Tumors and Cancer Mechanisms.

Tumors and Cancer Mechanisms

GC 7020 - Human Genetics

University of Cincinnati

Not all tumors are cancerous. Benign tumors grow but cannot spread or turn other cells in the

body into tumors. Benign tumors are self contained, non cancerous growths that cannot spread.

Benign tumors can grow and put pressure on surrounding cells causing some problems. Benign

and cancerous cells arise from single cells and are clonal. Usually they occur in somatic cells

and are not passed on to the next generation. Genetic alterations lead to cancer with increasingly

aggressive growth with each mutation. Cancerous cells are metastatic and invasive, they can

detach and invade other parts of the body to form malignant tumors. Rates vary for different

forms of cancer, varies by sex, age, and various environmental components. ⅓ Americans will

get cancer during their lifetime, ¼ Americans will eventually die of cancer. Cancer is a genetic

disease, cancer risk for some cancers runs in families (heritable), most cancers require multiple

mutations to cause cancer (at least two). Not all have the same risk for cancer, some predisposed

by inheriting 1+ mutations that can lead to cancer. Being predisposed does not mean you will

definitely get cancer, you inherit 1+ mutations but require environmental insult to cause

additional mutations which triggers cancer. Alfred Knudsen, two hit hypotheses for cancer. The

cell cycle is commonly affected in cancer, one or more of the mutations leading to cancer alter

the cell cycle. Cell cycle controls cell division and growth. Cancer cells keep dividing and are

immortal (don't seem to have programmed cell death). Checkpoints regulate cell division and

growth in interphase, some genes suppress cell division (tumor suppressor genes), other genes

are regulatory genes (proto-oncogenes) that turn on and maintain cell division. Retinoblastoma

was the first cancer to be directly associated with a genetic abnormality (deletions or mutation

of the chromosome 13 q14 band). Retinoblastoma can occur sporadically (no family history)

or it can be inherited. If a genetic mutation is found, there is a 45-50% chance that the parents

will have another child with retinoblastoma. If no mutation is found, the risk of having a second

child with retinoblastoma is 2-5%. The average age of children with retinoblastoma is 18

months. More than 75% of children with retinoblastoma are first noted to have a white pupil

(leukocoria), poorly aligned eyes (strabismus), or a red and painful eye (usually due to

glaucoma). Other eye diseases which can cause these symptoms include congenital cataract,

toxocara canis, coat disease, and persistent hypertrophic primary vitreous (PHPV). These

diseases may look like retinoblastoma, but by performing an examination under anesthesia,

specialized blood tests, CAT scans, and ultrasound evaluations, ophthalmic oncologists can

diagnose intraocular retinoblastoma in over 95% of cases. In order to be 100% correct all the

time, eye cancer specialists would have to perform a biopsy. Biopsies of intraocular

retinoblastoma are avoided in order to prevent cancer cells from spreading outside the eye.

Retinoblastoma has two forms, when one eye is affected it is likely sporadic, and when both

eyes are affected it is likely inherited. Breast cancer genes, 85-90% of women with BRCA I

mutation will get cancer. 1/200 have the allele. BRCA 1 and 2 dominant. Retroviruses are viral

causes of cancer; DNA viruses: SV40, Polyoma, Adenovirus; RNA viruses: Rouse Sarcoma

virus, Mouse Mammary tumor virus. In Rous Sarcoma Virus, gag, pol, and env allow the virus

to infect cells and replicate, but not cause tumors, onc allows virus to also cause tumors. So

gag-pol-env is a non tumor forming retrovirus, gag-pol-env-onc is a tumor forming retrovirus.

Aflatoxin is produced by two fungi called Aspergillus flavus and Aspergillus parasiticus, these

toxins occur naturally and are found in a wide range of commodities (including peanuts) used

for animal and human consumption. Aflatoxin is known to be carcinogenic at one part per

billion. Development of peanut germplasm with resistance to Preharvest Aflatoxin

Contamination. Colon cancer requires 5-7 mutations in the same cell, risk increases with age.

The colon cancer model is a multi step model, number and order of mutations important in

tumor formation. APC (Adenomatous Polyposis Coli) is a tumor suppressor gene, 2 copies are

needed to go to the next stage. K-ras makes polyp form an adenoma, Polyp: benign tumors

made up of clones of cells,

Adenoma: intermediate stage tumor with fingerlike projections. APC is part of the pathway

that can either promote cell proliferation or cell death. DCC (commissural axons expressed in

colorectal cancer = DCC), DPC4, JV-18 are all tumor suppressor genes. 2 copies of p53 gene

cause late stage to become cancerous. P53 is a transcription factor that can be involved in cell

death of damaged DNA cells. Oncogenes are genes associated with the stimulation of cell

division, cancers that result from only one mutant allele of the gene. Growth factors or receptors

for growth factors: PDGF: platelet derived growth factor (brain and breast cancer), erb-B:

receptor for epidermal growth factor (brain and breast cancer), erb-B2: receptor for growth

factor (breast, salivary, and ovarian cancers), RET: growth factor receptor (thyroid cancer).

