Extracellular Matrix Interactions Research Articles

Visible light photo-crosslinking of biomimetic gelatin-hyaluronic acid hydrogels for adipose tissue engineering

Tissue engineering (TE) of adipose tissue (AT) is a promising strategy that can provide 3D constructs to be used for in vitro modelling, overcoming the limitations of 2D cell cultures by closely replicating the complex breast tissue extracellular matrix (ECM), cell-cell, and cell-ECM interactions. However, the challenge in developing 3D constructs of AT resides in designing artificial matrices that can mimic the structural properties of native AT and support adipocytes biological functions. Herein, we developed photocrosslinkable hydrogels by employing gelatin methacrylate (GelMA) and hyaluronic acid methacrylate (HAMA) to mimic the collagenous and glycosaminoglycan components of AT microenvironment, respectively. The physico-mechanical properties of the hydrogels were tuned to target AT biomimetic properties by varying the hydrogel formulation (with or without hyaluronic acid), and the amount of photoinitiator (ruthenium/sodium persulfate) used to crosslink the hydrogels via visible light. The physical and mechanical properties of the developed hydrogels were tuned by varying the material formulation and the photoinitiator concentration. Preadipocytes were encapsulated inside the hydrogels and differentiated into mature adipocytes. Findings enlightened that HAMA addition in hybrid hydrogels boosted an increased lipid accumulation. The engineered biomimetic adipocyte-based constructs resulted promising as scaffolds or 3D in vitro models of AT.

Dynamic duo: Cell–extracellular matrix interactions in hair follicle development and regeneration

Ectodermal organs, such as hair follicles, originate from simple epithelial and mesenchymal sheets through a complex developmental process driven by interactions between these cell types. This process involves dermal condensation, placode formation, bud morphogenesis, and organogenesis, and all of these processes require intricate interactions among various tissues. Recent research has emphasized the crucial role of reciprocal and dynamic interactions between cells and the extracellular matrix (ECM), referred to as the “dynamic duo”, in the development of ectodermal organs. These interactions provide spatially and temporally changing biophysical and biochemical cues within tissues. Using the hair follicle as an example, this review highlights two types of cell–ECM adhesion units—focal adhesion-type and hemidesmosome-type adhesion units—that facilitate communication between epithelial and mesenchymal cells. This review further explores how these adhesion units, along with other cell–ECM interactions, evolve during hair follicle development and regeneration, underscoring their importance in guiding both developmental and regenerative processes.

Breast Cancer: Extracellular Matrix and Microbiome Interactions.

Breast cancer represents the most prevalent form of cancer and the leading cause of cancer-related mortality among females worldwide. It has been reported that several risk factors contribute to the appearance and progression of this disease. Despite the advancements in breast cancer treatment, a significant portion of patients with distant metastases still experiences no cure. The extracellular matrix represents a potential target for enhanced serum biomarkers in breast cancer. Furthermore, extracellular matrix degradation and epithelial-mesenchymal transition constitute the primary stages of local invasion during tumorigenesis. Additionally, the microbiome has a potential influence on diverse physiological processes. It is emerging that microbial dysbiosis is a significant element in the development and progression of various cancers, including breast cancer. Thus, a better understanding of extracellular matrix and microbiome interactions could provide novel alternatives to breast cancer treatment and management. In this review, we summarize the current evidence regarding the intricate relationship between breast cancer with the extracellular matrix and the microbiome. We discuss the arising associations and future perspectives in this field.

Transcriptome analysis of human dental pulp cells cultured on a novel cell-adhesive fragment by RNA sequencing

