Personalized Med Flashcards
1
Q
Describe the treartment of dx
A
2
Q
What causes disease?
A
Diseases are partially the results of gene expressions and regulations
3
Q
Use of Genomics
A
Genomics provides better understanding on the development and progression of diseases such as cancer and cardiovascular disease
Genomics also ensures patients’ safety by providing information on drug metabolism and drug-drug interaction
4
Q
Goal of parmacogenomics
A
Our goal of pharmacogenomics is to achieve 4 “right”
Right patient
Right drug
Right time
Right dose
5
Q
Describe the cells in the human body
A
Around 30-40 trillion cells
Over 200 different types, such as neurons, epithelial cells and red blood cells
As many as 100 billion cells die each day and replaced by new cells
6
Q
How are new cells made? What is this process called?
A
New cells are made by cell division (one mother cell divides into two daughter cells)
Each cell division process is called a “cell cycle”
7
Q
Describe interphase of the cell cycle
A
G1 (Gap 1): cell grows and prepares for DNA replication
S (synthesis): DNA replication
G2 (Gap 2): cell continues to grow and prepares for mitosis
M (mitosis): cell stops growth and starts division
G0 (Gap 0): cell has left the cell cycle and stopped dividing
Checkpoints: one in G1 and one in G2 and apoptosis starts if anything goes wrong
G1 checkpoint: DNA Synthesis
G2 checkpoint: preparation for mitosis
R (restriction point): cell commits to the cycle for division- IN G1
8
Q
Describe mitosis
A
M phase
Prophase: condensation of chromatin and disappearance of nucleus
Metaphase: chromosomes align on the metaphase plate
Anaphase: chromosomes split and move to the opposite poles of the cell
Telophase & cytokinesis: spindle disappears, nucleus reforms and mother cell divides into two daughter cells
Anaphase checkpoint
9
Q
When are growth factors no longer required in the cell cycle?
A
No more growth factors after the R point
10
Q
Cell Cycle Checkpoints
A
11
Q
How many chromosmes in the human body?
A
23 pairs of chromosomes in human
12
Q
What is a chromosme?
A
Complex of a DNA molecule and proteins
13
Q
DNA SHape.How many base pairs?
A
DNA molecule: linear double-stranded (50 – 250 million base pairs)
14
Q
How many genes in a chromosme? How many base pairs?
A
Average chromosome: 2500 – 5000 genes within 130 million base pairs
15
Q
Microband
A
Microband: 3 – 5 million base pairs and 60 – 120 genes
16
Q
Do chromsomes all code for genes?
A
Only 10% of human chromosomes code for genes
Rest of human chromosomes: may play regulating roles
17
Q
Cell Cycle and Growth Factors
A
Before R, need growth factors (cell cycle stimulated by growth factors)
Past R, growth factors are not required anymore
18
Q
What stimulates cell cycle?
A
Cell cycle stimulated by growth factors
19
Q
How is DNA compacted? What does it do?
A
DNA is wrapped around histones
A histone is a protein that provides structural support for a chromosome.
20
Q
Describe histones
A
A nucleosome is a section of DNA that is wrapped around a core of proteins.
DNA is a linear molecule
DNA molecule is condensed –> Wrapped around histones –> Each one has 2, get an octomer, DNA wraps around on the surface –> H1 stabilizes nucleosomes by binding to the dyad region between the entry and exit sites of DNA. (acts as a lock in space)
Highly compacted Need to open it up to do protein synthesis –> Must be in linear form
Linker DNA describes the non-nucleosomal DNA connecting two or more nucleosomes in an array.
21
Q
What is a gene?
A
A portion of chromosomal DNA sequence required for the production of a polypeptide (protein) or a functional RNA molecule
22
Q
Size of a gene?
A
Size: small (1.5 kb) – large (2000 kb)
23
Q
What sequences are in a gene?
A
Include the coding sequence and adjacent sequence required for regulation of expression (such as promoters)
24
Q
What size is mature mRNA?
A
Mature mRNA is about 1/10 of the gene size (RNA splicing)
25
What is RNA splicing?
RNA splicing: precursor mRNA → mRNA
26
Describe the genetic code?