PDGF plays a critical role in cellular proliferation and development. The biologically active

form is a dimer formed from the A and B chains. PDGF is active to a differing degree depending

on which dimer is formed (AA, AB, or BB). The PDGF Receptor is also a dimer and can form

from the combination of the alpha and beta chains in any order (alpha-alpha, alpha-beta, beta-

beta). Only cells that express PDGF receptors can respond to PDGF (the ligand). Each cell

would have thousands of receptor copies, magnitude of a response varies with the extracellular

ligand concentration; the dose response relationship. Cytoplasm relays in stimulatory signaling

pathways: Ki-ras: activated by active growth factor receptor proteins (lung, ovarian, colon,

pancreatic cancer), N-ras: activated by active growth factor receptor proteins (leukemias), c-

src: protein kinase that becomes overactive in phosphorylation of target proteins. Transcription

factors that activate growth promoting genes, c-myc: activates transcription of growth

stimulation genes (leukemia, breast, stomach, and lung cancer), N-myc: (nerve and brain

cancer), L-myc: (lung cancer), c-jun and c-fos: function as transcription factors. N-myc is a

transcription factor, part of a complex regulatory network implicated in the control of diverse

aspects of cellular physiology including cell proliferation and apoptosis. Other types of

molecules: Bcl-2: normal protein blocks cell suicide (lymphoma), Bcl-1: codes for cyclin D1,

stimulatory protein of the cell cycle (breast, neck, head cancers), MDM2: codes for antagonist

of p53 (sarcomas). Tumor suppressor genes are genes associated with inhibition of cell

division, cancers that require both alleles of the gene to be altered. Cytoplasmic proteins: APC

(colon and stomach cancers), DPC4: codes for relay molecule in cell division inhibitory

pathway (pancreatic cancer), NF-1: codes for protein that inhibits a stimulating stimulatory Ras

protein (brain, nerve, leukemia), NF-2: (brain and nerve cancers). Nuclear proteins, MTS1:

codes for p16 protein, brake on cell cycle clock (many cancers), RB: codes for pRB protein,

master brake on cell cycle (retinoblastoma, bone, bladder, lung, and breast cancer), p53: codes

for p53 protein, halts cell cycle in G1 and induces cell suicide (many cancers), p16: inhibits

cyclin D-dependent kinase activity, WT1: (Wilms tumor of the kidney), BRCA1: functions in

repair of damage to DNA (breast and ovarian cancers), BRCA2: functions in repair of damage

to DNA (breast cancer). Location not clear, VHL (kidney cancer), mutation of the von Hippel-

Lindau tumor suppressor (VHL) is associated with the majority of renal carcinomas and also

with VHL syndrome, VHL regulated degradation of HIF-1 and levels of vascular angiogenic

growth factors (VEGF-1). VHL protein and how it acts with hypoxia inducible factor (HIF), if

the VHL protein isn't working right it affects some other proteins and the cell begins to think it

isn't getting enough oxygen. Starts to make some new blood vessels to bring more oxygen,

vascular tumors begin to form. VHL protein interacts with a number of other proteins and

enzymes, each of which also has to be normal for this process to work. Carcinogenic causes

cancer, mutanogenic causes mutations. Ames Test: bacterial test for mutation, an extract of rat

liver homogenate (S9) is mixed with a strain of his- bacteria. In the absence of histidine, the

bacteria are unable to grow on minimal medium (control result), when mixed with a suspected

mutagen (X), the presence of revertant colonies indicates that some his- bacteria have mutated

(reverted) to his+ and therefore that substance X is a mutagen. Translocations have caused

cancer, hybrid genes due to translocations. Reciprocal translocation leads to chronic

myelogenous leukemia. Loss of heterozygosity associated with tumor suppressor genes and

tumors. Loss of heterozygosity (LOH) is when a gene that originally had two alleles loses one

allele. Loss of alleles comparing urine with blood samples in bladder cancer. Little to no

information on the strange karyotype of tumors. Poor repair of double stranded breaks in

tumors. Chromosomal instability: extra or missing chromosomes and rearrangements.

Microsatellite instability: DNA level change in number of repeats in tumors. Chromosomal

instability arises three ways. Tumor cells lose the spindle checkpoint; tumor cells are unable to

proceed through the cell cycle despite having DNA damage, structural chromosomal

abnormalities can be a by-product of DNA replication attempts on damaged DNA; tumors may

replicate to the point that the telomeres become too short to protect the chromosome ends,

which leads to structural abnormalities. Spindle checkpoint should prevent chromosome

segregation at mitosis until all chromosomes are correctly attached to the spindle fibers. APC

gene may be involved, very early adenoma cells that are APC- have abnormal mitotic spindles

leading to chromosomal instability. BASC (BRCA1-Associated Genome Surveillance

Complex) involved in detecting and signalling DNA damage (conserved across eukaryotes).

ATM is an early damage sensing component of BASC. ATM is a very large protein that relays

the signal to other targets, homozygous ATM loss causes AT (Ataxia telangiectasia),

heterozygotes ATM at increased risk for breast cancer. Nibrin: complexes with MRE11 and

RAD50 proteins to form part of BASC, lack of nibrin causes Nijmegan breakage syndrome

(clinically similar to AT, but includes microcephaly and growth retardation instead of ataxia).

BRCA1: product of first known breast cancer gene, very large protein, multiple functional

domains that forms part of BASC, also functions in recombination, chromatin remodeling and

control of transcription. BRCA2 has no structural similarity to BRCA1, shares many functions

with BRCA1, cause of some hereditary breast cancer, cause one form of Fanconi Anemia, also

can cause a recessive syndrome of congenital abnormalities, progressive bone marrow failure,

cellular hypersensitivity to DNA damage, and a predisposition to cancer. Cells with defects in

the DNA damage signalling system proteins have trouble repairing double stranded breaks.

