Extracellular Matrix Interactions Research Articles

CAPN1 is a novel biomaker of patients with AML based on comprehensive analysis

ABSTRACT Acute myeloid leukemia (AML) is a common hematologic malignancy in adults. Recent studies investigating the potential pathogenesis of AML have significantly advanced our understanding of this disease. While cytogenetics and molecular abnormalities are crucial for confirming chemotherapy response and long-term outcomes, there are additional potential therapeutic targets and prognostic factors. The CAPN1 gene, which encodes a large subunit of the ubiquitous enzyme calpain, has not been extensively studied in hematological diseases. In this study, we used data from the TCGA public database to perform a bioinformatic analysis and found that CAPN1 is differentially expressed in multiple cancers and is associated with an unfavorable prognosis in AML. We employed R software and websites such as David and STRING to conduct differential analysis, GO and KEGG analysis, and explore the correlation between CAPN1 and physiological processes and key pathways. Our findings suggest that CAPN1 is significantly associated with the structure of the extracellular matrix and receptor-ligand interactions, indicating its potential role in disease progression. Additionally, we used CYBERSORT and ssGSEA to analyze the immune environment of CAPN1 and found that it is associated with most immune components, particularly CD56 cells and neutrophils. In conclusion, CAPN1 is a key prognostic gene in AML that is significantly correlated with disease progression, clinical features, and immune invasion.

Engineering Cell Microenvironment Using Nanopattern-Derived Multicellular Spheroids and Photo-Crosslinked Gelatin/Hyaluronan Hydrogels.

Cell cultures of dispersed cells within hydrogels depict the interaction of the cell-extracellular matrix (ECM) in 3D, while the coculture of different cells within spheroids combines both the effects of cell-cell and cell-ECM interactions. In this study, the cell co-spheroids of human bone mesenchymal stem cells/human umbilical vein endothelial cells (HBMSC/HUVECs) are prepared with the assistance of a nanopattern, named colloidal self-assembled patterns (cSAPs), which is superior to low-adhesion surfaces. A phenol-modified gelatin/hyaluronan (Gel-Ph/HA-Ph) hydrogel is used to encapsulate the multicellular spheroids and the constructs are photo-crosslinked using blue light. The results show that Gel-Ph/HA-Ph hydrogels with a 5%-to-0.3% ratio have the best properties. Cells in HBMSC/HUVEC co-spheroids are more favorable for osteogenic differentiation (Runx2, ALP, Col1a1 and OPN) and vascular network formation (CD31+ cells) compared to HBMSC spheroids. In a subcutaneous nude mouse model, the HBMSC/HUVEC co-spheroids showed better performance than HBMSC spheroids in angiogenesis and the development of blood vessels. Overall, this study paves a new way for using nanopatterns, cell coculturing and hydrogel technology for the generation and application of multicellular spheroids.

Multiple Myeloma Cell Simulation Using an Agent-Based Framework Coupled with a Continuous Fluid Model

Bone marrow mechanical conditions play a key role in multiple myeloma cancer. The complex mechanical and chemical conditions, as well as the interactions with other resident cells, hinder the development of effective treatments. Agent-based computational models, capable of defining the specific conditions for every single cell, can be a useful tool to identify the specific tumor microenvironment. In this sense, we have developed a novel hybrid 3D agent-based model with coupled fluid and particle dynamics to study multiple myeloma cells’ growth. The model, which considers cell–cell interactions, cell maturation, and cell proliferation, has been implemented by employing user-defined functions in the commercial software Fluent. To validate and calibrate the model, cell sedimentation velocity and cell proliferation rates have been compared with in vitro results, as well as with another previously in-house developed model. The results show that cell proliferation increased as cell–cell, and cell–extracellular matrix interactions increased, as a result of the reduction n maturation time. Cells in contact form cell aggregates, increasing cell–cell interactions and thus cell proliferation. Saturation in cell proliferation was observed when cell aggregates increased in size and the lack of space inhibited internal cells’ proliferation. Compared with the previous model, a huge reduction in computational costs was obtained, allowing for an increase in the number of simulated cells.

In Vitro Profiling of the Extracellular Matrix and Integrins Expressed by Human Corneal Endothelial Cells Cultured on Silk Fibroin-Based Matrices.

