Methods in Molecular Biology

Non-small cell lung cancer (NSCLC) is a predominant form of lung cancer characterized by its aggressive nature and high mortality rate, primarily due to late-stage diagnosis and metastatic spread. Recent studies underscore the pivotal role of mitophagy, a selective form of autophagy targeting damaged or superfluous mitochondria, in cancer biology, including NSCLC. Mitophagy regulation may influence cancer cell survival, proliferation, and metastasis by modulating mitochondrial quality and cellular energy homeostasis...

Volumetric muscle loss (VML) is one of the major types of soft tissue injury frequently encountered worldwide. In case of VML, the endogenous regenerative capacity of the skeletal muscle tissue is usually not sufficient for complete healing of the damaged area resulting in permanent functional musculoskeletal impairment. Therefore, the development of new tissue engineering approaches that will enable functional skeletal muscle regeneration by overcoming the limitations of current clinical treatments for VML injuries has become a critical goal...

Microbial dysbiosis is an important trigger in the development of oral diseases. Oral keratinocytes or gingival epithelial cells (GECs) offer protection against various microbial insults. Recent studies suggest that GECs expressed higher level of bitter taste receptor 14 (T2R14) compared to other taste receptors and toll-like receptors and act as innate immune sentinels. Macroautophagy or autophagy is a cellular conserved process involved in the regulation of host innate immune responses against microbial infection...

The extracellular matrix (ECM) is a noncellular component of tissues that provides structural and biochemical support to cells. The purpose of decellularization is to provide a tissue-specific niche to preserve the architecture, composition, and signaling molecules of the ECM. The current protocol discusses the standardization of chondrocyte isolation and the preparation of acellular ECM as a bioink additive from human native articular cartilage. Isolated chondrocytes with bioink additives provide a tissue-specific microenvironment...

Protein-protein interactions (PPIs) are known to be involved in most cellular functions, and a detailed knowledge of such interactions is essential for studying their role in normal and pathological conditions. Significant progress is being made in the identification of PPIs through advances in computational methods. In particular, the AlphaFold2 machine learning-based model has been shown to accelerate drug discovery process by predicting the 3D structure of protein complexes. In this chapter, a straightforward protocol for predicting interprotein interactions between PAR-3 and its protein partner adapter molecule crk is provided...

Maintenance of hematopoietic stem cell (HSC) function is an orchestrated event between multiple cell types, and crosstalk between these cell types is an essential part of HSC regulation. Among the cell groups of the niche involved in this process are a group of bone-resident macrophages known as osteomacs (OM). Previously, it was demonstrated that OM and osteoblasts contained within neonatal calvarial cells are critical to maintain hematopoietic function. Additionally, interactions between neonatal calvarial cells and megakaryocytes further enhance this hematopoietic activity...

Germ stem cell (GSC) niches are fundamental for the maintenance of the immortal germ cell lineage across generations. In the nematode Caenorhabditis elegans, the simple GSC system has served as an important model for understanding stem cell biology and underlying genetic architecture. GSC niche activity in C. elegans is highly sensitive to subtle environmental and genetic variation. Quantifying variation in the C. elegans GSC niche is therefore essential; however, most methods to do so remain labor-intensive and time-consuming when screening large numbers of individuals...

The co-culture method is a simple type of cell culture method used to evaluate the effects of communication between various types of cells in an in vitro setting. In the co-culture method, two or more eukaryotic cell types, or eukaryotic and prokaryotic cells, are cultured together. The co-culture method reflects in vivo cell behaviors and thereby emerges as a pivotal technique with diverse applications in cancer research and cell biology. Two categories of co-culture methods (indirect methods and direct methods) are well known...

Vernal keratoconjunctivitis (VKC) is a serious eye allergy characterized by poorly understood pathogenic mechanisms and a lack of effective treatments. Autophagy, a process involved in both triggering and suppressing immune and inflammatory responses, plays a role in VKC's pathophysiology. Understanding autophagy's involvement in VKC could lead to new treatment possibilities, such as utilizing specific topical substances to induce or inhibit autophagy and prevent severe complications of this eye condition. In our current protocol, we present a robust methodology established in our laboratory for studying autophagy in primary conjunctival fibroblasts...

Embryonic wound repair proceeds with complete regeneration of the tissue without any scar formation, whereas tissue repair in adults usually results in scars and the tissue does not completely regain its preinjured state. Wound-induced hair neogenesis (WIHN) in adult rodents results in de novo hair follicle formation in the center of large wounds, mimicking regeneration processes seen in fetal tissue. The investigation of WIHN therefore provides a unique quantitative framework for scrutinizing the mechanistic underpinnings of regenerative repair, which can have clinical implications in the context of scarless healing...

