spatial/scRNA imputation via deep learning. In the melanoma dataset, we identified tumor cells, major TME cell types, and rare immune cell types (TCF7+ stem-like T-cells and CD3+TCRα+PAX5+CD79a+ B/T dual-expressor lymphocytes enriched in tertiary lymphoid structures). All cell types were validated in scFFPEseq. As immune R-L interactions are critical therapeutic targets, we developed a novel computation method to quantify spatial R-L interactions by accounting for cell-cell distance, identifying spatially informed R-L pairs that differ from dissociation-based inferences. CNV inference from melanoma scFFPEseq revealed intratumoral heterogeneity (ITH). We therefore adapted the conditional variational autoencoder ENVI to simultaneously incorporate scRNA and MERFISH spatial data into a unified latent embedding. ENVI-ITH successfully learned ITH subgroup information, enabling imputation of phylogenetic lineages on spatial MERFISH. CTCL MERFISH data revealed major TME cell types, yet separation of malignant vs benign T-cells by clustering and marker approaches is hindered by their overlapping gene expression. To overcome this barrier, we deployed ENVI to impute patient-specific malignant and benign TCR clonotypes by training on the matched scVDJ/RNA data, yielding an ENVI-TCR pipeline that can delineate malignant vs benign T-cells in situ. We validated the spatial pattern of malignant T-cells by patient-specific in situ TCR probes. In sum, we have interrogated the melanoma and CTCL TME by MERFISH and presented a novel computational framework for robustly co-embedding scRNA data with imaging-based ST to spatially resolve melanoma ITH and malignant/benign T-cell populations. We believe this approach will be highly impactful for melanoma and CTCL and can be broadly applied to other solid tumors and lymphomas. Citation Format: Zichao Liu, Xiaofei Song, Jiang He, Justin He, Jodi Balasi, Jeffrey H. Chuang, Pei-Ling Chen. Dissection of melanoma and cutaneous lymphoma spatial molecular architecture by multimodal single-cell and spatial transcriptomics with generative AI [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 1143.

Abstract 6853: Spatial proteomic and transcriptomic characterization of the inflammatory landscape of formalin fixed paraffin embedded Barrett’s esophagus tissues

Abstract Esophageal adenocarcinoma (EAC), a significant cause of morbidity and mortality, develops from its metaplastic precursor lesion termed Barrett’s esophagus (BE). BE progresses to EAC within an inflammation rich environment, however a detailed understanding of the types of inflammatory cells present, how that population changes over time or diagnosis, and the related immunomodulatory pathways that may mediate BEs progression is still understudied. Traditional immunohistochemistry is often inadequate to provide detailed information about a broad number of cells, local cellular proportions, and cellular heterogeneity; while bulk or single cell RNA sequencing lose the spatial context and relationships between the stroma and epithelium. Utilizing modern multiplex profiling technologies such as Nanostring’s GeoMx digital Profiler (DSP) aid in identifying both cellular composition and distribution of cells within the epithelium and stroma. Therefore, our aim of this study was to determine the suitability of the DSP platform for analyzing formalin fixed paraffin embedded (FFPE) endoscopic samples of BE and determine any differences between non-dysplastic BE (NDBE) samples from patients who eventually progressed (progressors) compared to those who did not (non-progressors), with the goal to gain deeper insights about cellular composition and spatial distribution of immune cells that may dictate progression of BE. Our secondary goal was to investigate the relationship of these cells to the BE epithelial cells through understanding the immune signaling and regulatory pathways. Our pilot study utilizing a 49-plex antibody panel on 7 NDBE samples from progressors and 8 NDBE samples from non-progressors showed good quality metrics and deciphered an immune rich microenvironment in BE with several immune markers including CD66b (neutrophils), CD14 (monocytes), CD68 (macrophages) and CD56 (NK cells) being overexpressed in the stroma of progressors compared with non-progressors, corrected p value less than 0.05. The myeloid activation marker CD80 was overexpressed in the BE epithelial cells of progressors. To determine how spatial transcriptomic profiling performed in FFPE endoscopic samples, 1,812 transcripts within 48 regions of interest of four BE, HGD, and EAC samples was interrogated. Only 36 (2%) probes fell below the limit of detection quality threshold. Thus, our pilot results show that robust proteomic and transcriptomic profiling can be obtained from endoscopic BE biopsies using this system. Based on these results, we systematically interrogated the immune cell makeup and distribution as well as their related inflammatory and immunoregulatory pathways in 40 NDBE biopsies (20 progressors and 20 with stable non-progressing disease) within discrete compartments (stroma and epithelium) through spatial whole transcriptome profiling. Citation Format: Qurat ul Ain, Nicola Frei, Amir M. Khoshiwal, Pim Stougie, Robert Odze, Sophie Camilleri-Broet, Lorenzo Ferri, Lucas C. Duits, Jacques Bergman, Matthew D. Stachler. Spatial proteomic and transcriptomic characterization of the inflammatory landscape of formalin fixed paraffin embedded Barrett’s esophagus 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 6853.

