Pharmacogenomics Flashcards
Personalized medicine is the optimization of what 3 things?
- Drug
- Disease
- Human body
What are the 4 “rights” of pharmacogenomics?
- Right patient
- Right drug
- Right time
- Right dose
Diseases are partially the result of gene ___________ and ____________
expression; regulations
The human body contains around __-__ ________ cells
30-40 trillion
What is G1 phase?
Cell grows and prepares for DNA replication
What is S phase?
DNA replication
What is G2 phase?
Cell continues to grow and prepares for mitosis
What is M phase?
Cell stops growth and starts division
What is G0 phase?
Cell has left the cell cycle and stopped dividing
Where are the 3 cell cycle checkpoints?
What is the purpose of these checkpoints?
One in G1, one in G2, and one in anaphase - apoptosis starts if anything goes wrong
- G1 checkpoint = DNA synthesis
- G2 checkpoint = preparation for mitosis
- Anaphase checkpoint = checks attachment of mitotic spindle
What is R in the cell cycle (restriction point)?
Cell commits to the cycle for division
When in the cell cycle is the restriction point (R)
In G1
What are the 5 components of the M phase (mitosis)?
- Prophase
- Metaphase
- Anaphase
- Telophase
- Cytokinesis
What is happening in prophase?
Condensation of chromatin and disappearance of nucleus
What is happening in metaphase?
Chromosomes align on the metaphase plate
What is happening in anaphase?
Chromosomes split and move to the opposite poles of the cell
What is happening in telophase & cytokinesis?
Spindle disappears, nucleus reforms, and mother cell divides into 2 daughter cells
DNA molecule contains __-___ _______ base pairs
50-250 million
Average chromosome molecule contains ____-____ genes within ___ _______ base pairs
2500-5000; 130 million
A microband contains _ - _ _______ base pairs and __-___ genes
3-5 million; 60-120
Only __% of human chromosomes code for genes
10%
What is a gene?
A portion of chromosomal DNA sequence required for the production of a polypeptide (protein) or a functional RNA molecule
- Includes the coding sequence and adjacent sequence required for regulation of expression (such as promoters)
Mature mRNA is about _/__ of the gene size
1/10
RNA splicing is?
Precursor mRNA –> mRNA
What is the path of gene expression?
Gene –> mRNA –> protein
Know the difference between transcription and translation
Transcription = Gene –> mRNA
Translation = mRNA –> protein
Only ~_____ genes are expressed in a typical human cell
15,000
What are promoters?
Why are they required?
Where are they typically located?
- DNA sequences that “promote” gene expression
- Required for DNA transcription (i.e., mRNA synthesis)
- Typically located upstream of the genes
What do promoters do? (4)
- RNA polymerase binding site
- Direct the exact place to initiate DNA transcription
- Determine when and how a gene is transcribed
- Promoter methylation represses gene transcription
The entire DNA genome contains ~_ _______ base pairs
3 billion
What is the Encyclopedia of DNA elements (ENCODE)?
Annotation of functional elements encoded in human genome
What are gene-switches?
What do they contribute to?
Non-gene parts of DNA contributing to human diseases such as:
- Multiple sclerosis
- Lupus
- Rheumatoid arthritis
- Crohn’s disease
Genomics is an interdisciplinary study of human genome, including these 5 things:
- Structure
- Function
- Mapping and annotation
- Regulation
- Evolution
Disease development results as an interaction between _______ and ____________
genome; environment
What are the 5 types of genomic studies?
- Structural genomics
- Functional genomics
- Comparative genomics
- Genetic mosaicism
- Genome-wide association
What is structural genomics?
Structures of proteins encoded by the whole genome
What is functional genomics?
Regulation of different biological functions regulated by the genome
What is comparative genomics?
Genomic variances between different species
What is genetic mosaicism?
DNA mutations in the genome and underlying mechanisms
What is genome-wide association?
Genetic markers and association with phenotypes (e.g., diseases)
Genomics studies have four essential parts. What are they?
- Genetic variations
- Gene expressions
- Gene regulations
- Gene correlations
What are the 5 types of genetic variations?
