Question

1. Give examples of a personalized medicine.

2. What is Biomarker and how can it be used to identify cancer cells?

3 How are chemical compound libraries related to high throughput screening .

4. What is the value of Microarray technology?

4. How does DNA synthesizer make Oligonucleotides

5. Of what value are Oligonucleotides?

6. What are the three uses of peptides in medicinal biotechnology ?

7. How does pharmacogenetics allow for the development of personalized medicines?

Answer 1

1. Give examples of a Personalized medicine

• Unlike the theory of one drug that fits all models, personalized medicine is a tailored medical model.
• In this model, all patients with the same diagnosis don't receive the same treatment, rather it stratifes people into groups based on their unique genetic profile.
• Techniques like DNA sequencing, RNA seq and genome wide association studies help in studying patient's molecular profile.
• Diagnostic tests like medical imaging, PET, MRI etc also help in testing of several biomarkers associated with certain diusease.
• eg of Personalized medicine-
• (1.) Some breast cancer patients over express a protein called HER-2 and they don't respond well to standard treatments. Trastuzumab medicine for HER2 patients successfully reduces reccurrence in of cancer.
• (2.) B-Raf protein is mutated and over- expressed in case of melanoma . This protein direct cell growth. Cancer patients that show V60B-RAF positive mutation are treated with it's inhibitor Vemurafenib.

2.  What is Biomarker and how can it be used to identify cancer cells

• A biomarker is a gene or a protein that is present in and is associated with a certain pathology or a disease.
• A biomarker used to identify cancer cells and is indicative of it is called a cancer biomarker. It is a molecule secreted either by tumor cells or by the body in response to a tumor.
• As cancer arises due to genetic or epigenetic changes that leads to genetic alterations in DNA such as mutations or rearrangements, which turn affects gene expression and hence leads to synthesis of altered protein and thereby altered metabolites are synthesised.
• So, the biomarkers present to identify cancer cells are genetic, proteomic and metabolic in nature.
• Genetic biomarkers are tested using PCR, microarray or FISH technologies.
• Immunoassays (antibody based detection), Mass spectrometry etc can be used to detect protein markers.
• Metabolite biomarkers are tested using approaches like NMR, HPLC, etc.
• The biomarkers can be detected from blood, serum, urine, stool or other body fluids and in certain cells or tissues of the body.
• If these biomarkers are present above a cut-off value (that is based on it's presence in non- cancerous patiemts), it means true- positive, that is the assay is sensitive and biomarker is truly indicative of cancer in the patient's body.
• A genomic biomarker present in blood is mutated BRCA1 and BRCA2. this is indicative of breast cancer. It is tested using DNA sequencing. Ras mutations, another genomic marker in blood, indicative of colon and lung cancer, tested using PCR.
• A protein specific marker, PSA (Prostate specific antigen), found in serum, tested using immunoassay is indicative of prostate cancer.
• A metabolomics marker, 1-hydroxyprene detected in urine using HPLC is indicative of cancer in lungs.
• Fecal sample required to detect colorectal cancer.

3. How are chemical compound libraries related to high throughput screening .

• A chemical library is a collection of stored chemicals, that are stored in online databases. They are mainly used in drug discovery during high throughput screening (HTS).
• HTS is the process of drug discovery. It is used to test millions of potential, active compounds that can be used as drugs for a treatment of a particular disease in short time frame.
• In HTS, samples or targets such as cells, enzymes, etc are placed in wells of well plate. Different, potential chemicals are added to these wells. Reaction is allowed to be carried out in these wells. These steps are replicated many times. The wells that show a positive reaction are chosen, and the chemical compound that was added to those wells are identified. These chemical compounds showing positive results are known as hits. These hits are narrowed down and are used for latter steps of drug designing.
• Chemical or compound libraries serve as the source of chemicals that are added to these targets and potentially may be used as a drug in treatment of a medical condition.

4. What is the value of Microarray technology?

• Microarray is a molecular tool that helps in quantification of thousands of genes transcripts from a given cell.
• A microarray is a chip divided into rows and columns. Each cell of this chip contains DNA fragments or oligonucleotides of known sequence. Reverse transcribed transcripts of samples hybridize to these oligonucleotides placed on the chip. This binding helps in detection of specific transcripts, that may be associated with a disease state or any medical abnormality. This is a basic DNA microarray
• Genotyping, a kind of microarray identifies Single Nucleotide Polymorphisms (SNPs). This helps to identify genetic variation in individuals and populations.
• CGH (Comparative Genomic hybridization), a microarray- it's used to identify genomic insertions, deletions or copy number changes in chromosomal regions. It is a cytogenetic approach that helps in identification of congenital anomalies like autism and some mental retardation disorders.
• Splice variants is a microarray platform that helps to identify genes whose splice variants produce abnormal proteins that trigger disease development.