Abstract 2884: Resistance to pan-FGFR inhibition is determined by the EMT phenotype associating with clinical outcome in HNSCC

Abstract Receptor tyrosine kinases (RTK) and integrins coalesce at focal adhesions. These cell membrane areas serve as huge signaling hubs critically contributing to central aspects of cancer cell survival and therapy resistance. Despite the fact that these receptors mutually interact, co-dependencies between these receptors and associated therapeutically exploitable vulnerabilities remain largely unclear in HPV-negative head and neck squamous cell carcinoma (HNSCC). Here, we evaluated the cytotoxic and radiochemosensitizing potential of targeting 10 RTK and β1 integrin in up to 20 different 3D matrix grown HNSCC cell models. RNA sequencing and protein-based biochemical assays were performed for molecular and pathway characterization. Bioinformatically identified transcriptomic signatures were applied to patient cohorts to show clinical relevance. Our observations demonstrate that fibroblast growth factor receptors (FGFR 1-4) present with the strongest cytotoxic and radiosensitizing potential, both as monotherapy and in combination with β1 integrin inhibition, surpassing the efficacy of the other investigated RTK. Pharmacological pan-FGFR inhibition elicited a variable response spectrum ranging from cytotoxicity/radiochemosensitization to resistance/radioprotection. Transcriptomic characterization revealed an association of these contrasting responses to FGFR inhibition with a mesenchymal-to-epithelial transition (MET) for sensitive cell models and a partial epithelial-to-mesenchymal transition (EMT) for resistant cell models. Accordingly, deactivation of EMT associated kinases like EGFR, PKC and PAK proved effective in diminishing the adaptive FGFR-driven resistance. Importantly, the translation of the adaptive resistance profiles to HNSCC patient cohorts showed its prognostic value and provided conclusive validation of the presence of EMT-related vulnerabilities that can be strategically used for therapeutic intervention. In conclusion, our study demonstrates that pan-FGFR inhibition induces both a highly beneficial radiochemosensitizing and a detrimental radioprotective effect in HNSCC cell models. Adaptive EMT-associated resistance appears to be of clinical importance, and we provide effective molecular approaches to exploit this therapeutically. Citation Format: Felix Broghammer, Mahesh Gouda, Irina Korovina, Cornelia Brunner, Robert P. Coppes, Olivier Gires, Michael Seifert, Nils Cordes. Resistance to pan-FGFR inhibition is determined by the EMT phenotype associating with clinical outcome in HNSCC [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 2884.