Four types of nucleotides in DNA: A, T, G and C
Pairs: A-T and G-C
Four types of nucleotides in mRNA: A, U, G and C
Pairs: A-U and G-C
27
Gene Expression
Gene expression: Gene mRNA protein
Transcription: Gene mRNA
Translation: mRNA protein
28
How many genes expressed in human cells?
Only ~15,000 genes expressed in a typical human cell
Expression varies from one cell to another
28
Eukaryotic gnese contain....
Eukaryotic genes: exons and introns
29
What is involved in disease?
Gene malfunction is involved in many diseases, such as TP53 in different types of cancer
30
Describe what are promoters?
DNA sequences that “promote” gene expression
Required for DNA transcription (i.e., mRNA synthesis)
Typically located upstream of the genes
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
31
When did the human genome project start? WHo?
Initiated in 1990 and finished in 2006
Funded by the US Department of Energy and the National Institutes of Health and involved research institutes from six countries
32
What did the human genome discover?
Complete DNA sequence of human
Most complex and largest genome (up to now)
33
Nuclear DNA vs Mitochondrial DNA
Nuclear DNA genome: 22 pairs of autosomes (diploid) and 2 sex chromosomes (X and Y): ~ 3 billion base pairs
~19,000 genes
Mitochondrial DNA genome: ~ 17 thousand base pairs
38 genes
34
What is required to read a genome?
ENCyclopedia Of DNA Elements (ENCODE)
Annotation of functional elements encoded in human genome
35
What are gene switches?
Gene switches: non-gene parts of DNA contributing to human diseases such as:
Multiple sclerosis
Lupus
Rheumatoid arthritis
Crohn’s disease
36
Who termed the term genomics and when?
The term “genomics” was coined in 1986 by Tom Roderick (Jackson Laboratory, Maine)
37
What is genomics?
Genomics is an interdisciplinary study of human genome
Structure
Function
Mapping and annotation
Regulation
Evolution
Understand disease development – interaction between genome and environment
38
Describe the different types of genomic studiues?
39
What are the four essential parts of genomics?
Genetic variations
Gene expressions
Gene regulations
Gene correlations
40
Types of Genetic Variations
Single nucleotide polymorphisms (SNPs)
Copy number variations (CNVs)
Insertions and deletions
Large scale variations
Structural variations
41
Most common Genetic VAriation
SNP's
42
What are SNP's?
Small stretches of DNA that differ in only one base
43
SNP Frequency
Frequency: 1 in 1,000 bases to 1 in 100-300 bases
44
Whatdo SNP's distinguish?
Serve to distinguish individual genetic material
45
How many SNP's have been discovered? Are SNP's common?
Millions of SNPs have been discovered
SNPs comprise ~80% of known polymorphisms
Most common type of genetic variation among people
46
How many SNPS in a gene?
Each gene: ~5 coding SNPs
47
Importance of SNPS's
Important in understanding the genetic basis of human diseases
Relationships between SNPs and drug response
48
SNP's Exqample
CYP450 polymorphisms and CYP450 SNPs – decide drug metabolism and activity
Most common is SNPS in CYP450 –> we know all of them
49
Describe where SNP's occur in agene and its importance?
If in non-coding region, nothing happens (most often)
Regulatory –> often will increase or decrease transcription
Coding region –> First or second letter, you get different protein (whether the protein is functional, not functional or partially functional, depends on tests)
3rd Letter often get same protein
50
Describe the presence of SNP's
SNPs are very common in the human population
Between any two people, there is an average of one SNP every ~1250 bases
51
What is the difference between a coding SNP and non-coding SNP_?
Coding SNPs and non-coding SNPs
Some SNPs have phenotype effects – coding SNPs
Most of the SNPs have no phenotypic effect – non-coding SNPs
Venter et al. estimate that < 1% of human SNPs impact protein function
52
What is a CNV?
Variation among people in the number of copies for a particular gene or DNA sequence
53
CNV are a source of....
A source of genetic diversity
54
How do CNV's occur?
Recombination-based and replication-based mechanisms
55
Compare CNVS to SNP's
Higher de novo locus-specific mutation rate than for SNPs
56
What are the predominate mechanisms of gejnome evolution?