Developing a scaffold for culturing human corneal endothelial (HCE) cells is crucial as an alternative cell therapeutic approach to bridge the growing gap between the demand and availability of healthy donor corneas for transplantation. Silk films are promising substrates for the culture of these cells; however, their tensile strength is several-fold greater than the native basement membrane which can possibly influence the dynamics of cell-matrix interaction and the extracellular matrix (ECM) secreted by the cells in long-term culture. In our current study, we assessed the secretion of ECM and the expression of integrins by the HCE cells on Philosamia ricini (PR) and Antheraea assamensis (AA) silk films and fibronectin-collagen (FNC)-coated plastic dishes to understand the cell-ECM interaction in long-term culture. The expression of ECM proteins (collagens 1, 4, 8, and 12, laminin, and fibronectin) on silk was comparable to that on the native tissue. The thicknesses of collagen 8 and laminin at 30 days on both PR (4.78 ± 0.55 and 5.53 ± 0.51 μm, respectively) and AA (4.66 ± 0.72 and 5.71 ± 0.61 μm, respectively) were comparable with those of the native tissue (4.4 ± 0.63 and 5.28 ± 0.72 μm, respectively). The integrin expression by the cells on the silk films was also comparable to that on the native tissue, except for α3 whose fluorescence intensity was significantly higher on PR (p ≤ 0.01) and AA (p ≤ 0.001), compared to that on the native tissue. This study shows that the higher tensile strength of the silk films does not alter the ECM secretion or cell phenotype in long-term culture, confirming the suitability of using this material for engineering the HCE cells for transplantation.

Anoikis in phenotypic reprogramming of the prostate tumor microenvironment.

Prostate cancer is one of the most common malignancies in males wherein 1 in 8 men are diagnosed with this disease in their lifetime. The urgency to find novel therapeutic interventions is associated with high treatment resistance and mortality rates associated with castration-resistant prostate cancer. Anoikis is an apoptotic phenomenon for normal epithelial or endothelial cells that have lost their attachment to the extracellular matrix (ECM). Tumor cells that lose their connection to the ECM can die via apoptosis or survive via anoikis resistance and thus escaping to distant organs for metastatic progression. This review discusses the recent advances made in our understanding of the signaling effectors of anoikis in prostate cancer and the approaches to translate these mechanistic insights into therapeutic benefits for reducing lethal disease outcomes (by overcoming anoikis resistance). The prostate tumor microenvironment is a highly dynamic landscape wherein the balance between androgen signaling, cell lineage changes, epithelial-mesenchymal transition (EMT), extracellular matrix interactions, actin cytoskeleton remodeling as well as metabolic changes, confer anoikis resistance and metastatic spread. Thus, these mechanisms also offer unique molecular treatment signatures, exploitation of which can prime prostate tumors to anoikis induction with a high translational significance.

Abstract 2209: A proteomic-based prognostic signature of pancreatic adenocarcinoma