Abstract 1846: Integrative histopathologic, proteomic, phosphoproteomic, genomic, and transcriptomic characterization of renal cell carcinoma

Abstract Although histologically defined subtypes exist, renal cell carcinoma (RCC) is a heterogenous disease, resulting in various treatment outcomes and prognosis. Here, we conduct comprehensive profiling of RCC with histopathologic, proteomic, phosphoproteomic, genomic, and transcriptomic analyses on tumor and paired adjacent normal tissues from 113 patients. RCC tumors are distinctly separated from corresponding normal tissues through multi-omics clustering, a distinction further supported by pathway analysis. In addition, various hallmarks of cancer were differentially observed at the individual patient level, highlighting the intertumoral heterogeneity of RCC. Proteomic subtyping classifies RCC tumors into four subtypes (C1-4) with distinct phosphoproteomic, genomic, and transcriptomic characteristics with prognostic and predictive implications. Among these subtypes, C1-3 were almost composed of clear cell RCC (ccRCC; 96.8%), whereas C4 was composed of non-clear cell RCC (nccRCC) or other types of cancer (100.0%). Among each subtype, C1 (N=37) exhibits the strongest adaptive immune response and angiogenesis with favorable prognosis after surgical resection. C2 (N=39) was characterized with enrichment in DNA repair pathways and alteration in VHL (100.0%) along with BAP1 (24.0%) genes. C3 (N=19) was associated with enrichment in inflammatory response with dismal prognosis and therapeutic resistance to tyrosine kinase inhibitors targeting vascular endothelial growth factor receptors. C4 (N=18) was exclusively enriched with nccRCC with active mitochondrial and oxidation phosphorylation. Transglutaminase 2 (TGM2), a crosslinking enzyme, is identified as a potential marker with therapeutic implication for ccRCC. Collectively, this study reports a large-scale multi-omics-based approach of RCC, providing insights into biologic underpinning and evidence for rational treatment selection as well as linking the multi-omics-derived phenotypes to clinical outcomes of ccRCC. Citation Format: Woo Sun Kwon, Chang Gon Kim, Harim Koo, Woo Kyun Bae, Eu Chang Hwang, Won Sik Ham, Nam Hoon Cho, Jason K. Sa, Jong Bae Park, Sun Young Rha. Integrative histopathologic, proteomic, phosphoproteomic, genomic, and transcriptomic characterization of renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1846.

Abstract 3786: Genomic and transcriptomic characterization of peritoneal, lung and liver metastases of colorectal carcinoma reveals site-specific differences

Abstract Background: Metastasis in colorectal cancer (CRC) is a critical factor in patient outcomes, with 20% of patients affected at the time of diagnosis and up to 50% developing metachronous metastatic disease later on. Despite the growing importance of metastatic sites as independent predictors of overall survival (OS) and the ongoing development of new treatments, there has been limited effort to personalize systemic treatment based on specific metastatic locations. Aim: This study aims to compare the genomic landscape of different metastatic sites in CRC to detect novel diagnostic and therapeutic targets. Methods: DNA whole-genome-sequencing and RNA gene expression data from metastatic CRC samples were retrieved from the Hartwig Medical Foundation (HMF). Single nucleotide variants (SNVs), somatic copy number aberrations (SCNAs) and structural variants (SVs) were reported by HMF with their pipelines. In addition, focal amplifications and deletions were identified using GISTIC2 (v6.15.30). We included 464 microsatellite stable samples derived from liver metastases (n=369), peritoneal metastases (n=58) and lung metastases (n=37). We compared DNA mutation frequencies between tumors from different metastatic sites (two-sided Mann-Whitney tests) and performed differential gene expression and pathway enrichment analysis. Results: Liver metastases had the highest number of focal SCNAs per sample (median 33 vs 17 in peritoneum (p < 0.001); vs 18 in lung (p < 0.001)). Furthermore, we observed 39 site-specific SCNAs in liver, 9 in peritoneal and 15 in lung metastases. Of these, the most significant focal SCNAs were an amplification within 20q13.12 (79%) and deletion within 1p35.3 (64%) in peritoneal metastases and a deletion within 18q21.1 (84%) in lung metastases. Furthermore, peritoneal metastases displayed less genomic instability, featuring lower ploidy (median 2.65 vs 2.94 in liver (p=0.025); vs 3.15 in lung (p=0.025)) and lower aneuploidy scores (median 19 vs 26 in liver (p=0.016); vs 30 in lung (p=0.016)) while having no significant differences in tumor mutational burden or individual SNVs. Analysis of SVs revealed that peritoneal metastases exhibited fewer deletions (≥10kb; 1.3x fold change increase in liver and lung) and fewer duplications (≥1kb; 1.4x fold change increase in liver). Differential gene expression analysis uncovered higher expression of gene sets involved in the apical junction and the TGF-beta-signaling pathway in peritoneal metastases. Conclusion: Specific focal SCNA and differences in genomic instability exhibit an association with preferential organotropism in CRC metastasis and could offer potential targets for the development of new diagnostic and therapeutic approaches. Citation Format: Nerma Crnovrsanin, Soufyan Lakbir, Renske d. Wit, Steven L. Ketelaars, Niels F. Kok, Petur Snaebjornsson, Gerrit A. Meijer, Sanne Abeln, Remond J. Fijneman. Genomic and transcriptomic characterization of peritoneal, lung and liver metastases of colorectal carcinoma reveals site-specific differences [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 3786.