AimThe aim of the present work was to find an efficient method for safe and reliable expansion of human dental pulp cells (hDPCs) in vitro. Here, we examined the effect of a novel recombinant E8 fragment of Laminin-511 (iMatrix-511) in hDPCs regarding viability and cell spreading. Further, we investigated the underlying mechanisms governing its effects in hDPCs using RNA sequencing (RNA-seq). MethodologyhDPCs were obtained from caries-free maxilla third molars (n = 3). CCK-8 assay was conducted to measure the viability of cells cultured on iMatrix-511 and two other ECM proteins. Cell morphology was observed by phase contrast microscope. RNA-seq of hDPCs cultured on iMatrix-511 or noncoated control was performed on Illumina NovaseqTM 6000 platform. ResultsiMatrix-511 (0.5 μg/cm2) enhanced the viability of hDPCs to an extent better than COL-1 and gelatin. Short term culture of hDPCs on iMatrix-511 resulted in 233 differentially expressed genes (DEGs). The top 12 most upregulated genes were XIAP, AL354740, MRFAP1, AC012321, KCND3, TMEM120B, AC009812, GET1-SH3BGR, CNTN3, AC090409, GEN1 and PIK3IP1, whereas the top 12 most downregulated genes were SFN, KRT17, RAB4B-EGLN2, CSTA, KCTD11, ATP6V1G2-DDX39B, AC010323, SBSN, LYPD3, FOSB, AC022400 and CHI3L1.qPCR validation confirmed the significant upregulation of GEN1, KCND3, PIK3IP1 and MRFAP1. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed, with genes enriched in various extracellular matrix interaction, estrogen and fat metabolism-related functions and pathways. ConclusionsiMatrix-511 facilitated spreading and proliferation of hDPCs. It enhances expression of anti-apoptotic genes, while inhibits expression of epidermis development-related genes.

Natural Hydrogels Support Kidney Organoid Generation and Promote In Vitro Angiogenesis.

To date, strategies aiming to modulate cell to extracellular matrix (ECM) interactions during organoid derivation remain largely unexplored. Here renal decellularized ECM (dECM) hydrogels are fabricated from porcine and human renal cortex as biomaterials to enrich cell-to-ECM crosstalk during the onset of kidney organoid differentiation from human pluripotent stem cells (hPSCs). Renal dECM-derived hydrogels are used in combination with hPSC-derived renal progenitor cells to define new approaches for 2Dand 3Dkidney organoid differentiation, demonstrating that in the presence of these biomaterials the resulting kidney organoids exhibit renal differentiation features and the formation of an endogenous vascular component. Based on these observations, a new method to produce kidney organoids with vascular-like structures is achieved through the assembly of hPSC-derived endothelial-like organoids with kidney organoids in 3D. Major readouts of kidney differentiation and renal cell morphology are assessed exploiting these culture platforms as new models of nephrogenesis. Overall, this work shows that exploiting cell-to-ECM interactions during the onset of kidney differentiation from hPSCs facilitates and optimizes current approaches for kidney organoid derivation thereby increasing the utility of these unique cell culture platforms for personalized medicine.

Proteomic profiling of mesenchymal stem cell-derived extracellular vesicles: Impact of isolation methods on protein cargo.

Extracellular vesicles (EVs) are nanosized vesicles with a lipid bilayer that are secreted by cells and play a critical role in cell-to-cell communication. Despite the promising reports regarding their diagnostic and therapeutic potential, the utilization of EVs in the clinical setting is limited due to insufficient information about their cargo and a lack of standardization in isolation and analysis methods. Considering protein cargos in EVs as key contributors to their therapeutic potency, we conducted a tandem mass tag (TMT) quantitative proteomics analysis of three subpopulations of mesenchymal stem cell (MSC)-derived EVs obtained through three different isolation techniques: ultracentrifugation (UC), high-speed centrifugation (HS), and ultracentrifugation on sucrose cushion (SU). Subsequently, we checked EV marker expression, size distribution, and morphological characterization, followed by bioinformatic analysis. The bioinformatic analysis of the proteome results revealed that these subpopulations exhibit distinct molecular and functional characteristics. The choice of isolation method impacts the proteome of isolated EVs by isolating different subpopulations of EVs. Specifically, EVs isolated through the high-speed centrifugation (HS) method exhibited a higher abundance of ribosomal and mitochondrial proteins. Functional apoptosis assays comparing isolated mitochondria with EVs isolated through different methods revealed that HS-EVs, but not other EVs, induced early apoptosis in cancer cells. On the other hand, EVs isolated using the sucrose cushion (SU) and ultracentrifugation (UC) methods demonstrated a higher abundance of proteins primarily involved in the immune response, cell-cell interactions and extracellular matrix interactions. Our analyses unveil notable disparities in proteins and associated biological functions among EV subpopulations, underscoring the importance of meticulously selecting isolation methods and resultant EV subpopulations based on the intended application.

Targeting the core program of metastasis with a novel drug combination.