Abstract Introduction: Pancreatic cancer has a very poor prognosis, with no established prognostic biomarkers in clinical use. This project aims to identify a prognostic proteomic-based signature for pancreatic adenocarcinomas. Methods: Fresh frozen tumors and matched normal samples from 125 patients were prepared for proteomic analyses using data-independent acquisition mass spectrometry (DIA-MS). Differential expression analyses were conducted on the normalized protein matrix to identify the top differentially expressed proteins (DEP) within the tumor samples. DEP were subjected to crosstalk and pathway enrichment analysis (PEA). Survival analysis based on initial univariate and subsequent 100 runs of multivariate Cox regression with Least Absolute Shrinkage and Selection Operator (LASSO) was performed to obtain a reduced list of candidate proteins associated with Overall Survival (OS). The proteins that appeared in greater than 95% of the LASSO runs were then used in a multivariate Cox model with recursive feature selection, which yielded the final 29 proteins. A risk score was built from the final 29 proteins. Consensus clustering was performed on the median absolute deviation-based top 20% highly variable proteins in tumor samples to identify proteomic-based subtypes. Results: Proteomic analyses revealed 5614 proteins identified from 599 sample runs. Differential expression analyses revealed 398 DEP in tumor samples (FDR-adjusted p-value <0.05, and |logFC|>1). PEA showed that these proteins were related to focal adhesion, extracellular matrix interaction (ECM), angiogenesis, and PI3K signaling pathways. A total of 803 proteins were significantly associated with OS in a univariate Cox regression analysis (p<0.05). PEA on the top 200 proteins associated with poorer OS revealed pathways related to focal adhesion, PI3K signaling, ECM and hypoxia-induced factor-1. Using LASSO multivariate Cox regression modeling, a 29-protein signature was identified, from which a risk score was calculated that dichotomized patients into high- and low-risk groups in terms of OS (Hazard ratio (HR) 2.8, 95% Confidence Interval (CI) [2.3, 3.3], concordance index of 0.91). This risk score was also prognostic for recurrence and three-year survival (both p<0.0001). A multivariate Cox regression model adjusted for other clinical variables revealed a significant association of the risk score with OS (HR 2.91, 95% CI [2.4, 3.5], p<0.001) while maintaining the concordance index (0.907). Consensus clustering analyses revealed four proteomic-based clusters, with cluster 3 showing the worst OS (p<0.001), independent of other clinical variables. PEA on the DEP within cluster 3 showed upregulation of proteins related to cell adhesion, angiogenesis, and immune-related pathways. Conclusion: A 29-protein signature identified a sub-group of patients with pancreatic adenocarcinoma with a poorer prognosis independent of clinical variables. Citation Format: Adel T. Aref, AKM Azad, Asim Anees, Mohashin Pathan, Jason Grealey, Daniela-Lee Smith, Erin M. Humphries, Daniel Bucio-Noble, Jennifer M. Koh, Erin Sykes, Steven G. Williams, Ruth Lyons, Natasha Lucas, Dylan Xavier, Sumit Sahni, Anubhav Mittal, Jaswinder S. Samra, John V. Pearson, Nicola Waddell, Peter G. Hains, Phil J. Robinson, Qing Zhong, Roger R. Reddel, Anthony J. Gill. A proteomic-based prognostic signature of pancreatic adenocarcinoma [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 2209.

A2AR as a Prognostic Marker and a Potential Immunotherapy Target in Human Glioma.

Gliomas are considered one of the most malignant tumors in the body. The immune system has the ability to control the initiation and development of tumors, including gliomas. Thus, immune cells find themselves controlled by various molecular pathways, inhibiting their activation, such as the immunosuppressive adenosine 2A receptor (A2AR). Our objective was to establish the expression profile and role of A2AR at the transcriptomic level, using real-time RT-PCR in Moroccan glioma patients, in addition to TCGA and CGGA cohorts. The real-time RT-PCR results in Moroccan patients showed that high expression of this gene was associated with poor survival in males. Our study on the CGGA cohort corroborated these results. In addition, there was a positive association of A2AR with T-cell exhaustion genes. A2AR also correlated strongly with genes that are primarily enriched in focal adhesion and extracellular matrix interactions, inducing epithelial mesenchymal transition, angiogenesis, and glioma growth. However, in the TCGA cohort, the A2AR showed results that were different from the two previously examined cohorts. In fact, this gene was instead linked to a good prognosis in patients with the astrocytoma histological type. The correlation and enrichment results reinforced the prognostic role of A2AR in this TCGA cohort, in which its high expression was shown to be related to lymphocyte differentiation and a successful cytolytic response, suggesting a more efficient anti-tumor immune response. Correlations and differential analyses based on A2AR gene expression, to understand the cause of the association of this gene with two different prognoses (CGGA males and TCGA Astrocytoma), showed that the overexpression of A2AR in Chinese male patients could be associated with the overexpression of extracellular adenosine, which binds to A2AR to induce immunosuppression and consequently a poor prognosis. However, in the second group (TCGA astrocytomas), the overexpression of the gene could be associated with an adenosine deficiency, and therefore this receptor does not undergo activation. The absence of A2AR activation in these patients may have protected them from immunosuppression, which could reflect the good prognosis. A2AR can be considered a promising therapeutic target in male CGGA and Moroccan patients with gliomas.