Integrated Transcriptomic and Proteomic Characterization of a Chromosome Segment Substitution Line Reveals the Regulatory Mechanism Controlling the Seed Weight in Soybean

Soybean is the major global source of edible oils and vegetable proteins. Seed size and weight are crucial traits determining the soybean yield. Understanding the molecular regulatory mechanism underlying the seed weight and size is helpful for improving soybean genetic breeding. The molecular regulatory pathways controlling the seed weight and size were investigated in this study. The 100-seed weight, seed length, seed width, and seed weight per plant of a chromosome segment substitution line (CSSL) R217 increased compared with those of its recurrent parent ‘Suinong14’ (SN14). Transcriptomic and proteomic analyses of R217 and SN14 were performed at the seed developmental stages S15 and S20. In total, 2643 differentially expressed genes (DEGs) and 208 differentially accumulated proteins (DAPs) were detected at S15, and 1943 DEGs and 1248 DAPs were detected at S20. Furthermore, integrated transcriptomic and proteomic analyses revealed that mitogen-activated protein kinase signaling and cell wall biosynthesis and modification were potential pathways associated with seed weight and size control. Finally, 59 candidate genes that might control seed weight and size were identified. Among them, 25 genes were located on the substituted segments of R217. Two critical pathways controlling seed weight were uncovered in our work. These findings provided new insights into the seed weight-related regulatory network in soybean.

Comparative transcriptomic characterization of the ovary in the spawning process of the mud crab Scylla paramamosain.

Oviposition is induced upon mating in most insects. Spawning is a physiological process that is fundamental for the reproduction of Scylla paramamosain. However, the molecular mechanisms underlying the spawning process in this species are poorly understood. Herein, comprehensive ovary transcriptomic analysis was conducted at the germinal vesicle breakdown stage (GVBD), spawning stage, 0.5 h post-spawning stage, and 24 h post-spawning stage of S. paramamosain for gene discovery. A total of 67,230 unigenes were generated, and 27,975 (41.61%) unigenes were annotated. Meanwhile, the differentially expressed genes (DEGs) between the different groups were identified, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was subsequently conducted. These results suggested that octopamine (OA) and tyramine (TA) could induce oviposition, while dopamine (DA) and serotonin (5-hydroxytryptamine [5-HT]) inhibit oviposition. The 20-hydroxyecdysone (20E) and methyl farnesoate (MF) signal pathways might be positively associated with oviposition. Furthermore, numerous transcripts that encode neuropeptides and their G-protein-coupled receptors (GPCRs), such as CNMamide, RYamide, ecdysis-triggering hormone (ETH), GPA2/GPB5 receptor, and Moody receptor, appear to be differentially expressed during the spawning process. Eleven unigenes were selected for qRT-PCR and the pattern was found to be consistent with the transcriptome expression pattern. Our work is the first spawning-related investigation of S. paramamosain focusing on the ovary at the whole transcriptome level. These findings assist in improving our understanding of spawning regulation in S. paramamosain and provide information for oviposition studies in other crustaceans.