Cancer Biology

Patient-derived glioblastoma (GBM) cells are valuable models for GBM research due to their rarity and the highly lethal nature of this cancer. Preserving these cells through long-term cryopreservation is therefore essential for advancing future investigations. However, recent studies have reported that standard cell recovery protocols are inefficient, resulting in poor cell survival and limited regrowth. Here, we established an optimized culture protocol that enhances the recovery and expansion of patient-derived GBM cells by combining Matrigel with an increased concentration of fetal bovine serum (FBS). This approach significantly improves cell attachment and recovery after thawing cells that have been cryopreserved for more than a decade. Importantly, the recovered cells retain key phenotypic characteristics and remain suitable for downstream applications, including drug testing and spheroid formation. Together, this optimized protocol provides a novel strategy to increase the availability of patient-derived GBM cells by improving their efficient recovery from long-term cryopreservation, thereby maximizing their utility in GBM research.

Breast cancer (BC) is the most frequently diagnosed malignancy in women and a leading cause of cancer-related mortality worldwide. Current clinical management relies on molecular classification—based on estrogen receptor (ER), progesterone receptor (PR), HER2, and Ki67 expression—to guide prognosis and therapy. Triple-negative breast cancer (TNBC), which lacks ER, PR, and HER2 expression, represents 15%–20% of cases and is characterized by aggressive behavior, early recurrence, and a paucity of targeted treatment options. These challenges underscore the urgent need for improved preclinical models that better recapitulate tumor biology to accelerate therapeutic discovery. While conventional monolayer (2D) cultures have contributed significantly to cancer research, they fail to mimic critical features of the three-dimensional (3D) tumor microenvironment (TME), thereby limiting clinical translation. To address this gap, 3D spheroid models have emerged as a powerful intermediary, more accurately replicating in vivo conditions such as cell–cell and cell–matrix interactions, nutrient and oxygen gradients, and the development of hypoxic cores. These features make spheroids a physiologically relevant platform for studying complex processes like metastasis, drug resistance, and treatment response. Here, we present a robust, simple, and cost-effective protocol for generating uniform 3D spheroids. Our method enables consistent monitoring of spheroid formation and growth over time, with quantitative, image-based size analysis to ensure reproducibility and scalability. Designed for flexibility, the protocol is broadly applicable across diverse cell types, effectively bridging the gap between traditional 2D cultures and complex in vivo studies. By providing an accessible and reliable model of the 3D TME, this protocol opens new avenues for high-throughput drug screening, mechanistic studies of tumor progression, and the advancement of personalized medicine strategies in breast cancer and beyond.

Extracellular vesicles (EVs) are nanoscale particles secreted by all cells and present in all biological fluids, where they carry molecular cargo reflective of health and disease states. Their diagnostic potential is often obscured by the high abundance of non-EV proteins and lipoproteins (e.g., albumin, apolipoproteins) that complicate proteomic analysis of primary biofluids, such as ascites fluid. Conventional isolation strategies face a persistent trade-off between EV purity and yield. To overcome this, a magnetic bead-based protocol (Mag-Net) to enrich EVs according to electrochemical surface charge using strong anion-exchange chemistry (SAX) was adapted for proteomics. Our workflow is specifically adapted to ascites fluid from human or murine sources. This approach effectively separates EVs from high-abundance proteins and lipoproteins, enabling proteomic profiling from as little as 2 μL of ascites fluid. Demonstrated in both murine and human ovarian cancer models, Mag-Net offers a reproducible, scalable, and automation-ready solution for EV isolation from various biofluids.

Prostate carcinoma (PCa) progression is strongly influenced by the surrounding tumor microenvironment, where cancer-associated fibroblasts (CAFs) represent the most abundant and functionally relevant stromal population. Despite their importance, the lack of stable cell lines representing CAF phenotypes limits the study of stromal–tumor interactions. To address this limitation, we provide an optimized protocol for isolating CAFs from fresh human PCa biopsies based on a mechanical procedure exploiting the specific CAF ability to migrate out from the tumor explants. This approach preserves tissue architecture and maintains CAF viability and phenotype. The resulting ex vivo CAF cultures provide a suitable model to investigate CAF biology within the tumor microenvironment.

Breast cancer remains one of the most prevalent and deadly malignancies affecting women worldwide. Its progression and metastatic behavior are driven by complex mechanisms. To develop more effective therapeutic strategies, it is crucial to understand tumor growth, angiogenesis, and microenvironmental interactions. Although traditional in vivo models such as murine xenografts have long been used to study tumor biology, these approaches are often time-consuming, costly, and ethically constrained. In contrast, the chick embryo chorioallantoic membrane (CAM) assay offers a rapid, cost-effective, and ethically flexible alternative for evaluating tumor development and angiogenesis. This protocol describes an in ovo CAM-based xenograft model in which human breast cancer cells are implanted onto the vascularized CAM of chick embryos. This method enables real-time evaluation of tumor growth. Furthermore, the model allows for manipulation of experimental conditions, including pharmacological treatments or genetic modifications, to study specific molecular mechanisms involved in breast cancer progression. The major advantages of this protocol lie in its simplicity, reduced cost, and capacity for high-throughput screening, making it a valuable tool for translational cancer research.