CNV's - Gene duplication and exon shuffling – predominant mechanism for genome evolution
56
CNV's are present in what% of human genome?
13% of human genome DNA
57
What dx's are CNV's associated swith?
Associated with diseases such as cancer, autism, lupus, autoimmune disorders and stroke
58
Describe the types of CNV's
Inversion > Sill same number of genes –> Not the same –> Shifting the reading frame –> May be a shift when do inversion –> May get new protein or no protein (assume copy number is reduced - copy number reduced by 1)
Remeber have 2 copies (one from each)
59
SULT 1A1 CNV
Ethnicity is related to the copy number variations
If the drug is prescribed to African American, higher chance they are a rapid metabolizer –> Faster metabolizer, can give higher dose (same level of drug in the body)
One copy means slow metabolizer –> Give same dose may be toxic for them
60
What aare INDEL's. Where do they occur?
Insertions and deletions (INDELs)
Small pieces of DNA
61
INDEL's are a source of what?
Alternative form of natural genetic variation
62
INDEL's Database
Emory University: created a map of 415,436 unique INDELs
63
INDEL's Effecton Humans
Likely to have a major impact on humans, including health and susceptibility to diseases
64
Categories of INDEL's
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)
Transposon: may contain multiple genes
Random DNA sequence insertions or deletions
65
INDEL Examples in Disease
Cystic fibrosis
Three-base-pair deletion in CFTR gene (ΔF508)
Huntington’s disease
Triplet repeat expansions (> 35 CAG repeats in gene HTT)
Breast cancer
6.2-kb deletion of BRCA2 gene
66
What are large scale variations?
Large portions of DNA repeated or missing for no known reasons in healthy persons
Associated with copy number variation of many genes
Large-scale copy-number variation (LCV)
This heterogeneity may underlie disease susceptibility
67
Structural Variations Prevalence and Types
Extremely common in human populations
Involved kilobase- to megabase-sized deletions, duplications, insertions, inversions and complex combinations of rearrangements
Genome structural changes are involved
68
Where do structural variations occur?
Hot spots: regions with a lot of variation and often associated with genetic disorders and diseases
Example: short arm of chromosome 1
69
Dletion Strucxtural VAriation
If happens on one chromosme, copy number of genes that are in segment is 1
If happens on both chromosmes, copy number of genes is 0
70
Duplication Structural VAriation
Copynumber of gnees in segment increases by 1 if only on the one chromosome
71
Inversion Structural VAriation
An inversion that does not include the centromere is called a paracentric (away from the centre) inversion. Both breaks are in the same arm of the chromosome.
An inversion that includes the centromere is called a pericentric (around the centre) inversion. May alter cell dividion and spindle attachment.
72
Balaced Translocation Structural VAriation
73
Unbalanced translocation structural variation
More purple genes as not balanced (unequal)
74
Balanced vs unbalnced structural variation
Structural rearrangements are defined as balanced if the complete chromosome set is still present though rearranged, and unbalanced if there is additional or missing information.
Unbalanced rearrangements include deletions, duplications, or insertions of a chromosome segment.
75
Phildel[phia CVhromosme
Balanced translocation of chromosomes 9 and 22
Create BCR-ABL fusion gene
Lead to acute lymphocytic leukemia (ALL) and chronic myeloid leukemia (CML)
76
Genomics vs Genetics
77
Describe the OMICs
78
Pharamcogneomics vs pharamacogenetiucs
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
79
What is pharamcogneomics used for?
Determining appropriate dosing
Avoiding unnecessary toxic treatments
Ensuring maximal efficacy
Reducing adverse side effects
Developing novel treatments
Explaining variable response to drugs
80
Tamoxifen and CYP 2D6.
Describe 2D6 SNPS's and metabolo9sm?
Tamoxifen is used to treat breast cancer
Converted by CYP2D6 to endoxifen to be active
6-10% European population deficient CYP2D6
Efficacy is likely to be low
Seek alternative treatments
CYP2D6 – 114 SNPs and metabolize 223 drugs
Possible drug interactions
81
Genotype-phenotype relationships of CYP2D6 (Caucasians in Sweden)
82
CYP 3A4 Polymorphisms are....
ethnicity related
83
Most common CYP enzyme for drug metabolism
CYP 3A4
84
Pharamcogenomic biomarkers can describe....
