Methods in Molecular Biology

Single-cell RNA-sequencing (scRNA-seq) is a powerful technique that can barcode individual cells and thus used to obtain a gene expression profile for every individual cell within a tissue. This makes scRNA-seq an excellent method for characterizing rare cell populations such as stem cells. We describe how scRNA-seq can be utilized to examine limbal epithelial stem cell population as well as investigate the contribution of autophagy to the function of limbal epithelial stem cells. To accomplish this, we used the Beclin1 heterozygous (Beclin1 het) mouse, a well-established model of autophagy deficiency...

Autophagy is a key process that maintains cellular homeostasis. Autophagy contributes to various physiological and pathophysiological processes. Development of methodologies for autophagy detection has greatly facilitated the research on autophagy. Among these methodologies, GFP-LC3 reporter has been popularly used in the literature. In this chapter, we will detail step-by-step the GFP-LC3 reporter protocol we have adapted in our lab. This protocol begins with the generation of lentivirus expressing GFP-LC3...

Paraxial mesoderm in the early embryo is segmented into epithelial blocks called somites that establish the metameric organization of the vertebrate body plan. Somites are sequentially formed from head to tail in a rhythmic manner controlled by an oscillating gene regulatory network known as the segmentation clock. We know very little about this important process during human development due to limited access to human embryos and ethical concerns. To bypass these difficulties, model systems derived from human pluripotent stem cells have been established...

Melanoma, a severe type of skin cancer, poses significant management challenges due to its resistance to available treatments. Despite this obstacle, the high immunogenicity of melanoma renders it amenable to immune therapy, and NK cells have been identified as possessing anti-tumor properties in immunotherapy. The development of chimeric antigen receptor (CAR)-modified NK cells, or CAR-NK cells, has shown potential in enhancing immunotherapeutic regimens. To achieve this, researchers have explored various sources of NK cells, including those derived from the placenta, which offers benefits compared to other sources due to their limited ex vivo expansion potential...

Flow cytometry and immunohistochemistry techniques both determine the target protein by immunolabeling. Flow cytometric analysis quantifies total number of fluorescent labeled cells and qualify sup-populations according to size and granularity. Immunohistochemistry is able to map immune-labeled cells and extracellular matrix components under light and electron microscope by enzyme or fluorescent molecules. Real-time identification, in-time classification, and final plotting of spermatogonial lineage are of crucial importance for monitoring the fertility potential of spermatogonial stem cell microenvironment and predicting progress of spermatogenesis...

Natural killer (NK) cells are a part of a sophisticated immune system that is necessary for the skin because it is a crucial organ that is continually exposed to environmental influences. Recent studies have shown that NK cell incorporation into three-dimensional (3D) organotypic culture systems for human skin stem cells provides a physiologically relevant environment to study the interactions between immune cells and skin cells, making it a powerful tool for simulating skin diseases and researching these interactions...

Psoriasis is a chronic, inflammatory, autoimmune disease with systemic symptoms including seborrheic psoriasis, pustular lesions, plaque lesions, intestinal eruptions, and sometimes arthritis. Moreover, most of the psoriatic subjects report life challenges due to the condition, impacting social activities and daily tasks. Generally, psoriasis treatment options depend on the severity, coexisting conditions, and medical availability. Although psoriasis therapies reduce symptoms and appearance, still it is not curable...

Cancer is a heterogeneous disorder of uncontrolled growth of cells, which has proven to be a major burden worldwide. Many treatment options are available for cancer therapy, yet side effects and drug resistance remain major hurdles. Therefore, it is necessary to develop novel drugs for cancer therapy. Anti-cancer peptides (ACPs) are attractive candidates with remarkable potency, low toxicity, and high specificity advantages. However, traditional experimental identification of ACPs is time-consuming and expensive...

Protease inhibitors of the alpha-macroglobulin family (αM) have a unique mechanism that allows them to trap proteases that is dependent not on the protease's class, but rather on its cleavage specificity. Proteases trigger a conformational change in the αM protein by cleaving within a "bait region," resulting in the sequestering of the protease inside the αM molecule. This nonspecific inhibitory mechanism appears to have arisen early in the αM family, and the broad protease-trapping capacity that it allows may play a role in pathogen defense...

The yeast surface display platform provides a powerful approach for screening protein diversity libraries to identify binders with an enhanced affinity toward a binding partner. Here, we describe an adaptation of the approach to identify binders with enhanced specificity toward one among multiple closely related binding partners. Specifically, we describe methods for engineering selective matrix metalloproteinase (MMP) inhibitors via yeast surface display of a tissue inhibitor of metalloproteinase (TIMP) diversity library coupled with a counter-selective screening strategy...