We previously reported that metastases are generally characterized by a core program of gene expression that activates tissue remodeling/vascularization, alters ion homeostasis, induces the oxidative metabolism, and silences extracellular matrix interactions. This core program distinguishes metastases from their originating primary tumors as well as from their destination host tissues. Therefore, the gene products involved are potential targets for anti-metastasis drug treatment. Because the silencing of extracellular matrix interactions predisposes to anoiks in the absence of active survival mechanisms, we tested inhibitors against the other three components. Individually, the low-specificity VEGFR blocker pazopanib (in vivo combined with marimastat), the antioxidant dimethyl sulfoxide (or the substitute atovaquone, which is approved for internal administration), and the ionic modulators bumetanide and tetrathiomolybdate inhibited soft agar colony formation by breast and pancreatic cancer cell lines. The individual candidate agents have a record of use in humans (with limited efficacy when administered individually) and are available for repurposing. In combination, the effects of these drugs were additive or synergistic. In two mouse models of cancer (utilizing 4T1 cells or B16-F10 cells), the combination treatment with these medications, applied immediately (to prevent metastasis formation) or after a delay (to suppress established metastases), dramatically reduced the occurrence of disseminated foci. The combination of tissue remodeling inhibitors, suppressors of the oxidative metabolism, and ion homeostasis modulators has very strong promise for the treatment of metastases by multiple cancers.

A multiscale dynamic model of cell–substrate interfaces

Cell–extracellular matrix (ECM) interactions play a pivotal role in many functions of cells, for example, sensing, signaling, migration, and gene expression. The spatial–temporal dynamic evolution of cell–substrate adhesions involves complicated mechano-bio-chemical coupling mechanisms of integrin, adaptor and signaling proteins, as well as the interplay between the cytoskeleton and ECM. In this paper, we establish a multiscale dynamic model of cell–substrate interfaces considering intermolecular force transmission pathways, i.e., intra- and extra-cellular bond dynamics, and mechanochemical coupling regulations. To illustrate its applications, this model is used to reproduce several adhesion-related experimental phenomena of cells, including substrate rigidity sensing, actin-assisted focal adhesion formation, and biphasic interface stress–actin speed relation. The results suggest that the cluster growth patterns are mediated by the intermolecular force transmission pathway and the actin flow speed, and that the integrin–ligand (IL) bond strengthening tends to inhibit the motion of clusters. We reveal that the monotonic-to-biphasic transition of force transmission and adhesion assembly is regulated by the bond rupture mechanosensitivity of integrin adhesion complexes (IACs). It is also demonstrated that this multiscale dynamic model can well describe the spatial–temporal evolutions of collective cell–substrate adhesions with the effects of actin flow and substrate deformation, and can also capture the morphological features of adhesion clusters and related interface force transmissions. This work provides a theoretical tool for studying mechano-biochemical mechanisms of cell–substrate interactions and for understanding various subcellular and cellular dynamic processes in, for example, tumors.

#1004 Single-nucleus RNA sequencing identifies upregulated antigen presentation, apoptosis, mTORC1 signaling and EMT in primary FSGS podocytes