Pharmacogenomic biomarkers may describe:
Drug exposure
Drug dosing
Clinical outcome
Adverse effects
Drug target
MOA (mechanism of action)
85
When analyzing drug metabolism, is one metabolism pathway enough if patient does not have anothe rpathway?
Yes
86
Phenytoin Metabolism
CYP2C9 activity is decreased in individuals with genetic variants such as the CYP2C9*2 and CYP2C9*3 alleles.
Carriers of variant alleles, resulting in intermediate (e.g., *1/*3, *2/*2) or poor metabolism (e.g., *2/*3, *3/*3) have decreased clearance of phenytoin.
Other decreased or nonfunctional CYP2C9 alleles may also result in decreased clearance of phenytoin (e.g., *5, *6, *8, *11).
Poor Metabolizer:
White - 2-3%
Asian - 0.5-4%
African American <1%
Intermediate Metabokizer:
White - 35
Asian - 15-36
African American 24%
87
Describe the basis of personalized medicine?
Right drug, right patient and right dose
P4 medicine
Predictive
Preventative
Personalized
Participatory
88
Pharamcogenomic genotyping real world use
drug development and pharmacy practice
89
DNA Sequencing Costs. What can it dtetc?
Whole genome sequencing (WGS) – Cost: $1,000 – $3,000
Whole genome exon sequencing (WGES or WES) – Cost: $1,000 – $2,000
Diseases: point mutations, deletions, insertions, SNPs, structural variations, etc.
Detect family disease history
90
Define Biochip
Biochip: an array of selected biomolecules immobilized on a surface
91
Define Microarray
Microarray: a rapid method of sequencing and analyzing genes
92
Biochip Technologies
PCR on a chip
Customized microarray with miniaturized PCR reactor for amplification
Gene profiling array (Affymetrix)
Human genotyping, CNVs, transcriptome analysis, etc.
Arrayit® H25K (Arrayit)
25,509 human gene sequences and 795 controls
AmpliChip CYP450 (Roche)
> 15,000 oligonucleotide probes
Example: 29 polymorphisms and mutations for CYP2D6
93
What is PharmGKB?
Annotating drug labels containing pharmacogenomics information approved by US Food and Drug Administration (FDA), European Medicines Agency (EMA), Swiss Agency of Therapeutic Products (Swissmedic), Pharmaceuticals and Medical Devices Agency, Japan (PMDA) and Health Canada (Santé Canada) (HCSC)
94
Describe Duchenne Muscular Dystrophy
Happens in 1 in 3,500 male births (X-chromosome linked, muscle weakness, scar tissue formation, inflammation, etc.)
Caused by mutations in the dystrophin gene (DMD)
Gene DMD is the largest known human gene, spanning approximately 2.5 MB on the X-chromosome
Gene DMD has 79 exons
Mutations in gene DMD occur throughout the whole length, prevalently characterized by large deletions and single point mutations
95
Describe etelpirsen drug?
Exon skipping therapy
Treat, not cure, of some types of DMD
Cause excision of exon 51 during pre-mRNA splicing
The shortened dystrophin has ~ 50% of normal function
96
Eptilersen MOA
97
Selective FDA and EMA approved biomarkers for molecular pathology testing
98
Vitrakvi (Larotrectinib)
First FDA-approved cancer drug targeted to genetic mutation, not cancer type (November 2018)
For adults and children with solid tumors that test positive for NTRK gene fusions without a known acquired resistance mutation
Known acquired resistance mutations – G623R, G696A, and F617L
Cost in Canada: per 28-day cycle (Year 2021)
Pediatric patients: $8207
Adult patients: $11,724
99
SNP Genotyping. How many panels?
High resolution genome-wide association of SNPs to risk profiles of common diseases
SNP panels: 300,000 – 1,000,000
100
Association studies of SNP genotyping?
SNPs and disease susceptibility
SNPs and drug responses, such as insertions/deletions of ACE gene on β-blockers
SNPs and treatment outcome (beneficial or adverse)
101
SNPs related to Vitamin D and breast cancer risk
Heterozygotes of one SNP (rs12239582) 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
102
Warfarin USe. Issue with Warfarin?