Telomeres are the ends of human chromosomes and are protected by repeat sequences

(TTAGGG). Maintained by RNA-containing enzyme Telomerase, which is present in human

germline, but absent in most somatic tissues. Senescence is when cells stop dividing.

Fibroblasts that survive past senescence (with p53 gene damage or retinoblastoma protein or

with viral oncogenes) hit crisis and have gross abnormalities, but have acquired telomerase and

become immortal. Excessive division leads to depletion of telomeres and crisis. Clones are

identical copies of cells derived from a single ancestor. Cloning of cells is common, cloning of

animals is not routine. Cloning animals is difficult. Nuclear fusion is not related to DNA

cloning, two atomic nuclei combine to form a bigger nucleus. Restriction enzymes are DNA

cutting proteins. Recombinant DNA has been artificially combined from two different

organisms. Restriction Fragment Length Polymorphisms (RFLPs): digesting DNA with

restriction endonucleases is another method of detecting polymorphisms. Restriction

endonucleases are bacteria's way of defending itself against invading DNAs. A restriction

enzyme cleaves double stranded DNA at a specific recognition sequence. The smaller

fragments will run more quickly when electrophoresed through an agarose gel. Can

differentiate between the different size fragments. Restriction enzymes are usually named after

the bacterial species from which they were derived. Named using the first letter of the genus

name and the first two letters of the species name. The number refers to the particular enzyme

derived from that species. Alu I was the first enzyme derived from Arthrobacter luteus. There

are hundreds of different restriction endonucleases, recognizing hundreds of different

recognition sequences. It is possible to construct a haplotype or genotype by typing an

individual for many different restriction enzymes. Vector serves as a carrier for DNA fragments

into cells where they can be replicated. Plasmids often used, self replicating circular molecules

of DNA, found in cytoplasm of bacterial cells, pBR322 is a common vector. Clones are small

so it takes many clones to hold the genome, the genome is big. A library is a collection of clones

that contain all of the DNA sequences of an individual. Would take 8.1 million plasmids

averaging 1700 bases (1.7kb) to cover all the genetic information from a single human cell.

Bigger vectors have been made/found. YAC: would take 3000 YACs, BAC, Cosmids: small.

Plasmid is an extrachromosomal circular DNA molecule that autonomously replicates inside

the bacterial cell; cloning limit: 100 to 10,000 base pairs or 0.1-10 kilobases (kb). Phage are

derivatives of bacteriophage lambda; linear DNA molecules, whose region can be replaced

with foreign DNA without disrupting its life cycle, cloning limit: 8-20 kb. Cosmids: an

extrachromosomal circular DNA molecule that combines features of plasmids and phage;

cloning limit - 35-50 kb. Bacterial artificial chromosomes (BAC) based on bacterial mini-F

plasmids, cloning limit: 75-300 kb. Yeast artificial chromosomes (YAC) an artificial

chromosome that contains telomeres, origin of replication, a yeast centromere, and a selectable

marker for identification in yeast cells, cloning limit: 100-1000 kb. Steps of cloning with any

vector: prepare the vector and DNA to be cloned by digestion with restriction enzymes to

generate complimentary ends, then ligate the foreign DnA into the vector with the enzyme

DNA ligase, then introduce the DNA into the bacterial cells (or yeast cells for YACs) by

transformation, then select cells containing foreign DNA by screening for selectable markers

(usually drug resistance). Length polymorphisms, simple PCR-able insertions and deletions,

VNTRs (variable number of tandem repeats), STRs (short tandem repeats, 2-6 bases),

minisatellites (10-100s of bases). Direct sequencing: dideoxy terminator method, chemical

cleavage method. Comparative sequencing: SSCP (single strand conformation

polymorphisms), heteroduplex analysis, denaturing HPLC, chemical and enzymatic cleavage

of heteroduplexes. DNA sequencing chip technology. RFLPs: digesting DNA with restriction

endonucleases is another method of detecting polymorphisms. Restriction endonucleases are

bacteria's way of defending itself against invading DNAs (viruses, plasmids). A restriction

enzyme cleaves double stranded DNA at a specific recognition sequence. Southern blotting,

digest genomic DNA with restriction enzyme, run it out on a polyacrylamide gel, transfer the

gel to a solid membrane (nitrocellulose, nylon, etc) and dry it onto the membrane, wash the

membrane with a labeled probe that is specific to the region you want to visualize, then rinse

away all the unbound probe. Then place the gel/filter into a sealed cassette with a piece of

autoradiograph (x-ray) film. The radioactive decay of the probe will expose the film. Only the

radioactively labeled bands will expose the film. In automated sequencing, the ddNTPs are

each labeled with a different fluorescent label. (ddGTP is one color, ddATP another, ddCTP

another, ddTTP another color). All the fragments start at the 5 end (beginning) of the fragment,

but end on every possible nucleotide. The last nucleotide in every fragment is the ddNTP and

is color coded. When the bands are electrophoresed through a denaturing polyacrylamide gel,

they pass in front of a laser detection system at the bottom (positive) end of the gel. The laser

excites the fluorescent label and a CCD detector records the color of the band passing by the

detector. The bands are ordered by size, smallest to largest. So the first fragment is 1 bp long,

the second is 2-bp long, etc. and are color coded to reveal the identity of the last base. Maxam-

Gilbert chemical cleavage methods, for chemical cleavage sequencing, the DNA is treated with

chemicals that damage only specific nucleotides. In this case, the DNA is 5 end labeled with a

radioactive label, then in four separate tubes, the DNA is reacted with chemical agents that

damage different specific bases. For chemical cleavage sequencing, the DNA is treated with

chemicals that damage only specific nucleotides.