Our genome is duplicated during every round of cell division through the process of DNA replication, but this fundamental process is subjected to various stresses arising from endogenous or exogenous sources. Thus, studying replication dynamics is crucial for understanding the mechanisms underlying genome duplication in physiological and replication stress conditions. Earlier, radioisotope-based autoradiography and density-labeling methods were used to study replication dynamics, which were limited in spatial resolution, representing only average estimates from many DNA samples. Here, we describe a DNA fiber assay that utilizes different thymidine analog incorporation, like 5-chloro-2’-deoxyuridine (CldU) and 5-iodo-2’-deoxyuridine (IdU), into replicating DNA. Such labeled DNA can be stretched and fixed on silanized glass slides, which are denatured with mild acidic treatment to expose the labeled nascent DNA. This DNA can then be visualized by using primary antibodies against CldU and IdU, followed by fluorophore-conjugated secondary antibodies, and observing them using a fluorescence microscope. The DNA fiber assay allows the visualization of individually replicating DNA at a single-molecular resolution and is highly quantitative, high-throughput, and easily reproducible. This technique offers insights into different replication parameters, like rate of DNA synthesis, extent of reversed fork protection, restart of stalled forks, and fork asymmetry under untreated or replication stress conditions at a single-molecule level.

The extracellular matrix (ECM) critically shapes melanoma progression and therapeutic response, yet commonly used matrices such as Matrigel fail to capture tissue- and disease-specific ECM properties. This protocol provides a streamlined and scalable method for generating murine, tissue-specific ECM hydrogels from skin, lung, and melanoma tumors, therefore overcoming the restricted materials of mouse-derived ECM. The workflow integrates tissue-tailored decellularization, lyophilization, mechanical fragmentation, pepsin digestion, and physiological polymerization to produce hydrogels that reliably preserve fibrillar collagen architecture and organ-specific ECM cues. Decellularization efficiency and ECM integrity are validated by DNA quantification, H&E staining, and Picrosirius Red staining analysis. These hydrogels provide a species- and tissue-matched platform for studying melanoma–ECM–immune interactions, pre-metastatic niche features, and therapy-induced ECM remodeling. Overall, this protocol offers a reproducible and physiologically relevant ECM model that expands experimental capabilities for melanoma biology and treatment-resistance research and that can be easily extended to other tumors and tissues.

Immunohistochemistry (IHC) and immunofluorescence (IF) are fundamental molecular biology techniques to assess protein expression. However, the melanin present normally in the eye in the uveal tract (choroid, iris, and ciliary body) and the retinal pigment epithelium (RPE) poses a significant challenge for IHC and IF. This is because melanin interferes with both chromogenic and fluorescent detection methods. Additionally, formalin fixation, which is commonly used for IHC, can result in shrinkage and loss of cellular detail in the eye. This protocol provides an optimized approach using Davidson’s fixative with a hydrogen peroxide bleaching step to eliminate melanin interference in the mouse eye, improving the quality and interpretability of IHC analyses of the uveal tract and RPE. It is particularly useful for the analysis of uveal melanoma.

Immunopeptidomics enables the identification of peptides presented by major histocompatibility complex (MHC) molecules, offering insights into antigen presentation and immune recognition. Understanding these mechanisms in hypoxic conditions is crucial for deciphering immune responses within the tumor microenvironment. Current immunopeptidomics approaches do not capture hypoxia-induced changes in the repertoire of MHC-presented peptides. This protocol describes the isolation of MHC class I-bound peptides from in vitro hypoxia-treated cells, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. It describes optimized steps for cell lysis, immunoaffinity purification, peptide elution, and MS-compatible preparation under controlled low-oxygen conditions. The method is compatible with various quantitative mass spectrometry approaches and can be adapted to different cell types. This workflow provides a reliable and reproducible approach to studying antigen presentation under hypoxic conditions, thereby enhancing physiological relevance and facilitating deeper immunological insights.

Research on brain disorders, particularly in the field of oncology, requires in vivo models to evaluate various therapeutic approaches, including intracerebral drug delivery. To meet this requirement, the implantation of intracerebral cannulas offers a reliable method for administering candidate therapeutics directly into the brain. This protocol describes a surgical technique for cannula implantation in mice, enabling repeated administration of therapeutic compounds in the context of glioblastoma treatment. The method was designed with an emphasis on using accessible, easy-to-handle, and sterilized tools to optimize surgical outcomes. Particular attention was also given to animal welfare, notably through refined procedures for asepsis, anesthesia, and postoperative care.