Targeting dysregulated protease expression and/or abnormal substrate proteolysis, highly selective inhibition of pathogenic proteases by monoclonal antibodies (mAbs) presents an attractive therapeutic approach for the treatment of diseases including cancer. Herein, we report a functional selection method for protease inhibitory mAbs by periplasmic co-expression of three recombinant proteins-a protease of interest, an antibody Fab library, and a modified β-lactamase TEM-1. We validate this approach by isolation of highly selective and potent mAbs inhibiting human matrix metalloproteinase 9 (MMP9)...

The membrane-bound matrix metalloproteinase 14 (MMP14, also known as MT1-MMP) plays important roles in the remodeling of the extracellular matrix during various cellular processes such as cancer metastasis, angiogenesis, and wound healing through its proteolytic activity. There are no known MMP14-specific inhibitors to date, and hence identification of MMP14-specific inhibitors will be beneficial for finding potential therapeutics for various diseases, including cancer and inflammation. High-throughput screening (HTS) assays have become a common way to search for new small compounds, peptides, and natural products...

Hematopoiesis is the process through which all mature blood cells are formed and takes place in the bone marrow (BM). Acute myeloid leukemia (AML) is a blood cancer of the myeloid lineage. AML progression causes drastic remodeling of the BM microenvironment, making it no longer supportive of healthy hematopoiesis and leading to clinical cytopenia in patients. Understanding the mechanisms by which AML cells shape the BM to their benefit would lead to the development of new therapeutic strategies. While the role of extracellular matrix (ECM) in solid cancer has been extensively studied during decades, its role in the BM and in leukemia progression has only begun to be acknowledged...

The utilization of tumor spheroids and organoids has greatly facilitated mechanistic understanding of tumor growth and invasion and lead to more effective high-throughput analysis of potential chemotherapeutic agents. In spheroid and organoid systems, tumor invasion occurs in three dimensions and monitoring this behavior can be data intensive. Quantitative correlation of tumor invasion with protease activity can further exacerbate data storage issues. The present method utilizes the "Hit Pick" approach to provide quantitative analysis and correlation of tumor invasion and membrane type 1 matrix metalloproteinase (MT1-MMP) activity in a rapid fashion with greatly reduced data storage requirements compared with standard image analysis approaches...

Cancers have a complex relationship with the surrounding environment that regulates everything from progression to response to treatment. Cell-cell and cell-matrix interactions are heavily influenced by protease biology. Studies on the tumor microenvironment have revealed a new complexity for proteases, describing novel substrates for classic proteases, and protease-independent roles for these enzymes. The rapid expansion of 3D in vitro model systems provides excellent tools to study the intricate influence of proteases on the tumor microenvironment...

The platelet-derived microparticles (PMPs) have been connected with tumor progression and metastatic dissemination. PMPs infiltrate solid tumors and transfer platelet-derived cargo to cancer cells. The functional roles of PMPs in cancer progression are still poorly understood. PMPs, incorporated by colorectal cancer (CRC) cells, were shown to upregulate the expression and activity of matrix metalloproteases (MMPs). To investigate the impact of PMPs on the invasive potential of CRC, we established the protocol of dequenched gelatin (DG), fluorescein conjugate assay...

Membrane-type 1 matrix metalloproteinase (MT1-MMP, also called MMP14) is one of the significant cell invasion drivers. MT1-MMP has been shown to play a crucial role in cancer invasion, cartilage degradation in rheumatoid arthritis, angiogenesis, and collagen homeostasis in different stromal tissues. Thus, investigating MT1-MMP activities in different cell types is of interest to investigators in different research fields. Several methods are available to assess the unique biological activity of MT1-MMP in the cells...

Some cancer cells form highly regulated structures, termed invadopodia, which mediate local, enzymatic degradation of extracellular matrix and facilitate cancer cell invasion and migration during metastatic progression. Understanding invadopodium formation and function in cancer cells is therefore an important strategy to find novel clinical approaches to interfere with metastasis. Invadopodia are F-actin-rich protrusions that form on the advancing edge of cells, supported by complex molecular interactions at the cell membrane...

Collagen-I (Col) and hyaluronic acid (HA) are two of the most important extracellular matrix (ECM) components. While collagen serves as the main structural feature of the ECM and is an important ligand for integrin-based adhesions, HA acts as a ligand for the transmembrane glycoprotein CD44. However, most studies on cancer invasion utilize 3D collagen matrices, thereby ignoring the importance of HA-CD44 interactions. Here, we describe the process of fabricating Col-HA gels with varying Col/HA ratios, which can be used to suitably mimic the tumor microenvironment...

Silencing expression with short interfering RNA (siRNA) is a rapid and cost-effective way to analyze the involvement of target genes in a range of biological processes. Here we describe isolation of primary human monocytes from peripheral blood and their in vitro differentiation to macrophages, followed by electroporation with siRNA to silence expression of a disintegrin and metalloproteinase 17 (ADAM17). This enables evaluation of ADAM17's role in cleaving transmembrane proteins, such as its prototypic substrate tumor necrosis factor (TNF), by enzyme-linked immunosorbent assay (ELISA), flow cytometry, or immunoblotting...