Reprogramming of the Genome-Wide DNA Methylation Landscape in Three-Dimensional Cancer Cell Cultures

During the last century, 2D cell cultures have been the tool most widely used to study cancer biology, drug discovery, genomics, and the regulation of gene expression at genetic/epigenetic levels. However, this experimental approach has limitations in faithfully recreating the microenvironment and cellular processes occurring in tumors. For these reasons, 3D cell cultures have recently been implemented to optimize the conditions that better recreate the biological and molecular features of tumors, including cell-cell and cell-extracellular matrix (ECM) interactions, growth kinetics, metabolic activities, and the development of gradients in the cellular microenvironment affecting the availability of oxygen and nutrients. In this sense, tumor cells receive stimuli from the local environment, resulting in significant changes in their signaling pathways, gene expression, and transcriptional and epigenetic patterns. In this review, we discuss how different types of 3D cell culture models can be applied to characterize the epigenetic footprints of cancer cell lines, emphasizing that DNA methylation patterns play an essential role in the emergence and development of cancer. However, how 3D cancer cell cultures remodel the epigenetic programs is poorly understood, with very few studies in this emerging topic. Here, we have summarized the studies on the reprogramming of the epigenetic landscape of DNA methylation during tumorigenesis and discuss how it may be affected by microenvironmental factors, specifically in 3D cell cultures.

Stiff Extracellular Matrix Promotes Invasive Behaviors of Trophoblast Cells.

The effect of extracellular matrix (ECM) stiffness on embryonic trophoblast cells invasion during mammalian embryo implantation remains largely unknown. In this study, we investigated the effects of ECM stiffness on various aspects of human trophoblast cell behaviors during cell-ECM interactions. The mechanical microenvironment of the uterus was simulated by fabricating polyacrylamide (PA) hydrogels with different levels of stiffness. The human choriocarcinoma (JAR) cell lineage was used as the trophoblast model. We found that the spreading area of JAR cells, the formation of focal adhesions, and the polymerization of the F-actin cytoskeleton were all facilitated with increased ECM stiffness. Significantly, JAR cells also exhibited durotactic behavior on ECM with a gradient stiffness. Meanwhile, stiffness of the ECM affects the invasion of multicellular JAR spheroids. These results demonstrated that human trophoblast cells are mechanically sensitive, while the mechanical properties of the uterine microenvironment could play an important role in the implantation process.

Cellular and Molecular Mechanisms of Intestinal Fibrosis.

Intestinal fibrosis associated stricture is a common complication of inflammatory bowel disease usually requiring endoscopic or surgical intervention. Effective anti-fibrotic agents aiming to control or reverse intestinal fibrosis are still unavailable. Thus, clarifying the mechanism underpinning intestinal fibrosis is imperative. Fibrosis is characterized by an excessive accumulation of extracellular matrix (ECM) proteins at the injured sites. Multiple cellular types are implicated in fibrosis development. Among these cells, mesenchymal cells are major compartments that are activated and then enhance the production of ECM. Additionally, immune cells contribute to the persistent activation of mesenchymal cells and perpetuation of inflammation. Molecules are messengers of crosstalk between these cellular compartments. Although inflammation is necessary for fibrosis development, purely controlling intestinal inflammation cannot halt the development of fibrosis, suggesting that chronic inflammation is not the unique contributor to fibrogenesis. Several inflammation-independent mechanisms including gut microbiota, creeping fat, ECM interaction, and metabolic reprogramming are involved in the pathogenesis of fibrosis. In the past decades, substantial progress has been made in elucidating the cellular and molecular mechanisms of intestinal fibrosis. Here, we summarized new discoveries and advances of cellular components and major molecular mediators that are associated with intestinal fibrosis, aiming to provide a basis for exploring effective anti-fibrotic therapies in this field.

Triple-negative mouse breast cancer initiating cells show high expression of beta1 integrin and increased malignant features.