- SNPs
- CNVs
- Insertions and deletions
- Large scale variations
- Structural variations
The most common type of genetic variation among people is?
SNPs
What is a SNP?
Small stretches of DNA that differ in only one base
SNPs serve to distinguish __________ _______ ________
individual genetic material
SNPs are important for what 2 reasons?
- Important in understanding the genetic basis of human diseases
- Relationships between SNPs and drug response
Between any two people, there is an average of one SNP every ~____ bases
1250
Some SNPs have phenotype effects. These are called?
Coding SNPs
Most of the SNPs have no phenotypic effect. These are called?
Non-coding SNPs
Estimate how many SNPs are present between two people.
How many will be in the coding region?
Genome size = 3 billion base pairs
So, 3,000,000,000/1250 = 2,400,000
Coding is only 10%, so 2,400,000 x 0.1 = 240,000
What are 2 mechanisms of copy number variations (CNVs)?
- Recombination-based
- Replication-based
What are copy number variations (CNVs)?
Variation among people in the number of copies for a particular gene or DNA sequence
The predominant mechanisms for genome evolution are? (2)
Gene duplication and exon shuffling
What are the 5 categories of INDELs?
- Insertions or deletions of single base pairs
- Expansions by only one base pair (monomeric base pair expansions)
- Multi-base pair expansions of 2-15 repeats
- Transposon insertions (insertions of mobile elements)
- Random DNA sequence insertions or deletions
How are INDELs related to the following diseases:
1. Cystic fibrosis
2. Huntington’s disease
3. Breast cancer
- Three-base-pair deletion in CFTR gene
- Triplet repeat expansions (>35 CAG repeats in gene HTT)
- 6.2-kb deletion of BRCA2 gene
What are large scale variations?
- Large portions of DNA repeated or missing for no known reasons in healthy persons
- Large scale copy-number variations (LCVs)
- This heterogeneity may underlie disease susceptibility
What are structural variations? (2)
- Involved in kilobase- to megabase-sized deletions, duplications, insertion, inversions and complex combinations of rearrangements
- Genome structural changes are involved
What are “hot spots” relating to structural variations? Example?
Hot spots: regions with a lot of variation and often associated with genetic disorders and diseases
- E.g., short arm of chromosome 1
What are the 5 types of structural variations?
- Deletion
- Duplication
- Paracentric inversion
- Balanced translocation
- Unbalanced translocation
What is a Philadelphia chromosome? (3)
- Balanced translocation of chromosomes 9 and 22
- Create BCR-ABL gene
- Leads to acute lymphocytic leukemia (ALL) and chronic myeloid leukemia (CML)
What valuable information may SNP genotyping provide?
a) Disease susceptibility
b) Drug response
c) Treatment outcome
d) Adverse drug reaction
e) All of the above
f) None of the above
e)
Compare genetics to genomics. Should know 3 major differences between them.
Genetics:
1. Study of heredity
2. Specific gene
3. Function and composition of a single gene
Genomics:
1. Study of entirety
2. Entire genome
3. Address all genes and their relationships
What is an exon?
What is an intron?
Exon: a portion of a gene that encodes amino acids
Intron: a portion of a gene that does not encode amino acids
What is the difference between pharmacogenomics and pharmacogenetics?
Pharmacogenomics:
- Development of drug therapies (drug and dose) to compensate for genetic differences in patients
Pharmacogenetics:
- Study the genetic basis for variability in drug response
Our goals as a pharmacist (in terms of pharmacogenomics) is? (4)
- Determining appropriate dosing
- Avoiding unnecessary toxic treatments
- Ensuring maximal efficacy
- Reducing adverse side effects
Tamoxifen and CYP2D6. Tamoxifen is used to treat breast cancer. What is the issue here regarding the European population?
6-10% of the European population is deficient in CYP2D6
- Efficacy likely to be low
- Seek alternative treatment
Pharmacogenomic biomarkers for drug labeling (FDA) may describe: (6)
- Drug exposure
- Drug dosing
- Clinical outcome
- Adverse effects
- Drug target
- MOA
What is P4 medicine?