Abstract Background and Aims Primary focal segmental glomerulosclerosis (FSGS) is associated with irreversible podocyte damage, but the underlying cause and pathophysiology are incompletely understood. Furthermore, diagnostic markers that allow reliable differentiation between primary and secondary FSGS subtypes are lacking. We applied single-nucleus RNA-sequencing (snRNA-seq) on podocytes of patients with primary or secondary (maladaptive) FSGS, to identify subtype-specific differentially expressed genes and pathways. Method We used droplet-based snRNA-seq (10X Genomics Chromium) on cryopreserved kidney biopsy cores from human patients with newly diagnosed primary FSGS (n = 9, all nephrotic), maladaptive FSGS (n = 9, not nephrotic), proteinuric controls (PLA2R-positive membranous nephropathy (PLA2R+ MN), n = 3), and healthy controls (pre-perfusion biopsies, n = 4). Differential gene expression (DGE) analysis was done with a pseudobulk method provided by the EdgeR R-package to reduce bias and false discoveries. The fGSEA R-package was used for subsequent gene set enrichment analysis. Results We identified a total of 120 751 high-quality nuclei, of which 2 471 were podocytes (Fig. 1A). DGE analysis identified the top 20 differentially expressed genes (DEGs) per diagnosis (Fig. 1B). Remarkably, primary FSGS podocytes showed more transcriptional similarity to PLA2R+ MN podocytes, compared to maladaptive FSGS podocytes. This underscores the heterogeneity of patients with FSGS and shows that heavy proteinuria, regardless of the underlying diagnosis, may be associated with a distinct transcriptional profile in podocytes. Upregulated genes in primary FSGS podocytes included TIMP1, BTG2, ZNF44, EHD4, ZNF250, ECM1, SEMA4G, PHLDB1, and HDAC5. Upregulation of the matrix metalloproteinase inhibitor TIMP1 may possibly contribute to the development of glomerulosclerosis. Upregulation of BTG2 has previously been found to be pathogenic in FSGS by promoting epithelial-mesenchymal transition (EMT)-induced podocyte injury [1]. Next, gene set enrichment analysis on the identified DEGs in primary FSGS podocytes showed upregulation of pathways involved in antigen presentation (driven by upregulation of HLA-A, HLA-B, HLA-C, HLA-E and B2M), mTORC1 signaling, apoptosis and EMT (Fig. 1C). In maladaptive FSGS, upregulated pathways were mainly involved in extracellular matrix interaction. This may correlate with the significantly higher degree of chronic damage on kidney biopsy in the maladaptive FSGS patients (median Mayo Clinic Chronicity Score of 6.0, IQR [4.0-7.0]) vs. primary FSGS (2.0, [1.0-4.0]) and PLA2R+ MN (1, IQR [1.0-1.5]) (Kruskal-Wallis test, P = 0.007). Conclusion Our results corroborate previous studies that implicate apoptosis, mTORC1 signaling, EMT and auto-immunity in primary FSGS. Our future work will focus on cell-cell interactions within the glomerular niche and validation studies of candidate podocyte-specific genes.

Patterning and folding of intestinal villi by active mesenchymal dewetting

Tissue folds are structural motifs critical to organ function. In the intestine, bending of a flat epithelium into a periodic pattern of folds gives rise to villi, finger-like protrusions that enable nutrient absorption. However, the molecular and mechanical processes driving villus morphogenesis remain unclear. Here, we identify an active mechanical mechanism that simultaneously patterns and folds the intestinal epithelium to initiate villus formation. At the cellular level, we find that PDGFRA+ subepithelial mesenchymal cells generate myosin II-dependent forces sufficient to produce patterned curvature in neighboring tissue interfaces. This symmetry-breaking process requires altered cell and extracellular matrix interactions that are enabled by matrix metalloproteinase-mediated tissue fluidization. Computational models, together with invitro and invivo experiments, revealed that these cellular features manifest at the tissue level as differences in interfacial tensions that promote mesenchymal aggregation and interface bending through a process analogous to the active dewetting of a thin liquid film.

Transcriptional signatures of fentanyl use in the mouse ventral tegmental area.

Synthetic opioids such as fentanyl contribute to the vast majority of opioid-related overdose deaths, but fentanyl use remains broadly understudied. Like other substances with misuse potential, opioids cause lasting molecular adaptations to brain reward circuits, including neurons in the ventral tegmental area (VTA). The VTA contains numerous cell types that play diverse roles in opioid use and relapse; however, it is unknown how fentanyl experience alters the transcriptional landscape in specific subtypes. Here, we performed single nuclei RNA sequencing to study transcriptional programs in fentanyl-experienced mice. Male and female C57/BL6 mice self-administered intravenous fentanyl (1.5μg/kg/infusion) or saline for 10days. After 24 h abstinence, VTA nuclei were isolated and prepared for sequencing on the 10× platform. We identified different patterns of gene expression across cell types. In dopamine neurons, we found enrichment of genes involved in growth hormone signalling. In dopamine-glutamate-GABA combinatorial neurons, and some GABA neurons, we found enrichment of genes involved in Pi3k-Akt signalling. In glutamate neurons, we found enrichment of genes involved in cholinergic signalling. We identified transcriptional regulators for the differentially expressed genes in each neuron cluster, including downregulated transcriptional repressor Bcl6, and upregulated transcription factor Tcf4. We also compared the fentanyl-induced gene expression changes identified in mouse VTA with a published rat dataset in bulk VTA, and found overlap in genes related to GABAergic signalling and extracellular matrix interaction. Together, we provide a comprehensive picture of how fentanyl self-administration alters the transcriptional landscape of the mouse VTA that serves as the foundation for future mechanistic studies.

Glycosaminoglycan-Mediated Interactions in Articular, Auricular, Meniscal, and Nasal Cartilage.