Autophagy is an evolutionarily conserved process providing the energy that cells need to survive, especially in stress situations, through catabolic processes. Considering the dual role of autophagy in cancer cells depending on the cellular context, it is crucial to comprehend the effect of drug candidates put forward to prevent cancer through the autophagy pathway. The CYTO-ID® Autophagy Detection Kit allows a rapid, specific and quantitative measurement of autophagic activity at the cellular level using a 488 nm-excitable green fluorescent detection reagent via flow cytometer...

Linking phenotypes to genetic components has been an essential part of novel drug discovery, and screening methods have been widely employed to achieve such a goal. Screens can be conducted in either pooled or arrayed formats. Although arrayed screenings provide a better and cheaper alternative in small scale, the larger-scale screenings are conducted in pooled manner. With its adaptability to various models and conditions, CRISPR/Cas9 technology provides an invaluable alternative to classical and RNAi-based screening methods...

Leishmaniasis is a neglected tropical disease caused by numerous species of Leishmania parasites, including Leishmania major. The parasite is transmitted by several species of sandfly vectors and infects myeloid cells leading to a myriad of inflammatory responses, immune dysregulations, and disease manifestations. Every cell undergoes autophagy, a self-regulated degradative process that permits the cells to recycle damaged or worn-out organelles in order to maintain cellular health and homeostasis. Studies have shown that Leishmania modulates their host cell autophagic machinery and there are indications that the parasite-specific autophagic processes may be valuable for parasite virulence and survival...

Myriad proteins are involved in the process of autophagy, which they participate in via their protein-protein interactions (PPI). Herein we outline a methodology for examining such interactions utilizing the case of intrinsically disordered protein (IDP) TNIP1 and its interaction with linear M1-linked polyubiquitin. This includes methods for recombinant production, purification, immuno-identification, and analysis of an IDP associated with autophagy, its ordered binding partner, and means of quantitatively analyzing their interaction...

The exquisite balance between cellular prosurvival and death pathways is extremely necessary for homeostasis. Different forms of programmed cell death have been widely studied and reported such as apoptosis, necroptosis, pyroptosis, and autophagy. Autophagy is a catabolic process important for normal cellular functioning. The main aim of this machinery is to degrade the misfolded or damaged proteins, unuseful organelles, and pathogens, which invade the cells, thereby maintaining cellular homeostasis and assuring the regular renewal of cell components...

Non-small cell lung cancer (NSCLC) is among the most malignant tumors with high propensity for metastasis and is the leading cause of cancer-related death globally. Most patients present with regional and distant metastasis, associated with poor prognosis. Lipids may play an essential role in either activating or inhibiting detachment-induced apoptosis (anoikis), where the latter is a crucial mechanism to prevent metastasis, and it may have a cross-talk with autophagy. Autophagy has been shown to be induced in various human cancer metastasis, modulating tumor cell motility and invasion, cancer cell differentiation, resistance to anoikis, and epithelial to mesenchymal transition...

In this chapter, we provide a method to purify and culture embryonic melanocytic stem cells that express green fluorescent protein in a cell-type specific manner. Isolation of melanocytic lineage cell populations that are >98% pure is accomplished through the use of GFP-based fluorescence activated cell sorting. We also provide a method to culture the purified melanoblasts and to analyze their proliferation, apoptosis, and motility properties.

Autophagy is an evolutionarily conserved process that aims to maintain the energy homeostasis of the cell by recycling long-lived proteins and organelles. We have very recently demonstrated that lipophagy, a special form of autophagy, mediates the association of the lipid droplets (LDs) with lysosomes to deliver the lipid cargo within the LDs to lysosomes for degradation in order to release free cholesterol required for steroid synthesis in human ovary and testis. In this chapter, we describe live cell confocal microscopy technique that allows us to monitor real-time cholesterol trafficking and the association of cholesterol-laden LDs with lysosome (lipophagy) in human granulosa cells...

Exosomes are small membrane-derived vesicles that transmit DNA constituents, mRNAs, microRNAs, and proteins from donor cells to a receiver cell. Various cells comprising of mesenchymal, immune, and cancer cells discharge exosomes. Cancer cell exosomes form the entry and reprogramming of essentials connected to a tumor environment. Melanoma-derived exosomes transport diverse proteins such as c-MET and RAB27a, which leave a melanoma mark. Increased mesenchymal epithelial transition (MET) expressions in serum exosomes have been considered an indicator of disease progression...

Short hairpin RNA (shRNA) is a technique used to silence gene expression stably in various cells. There are however several reported problems. First, the cloning of oligos can lead to ligation of multiple copies; second, premature termination of sequencing reaction during confirmation of hairpin template; third, microdeletions/substitutions in hairpin during cloning; and fourth, off target effects. In this chapter, we have described a retrovirus transduction-based protocol that can be used on cells in culture without encountering any of the reported issues...