Anticoagulant (blood thinner)
Treat blood clots such as deep vein thrombosis and pulmonary embolism
Prevent stroke
Prevent clots by interfering with the production of vitamin K
Warfarin causes more emergency department visits among the elderly than any other drug
103
Describe the metabolism of warfarin
Warfarin is metabolized by CYP2C9
CYP2C9 (39 SNPs)
CYP2C9*1 – wild type
CYP2C9*2 (R144C) – slow metabolizer
CYP2C9*3 (I359L) – slow metabolizer
People with these CYP2C9 variants generally need lower warfarin doses
104
How can CNV be profilled?
Detected with high-throughput scanning technologies such as comparative genomic hybridization (CGH) and high-density SNP microarrays
105
Examples of CNV Profiling
HapMap DNA collection: > 1,000 CNVs ranging from 1 kb to 3 Mb
Digital array for CNV detection
CNVnator: CNV discovery and genotyping in a population
106
What is gene expression profilling?
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 responses
107
How many personalized drugs approved?
One in every 4 drugs approved by the FDA was a personalized medicine (2013-2017)
Approved 16 personalized therapies in 2017 and 17 personalized therapies in 2021
Account for >25% of FDA approvals in each year between 2015 and 2021
108
Imatinib
Approved for chronic myelogenous leukemia (CML) and acute lymphocytic leukemia (ALL)
Inhibit BCR-ABL tyrosine kinase
Inhibit proliferation and induce apoptosis in BCR-ABL positive cells
Tablets: 100 mg and 400 mg
CML: 400 mg daily; ALL: 600 mg daily
109
Classification of Breast Cancer
Three surface receptors: estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2)
ER and PR: hormone receptors
HER2: growth factor receptor
Luminal A: ER+ and/or PR+, HER2-
Luminal B: ER+ and/or PR+, HER2+
HER2: ER-, PR-, HER2+
Triple-negative: ER-, PR-, HER2-
Normal-like: similar to luminal A
110
Palbocib MOA
First CDK4/6 inhibitor
Inhibit cyclin-dependent kinases CDK4 and CDK6
Block the phosphorylation of Rb
Prevent cancer cells to pass the R point
Arrest cancer cells in G1 phase
111
Palbocib Combination
In combination with an aromatase inhibitor or fulvestrant to treat HR+, HER2- advanced or metastatic breast cancer
112
Palbocicilib Dose
Dose: 125 mg orally with food, once daily for 21 consecutive days followed by 7 days off treatment
113
Tratusuzumab Approval and MOA
Approved for HER2-subtype breast cancer
Monoclonal antibody targeting HER2/neu/Erbb2 protein
Bind to subdomain IV of HER2 protein
114
Trastuzumab Dose
IV infusion (1st: 90 min; if well-tolerated: 30 min)
115
Trastuzumab A/E
ADRs: chills, fever, body pain, weakness, nausea
116
Pertuzumab MOA, Approval
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
Trastuzumab + pertuzumab + docetaxel for metastatic and recurrent HER2+ breast cancer
117
TDM1 MOA, DOSE,
Conjugate of trastuzumab (T) and emtansine (DM1)
Emtansine, which is a potent cytotoxic agent, is cleaved from T-DM1 and released inside breast cancer cells
Treat HER2+ metastatic breast cancer and early-stage HER2+ breast cancer after surgery
Intravenous injection every three weeks
14 cycles in total for early-stage HER2+ breast cancer
118
Lapatanib
Dual tyrosine kinase inhibitor that can reversibly bind to the ATP-binding pockets of both EGFR and HER2
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 overexpress HER2
119
Geftinib
Inhibitor of epidermal growth factor receptor (EGFR)
Signaling via EGF-EGFR promotes DNA synthesis, proliferation, migration and survival
Prescribed for non-small cell lung cancer (NSCLC) with EGFR exon 19 deletion or exon 21 L858R mutation
120
Cetuximab
Monoclonal antibody against EGFR
Used for treatment of head and neck cancer and colorectal cancer
