Genes and Cancer Biology

9 / 11 lecture

chromosomes: somatic cells vs germline cells

• within the nucleus of every cell is the genetic code responsible for the structure and function of the human body

• cells are subdivided into

  • germline cells (gametes: sperm and egg cells)

  • somatic cells (all other cells)

chromosomes: numbers

• somatic cells contain 23 pairs of chromosomes

  • 22 pairs of autosomes

    • each pair is nearly identical in appearance and DNA sequence

    • they are homologous

  • 1 pair of sex chromosomes

    • 2 homologous X chromosomes in people AFAB

    • 1 non-homologous pair of X and Y chromosomes in people AMAB

• germline cells contain 23 single copies of chromosomes

autosomes

• code for every protein and enzyme that your body produces

• you get one copy of chromosomes from one parent and another copy from your other parent

genes and DNA: components

• each chromosome is composed of deoxyribonucleic acid (DNA) and histone proteins

  • DNA provides the genetic code for the synthesis of proteins

  • histone proteins help DNA fold into chromosomes

• each strand of DNA is made up of sequences of 4 nucleotides

  • nucleotide: nitrogenous base, deoxyribose, phosphate

  • four nitrogenous bases:

    • two purines: adenine and guanine

    • two pyrimidines: cytosine and thymine

purines

• adenine

• guanine

pyrimidines

• cytosine

• uracil

• thymine

genes and DNA: hydrogen bonds

• strands of DNA are held together by hydrogen bonds connecting the nitrogenous bases

  • adenine forms a bond with thymine

  • guanine forms a bond with cytosine

• resulting structure is a double helix

cell division: the cell cycle

• DNA needs to replicate to preserve genetic information when cells divide

• the cell cycle represents the process of cell division

  • G₀ → the resting and repairing phase

    • most cells are in this phase and carrying out the job they were specialized to do

  • G₁ → cell is preparing for DNA synthesis

  • S phase → DNA synthesis

  • G₂ → cell is preparing for mitosis

  • M → mitosis

    • prophase, metaphase, anaphase, telophase

  • every step that isn’t mitosis is considered interphase

Cell Division: S phase

1. DNA molecule unwinds and opens up to expose the nucleotide bases

2. DNA polymerase moves along the template strand of DNA and creates a complementary strand of DNA based on the nucleotides in the template

• cytosine and guanine line up

• adenine and thymine line up

3. DNA polymerase “proofreads” the complementary strand

• if the base is not complementary it is excised and replaced

4. once the strand has been completely replicated, there are two identical chromosomes

cell division: Mitosis (M phase) - prophase

• once DNA replication has completed (during interphase), the cell can divide

• the DNA coils, shortens and thickens to produce the chromosomes

• the chromosomes are visible as two identical halves (chromatids) attached at a single point (centromere)

cell division: Mitosis (M phase) - metaphase

• the chromosomes line up at the cellular equator in the middle of the cell

• spindle fibers radiate from centrioles at each pole of the cell to the centromere

cell division: Mitosis (M phase) - anaphase

• the centromere split and the sister chromatids are pulled apart toward opposite poles

cell division: Mitosis (M phase) - telophase

• the new nuclear envelope is formed

• spindle fibers disappear

• cell divides

• the end result is two daughter cells that contain the same genetic information (diploid)

cell division: meiosis I

• the process by which gametes (sex cells) are formed

  • will end up with half of the genetic information

• the DNA replicates during interphase

• prophase I: replicated chromosomes coil up

• metaphase I: homologous chromosomes line up on equator of cell opposite one another

  • spindle fibers radiate from the centrioles and attach to centromere

• anaphase I: homologous chromosomes are pulled to opposite poles of the cell

• telophase I: nuclear envelope forms and cell divides into two daughter cells

cell division: meiosis II

• metaphase II: chromosomes line up along the equator again

  • spindle fibers radiate from the centrioles and attach to centromere

• anaphase II: chromatids are pulled apart and move toward opposite poles

• telophase II: cell divides into two germ cells

  • each germ cell now has half the genetic information (haploid)

mutations during cell division: polyploidy

• cells that have a multiple of the normal number of chromosomes (23)