Dimethylsulfate cleaves G, Formic acid and piperidine cleaves A + G, Hydrazine cleaves T +

C, Hydrazine, NaCl + piperidine cleaves C. Mulitlocus minisatellite repeat polymorphisms

create a huge number of polymorphic alleles, such that no two humans are expected to match

exactly for all alleles. STRs provide more genetic information and are easier to analyze,

making them better markers for genome mapping. High mutation rates make STRs more

informative but can introduce noise when tracking inheritance. We used to get specific

genes/alleles into crops or animals by using traditional breeding methods like selective

breeding, hybridization, and mutagenesis, which were slow and imprecise ways of introducing

desired traits. We want genes that improve traits like pest resistance, disease resistance, drought

tolerance, growth rate, nutrition, and overall productivity. Edible vaccines are vaccines

produced in genetically modified plants that you can eat to trigger an immune response. Edible

vaccines are useful because they are cheap, easy to distribute, needle-free, and require no

refrigeration, making them ideal for mass vaccination. We want to make transgenic animals to

improve traits like disease resistance or growth, produce valuable proteins or medicines, and

create better models for studying human diseases. A natural protein produced in the milk of

GEM and other transgenic cows kills the bacteria that cause mastitis. Agresearch plans to

transfer a copy of the human gene responsible for producing myelin basic protein (MBP) into

Friesian cows. The plan is then to harvest large amounts of MBP from the milk of the transgenic

cows for testing on MS sufferers. MS is a chronic disease of the central nervous system that

scientists believe is caused by the patchy degeneration of the myelin sheath that coats nerves

in the brain and spinal cord. In animals showing clinical signs of the disease, recovery can be

helped by ingestion of myelin basic protein. Tracy was a transgenic ewe that had been

genetically modified so that her milk produced a human protein called alpha antitrypsin, a

potential treatment for cystic fibrosis. Sheep in Beltsville Maryland were transgenic, carrying

a gene that may block a common virus that depresses the immune system of sheep. Targeted

transgenic cloned sheep, scientists knocked out the gene for a-1,3 galactosyl transferase in

somatic pig cells using homologous recombination. These cells can be used in combination

with porcine nuclear transfer to produce knockout pigs whose cells and organs are devoid of

gal-a-1,3-gal sugar residues. A key step in overcoming hyperacute rejection associated with the

transplantation of xenogenic tissues. Targets for genetic modification in cows include:

knockout of the bovine prion (PrP) gene to produce cattle resistant to BSE (mad cow disease).

Knockout of allergenic milk protein genes for use in the production of infant formulas. A

number of companies have human therapeutic protein products that are isolated from the milk

of transgenic livestock (sheep, cows, goats, and rabbits) in the late stage clinical trial. Human

anti-thrombin III (blood coagulation inhibitor), AAT (alpha-1-antitrypsin) for treatment of

cystic fibrosis, alpha-glucosidase for treatment of Pompe’s disease. All of these products were

produced via microinjection of the desired human gene, under control of a mammary gland

specific promoter, into fertilized zygotes. A type of transgenic fish, when introduced into a wild

population, could in theory wipe all of the individuals out. Fish have human growth hormone

gene hGH, which increases growth rate and final size. Large GMO males were attracting many

females from the wild population, 4x as many as their wild rivals. Predicted hGH gene would

then spread quickly through the population. Noticed that only ⅔ of the GMO fish would survive

the sexual maturity compared to the wild populations. Spread of the hGH could make wild

populations dwindle and become extinct. Used a computer model to see how long it may take

for 60 transgenic fish to affect a wild population of 60,000. Results suggested the wild

population would be extinct within 40 years. An anti-Darwinian phenomenon has developed,

the researchers suggest the least fit individual has the most successful rate of reproduction.

Transgenic fish offer nearly every kind of exposure route as mice, can be exposed at low-dose

realistic levels, cheaper to use, less controversial. Scientists are breeding genetically modified

fish to harvest a precious blood coagulant that they hope will one day staunch heavy bleeding

in haemophiliacs or gunshot victims. Inserted genes into Tilapia, so that its liver secretes

Human Coagulation Factor VII into its bloodstream. Proteomics: understanding the function

of genes, proteins in an organism, how proteins interact with the environment, finding proteins

that are markers for disease, ID proteins as targets of drugs to fight disease. Ethical concerns

about genomics: need to protect personal genetic info, genome and behavior, genome and

ethnicity, genome and health care/insurance, sharing genetic info with patients and free access

to data. Gene therapy is a medical technique that treats disease by altering genes, usually by

adding, fixing, or editing DNA, but it faces challenges like delivery problems, immune

reactions, and raises ethical concerns about safety, fairness, and potential misuse such as

germline editing or “designer babies.” Genetic counseling, provides facts about diagnosis,

progression, management, treatment for disorder, heredity contributes to disorder. Many

animal behaviors are genetically programmed (like migration, mating rituals), and genes

heavily influence human behaviors (personality, predispositions to addiction, intelligence),

alongside environment. But human behavior is rarely strictly determined, as learning and

experience modify genetic tendencies making free will a complex concept where our choices

arise from gene-environment interplay. Suckling response is a reflex in newborn mammals,

grasping is where newborns grasp objects placed in their hands, both are genetically

determined. One of the biggest problems with behavioral genetics is defining the phenotype.

