Genetics Final Exam

Most Common Cancers

US: Skin Cancer
World: Lung Cancer

G1/S Checkpoint

Cell monitors size and DNA integrity

Loss: gene amplification, chromosomal rearrangements, lack of apoptosis

G2/M Checkpoint

Cell monitors DNA synthesis and damage

Loss: translocations

M Checkpoint

Cell monitors spindle formation and attachment to kinetochores

Loss: polyploidy and aneuploidy

Cyclins and Kinases

Control passage through cell cycle

Cancer Driver Genes

Tumor Suppressor Genes, Oncogenes, DNA Damage Response (DDR) genes

Tumor Suppressor Genes

E.g. BRCA1 and BRCA2

LOF, recessive

Oncogenes

Ras (HRAS, KRAS, NRAS)

GOF, dominant

DNA Damage Response (DDR) genes

E.g. ARID1A

Usually recessive

Sustaining proliferative signaling

Cancer cell stimulate own growth without external signals

Evading growth suppressors

Cancer cells ignore tumor suppressor genes

Resisting cell death

Avoid apoptosis

Enabling replicative immortality

Cancer cells activate telomerase and become undifferentiated

Genome Instability and Mutation

Increased mutation rates

Non-mutational Epigenetic Reprogramming

Epigenetics change

PARP1 in BRCA1/2 Cancer

PARP1 is DDR protein, and PARPi causes synthetic lethality by stopping PARP1 from repairing small damages

Synthetic Lethality

One copy of an allele is viable but two copies leads to cell death

Organismal Hallmarks of Aging

Loss of skin elasticity, Hair loss/greying, Menopause, Cognitive impairment, Muscle strength,

Age-related diseases: lung disease, stroke, cardiovascular disease, diabetes, kidney failure, osteoarthritis, cancer, dementia & Alzheimer’s

Cellular/Molecular Hallmarks of Aging

Altered intercellular communication

Stem cell exhaustion

Cellular senescence

Mitochondrial dysfunction

Deregulated nutrient-sensing

Loss of proteostasis

Epigenetic alterations

Telomere attrition

Genomic instability

Mitochondrial Dysfunction (with Aging)

Susceptible to mutations which affects efficiency of oxidative phosphorylation (making ATP) and increasings ROS (reactive oxygen species)

DNA Damage (with Aging)

Genomic instability, Stem cell exhaustion, Cellular senescence, Altered intercellular communication

Unrepaired DNA damage causes cells to sensece or undergo apoptosis, reduced stem cell regeneration, and disease

Telomere attrition (with Aging)

When telomeres get too short, cells undergo growth arrest or apoptosis—non-immortal cells

Generally longer=healthier, but mice and some human cancers are the exception

Associated with microplastics

Loss of protein homeostasis (with Aging)

Free radicals react with some amino acids (histidine, arginine, lysine, proline and methionine) to impact protein function. Proteins can also react with glucose, impacting the protein’s structure and function.

Epigenetic alterations (with Aging)

DNA methylation decreases with age except for CpG sites. Under-methylating leads to expression of repeat DNA.

Deregulated nutrient-sensing (with Aging)

Reducing caloric intake prevents diseases related to impaired metabolism.

Measuring Biological Age

Telomere length, epigenetic clocks, blood biomarkers, physiological tests (muscle strength, memory decline, etc)

Horvath’s Epigenetic Clock

Gathered methylation data from 7k people and found 353 age-related CpG sites to estimate biological age and chronological age. Sperm had very low biological age and cancer cells were sporadic

DNAm PhenoAge

Compared DNA 513 methylation sites with clinical biomarkers. Better than Horvath’s for disease/mortality prediction

Factors affecting biological aging

Physical Activity, Diet, Socioeconomic status, Education level, Smoking/Drinking, Metabolism (BMI, Diabetes), Menopause, Infections (HIV), Heart/Lung Function, Cancer, Male, Neuropsychiatric (PTSD, Depression, Schizophrenia, Alzheimer’s Parkinson’s)

APOE

Fat-binding protein that mediates cholesterol metabolism—associated with extreme longevity alongside lncRNA

CIRBP

Protein expressed in bowhead whales that increases NHEJ w/ more accuracy—extends life

Evolutionary Theories of Aging

Mutation accumulation theory, Antagonistic pleiotropy theory, Disposable soma theory

Mutation accumulation theory

Natural selection is blind to variants that impact organism AFTER reproduction

Antagonistic pleiotropy theory

Natural selection choose traits are beneficial when young and harmful when old (cell senescence: when young helps in development, wound healing, cancer prevention)

Disposable soma theory

Natural selection has limited energy budget between reproduction, growth, and aging

Cellular Potency

Ability for cells to become lots of specialized cells

Determined by DNA methylation, PcG and TrxG (group proteins that control epigenetics)

Totipotent

Cells become ANY cell type (Zygote starts are this)

Open genome: global DNA demethylation

Pluripotent

Cells become MANY cell types

No X-inactivation, genes for all differentiation off (by PcG), Promoter hypomethylated

Multipotent

Cells become MORE THAN ONE cell type

X-inactivation, lineage-specific genes for differentiation off (by PcG), Promoter hypermethylated