• triploidy: three copies of each chromosome

• tetraploidy: four copies of each chromosome

• nearly all triploidy and tetraploidy pregnancies are spontaneously aborted

mutations during cell division: aneuploidy

• cells that DO NOT have a multiple of 23 chromosomes

• usually due to nondisjunction (when chromosomes fail to separate during meiosis I)

• trisomy: three copies of one chromosome (trisomy 13, 18, or 21 can survive)

• monosomy: one copy of one chromosome (all are lethal)

• fertilized eggs containing no X chromosome cannot survive

trisomy 21: down syndrome

• 1 in 800 live births

• intellectually disabled

• clinical manifestations

  • low nasal bridge

  • epicanthal folds

  • protruding tongue

  • flat, low set ears

  • poor muscle tone

  • short stature

  • ~50% have congenital heart defects **

  • increased risk of respiratory illness

  • 54-90% have obstructive sleep apnea **

  • almost all develop symptoms of alzheimer’s disease by age 40 **

turner syndrome (45, X)

• syndrome characterized by presence of one X chromosome without a homologous X or Y chromosome

• absence of Y chromosome means these individuals are usually AFAB

• usually sterile: gonadal streaks rather than ovaries

• clinical manifestations

  • short stature **

  • webbing of the neck (~50%) **

  • sparse body hair **

  • normal intellectual development usually **

  • widely spaced nipples

  • coarctation (narrowing) of the aorta

Klinefelter syndrome (47, XXY)

• syndrome characterized by presence of two or more X chromosomes in addition to a Y chromosome

• presence of Y chromosome means these individuals are usually AMAB

• usually sterile

• clinical manifestations **

  • elevated stature

  • gynecomastia

  • small testes

  • sparse body hair

  • high pitched voice

  • some intellectual disability is common

abnormalities associated with chromosome structure

• some disorders are the result of abnormalities within the chromosome

• parts of chromosomes can be duplicated or lost during DNA replication and cell division

• oftentimes less severe

• missing information is usually more problematic than excess information

abnormal chromosome structure: deletion

• loss of a portion of the genetic material

• deleton

abnormal chromosome structure: duplication

• redundant genetic material in the chromosome

• duplicacation

abnormal chromosome structure: inversion

• reversal of the order of the genetic code resulting from 2 breaks

• insrevion

abnormal chromosome structure: translocation

• interchanging of material from 2 non-homologous chromosomes

abnormal chromosome structure: fragile sites

• microscopic breaks and gaps in DNA

cri du chat

• syndrome associated with deletion of the short arm of chromosome 5

• clinical manifestations

  • high pitched, cat-like cry **

  • wide-set eyes with prominent epicanthal fold **

  • intellectual disability **

  • low-set posterior rotated ears

  • low birth weight

  • smaller than normal head

  • heart defects

• survival is good

fragile X syndrome

• syndrome associated with multiple (> 200) repeats of a 3-nucleotide sequence in long arm of X chromosome (1 in 4000 males / 1 in 8000 females)

• leads to silencing of the genes, many of which are responsible for neuronal synaptic connections

• second most common cause of intellectual disability (after down syndrome) and autism

• clinical manifestations **

  • elongated face

  • enlarged genitals

  • intellectual disabilities (language delay, poor attention, signs of autism)

  • long hands and feet

  • large ears

  • mood disturbances (tantrums, anxiety, aggression)

  • sensory and motor deficits

fragile X phenotype

F → face elongated

R → repeats (CGG, CGG, CGG…)

A → ADHD

G → giant genitals

I → intellectual impairment

L → large hands/feet

E → ears protruding

X → extensible joints

DNA → genes → polypeptides

• sequences of nucleotides in DNA make up genes

  • the basic units of inheritance

• genes code for all the body’s proteins

  • structural proteins

  • enzymes

• proteins are made up of sequences of amino acids (there are 20 amino acids)

  • specific combination of amino acids creates a polypeptide

  • polypeptides are bound together and folded in a certain way (alpha helices or beta pleated sheets are most common) to form a protein

protein synthesis

• cookbook = DNA

• recipe = RNA

• dinner = protein

protein synthesis: transcription

• the cell needs to decipher the genetic code to know what protein to make

• this creates a messenger ribonucleic acid (mRNA) template (the recipe) from the DNA (the cookbook) for protein synthesis