Phenotypes refer to the observable behavior or trait. Defining it is difficult because behaviors

are complex, variable, and influenced by the environment. Accurate definition is critical for

linking behavior to genes. Poorly defined behaviors can lead to misleading genetic studies.

Behaviors are dynamic, context dependent, and influenced by multiple genes and the

environment making them harder to measure than physical traits. Single gene traits are

controlled by one gene and easier to map genetically, multiple gene traits are influenced by

many genes and the environment making them harder to map. There are some behaviors due

to mutations in a single gene but it is rare. Fruit fly foraging behavior and mendelian behavioral

disorders in humans. Single gene model vs polygenic model (many genes). Combination of

multiple genes interact to produce a unique phenotype. The environment often alters the

phenotype, making understanding and defining the phenotype difficult. Usually study extended

families expressing the trait. Try to determine inheritance patterns from the traits apparent

transmission in pedigrees. Linkage analysis between anonymous markers and the phenotype,

test for non random association with candidate gene alleles. Candidate genes are specific genes

that are believed to be related to a particular trait, like a disease or physical attribute. Defining

phenotype, uses published clinical guidelines but cannot define too narrowly, because it may

exclude people who truly have the trait or disorder, but cannot define too broad because you

may include people who don't really have the trait. Some mutations in genes lead to changes

in the structure of the nervous system (Alzheimers, Charcot Marie Tooth Syndrome,

Huntington Chorea). Other behavioral changes due to changes in function rather than structure

(Bipolar disorder, Schizophrenia). Animal models breed for behavioral phenotypes, can

inbreed, control mastings, can modify the genome (knockouts, directed mutations,

increased/decrease expression). Open field behavior in mice, some mice freeze in bright open

space, some are nervous and defecate/urinate a lot, some explore actively. Bred for strain of

mice that had these traits, found albino strain showed exploratory behavior and was highly

emotional, C57 strain was normal colored with low levels of emotional behavior. Crosses

showed OFB was a polygenic trait. Drosophila: many mutations associated with behaviors.

Learning mutants include: Dunce: cannot learn conditioned response, turnip: impaired in

learning conditioned response, rutabaga: impaired in several types of learning/memory. Sexual

behavior mutants include: fruitless: males court each other, savoir-faire: males unsuccessful in

courtship, coitus-interruptus: males stop copulation prematurely. Motor behavior mutants

include: flightless: lacks coordination in flying, sluggish: moves slowly, wings up: holds wings

perpendicular to body. Experiments used odor and electric shock, flies learned to avoid odor

that was accompanied by shock, mutations in cAMP gene led to flies that did not learn to avoid

shock. cAMP controls transcription and sets off cascades of biochemical reactions inside the

nervous system. cAMP is produced by enzymes and adenyl cyclase. Transgenic animals: cross

species of strains, put human genes in other animals to study expression, and effects of

treatments. Amyotrophic lateral sclerosis (ALS) is autosomal dominant in 10% of all cases.

Some individuals have SOD1 gene mutation on chromosome 21. Makes SOD1 protein toxic,

mice with this mutant version have muscle weakness and atrophy similar to affected humans

with ALS. Study these mice to see how SOD1 protein selectively damages some nerve cells,

ignores others. Huntington Disease, gene at 4p16.3, CAG repeat expansion, increase in CAG

leads to many glutamic acids inserted into the gene product which makes it toxic and kill nerve

cells. Damage occurs at the striatum and cerebral cortex of the brain, cells fill with cytoplasmic

and nuclear clusters of the mutant protein, degenerate and die. Leads to involuntary muscle

movements and progressive personality changes as more nerve cells die. Protein affected in

HD is called Huntingtin, large protein (Htt), stimulates production of BDNF protein (necessary

for survival of cells in the striatum), mutant Htt causes decrease in BDNF production (cells of

the striatum degenerate and die), causes gene product to lose function but also causes new toxic

state of gene product. Transplanting fetal stem cells (in mice) into affected regions leads to

partial restored function, nerve connections and behavior. Noam Chomsky has argued since all

humans learn language easily it is probably genetic, and found a large family with an autosomal

dominant speech/language disorder that mapped to chr7. Sporadic cases with the same

symptoms had a translocation, showing which gene was involved. Found FOXP2 mutation

changes amino acid, FOXP2 is a transcription factor that is very active in fetal brains. Looking

at chimps to see how FOXP2 differs, may lead to ability or inability to learn language.

Behavioral disorders: alcoholism, schizophrenia, bipolar disorder, neurotransmitter disorders.