Predictive
Preventative
Personalized
Participatory
What are the 2 types of DNA sequencing available and what are their costs roughly?
- Whole genome sequencing (WGS)
- $1000 - $3000 - Whole genome exon sequencing (WGES or WES)
- $1000 - $2000
What is DNA sequencing (WGS or WES) used for? (2)
- Diseases: point mutations, deletions, insertions, SNPs, structural variations, etc.
- Detect family disease history
What is a biochip?
An array of selected biomolecules immobilized on a surface
What is a microarray?
A rapid method of sequencing and analyzing genes
What are 4 biochip (DNA chip) technologies?
- PCR on a chip
- Customized microarray with miniaturized PCR reactor for amplification - Gene profiling array
- Human genotyping, CNVs, transcriptome analysis, etc. - Arrayit
- 25,509 human gene sequences and 795 controls - AmpliChip
- >15,000 oligonucleotide probes
What is happening in the DMD gene (Duchenne Muscular Dystrophy) that causes this disease?
Mutations in gene DMD occur throughout the whole length, prevalently characterized by large deletions and single point mutations
What medication is used to treat (not cure) DMD?
Eteplirsen
What is the MOA of eteplirsen? (3)
- Exon, skipping therapy
- Cause excision of exon 51 during pre-mRNA splicing
- The shortened dystrophin has ~50% of normal function
What is a drug target network?
1 drug may target multiple proteins
1 protein may be targeted by multiple drugs
What is larotrectinib (Vitrakvi)?
What is it used for?
- First FDA-approved cancer drug targeted to genetic mutation, not cancer type
- For adults and children with solid tumors that test positive for NTRK gene fusions without a known acquired resistance mutation
What is SNP genotyping?
High resolution genome-wide association of SNPs to risk profiles of common diseases
What are 3 association studies done with SNP genotyping?
- SNPs and disease susceptibility
- SNPs and drug responses, such as CYP2D6 polymorphism
- SNPs and treatment outcome (beneficial or adverse)
What are 5 clinical trials that can be done with SNP genotyping?
- Genotyping
- Molecular definition of diseases
- Correlation of drug response and adverse effects
- Prediction of dose response and adverse effects
- Pinpoint common SNP sets for patients who do not respond to a drug
In example 13: SNPs related to Vitamin D and breast cancer risk, what was going on? (2)
- Heterozygotes of one SNP have a statistically significant association with a low risk of breast cancer
- Diverse associations with breast cancer risk for a few of the tested SNPs, depending on whether vitamin D level was high or low
People with slow metabolizer variants of CYP2C9 generally need _____ warfarin doses
lower
What technologies are used to detect CNVs?
Detected with high-throughput scanning technologies such as comparative genomic hybridization (CGH) and high-density SNP microarrays
What is CNVnator?
What are the 3 benefits?
CNV discovery and genotyping in a population
Benefits:
- High sensitivity (86-96%)
- Low false-discovery rate (3-20%)
- High genotyping accuracy (93-95%)
What is gene expression profiling? (4)
- Measurement of the expression and activity of thousands of genes at once (genomics and transcriptomics)
- Get a global picture of cellular function
- Identify association of gene expression profiles with disease susceptibility and development, drug metabolism and adverse effects, etc.
- Identify drug design targets and predict drug response
What are 8 gene expression profiling technologies?
- DNA microarrays
- Differential gene expression (DEGs)
- Single-cell gene expression
- Gene expression profiling based on alternative RNA splicing
- Gene expression analysis on biopsy samples
- Serial analysis of gene expression (SAGE)
- Gene expression profiling of WBCs
- In vivo gene expression by molecular imaging
What do pharmacogenetic biomarkers demonstrate?
Inter-individual genetic differences on the pharmacokinetics, pharmacodynamics, efficacy, and safety of drug treatments
What therapeutic area has the most new FDA drug approvals with pharmacogenetics?
Oncology
What is imatinib approved for?