1. RNA polymerase binds to promoter site on DNA

• specifies the beginning of a genre

2. RNA polymerase opens the DNA to expose the nitrogenous bases

3. RNA nitrogenous bases that are complementary to the DNA nitrogenous bases line up to form mRNA

• cytosine and guanine line up

• adenine pairs up with uracil (similar to thymine)

4. termination sequence in DNA marks the end of the gene and terminates transcription

5. now you have a strand of mRNA

protein synthesis: removal of introns

• before moving into the cytoplasm, some RNA sequences are removed from the mRNA (introns)

• the function of these is unknown

protein synthesis: translation

• the mRNA molecule travels to a ribosome to build a polypeptide

  • each sequence of 3 nucleotides on the mRNA (codon) codes for a specific amino acid

  • molecules of transfer RNA (tRNA) in the cytoplasm have a sequence of 3 nucleotides (anticodon) that is complementary to the codon on the mRNA

  • each tRNA carries one amino acid

translation

1. mRNA binds to ribosome

2. the anticodon of a tRNA lines up with the codon on a mRNA

• The ribosome will look at the first 3 nucleotides (codon) and it corresponds to a specific amino acid (the amino acid is attached to a specific tRNA)

3. subsequent tRNA molecules bind to subsequent codons on mRNA

4. amino acids on adjacent tRNA molecules bind together to form a polypeptide

• As each tRNA attaches to the codon, the amino acid that is attached to each individual tRNA will string together and make a polypeptide chain

dominant and recessive alleles

• each gene occupies a locus on a chromosome

• different forms of a gene are called alleles

  • alleles may be dominant or recessive

    • dominant → characterized by capital letters, stronger expression

    • recessive → characterized by lowercase letters, weaker expression

  • a person receives one allele from each parent

genotype

• refers to the genetic makeup of the alleles

  • used to describe a characteristic

  • if the alleles from each parent are identical (both dominant or both recessive), a person is homozygous (BB or bb)

    • need to specify

      • homozygous dominant (BB)

      • homozygous recessive (bb)

  • if the alleles are NOT identical (one dominant and one recessive), they are heterozygous

phenotype

• refers to the observable trait in a person

  • a dominant trait will be observed when paired with another dominant allele (BB) or when paired with a recessive allele (Bb)

  • a recessive trail will only be observable when paired with another recessive allele (bb)

disease carriers

• a person is a carrier of a disease if they have the allele for a disease but are phenotypically normal

  • often this is because the disease causing allele is recessive

  • a homozygous dominant person (BB) does not carry the trait

  • a heterozygous person (Bb) carries the trait but will not exhibit signs of the disease

  • to express disease, both recessive alleles have to be present (bb)

  • ex

    • tay sachs

    • cystic fibrosis

cystic fibrosis

• AUTOSOMAL RECESSIVE

• mutation results in abnormal an ion channel for Cl- and HCO3- (decreased number and abnormal function)

• primarily affects:

  • lungs

  • pancreas

  • GI tract

  • sweat glands

  • vas deferens

cystic fibrosis clinical manifestations

• mucous accumulation in the lungs

  • increased reabsorption of Na and water from lumen of airway

  • mucous in airway is thick and tenacious

  • persistent airway obstruction

  • recurrent infections

• increased mucin production in GI tract

  • plugging of pancreatic ducts

  • GI disruption

• increased Na+ and Cl- in sweat due to poor absorption

cystic fibrosis diagnosis

• trypsinogen test for newborns: trypsinogen is elevated in CF

• sweat test

  • administer a medication to induce sweating

  • measure Cl- in sweat

Huntington Disease

• AUTOSOMAL DOMINANT

• repeats of a 3-nucleotide sequence contributes to extra long protein that is prone to fragment

• result is neuronal dysfunction and eventually death

Huntington Disease Clinical Manifestations

• onset of symptoms around age 45

  • many have already had children (their children are likely to have it too)

• motor signs (diagnostic)

  • involuntary movement (choreiform movements)

  • impaired voluntary movement (bradykinesia and lack of coordination)

• cognitive impairment

• depression

• death usually occurs 10-30 years after onset of symptoms

background on cancer

• second leading cause of death in the US (first leading cause is heart disease)