Alzheimer's, less than 50% of cases are genetic, there are clear genetic causes though. Normal

behavior variants: risk taking, a neurodevelopmental gene, called neuroD2, is related to the

development of an almond shaped area of the brain called the amygdala, the brain's emotional

seat. This gene also controls the emotional memory formation and development of the fear

response. Personality, sociality or antisocial behavior are all behavior variants. Risk raking loci:

Dopamine receptor D4 (DRD4): the 7 repeat allele of the DRD4 gene associated with increased

risk taking and novelty seeking behaviors. Serotonin transporter (5-HTTLPR): the “short” (s)

allele of the 5-HTTLPR gene is linked to increased risk aversion, while the “long” (l) allele is

associated with increased risk tolerance. CADM2 gene: CADM2 gene (cell adhesion molecule

2) associated with risk taking behavior. The immune system is the body's defense against

infection. Non specific response blocks entry of disease causing agents into the body, blocks

spread of infectious agents in the body. Specific response: immune reaction. Two lines of

defense: antibody mediated immunity and cell mediated immunity. Antibody mediated

immunity primary response is triggered first time the body encounters an antigen, lags, second

response is triggered by exposure to the same antigen, does not lag. Cell mediated immunity

primary response with lag phase, secondary response triggered after being re-exposed to

antigen, does not lag because of memory T cells. Inflammatory response, skin is a barrier to

bacteria, mites, fungi, these cannot penetrate dead skin layers. If organisms do penetrate dead

skin, or cells lining digestive, respiratory, or urinary tracts, inflammatory response happens.

Signals increase blood flow to the affected area, makes it red and warm, bacteria don't like heat,

this prevents growth. Mobilizes WBCs, raises metabolic rate of nearby cells. WBCs engulf and

destroy invading microorganisms. If infection persists capillaries become leaky and plasma

flows into surrounding tissue, causing swelling. Clotting factors in plasma trigger a cascade of

small blood clots that seal off the injured area to prevent organisms from escaping. Monocytes

(WBC’s that engulf pathogens and clean up debris) clean up dead viruses, bacteria, fungi, and

dead cells/debris. If an inflammatory response is not sufficient, an immune response is

triggered. Crohn disease affects 1/1000 individuals, ulcerative colitis, caused by error in the

immune system. Predisposition due to chromosome 16 mutation in NOD2 gene (receptor found

on surface of monocytes and other immune cells). The receptor signals a protein in the nucleus

to begin inflammatory response (detects molecules on the surface of bacterial cells),

inflammatory response in Crohn’s damages the intestinal wall. Atherosclerosis and

inflammatory response: LDLs get oxidized in arteries and damage arterial walls, this triggers

macrophages and monocytes to remove LDLs, but they cannot remove the oxidized LDLs and

it gets worse, triggering more WBC. Muscle covers the wound. Compliment system: chemical

defense system, supplements inflammatory response, kills microorganisms directly, working

with immune response system. Neutralisation: blocking the biological activity of their target

molecule, opsonisation: interact with special receptors on various cells, including

macrophages, neutrophils, basophils and mast cells allowing them to recognize and respond to

the antigen, complement activation: causes direct lysis by complement, complement

recruitment also enhances phagocytosis. Complement proteins are synthesized in the liver and

circulate in the bloodstream as active precursors. At the site of infection, the C1 activates C2,

etc through C9. C5 through C0 form a large cylindrical multiprotein complex (MAC). MAC:

membrane attack complex, embeds in plasma membrane of invading microbe creating a pore,

fluid flows in through pore due to osmotic gradient and bursts cell, proteins also guide

phagocytes to site of infection. Antigens: most are proteins or proteins combined with

polysaccharides, any molecule can be an antigen if it causes antibody production. Antibody is

a protein produced by the immune system in response to the presence of an antigen.

Lymphocytes are WBCs that originate in the bone marrow and mediate immune response,

formed by mitotic division of stem cells. When daughter cells migrate to the thymus they get

reprogrammed into T cells, mature T cells circulate in blood and concentrate in lymph nodes

and spleen. B cells mature in bone marrow and move directly to the circulatory system and

lymph system, they are genetically programmed to produce antibodies, each B cell produces

just one kind of antibody. Immune response has two parts: antibody mediated immunity and

cell mediated immunity. Antibody mediated immunity regulated by B cell production, defends

against invading bacteria and viruses. Cell mediated immunity regulated by T cell production,

attacks cells of the body infected with bacteria and viruses, and also protects against infection

by parasites, fungi, protozoans. One kind of T cell can even kill cancerous cells. Stages of

antibody mediated immune response: antigen detection, activation of T helper cells, antibody

production by B cells. A specific type of immune system controls each stage. Antibody

mediated immunity, the principal agent is B cell, B cell responds to bacteria, bacterial toxins,

and some viruses, and when activated, B cells form memory cells and plasma cells which

produce antibodies to these antigens. Cell mediated immunity, the principle agent is T cell, T

cells respond to cancer cells, virally infected cells, single celled fungi, parasites, and foreign

cells from organ transplants, when activated, T cells differentiate into memory cells, cytotoxic

cells, suppressor cells, and helper cells. Cytotoxic T cells attach the antigen directly.