Glycosaminoglycans (GAGs) are ubiquitous components in the cartilage extracellular matrix (ECM). Ultrastructural arrangement of ECM and GAG-mediated interactions with collagen are known to govern the mechanics in articular cartilage, but these interactions are less clear in other cartilage types. Therefore, this article reviews the current literature on ultrastructure of articular, auricular, meniscal, and nasal septal cartilage, seeking insight into GAG-mediated interactions influencing mechanics. Ultrastructural features of these cartilages are discussed to highlight differences between them. GAG-mediated interactions are reviewed under two categories: interactions with chondrocytes and interactions with other fibrillar macromolecules of the ECM. Moreover, efforts to replicate GAG-mediated interactions to improve mechanical integrity of tissue-engineered cartilage constructs are discussed. In conclusion, studies exploring cartilage specific GAGs are poorly represented in the literature, and the ultrastructure of nasal septal and auricular cartilage is less studied compared with articular and meniscal cartilages. Understanding the contribution of GAGs in cartilage mechanics at the ultrastructural level and translating that knowledge to engineered cartilage will facilitate improvement of cartilage tissue engineering approaches.

Proteomic characteristics of the aqueous humor in Uyghur patients with pseudoexfoliation syndrome and pseudoexfoliative glaucoma

Pseudoexfoliation syndrome (PEX) is characterized by the deposition of fibrous pseudoexfoliation material (PEXM) in the eye, and secondary glaucoma associated with this syndrome has a faster and more severe clinical course. The incidence of PEX and pseudoexfoliative glaucoma (PEXG) exhibits ethnic clustering; however, few proteomic studies related to PEX and PEXG have been conducted in Asian populations. Therefore, we aimed to conduct proteomic analysis on the aqueous humor (AH) obtained from Uyghur patients with cataracts, those with PEX and cataracts, and those with PEXG and cataracts to better understand the molecular mechanisms of the disease and identify its potential biomarkers. To this end, AH was collected from patients with cataracts (n = 10, control group), PEX with cataracts (n = 10, PEX group), and PEXG with cataracts (n = 10, PEXG group) during phacoemulsification. Label-free quantitative proteomic techniques combined with bioinformatics were used to identify and analyze differentially expressed proteins (DEPs) in the AH of PEX and PEXG groups. Then, independent AH samples (n = 12, each group) were collected to validate DEPs by enzyme-linked immunosorbent assay (ELISA). The PEX group exhibited 25 DEPs, while the PEXG group showed 44 DEPs, both compared to the control group. Subsequently, we found three newly identified proteins in both PEX and PEXG groups, wherein FRAS1-related extracellular matrix protein 2 (FREM2) and osteoclast-associated receptor (OSCAR) exhibited downregulation, whereas coagulation Factor IX (F9) displayed upregulation. Bioinformatics analysis suggested that extracellular matrix interactions, abnormal blood-derived proteins, and lysosomes were mainly involved in the process of PEX and PEXG, and the PPI network further revealed F9 may serve as a potential biomarker for both PEX and PEXG. In conclusion, this study provides new information for understanding the proteomics of AH in PEX and PEXG.

Abstract 6782: 3D-EXpress - an ex vivo platform using viably cryopreserved tumoroids for rapid assessment of targeted therapeutic outcomes

