Next-generation sequencing (NGS) technology has transformed the biomedical research landscape. Only a few years ago, high resolution genome or exome sequencing would be cumbersome and cost-restrictive, but current NGS technology platforms now allow for basic and clinical researchers to include these approaches for routine DNA and RNA sequencing needs. What are the different NGS sequencing approaches and how are they applied to oncology research?
Sarcomas are a group of aggressive heterogeneous tumors for which more than 100 histological subtypes have been defined1. Sarcomas are found in a variety of solid tissues, including bone and gastrointestinal stromal cells. Current treatment options include radiotherapy, surgical resection, targeted therapies, and chemotherapy, but these treatments have had limited efficacy on intermediate to high grade tumors. Investigations into the molecular and cellular mechanisms that drive sarcomas have helped identify potential biomarkers that can serve as potential therapeutic targets. In addition, recent studies have also focused on the tumor microenvironment (TME) within sarcomas and the roles of different immune cell subsets creating an immunosuppressive microenvironment. These observations directly inform novel immunotherapeutic approaches that are being examined in preclinical and clinical studies.
Gastrointestinal cancers are a heterogeneous group of cancers that can be caused by H. pylori bacterial or Epstein-Barr virus infection, chronic inflammation, or inherited or spontaneous genetic mutations. Advances in solid tumor immunotherapy for gastrointestinal cancers includes the development of methods that improve the screening, evaluation, and development of more precise and robust treatments. Breakthroughs in basic and translational research are leading to better treatment options for gastrointestinal cancer, and CRISPR/Cas9-based (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) gene editing technology is at the forefront of these discoveries.
Mouse models have been essential to the development of novel immunotherapies that target solid tumors and hematological malignancies. Several types of mouse models exist, and syngeneic mouse models offer several advantages for screening potential drugs and biologics since tumors are derived from the same genetic background as the mouse strain. Syngeneic tumor models are particularly useful for profiling tumor infiltrating lymphocytes (TILs) that are found within the tumor microenvironment (TME) of solid tumors.
Highlighted below is how immune profiling of TILs can be carried out in syngeneic mouse models and how this informs preclinical studies.
Acute myeloid leukemia (AML) is one of the most frequently occurring types of leukemia and can have widely varying treatment outcomes. Multiple mutations and cytogenetic abnormalities have been characterized in AML, and recent studies have been essential to defining specific mutations that confer resistance to standard chemotherapies or molecular inhibitors. A mutation in the tyrosine kinase domain of FMS-like tyrosine kinase 3 (FLT3) has been associated with resistance to FLT3 inhibitors, and molecular diagnostics are critical to identifying mutations that lead to treatment failure.
Plasmacytoid carcinoma of the urinary bladder – H&E Staining
Immunohistochemistry (IHC) is a technique that originates in the early twentieth century but continues to be a valuable method that forms the backbone of molecular pathology. IHC is used for histological examination of tissues and specifically detects the presence of a molecule, such as a tumor antigen. IHC uses antibody-based labeling in which the primary antibody detects the target of interest and the secondary antibody detects the primary antibody which is linked to a molecule for microscopic visualization. Many different secondary antibody labeling modalities exist, including fluorescence, enzyme-mediated reactions and colloidal gold, and different labels are suited to specific microscopy platforms.
Consider these five aspects of IHC as you implement this technique in preclinical cancer research:
Advances in preclinical oncology research are dependent on gaining insights into tumor biology and applying these insights to the development of novel diagnostics or therapeutics. Next-generation sequencing (NGS) technology has been instrumental in bridging basic immuno-oncology findings and preclinical applications. Here we provide an overview of NGS applications that are transforming preclinical oncology research.
Hematologic malignancies include a wide array of lymphomas and leukemias that affect different immune cell subsets. Acute myelogenous leukemia (AML) is one of the most commonly occurring leukemias in adults and children. AML is a highly heterogenous disease that can be caused by spontaneous gene mutations or chromosomal translocations, which results in the proliferation of dysfunctional myeloid cells. Cytogenetic and morphologic analyses have been the gold standard methods used in AML diagnosis, but flow cytometry-based protocols are becoming more widely used and validated as complementary diagnostic methods that can be coupled with these analyses to better guide treatment plans. Flow cytometry has also become an essential tool to understand AML progression and develop and evaluate novel therapeutics.
Consider these aspects of flow cytometry-based analysis of AML for exploratory or preclinical research.
Advances in molecular diagnostics and ex vivo drug sensitivity screening have greatly improved the use of targeted therapies for the treatment of chronic lymphocytic leukemia (CLL), such as B cell receptor signaling inhibitors, which include the Bruton tyrosine kinase (BTK) inhibitors like ibrutinib and acalabrutinib and the phosphoinositide 3-kinase (PI3K) inhibitors duvelisib and idelalisib, as well as the BCL2 inhibitor venetoclax. For most patients that are matched appropriately with these treatments, they show greatly improved progression-free survival and overall survival.
Bladder cancer is a relatively common form of cancer that is defined as either pre-invasive or invasive, and non-muscle invasive bladder cancer (NMIBC) is the most-commonly diagnosed subtype. NMIBC is typically treated by surgical resection and/or intravesical delivery of chemo- or immunotherapy-based adjuvant treatment, and long-term efficacy is monitored by urine testing or cystoscopy. Muscle-invasive bladder cancer (MIBC) is relatively resistant to current treatment options and occurs more frequently in men. MIBC also has high rates of morbidity and mortality, and novel therapies or combination therapies area being developed to better treat this form of bladder cancer.
Here we highlight recent findings about invasive bladder cancer biology and how these observations are informing the development of new therapies.