Triple-negative breast cancer (TNBC) is a subtype of breast cancer that exhibits aggressive tumor phenotypes, including rapid metastasis and tumor recurrence. Integrins belong to the family of transmembrane glycoproteins involved in regulating cell adhesion, proliferation, and differentiation through cell-cell and cell-extracellular matrix interactions. Aberrant β1 integrin signaling has been implicated in cancer invasion and metastasis processes. The present work aimed to investigate the role of β1 integrin in TNBC cancer progression using a mouse 4T1 cell line as a model system. We have sorted a subset of tumor-initiating cells (TICs) from the 4T1 cell line based on CD133 positivity by flow cytometry. RT-PCR and protein analysis studies showed the transcriptional upregulation of β1 integrin and its downstream target focal adhesion kinase in 4T1-TICs compared to parental 4T1 cells. In addition, the expression of β1 receptors in TICs is significantly higher than in parental population cells. Furthermore, in vitro cellular assays revealed that CD133+ TICs have higher clonogenic ability, invasion, and sphere formation potential. These findings suggest that β1 integrin has a potential role in TNBC invasion and metastasis. Hence, β1 integrin could be a possible factor for future targeted cancer therapies.

Abstract P6-13-01: EPITHELIAL-MESENCHYMAL TRANSITION AND TUMOR STEM CELLS NETWORK IDENTIFICATION IN BREAST CARCINOMAS: IN SILICO STUDY

Abstract INTRODUCTION: Breast cancer (BC) is the most prevalent malignant tumor in the female population, except for skin tumors. Despite therapeutic advances, over 20% of patients with localized disease will relapse. The research of epithelial-mesenchymal transition (EMT), tumor stem cells (TSC), and the biological mechanisms related to refractoriness and metastasis development is, therefore, an opportunity for new therapeutic strategies and better results. OBJECTIVES: To identify breast cancer cellular markers related to EMT and TSC according to their histological subtypes, stage and to analyze their relationship with clinical outcomes. METHODS: After selecting a public breast cancer patients database with interactome, we identified differentially expressed genes, their associated processes, coexpression networks and interactions with pathways related to the stem phenotype and epithelial-mesenchymal transition. The characterization of key genes and the correlation with histological subtypes and clinical outcome allowed us to determine a group of genes as potential breast cancer EMT/TSC prognostic markers. RESULTS: In the 989 patients studied, 1033 differentially expressed genes (DEGs) were found, categorized according to histological subtype (hormone receptor positive, HER2 positive, triple negative) and stage IV. Seven communities of gene coexpression were found, with the gray community showing greater interaction with hormone positive tumors, the green community with HER2 positive, and the turquoise community with the triple negative one. The hormone positive disease was related to extracellular matrix processes and neuronal communication, the HER2 positive to the extracellular matrix interaction and the triple negative tumors to mitotic processes. Investigation networks with EMT and TSC related genes demonstrated a strong correlation with HER2-positive and triple-negative tumors; being eight genes in HER2 positive subtypes correlated with survival (SYNDIG1, ​​COL10A1, SLC24A2, LINC00922, KLKP1, MMP11 and ECM2); and one of the hormone positive subtype (ITIH5). ECM2 was highlighted in terms of EMT/TSC connectivity and survival. CONCLUSION:The EMT/TSC processes are significant in the various subtypes of breast cancer and impact on survival, especially in the HER2 positive subtype. Citation Format: Vanessa Dybal, Bruno R. Cavalcante, Gisele V. Rocha, Clarissa Gurgel. EPITHELIAL-MESENCHYMAL TRANSITION AND TUMOR STEM CELLS NETWORK IDENTIFICATION IN BREAST CARCINOMAS: IN SILICO STUDY. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-13-01.

Role of GPR56 in Platelet Activation and Arterial Thrombosis.

The adhesion G protein-coupled receptor GPR56 mediates cell-cell and cell-extracellular matrix interactions. To examine the function of GPR56 in platelet activation and arterial thrombosis, we generated GPR56-knockout mice and evaluated GPR56 expression in human and mouse platelets. The results revealed that the levels of the GPR56 N-terminal fragment were significantly higher on the first day after myocardial infarction than on the seventh day in the plasma of patients with ST-segment-elevation myocardial infarction. Next, we investigated the effects of GPR56 on platelet function in vitro and in vivo. We observed that collagen-induced aggregation and adenosine triphosphate release were reduced in Gpr56 -/- platelets. Furthermore, P-selectin expression on the Gpr56 -/- platelet surface was also reduced, and the spreading area on immobilized collagen was decreased in Gpr56 -/- platelets. Furthermore, collagen-induced platelet activation in human platelets was inhibited by an anti-GPR56 antibody. Gpr56 -/- mice showed an extended time to the first occlusion in models with cremaster arteriole laser injury and FeCl3-induced carotid artery injury. GPR56 activated the G protein 13 signaling pathway following collagen stimulation, which promoted platelet adhesion and thrombus formation at the site of vascular injury. Thus, our study confirmed that GPR56 regulated the formation of arterial thrombosis. Inhibition of the initial response of GPR56 to collagen could significantly inhibit platelet activation and thrombus formation. Our results provide new insights for research into antiplatelet drugs.