Abstract Background: it has been a significant challenge to select, combine, and sequence the multiple FDA-approved IO therapies and pharmaceutical agents, highlighting the need to develop a precision oncology platform to explore novel combination treatments. 3D-EXpress is a unique ex vivo therapeutics testing platform using a biorepository of fresh patient tumoroids that were never dissociated, propagated, or reassembled to retain an intact microenvironment. Therefore, these specimens provide an excellent ex vivo platform to investigate the efficacy of therapeutics targeting the tumor microenvironment. Here, we employed the 3D-EXpress platform to compare the efficacy of different therapeutic modalities targeting tumor antigens and immune checkpoint ex vivo. Methods: Tumoroids measuring 150 μm in size retaining tumor cell heterogeneity, tumor-resident immune cells, stromal components, and extracellular matrix interaction were prepared from human endometrial and colorectal tumors. Tumoroids were cryopreserved and were selected based on tumor antigen status. Samples were treated for 72 hours ex vivo with antibody-drug conjugates, chimeric antigen receptor (CAR)T cells, or bispecific antibodies alone and in combinations. Treatment-mediated changes in tumor cell killing and tumor immune microenvironment were investigated. Results: 3D high throughput confocal imaging and Nilogen Oncosystem’s proprietary algorithm were used to detect and analyze treatment-induced tumor cell killing activity in tumoroids. The impact of ex vivo treatment by different modalities in combination with chemotherapeutic agents upon tumor resident immune cell populations was monitored by deep immune phenotyping and multiplex cytokine release assay. Based on the ex vivo responses tumors were assigned to treatment sensitive and resistant groups. Correlative analysis was performed and compared with detailed clinicopathologic data that is readily available for Biorepository tumors. Conclusions: The 3D-EXpress platform using cryopreserved 3D tumoroids with intact tumor microenvironment is an effective tool for the pre-clinical assessment of rational drug combinations for treatment of solid tumors. Furthermore, the 3D-EXpress platform provides unique insight into the microenvironment of both treatment responsive and non-responsive tumors and can aid in the development of patient-centered therapeutic regimens. Citation Format: Vanessa Garrido, Michelle Ataya, Nisha R. Dhanushkodi, Seth Currlin, Alliyah Humphrey, Jared Ehrhart, Rikhia Chakraborty. 3D-EXpress - an ex vivo platform using viably cryopreserved tumoroids for rapid assessment of targeted therapeutic outcomes [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 6782.

Abstract 2523: Predictive biomarkers for neoadjuvant FLOT4 chemotherapy response in gastroesophageal cancer: Results of multi-omics approach

Abstract Background: The FLOT4 chemotherapy regimen is a standard preoperative treatment for gastroesophageal junction (GEJ) and gastric cancer (GC), yet the response to this treatment is variable. Identification of predictive biomarkers is crucial for optimizing therapeutic strategies. This study aims to identify predictive biomarkers for FLOT4 treatment efficacy using a multi-omics approach. Methods: We conducted a preliminary differential gene expression analysis in diagnostic tissue pre-treatment and surgical resection post-treatment in six patients (two GEJ and four GC) who all exhibited a partial pathological response (G2) to neoadjuvant FLOT4 chemotherapy. Utilizing DESeq2 for differential gene expression and David pathway analysis for functional insights, we have begun to unravel the complex molecular response to treatment. Upcoming assays include blood gDNA and tumor tissue whole exome sequencing (WES), comprehensive methylation profiling, miRNA characterization, and proteomics via LC-MSMS. Results: Our preliminary data suggest alterations in gene expression associated with cell adhesion, extracellular matrix interaction, and immune response pathways. Three common genes (CXCL2, CXCL3, CXCL1) were identified among upregulated pathways in GEJ patients, while one common gene (IL1A) was observed in GC patients. These findings suggest a complex network of biological processes influenced by FLOT4. In-depth results, including whole-exome sequencing, methylation patterns, and miRNA profiles, will be completed and presented at the conference. Conclusion: These initial findings propose that changes in gene expression related to cellular architecture and immune response are indicative of a partial response to FLOT4 in both GEJ and GC patients. The identified genes and pathways may serve as potential biomarkers for predicting treatment outcomes. Future Directions: By the time of the conference, we anticipate including a more extensive patient cohort with complete response or no response to FLOT4, and comparative analyses with a FOLFOX treatment group. The integration of forthcoming WES, methylation, miRNA, and proteomics data will provide a more comprehensive molecular predictive model. Keywords: FLOT4 chemotherapy, gastroesophageal junction cancer, gastric cancer, predictive biomarkers, differential gene expression. Citation Format: Amira Al-Fahdi, Shoaib Al Zadjali, Ibrahim Al Haddabi, Anoopa Pullanhi, Muna Al Jabri, Aida Al Yayahee, Nada Al Shuaili, Nahad Al Mahrouqi, Mansour Al Moundhri. Predictive biomarkers for neoadjuvant FLOT4 chemotherapy response in gastroesophageal cancer: Results of multi-omics approach [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 2523.