Unipotent

Cells are STUCK as one cell type

X-inactivation, PcG silences all differentiation, TrxG turns on lineage-specific genes, Promoter hypermethylated

PcG/TrX

PcG:PRC2 writes H3K27me3 in pluripotent cells, PRC1 causes chromatin to condense in multi/unipotent cells

TrX: Unipotent cells have genes turned on by Trx writing H3K4me3

Hox Loci

Regulation body development, directed by morphogens

Control Development

TFs, Pioneer TFs, and RNA (non mRNA)

Phase 0

10 to 15 patients

Study pharmacodynamics and pharmacokinetics

Discovery Science

Studies in lab, including animal studies

Phase I

20 to 100 patients

Study in small amount of patients to determine maximum tolerable dose

single-ascending: different patients get higher amounts

multiple-ascending: each patients get more small doses

Phase II

50 to 100 patients

Study in more patients for drug effecacy (and more safety!)

Phase III

300 to 3000+ patients

Confirms safety/efficacy, but also for side effects and to compare to current treatments

Phase IV

In the Market

FDA-approved drugs are surveilled for long-term and rare effects, especially with new data groups

Pharmacodynamics

Study of the biochemical and physiological effects of drugs and their mechanisms of action (drug’s impact on the body)

Pharmacokinetics

Study of the absorption, distribution, metabolism, and excretion of drugs (often referred to as ADME) (body’s impact on a drug’s activity)

Pharmacogenomics

Study of how patients’ genomes impact their response to drugs

Personalized medicine

Tailoring patient care based on genomic sequence, environmental exposures/lifestyle, precise disease classification, personal/family health histories

Pharmacology

Interaction of chemicals with biological systems to yield therapeutic or other beneficial effects

Toxicology

Interaction of chemicals with biological systems to yield adverse effects

Where Drugs are metabolized (altered)

The liver (bioactivates and excretes)

CYP enzymes

Oxidize hydrophobic drug centers to be more hydrophilic to leave body, sometimes makes drugs more bioactive instead of eliminating

We have 57 and variants affect drug metabolism

ED50

Dose where 50% of patients benefit

TD50

Dose where 50% of patients experience toxic side effects

Therapeutic range

Therapeutic Index (TI)

TD50/ED50, want a large TI

Personalized Medicine Examples

CarT Therapy (cells recognize proteins only in cancer cells), Chemotherapy (choosing drug based on type of breast cancer ER/PR/HER2), Antibiotics (choosing drug bacteria isn’t resistant to), Diet (choosing food based on glycemic index)

Transposable Elements (TEs)

segments of DNA that can move to different locations

Most inactive (less than 0.05%)

Class I/Retrotransposons

Copy themselves into RNA then to DNA and then paste into a new location

~40-50% of human genome

LINE —> mRNA —> some protein (transposase and integrase) some mRNA —> transposase protein turns mRNA to cDNA and integrase protein inserts into genome

Class II/DNA transposons

Can just cut and paste themselves

~3% of human genome

Transposase binds to transposon, makes loop that cuts it out, inserts loop elsewhere, loop flattens out (gene for transposase on transposon), replicates by jumping during replication

Can’t jump anymore

Transposon Hypothesis

Theory that introns evolved from transposon jumping into coding sequences

Retrovirus

Transcribed into cDNA that’s inserted into chromosomes, e.g. syncytin proteins that made placenta for mother/child nutrient transfer and supressyn which binds to receptors to block invaders—common in placenta to protect germline

B and T cell receptors

do NOT have the same DNA as rest of cells

bind to antigens with high specificity

B+T cells replicate really quickly when infection happens to launch attach, and body remembers the activated cells for future infections

VDJ gene regions

Somatic recombination

1. D and J joins (everything between deleted)

2. V and D join (everything between deleted)

3. extra C and V are spliced out

Recombination Signal Sequences (RSS)

Flank individual V, D, and J regions

Allows Rag1 and Rag2 proteins to bind for cleavage

NHEJ mechanism is used to ligate ends together, slight variability each time

Affinity Maturation

Rapid replication with high mutation rate, ensure different levels of affinity to invader, highest affinity binds are replicated again

Somatic Hypermutation

Mechanism of affinity maturation

When BCR binds to antigen, AID deaminates C (turns to U) which causes mutations that affects affinity

Rag transposon Hypothesis

WDJ recombination originated from transposons jumping into receptor gene

Bacteriophage lysogenic cycle

Phage DNA incorporated into host’s genome

Bacteriophage lytic cycle

Phage DNA circular and separate from host DNA

Cas9

Type II single-effector nuclease

Knockout

Permanently removes or inactivates a gene

Knockdown

Temporarily reduces gene expression

Knock-in

Inserts new genetic material

Closest living relatives

Chimpanzees

Human Lost Genes

~80, smell, hair. smaller chewing muscles (myosin MYH16)

hCONDEL

human conserved deletions that are present in other species except humans

HAR

human accelerated regions that show more differences than expected, explained by genetic grift

Closest Non-Living Relative

Denisovans and Neanderthals

Genetic Distances

Other humans: ~0.6%

Chimps: ~2%

Most human variation is between individuals, not populations

STR

Short tandem repeats used for DNA profiling (identifying individuals)