An indentation-based framework for probing the glycosaminoglycan-mediated interactions of collagen fibrils

Microscale deformation processes, such as reorientation, buckling, and sliding of collagen fibrils, determine the mechanical behavior and function of collagenous tissue. While changes in the structure and composition of tendon have been extensively studied, the deformation mechanisms that modulate the interaction of extracellular matrix (ECM) constituents are not well understood, partly due to the lack of appropriate techniques to probe the behavior. In particular, the role of glycosaminoglycans (GAGs) in modulating collagen fibril interactions has remained controversial. Some studies suggest that GAGs act as crosslinkers between the collagen fibrils, while others have not found such evidence and postulate that GAGs have other functions. Here, we introduce a new framework, relying on orientation-dependent indentation behavior of tissue and computational modeling, to evaluate the shear-mediated function of GAGs in modulating the collagen fibril interactions at a length scale more relevant to fibrils compared to bulk tests. Specifically, we use chondroitinase ABC to enzymatically deplete the GAGs in tendon; measure the orientation-dependent indentation response in transverse and longitudinal orientations; and infer the microscale deformation mechanisms and function of GAGs from a microstructural computational model and a modified shear-lag model. We validate the modeling approach experimentally and show that GAGs facilitate collagen fibril sliding with minimal crosslinking function. We suggest that the molecular reconfiguration of GAGs is a potential mechanism for their microscale, strain-dependent viscoelastic behavior. This study reveals the mechanisms that control the orientation-dependent indentation response by affecting the shear deformation and provides new insights into the mechanical function of GAGs and collagen crosslinkers in collagenous tissue.

Characterizing Epithelial Wound Healing In Vivo Using the Cnidarian Model Organism Clytia hemisphaerica.

All animal organs, from the skin to eyes to intestines, are covered with sheets of epithelial cells that allow them to maintain homeostasis while protecting them from infection. Therefore, it is not surprising that the ability to repair epithelial wounds is critical to all metazoans. Epithelial wound healing in vertebrates involves overlapping processes, including inflammatory responses, vascularization, and re-epithelialization. Regulation of these processes involves complex interactions between epithelial cells, neighboring cells, and the extracellular matrix (ECM); the ECM contains structural proteins, regulatory proteins, and active small molecules. This complexity, together with the fact that most animals have opaque tissues and inaccessible ECMs, makes wound healing difficult to study in live animals. Much work on epithelial wound healing is therefore performed in tissue culture systems, with a single epithelial cell-type plated as a monolayer on an artificial matrix. Clytia hemisphaerica (Clytia) provides a unique and exciting complement to these studies, allowing epithelial wound healing to be studied in an intact animal with an authentic ECM. The ectodermal epithelium of Clytia is a single layer of large squamous epithelial cells, allowing high-resolution imaging using differential interfering contrast (DIC) microscopy in living animals. The absence of migratory fibroblasts, vasculature, or inflammatory responses makes it possible to dissect the critical events in re-epithelialization in vivo. The healing of various types of wounds can be analyzed, including single-cell microwounds, small and large epithelial wounds, and wounds that damage the basement membrane. Lamellipodia formation, purse string contraction, cell stretching, and collective cell migration can all be observed in this system. Furthermore, pharmacological agents can be introduced via the ECM to modify cell:ECM interactions and cellular processes in vivo. This work shows methods for creating wounds in live Clytia, capturing movies of healing, and probing healing mechanisms by microinjecting reagents into the ECM.