Abstract 5482: Spatial and multi-omic interrogation of the primary and recurrent glioblastoma microenvironment

Abstract Glioblastoma remains as one of the deadliest malignancies with most cases likely to recur. Recent work has focused on characterizing not only glioma cells, but the tumor microenvironment via single-cell and spatial transcriptomic technologies. This has improved our understanding of the high heterogeneity of this disease and described potential tumor domains. However, there is still a need to further understand the changes that occur between the primary and the recurrent lesion. We propose that a spatial, multi-omic characterization of matched primary and recurrent glioblastoma can yield insights into recurrence mechanisms occurring throughout the tumor microenvironment. We collected 22 IDH-WT glioblastoma samples from 12 patients (11 primary, 11 recurrent, 10 matched pairs) from the Mayo Clinic Neuroscience Biobank. We performed single-nucleus RNA sequencing (15 samples, 10 patients, 5 matched pairs) and proteomics (16 samples, 6 matched pairs) from fresh-frozen tissue, as well as spatial transcriptomics with 10x Visium (14 samples, 8 patients, 6 matched pairs) and 10x Xenium in-situ molecular imaging (6 samples, 2 matched pairs). Using spatial transcriptomics data, we identified regional subsets present in different proportions and distributions between primary and recurrent glioblastoma. These clusters were characterized with gene set and gene ontology analysis, identifying regions enriched with known glioma subtypes and cellular activity. Spatial-based cluster genes were consistent with significantly differentially expressed proteins. We used single-nucleus RNAseq and in-situ molecular imaging data from matched tissue samples to further interrogate relevant cell populations and location in the tumor micro-environment. We identified regions with enriched extra cellular matrix interaction and remodeling signatures to be highly expressed in recurrent glioblastoma. Primary glioblastoma was enriched with oligodendrocyte-like regions with high cell communication and extracellular vesicle signatures. This study will further our understanding of the changes in the mechanisms at play in the complex ecosystem of glioblastoma as it recurs. Citation Format: Jean R. Clemenceau, Paola Suarez-Meade, Alfredo Quiñones-Hinojosa, Tae Hyun Hwang. Spatial and multi-omic interrogation of the primary and recurrent glioblastoma microenvironment [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 5482.

Abstract A096: Blockade of LAIR1-collagen interaction enhances the therapeutic activity of BiTE-secreting T cells in ovarian cancer

Abstract Introduction: The tumor microenvironment (TME), abundant with collagen produced by cancer associated fibroblasts (CAFs), plays a critical role in evading the immune system and limiting the efficacy of cell therapies. High levels of collagen and CAF expression correlate with malignant potential, decreased T cell accumulation, and overall unfavorable clinical outcomes in ovarian cancer (OC). Finding ways to address this immunosuppressive TME is therefore critical to improving therapeutic options. We recently reported on the therapeutic potential of adoptively transferred T cells engineered to secrete a folate receptor alpha (FRα)-targeted bispecific T cell engager (FR-B T cells) to target a tumor antigen commonly overexpressed in OC. Transcriptional profiling following ACT revealed that effector-like FR-B T cells (FR-BE T cells) upregulated genes associated with extracellular matrix interaction, suggesting interaction with the tumor stroma may limit antitumor immunity by FR-B T cells. Our goal was to improve the effectiveness of FR-B T cells by inhibiting LAIR-1, a widely present immune checkpoint receptor that sends T cell inhibitory signals after binding to collagen-like domains, leading to T cell exhaustion. We hypothesized that interrupting the LAIR1-collagen pathway using a LAIR1 decoy (NC410, supplied by NextCure Inc.) could amplify the FR-BE T cell effector function, thereby improving the response. Methods: We utilized in vitro co-culture assays to understand the phenotype and mechanistic changes occurring at the level of the T cell/tumor interface when exposed to collagen, as well as effects of LAIR 1 pathway blockade with the addition of NC410. In vivo murine models were used to determine disease progression and overall survival (OS) following treatment with bispecific T cell engager-armed T cells ± LAIR1 blockade. Results: Phenotypic analysis of FR-B T cells revealed elevated LAIR-1 expression on FR-BE T cells. FRα+ OC lysis by FR-BE T cells was diminished in the presence of collagen, suggesting LAIR-1 signaling can suppress tumor attack. In vitro, the addition of NC410 enhanced the activity of FR-BE T cells when exposed to collagen, improving both FRα+ target cell lysis and partially restoring the production of IFN-γ by FR-BE T cells. In vivo, the combination of NC410 with FR-BE T cells led to improved tumor control compared to FR-BE T cell therapy alone. Conclusions: Our results highlight understanding the interactions between infiltrating immune cells and the immunosuppressive TME to better design combination therapies that improve duration and magnitude of immune attack on tumors. By blocking T cell/stromal interactions, FR-B T cell therapy can be further enhanced, creating a promising opportunity to improve the impact of adoptive cell therapy in OC. Citation Format: Sarah Werner, Nicole Gaulin, Jessie Chiello, Theja Giridharan, Anm Nazmul Khan, Sora Suzuki, Suzanne Hess, Sol Langermann, Emese Zsiros, Brahm H. Segal, A.J. Robert McGray. Blockade of LAIR1-collagen interaction enhances the therapeutic activity of BiTE-secreting T cells in ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr A096.