Chronic myelogenous leukemia (CML) and acute lymphocytic leukemia (ALL)
What is the MOA of imatinib? (2)
- Inhibit BCR-ABL tyrosine kinase
- Inhibit proliferation and induce apoptosis in BCR-ABL positive cells
What must be taken into account when making a breast cancer treatment plan? (7)
- Stage
- Menopausal status
- Hormone receptor status
- HER2 status
- Risk factors of recurrence
- Overall health condition
- Other breast cancer biomarkers
Breast cancer stage I: What are the steps of treatment? (5)
- Surgery (primary)
- Radiation therapy
- Hormonal therapy
- Chemotherapy (usually not offered)
- Targeted therapy (HER2+ and high risk of recurrence)
Breast cancer stage II: What are the steps of treatment? (5)
- Surgery (standard)
- Radiation therapy (including lymph nodes)
- Chemotherapy (adjuvant and neoadjuvant)
- Hormonal therapy
- Targeted therapy (HER2+ and high risk of recurrence)
Breast cancer stage III: What are the steps of treatment? (5)
- Chemotherapy (adjuvant and neoadjuvant)
- Targeted therapy (HER2+, ER+, or BRCA mutations)
- Surgery (before or after chemotherapy)
- Radiation therapy (after breast-conserving surgery)
- Hormonal therapy
Breast cancer IV: What are the steps of treatment? (3)
- Hormonal therapy
- Chemotherapy (reducing cancer growth within patient’s tolerance level of side effects)
- Monotherapy
- Combination therapy - Targeted therapy
What are the 3 surface receptors seen in breast cancer?
- Estrogen receptor (ER)
- Progesterone receptor (PR)
- Human epidermal growth factor receptor 2 (HER2)
ER and PR are _______ receptors
HER2 is a ______ ______ receptor
hormone; growth factor
What is the Luminal A classification of breast cancer?
ER+ and/or PR+, HER2-
What is the Luminal B classification of breast cancer?
ER+ and/or PR+, HER2+
What is the HER2 classification of breast cancer?
ER-, PR-, HER2+
What is the triple negative classification of breast cancer?
ER-, PR-, HER2-
What is the normal-like classification of breast cancer?
Similar to luminal A (ER+ and/or PR+, HER2-)
Palbociclib is the first…
CDK4/6 inhibitor
What is the MOA of palbociclib? (4)
Inhibit cyclin-dependent kinases CDK4 and CDK6
- Block the ppylation of Rb
- Prevent cancer cells to pass the R point
- Arrest cancer cells in G1 phase
How is palbociclib given?
In combination with an aromatase inhibitor or fulvestrant to treat HR+, HER2- advanced or metastatic breast cancer
(Also, give with food)
The main pathway of HER2 signaling is?
PI3K pathway
PI3K –> AKT –> mTOR –> transcription
Trastuzumab is approved for which subtype of breast cancer?
HER2
What is the MOA of trastuzumab? (2)
- Monoclonal antibody targeting HER2/neu/Erbb2 protein
- Bind to subdomain IV of HER2 protein
What are some ADRs associated with trastuzumab? (4)
- Chills
- Fever
- Body pain
- Weakness
What is the MOA of pertuzumab? (3)
- Monoclonal antibody binds to subdomain II of HER2 protein
- Block homodimerization of HER2 and heterodimerization of HER2-HER3
- Inhibit HER2-signaling pathway and decrease cell growth
What combination of medications is given for metastatic and recurrent HER2+ breast cancer (3)?
Trastuzumab + pertuzumab + docetaxel
What does emtansine do (when in combo in T-DM1 - ado-trastuzumab emtansine)?
Emtansine, which is a potent cytotoxic agent, is cleaved from T-DM1 and released inside breast cancer cells
When is T-DM1 used?
Treat HER2+ metastatic breast cancer and early-stage HER2+ breast cancer after surgery
What is the MOA of lapatinib?
Dual tyrosine kinase inhibitor that can reversibly bind to the ATP-binding pockets of both EGFR and HER2
When is lapatinib used? (2)
- In combination with capecitabine for treatment of advanced and metastatic HER2+ breast cancer
- In combination with letrozole for treatment of hormone receptor-positive metastatic breast cancer that overexpresses HER2
What is the MOA of gefitinib and cetuximab?
Inhibitor of EGFR