An interplay of matrix stiffness, dimensionality and adhesivity on cellular behavior

Cell-based assays are essential in vitro tools for understanding basic cell biology, pathophysiology of diseases and mechanism of drug actions most cancer studies have utilized two-dimensional (2D) cell culture methods, which have their shortcomings including lack of cell- extracellular matrix interactions and three-dimensional (3D) geometry, and inaccurate representation of cell polarity. Hence, 3D matrices are being increasingly used to study the effect of 3D niche on cell behavior. Till date, very few systematic studies have been done to show comparison of cell behavior when seeded on the surface and encapsulated inside the matrix. In this study, we fabricated poly(ethylene glycol) (PEG) and gelatin-based matrices using UV mediated photo-polymerization to establish 2D and 3D cell culture methods using breast cancer MDA-MB-231 cells. We have found that the adhesion and spreading of cells on the gel surface is different from that when embedded in gels. The stiffness of poly (ethylene glycol) diacrylate (PEGDA)-gelatin methacryloyl (GelMA) hydrogels with lower concentration of GelMA is lower than that with higher GelMA; further, those with higher overall concentration of polymers (>5%) retain their mechanical integrity and do not degrade even after 7 d. Physical characterization of these matrices demonstrate their optimal pore size, mechanical stiffness and degradation, which are further tunable for tissue engineering, regenerative medicine, drug delivery and cancer studies. Additionally, these semi-synthetic PEGDA-GelMA matrices are transparent in nature, thereby, allowing easy imaging of cells in 3D. The system developed here can be used for short and long term cell culture and can be potentially explored for cell migration and metastasis studies.

An indispensable role of TAZ in anoikis resistance promoted by OTUB1 deubiquitinating enzyme in basal-like triple-negative breast cancer cells

Aggressive cancers, such as triple-negative breast cancer (TNBC), are mostly fatal because of their potential to metastasize to distant organs. Cancer cells acquire various abilities to metastasize, including resistance to anoikis, an apoptotic cell death induced by loss of anchorage to the extracellular matrix. Transcriptional coactivator with PDZ binding motif (TAZ) and Yes-associated protein (YAP), the downstream effectors of the Hippo pathway, regulate cell- and tissue-level architectures by responding to mechanical microenvironments of cells, including the cell–extracellular matrix interaction. The Hippo pathway is frequently disrupted in cancer cells, and TAZ and YAP are irrelevantly activated, potentially resulting in anchorage-independent survival/proliferation of cancer cells and metastatic progression. The study aims to investigate the roles of TAZ and YAP in anoikis resistance in basal-like (BL) TNBC cells, which comprise a major subtype (>70%) of TNBC. We found that TAZ and YAP had nonredundant roles in anchorage-independent cancer cell survival or anoikis resistance. Particularly, TAZ was indispensable for anoikis resistance in BL-TNBC cells but not for survival of non-transformed mammary epithelial cells (MECs). In contrast, YAP, a paralog of TAZ, was indispensable for survival of both non-transformed MECs and cancer cells. Therefore, TAZ might be a preferable therapeutic target against dissemination of aggressive cancer cells without killing normal cells. Interestingly, TAZ was abnormally stabilized in BL-TNBC cells under non-adherent conditions, which promoted anoikis resistance. Furthermore, OTUB1, a deubiquitinating enzyme, was responsible for the stabilization of TAZ in detached BL-TNBC cells. Importantly, simultaneous high expression of TAZ and OTUB1 was associated with poor prognosis in BC. Thus, OTUB1 has emerged as a potentially druggable target. Successful inhibition of OTUB1 enzymatic activity is expected to downregulate TAZ and eventually prevents metastasis of aggressive cancers, such as BL-TNBC.

Spheroid Engineering in Microfluidic Devices.

Two-dimensional (2D) cell culture techniques are commonly employed to investigate biophysical and biochemical cellular responses. However, these culture methods, having monolayer cells, lack cell-cell and cell-extracellular matrix interactions, mimicking the cell microenvironment and multicellular organization. Three-dimensional (3D) cell culture methods enable equal transportation of nutrients, gas, and growth factors among cells and their microenvironment. Therefore, 3D cultures show similar cell proliferation, apoptosis, and differentiation properties to in vivo. A spheroid is defined as self-assembled 3D cell aggregates, and it closely mimics a cell microenvironment in vitro thanks to cell-cell/matrix interactions, which enables its use in several important applications in medical and clinical research. To fabricate a spheroid, conventional methods such as liquid overlay, hanging drop, and so forth are available. However, these labor-intensive methods result in low-throughput fabrication and uncontrollable spheroid sizes. On the other hand, microfluidic methods enable inexpensive and rapid fabrication of spheroids with high precision. Furthermore, fabricated spheroids can also be cultured in microfluidic devices for controllable cell perfusion, simulation of fluid shear effects, and mimicking of the microenvironment-like in vivo conditions. This review focuses on recent microfluidic spheroid fabrication techniques and also organ-on-a-chip applications of spheroids, which are used in different disease modeling and drug development studies.