Macrophages continuously move through the circulatory system and spaces between cells

searching for foreign antigens, when a macrophage runs into an antigen it engulfs it and

internalizes it, destroying it with enzymes, and small fragments of antigens move to the outer

surface of the macrophages plasma membrane. Macrophages may encounter a helper T cell

lymphocyte, surface receptors on the T cell make contact with the antigen fragment on the

macrophage, this activates the T cell. Activated T cells in turn identify and activate B cells that

can synthesize an antibody against the antigen encountered by the T cell. Activated B cells

divide and form two types of daughter cells (Plasma and B memory cells. Plasma cells

synthesize and secrete 2,000-20,000 antibody molecules per second into the bloodstream (live

only a few days), B memory cells form at this time and live months or years. Antibodies are

molecular weapons against antigens, Y shaped proteins bind to antigens in lock and key

manner, forming an antigen antibody complex. Antibodies are secreted by plasma cells,

circulate in blood and lymph systems, some antibodies attach to the surface of B cells,

antibodies belong to a class of molecules called immunoglobulins. Five classes: of

immunoglobulins (IgG, IgA, IgM, IgD, and IgE). Each has a unique size, structure, and

function. Consists of two identical long polypeptides (H chains) and two short identical

polypeptides (L chains) and these chains are held together by chemical bonds. Antibody

structure relates to its function, either to recognize and bind antigens or to inactivate the

antigen. One end of an antibody is an antigen combining site formed by the ends of the L and

H chains, recognizes and binds part of the antigen called the antigenic determinant, this

formation of the antibody antigen complex leads to the destruction of the antigen in several

ways. IgD present on the surface of many B cells, function is uncertain, may be surface receptor

for B cells, plays a role in activating B cells. IgM found on the surface of B cells and in the

plasma, B cells surface receptor for antigens secreted early in primary response, powerful

agglutinating agent. IgG is the most abundant immunoglobulin in blood plasma, produced

during primary and secondary response, and can pass through the placenta providing protection

to the fetus. IgA produced by plasma cells in the digestive and respiratory and urinary systems,

protects surface linings by preventing attachment of bacteria to surfaces of epithelial cells, also

present in tears and breast milk, protects lining of digestive, respiratory, and urinary systems.

IgE produced by plasma cells in skin, tonsils, and digestive and respiratory systems,

overproduction responsible for allergic reactions, including hay fever and asthma. Cannot code

for an antibody for every possible antigen, make combinations via recombination in three

clusters of antibody genes, the H chain genes on Chromosome 14, the Kappa L genes on

chromosome 2, and the lambda light genes on chromosome 22. Recombination takes place

during B cell maturation before antibody genes are transcribed and before antibody production

begins. In each antibody gene cluster, DNA segments that encode various portions of H and L

chains undergo recombination, each mature B cell encodes, synthesizes, and secretes only one

type of antibody. Allows 30,000 possible H chains and 3600 possible L chains, for several

hundred thousand possible combinations, other events in B cell maturation allow for billions

of possible antibody combinations from these few hundred segments at three loci. 3 types of T

cells in the immune system: Helper T cells activate B cells to produce antibodies, produce a

growth factor that stimulates B cell proliferation and differentiation, stimulates antibody

production by plasma cells, enhances activity of cytotoxic T cells. Suppressor T cells slow

down and stop the immune response (off switch), may inhibit immune reaction by decreasing

B and T cell activity and B and T cell division. Killer T cells find and destroy cells of the body

that are infected with a virus, bacteria or other infectious agent. Memory T cells remain in the

body waiting for the introduction of an antigen, when they proliferate and differentiate into

cytotoxic T cells, helper T cells, suppressor T cells and additional memory cells. If a cell

becomes infected with a virus, viral proteins appear on its surface, viral proteins recognized by

receptors on surfaçe of a killer T cell, T cell attaches to infected cells and secretes a protein that

punches holes in the plasma membrane of the infected cell. Cytoplasmic contents of infected

cells leak out through holes, the infected cell dies and is removed by phagocytes. B and T

memory cells are produced at first infections, they control resistance to second infection

(secondary immunity), second exposure to the same antigen results in immediate large scale

production of antibodies and killer T cells, much faster reaction than primary response.

Secondary immunity is why we get vaccinated. Vaccines stimulate production of memory cells

against a disease causing agent, vaccine is a weakened, disease causing antigen given orally or

injected, provokes primary response and memory cell production, second dose often given to

raise the number of memory cells (booster shot). Blood types determined by cell surface

antigens, 30 known antigens on blood cells, each constitutes a blood group or type, for

transfusions to work the donor and recipient must be identical or recipients immune system

will produce antibodies against donors surface antigens, clumping transfused cells, blocking

circulation in capillaries. Match ABO and RH systems for transfusions. Transfusion reactions,

Rh incompatibility, hemolytic reaction and rhogan. Transmission of HLA haplotypes, each

haplotype has four genes, each encoding a different antigen. Organ transplants: MHC HLA

systems must match, chances of a match are only 1/100,000, to 1/200,000. HLA alleles vary

wildly across ethnic and racial groups so matches across these groups are difficult.

Xenotransplants are animal-human transplants, using animals as donors to increase supply.