Increased glycolysis and cellular crosstalk in eosinophilic chronic rhinosinusitis with nasal polyps.

Chronic rhinosinusitis (CRS) is a chronic inflammatory disease of the sinonasal mucosa with distinct endotypes including type 2 (T2) high eosinophilic CRS with nasal polyps (eCRSwNP), T2 low non-eosinophilic CRS with nasal polyps (neCRSwNP), and CRS without nasal polyps (CRSsNP). Given the heterogeneity of disease, we hypothesized that assessment of single cell RNA sequencing (scRNA-seq) across this spectrum of disease would reveal connections between infiltrating and activated immune cells and the epithelial and stromal populations that reside in sinonasal tissue. Here we find increased expression of genes encoding glycolytic enzymes in epithelial cells (EpCs), stromal cells, and memory T-cell subsets from patients with eCRSwNP, as compared to healthy controls. In basal EpCs, this is associated with a program of cell motility and Rho GTPase effector expression. Across both stromal and immune subsets, glycolytic programming was associated with extracellular matrix interactions, proteoglycan generation, and collagen formation. Furthermore, we report increased cell-cell interactions between EpCs and stromal/immune cells in eCRSwNP compared to healthy control tissue, and we nominate candidate receptor-ligand pairs that may drive tissue remodeling. These findings support a role for glycolytic reprograming in T2-elicited tissue remodeling and implicate increased cellular crosstalk in eCRSwNP.

Unravelling the heterogeneity of oral squamous cell carcinoma by integrative analysis of single-cell and bulk transcriptome data.

Oral squamous cell carcinoma (OSCC) is a prevalent malignancy of the head and neck with rising global incidence. Despite advances in treatment modalities, OSCC prognosis remains diverse due to the complex molecular and cellular heterogeneity within tumours, as well as the heterogeneity in tumour microenvironment (TME). In this study, we utilized single-cell RNA sequencing (scRNA-seq) analysis to explore distinct subpopulations of tumour cells in OSCC tissues and their interaction with components in TME. We identified four major tumour cell subpopulations (C0, C1, C2 and C3) with unique molecular characteristics and functional features. Pathway enrichment analysis revealed that C0 primarily expressed genes involved in extracellular matrix interactions and C1 showed higher proliferation levels, suggesting that the two cell subpopulations exhibited tumour aggressiveness. Conversely, C2 and C3 displayed features associated with keratinization and cornified envelope formation. Accordingly, C0 and C1 subpopulations were associated with shorter overall and disease-free survival times, while C2 and C3 were weakly correlated with longer survival. Genomic analysis showed that C1 demonstrated a positive correlation with tumour mutation burden. Furthermore, C0 exhibited resistant to cisplatin treatment, while C1 showed more sensitive to cisplatin treatment, indicating that C0 might exhibit more aggressive compared to C1. Additionally, C0 had a higher level of communication with fibroblasts and endothelial cells in TME via integrin-MAPK signalling, suggesting that the function of C0 was maintained by that pathway. In summary, this study provided critical insights into the molecular and cellular heterogeneity of OSCC, with potential implications for prognosis prediction and personalized therapeutic approaches.

Modelling the complex nature of the tumor microenvironment: 3D tumor spheroids as an evolving tool.

Cancer remains a serious burden in society and while the pace in the development of novel and more effective therapeutics is increasing, testing platforms that faithfully mimic the tumor microenvironment are lacking. With a clear shift from animal models to more complex in vitro 3D systems, spheroids emerge as strong options in this regard. Years of development have allowed spheroid-based models to better reproduce the biomechanical cues that are observed in the tumor-associated extracellular matrix (ECM) and cellular interactions that occur in both a cell-cell and cell-ECM manner. Here, we summarize some of the key cellular interactions that drive tumor development, progression and invasion, and how successfully are these interactions recapitulated in 3D spheroid models currently in use in the field. We finish by speculating on future advancements in the field and on how these can shape the relevance of spherical 3D models for tumor modelling.