Abstract A020: Gene expression programs of cancer spread are targets for anti-metastasis treatments

Abstract The lack of specific anti-metastasis drugs is due to an incomplete understanding of the molecular mechanisms underlying this process, and hence a lack of potential drug targets. In the past, we have defined the genetic basis of cancer metastasis as aberrant expression or splicing by a unique set of developmentally non-essential stress response genes that physiologically mediate the homing of immune system cells. Thus, the genetic underpinning of metastasis is distinguishable from the genetic underpinnings for uncontrolled growth or immortalization (in contrast to oncogenes or tumor suppressor genes, metastasis genes are not mutated; when mutations do arise, they are typically located in the regulatory elements). More recently, we have expanded our research to gene expression programs with the goal to identify drug targets for combination therapies. Utilizing the gene expression profiles from 653 GEO datasets, we investigated the signatures by diverse cancers in various metastatic sites for common features and for site-specific characteristics. We corroborated the meta-analysis in a murine model. Metastases are generally characterized by a core program of gene expression that induces the oxidative metabolism, activates vascularization/tissue remodeling, silences extracellular matrix interactions, and alters ion homeostasis. This program distinguishes metastases from their originating primary tumors as well as from their target host tissues. For site specificity, the release from the primary tumor is associated with a suppression of functions that are important for the identity of the organ of origin, such as a down-regulation of steroid hormone responsiveness in the disseminated foci derived from prostate cancer. Metastases adjust to their target microenvironment by upregulating—even overexpressing—genes and genetic programs that are characteristic of that organ. Further, alterations in RNA and protein processing as well as immune deviation are common. Although the drug treatment of malignant tumors has made impressive progress in recent years, the successes have been achieved mostly against the primary tumors. Once a cancer has disseminated, the prognosis worsens dramatically. There is a paucity of suitable anti-metastasis drugs. Conceivably, chemotherapy of disseminated cancer might be more efficacious if selected to match the genetic makeup of the metastases rather than the organ of origin by the primary tumor. In this regard, new potential has opened up by our finding that the gene expression of metastases is characterized by a four-pronged core program, which is common to all metastases and distinguishes them from the primary tumor as well as from the target site. Drug combinations that suppress the genetic core program of metastasis may fill an important void in cancer chemotherapy. Our ongoing research has identified lead compounds that may lay the foundation for anti-metastasis combination chemotherapies. Citation Format: Gulimerouzi F. Fnu, Franz Hartung, Georg F. Weber. Gene expression programs of cancer spread are targets for anti-metastasis treatments [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr A020.

Three-Dimensional Cell Culture Methods in Infectious Diseases and Vaccine Research

Cells, the basic structures of all living organisms, reside in an extracellular matrix consisting of a complex three-dimensional architecture and interact with neighboring cells both mechanically and biochemically. Cell–cell and cell–extracellular matrix interactions form a three-dimensional network that maintains tissue specificity and homeostasis. Important biological processes in a cell cycle are regulated by principles organized by the microenvironment surrounding the cell. The conventional cell culture methods failed to mimic in vivo-like structural organization and are insufficient to examine features such as connectivity of cells, cellular morphology, viability, proliferation, differentiation, gene and protein expression, response to stimuli, and drug/vaccine metabolism. Three-dimensional cell culture studies are very important in terms of reducing the need for in vivo studies and creating an intermediate step. Three-dimensional cell culture methods have attracted attention in the literature in recent years, especially in examining the cellular distribution of organs in the presence of infectious diseases, elucidating the pathogenic mechanism of action of viruses, and examining virus–host interactions. This review highlights the use and importance of three-dimensional cell culture methods in the design and characterization of novel vaccine formulations and the pathogenesis of infectious diseases.