Two problems: compliment mediated rejection (cell surface proteins act as antigens that are

very different across species, trigger massive immediate immune response, compliment system

usually destroys organs within hours), T cell mediated rejection (same as in human organ

transplant, must suppress cellular rejection of transplant). Xenotransplants: cloned human

genes that suppress hyperacture rejection, genes injected into fertilized pig eggs, resulting

transgenic pigs carry human recognition antigens on their cells, appear human to the immune

system. Even with hyperacute rejection suppressed, still can have problems with T cell

mediated rejection of transplant, requires immunosuppressive drugs, weakens immune system

continuing rounds of infection, and may need to transplant bone marrow from donor pig to

human recipient (chimeric immune system). HLA and disease: ankylosing spondylitis (B27

allele), congenital adrenal hyperplasia (B47 allele), goodpasture syndrome (DR2 allele),

juvenile rheumatoid arthritis (DR5 allele), multiple sclerosis (DR2 allele), pernicious anemia

(DR5 allele), psoriasis (B17 allele), reuters syndrome (B27 allele), rheumatoid arthritis (DR4

allele), systemic lupus erythematosus (SLE) (DR3 allele). Allergen (weak antigens), allergic

reaction results when the immune system overreacts to weak antigens that do not evoke an

immune response to most people. Allergic reaction causes B cells to make IgE antibodies

instead IgG, IgE attach to mast cells in tissues (including nose and respiratory system). Shock:

mast cells release histamine granules and heparin into the circulatory system, triggers

inflammatory response (fluid accumulation, swelling, mucus secretion, can lead to life

threatening anaphylactic shock due to decrease in BP and constriction or airways in lungs).

Anaphylaxis is a severe onset allergic reaction. Autoimmune disorders: immune system attacks

own cells wrongly, IDDM: insulin dependent diabetes mellitus, clusters of cells in pancreas

make insulin, immune system kills these cells and lack of insulin leads to diabetes and requires

insulin shots to control blood sugar. X linked agammaglobulinemia (XLA) is a rare sex liked

recessive trait due to total absence of immunoglobulins and B cells. Acquired

immunodeficiency disorder (AIDS) is a collection of disorders that are caused by HIV

infection, HIV is a retrovirus, so it is an RNA virus that can make DNA copies of itself and

insert itself in other organisms' genomes. HIV has three components, protein coat, RNA

molecules, and reverse transcriptase enzyme. HIV: viral particle enclosed in a coat derived

from the plasma membrane of a T cell, virus selectively infects and kills T4 helper cells. Inside

the cell, RT transcribed RNA into DNA, viral DNA inserted into the human chromosome where

it sits for months or years. When an HIV infected T cell is called to act in an immune response,

viral genes are activated, new viral particles are formed and bud off the surface of the T cell,

rupturing and killing the T cell. Sets off a new round of infection, and as infection progresses,

T cells decrease, since T cells are the “master on switch” for the immune system, the ability to

mount an immune response decreases, eventually some infection leads to death. HIV

transmitted through bodily fluids, virus cannot live more than 1-2 hours outside the body,

cannot be transmitted by food, water, or casual contact. Epitopes are the part of the antigen that

is recognized by the immune system. Variation is increased by mutation, migration, and

balancing selection. Decreased by most selection and genetic drift. Hardy Weinberg Principle

predicts frequencies of genotypes in the next generation under certain assumptions. Genotype

frequencies are determined in part by the pattern of mating. Assumptions: 1. random mating,

non overlapping generations 2. Genotype frequencies will not be affected by migration,

mutation, and natural selection 3. Population must be large enough that random genetic drift

will not be a factor (allele frequency will not change due to sampling errors in small

populations), this ideally means population of infinite size, but for practical purposes, n>500

suffices to eliminate drift. Assumptions of H-W model: diploid organism, sexual reproduction,

non overlapping generations, two alleles per gene, allele frequencies identical in males and

females, random mating, population size very large, no migration, no mutation, no natural

selection on alleles under study. Frequency of AA = p^2, frequency of Aa = 2pq, frequency of

aa = q^2. A and s are the gametes of the previous generations, p + q = 1. Harvey Weinberg

equation: p^2 + 2pq + q^2 = 1. Dominance obscures the 1:1 relationship between genotype and

phenotype. Can still estimate allele frequencies from phenotype data if we assume H-w

proportions. When there is dominance, there is no possibility for a X^2 test of goodness of fit

to H-W-E because there are 0 df. Lack of df is why the calculated frequencies of Rh- and Rh+

fit the observed frequencies exactly. 2 classes -1 parameter -1 = 0. Chi square test is an

assessment of closeness of fit between the data and the prediction of the model. Degrees of

freedom for chi square values calculated as # of classes of data - number of parameters

estimated from the data -1. P value is the probability that chance alone could produce the

observed deviation from the model. A small p-value (p<0.05) means it is very unlikely that one

would observe those values by chance alone. Industrial melanism: moths in polluted areas,

where trees are darkened by pollution, tend to be dark, and moths in non polluted areas tend to

have light colored trees and light colored moths, presumably due to predators picking up the

contrast of moths on the different backgrounds. Heterozygotes are most frequent when allele

frequencies are 0.5. The ratio of heterozygotes to recessive homozygotes increases as recessive

alleles become rare. The ratio of heterozygotes to homozygous recessives is important for

disease genes. For cystic fibrosis, autosomal recessive defects in chloride transport leading to

abnormal glandular secretions, impaired digestion, respiratory infections, etc. Frequency of

recessive genotype in newborn caucasians is 1/1700 (0.00058), q-hat = 0.024, assuming

random mating and HWE frequencies of hets = 0.047 or 1/21 is a carrier. Het = 2pq = 2(1-q)q

= 2(.976)(.024) 0.047.