dr Naidoo L3 Flashcards
What is proteomics, and how does it contribute to the study of cancer and non-cancer tissues?
Proteomics involves studying the total protein content of cells and tissues. It provides a direct comparison of protein profiles between normal and disease tissues, such as cancer and non-cancer tissues. This helps identify differences in protein expression that could be indicative of underlying pathological conditions.
Explain the significance of MALDI-TOF technology in identifying proteins.
MALDI-TOF (Matrix-Assisted Laser Desorption/Ionization Time of Flight) technology is used for identifying proteins and establishing protein and peptide profiles. It enables accurate detection and measurement of proteins in tissues, making it possible to analyze the spatial distribution of proteins directly on tissue sections.
What is the importance of formalin-fixed paraffin-embedded (FFPE) tissue in clinical and research settings?
FFPE tissue is a clinical gold standard used for histological assessment. It preserves tissue architecture, allowing for further diagnostics, follow-up, and special stain re-examination. In research, FFPE tissue is valuable for analyzing DNA, RNA, and protein content, aiding in understanding disease mechanisms.
Describe the process of preparing FFPE tissue for protein analysis using MALDI-TOF MS.
FFPE tissue is subjected to an optimization procedure involving ethanol/methanol and chemical treatment. Proteins are extracted, and a sample is spotted on a MALDI target plate. The sample is overlaid with a matrix, and the target plate is used for further analysis using MALDI-TOF MS technology.
How is MALDI imaging used to analyze protein distribution in tissue sections?
MALDI imaging involves preparing tissue sections by antigen retrieval, trypsin digestion, and matrix coating. These prepared sections are then scanned using MALDI-TOF MS. The resulting images provide spatial distribution information about proteins directly on the tissue sections.
Explain the purpose and process of matrix aerosol deposition in MALDI imaging.
Matrix aerosol deposition is a crucial step in MALDI imaging. It involves gently depositing matrix on the tissue sample to enhance sensitivity and create reliable tissue preparation. A matrix aerosol is created and deposited on the tissue using vibrational vaporization techniques.
What are some potential applications of MALDI imaging in cancer research?
MALDI imaging can be applied to identify potential biomarkers for cancer detection and prognosis. It helps visualize differential protein expression between cancer and normal tissues, aiding in understanding disease mechanisms and developing targeted treatments.
In the context of lymphoma, how can MALDI imaging be used to identify biomarkers?
In lymphoma cases, such as diffuse large B cell lymphoma (DLBCL), MALDI imaging can help identify differentially expressed peptides and proteins. These profiles can serve as potential biomarkers for prognosis, early detection, and targeted treatments.
How does principal component analysis (PCA) contribute to the analysis of MALDI imaging data?
PCA is a statistical technique used to analyze complex data sets, like those obtained from MALDI imaging. It helps in reducing the dimensionality of the data while retaining its essential variation. In the context of lymphoma analysis, PCA can aid in identifying patterns and relationships within the data.
What are some challenges and limitations associated with using MALDI imaging for proteomic analysis?
While MALDI imaging is a powerful technique, it has limitations like the need for careful sample preparation, potential matrix effects, and challenges in accurately quantifying protein expression. Additionally, interpreting the data requires sophisticated computational tools and expertise.
How does the identification of differentially expressed peaks contribute to our understanding of lymphoma subtypes and HIV association?
Differentially expressed peaks in DLBCL subtypes (GC and ABC) from both HIV+ and HIV- cohorts provide insights into the molecular characteristics of different lymphoma types. These peaks can serve as potential markers for subtype differentiation and association with HIV infection.
What is the role of the Human Proteome Project in advancing cancer research?
The Human Proteome Project involves profiling peptides and proteins from healthy and cancer patients. This project enhances our understanding of the proteomic landscape and aids in identifying potential targets for therapeutic interventions. Many drugs are designed to target specific proteins, making this research crucial for cancer treatment advancements.