• incidence rate: the number of NEW CASES in a given time

  • incidence rates have increased since the 1960s

  • most likely a result of more screening rather than more diseases

• prevalence: the number of cases at a point in time

  • prevalence of many cancers has increased since the 1960s

• aging has led to more deaths due to cancer compared to other causes

• neoplasm = new growth

incidence / prevalence males vs females

mortality males vs females

• we don’t have good screenings for lung cancer

• many of the screenings only find something if it is late stage

etiology of cancer

• cancer is a complex, genetic disease

• genetic changes occur with age

• may occur by mutation or by epigenetic mechanisms

  • point mutations (one nucleotide)

  • translocations (large amounts of DNA)

  • repetition of certain gene sequences can increase expression of some genes (gene amplification)

  • epigenetics (methylation, etc.) may suppress expression of some genes

• these mutations change a normal cell into a malignant cell (malignant transformation)

etiology of cancer: oncogenes

• mutations of proto-oncogenes

  • normal genes that code for cellular growth and development (growth factors, growth factor receptors, transcription factors, etc.)

  • mutations convert proto-oncogenes into oncogenes

  • oncogenes increase cellular growth and development

  • ex

    • RAS: overexpression can lead to colorectal cancer and lung cancer

    • HER-2: overexpression can lead to breast cancer

etiology of cancer: tumor suppressor genes

• underactivity or silencing of tumor suppressing genes

  • genes that normally block cell division when DNA is damaged and induce apoptosis

  • mutation prevents activation of these genes

  • cancerous cells are not eliminated and cancer is allowed to grow

  • ex

    • BRCA-1 and BRCA-2 defect: promotes breast and ovarian cancer

    • APC gene mutation: promotes familial adenomatous polypoposis

influence of genetic changes in cancer

• will have an effect on:

  • proliferation → the process of cell division

  • differentiation → the process by which cells become specialized

  • maturity → differentiated cells that have reached full functional potential

differentiation

• regulated by genes and external stimuli (environment exposure to substances, cytokines, growth factors, etc.)

• all cells contain all genes

  • normally, only the genes for the specific, differentiated cell are active

  • as cells divide, they normally lose their ability to develop characteristics of other specialized cells

  • cancer doesn’t play by the rules

cancer’s effect on proliferation

• cells also normally lose their ability to proliferate

  • instead, tissues rely on progenitor/stem cells to grow

  • however, cancer doesn’t play by the rules

• stem cells: two properties

  • self-renewal

  • potency

cancer cell characteristics

• abnormal, rapid proliferation

• loss of cell differentiation

• genetic instability

• growth factor independence

• failure of cell density-dependent inhibition

• loss of cell cohesiveness and adhesion

• loss of anchorage dependence

• loss of cell-to-cell communication

• antigen expression

• production of enzymes, hormones, etc

• cytoskeletal changes

• “unlimited” life span

loss of cell differentiation (anaplasia) in cancer

• cells do not exhibit same features of differentiated cells

• more similar to embryonic cells rather than tissue or origin

• greater numbers of cells in mitosis due to rapid proliferation

• odd mitotic features (spindles)

• nuclei are odd in shape, may have abnormal number of chromosomes

• clumped chromatin

• large nucleoli

• classified from Grade I (well differentiated) to IV (poorly differentiated)

genetic instability in cancer

• inherent instability that contributes to development and progression of cancer

• high number of genetic mutations that would normally be corrected in normal tissue

  • lost/gained chromosomes, DNA insertions/deletions, etc

growth factor independence in cancer

• ability to proliferate without growth factor

• some produce their own growth factor

failure of cell density dependent inhibition in cancer

• cessation of growth when cells reach a pre-determined density is not active in cancer cells

• cancer cells will replicate in the absence of growth factor or just make their own growth factor

loss of cell cohesiveness and adhesion in cancer

• loss of tendency for cells to stick together

loss of anchorage dependence in cancer

• do not require anchorage to neighboring cells or extracellular matrix to grow and develop

• When the cancer cell breaks free, it can still multiply even though it is away from other tissues

  • Especially prevalent in ovarian cancer

  • If one cell from the ovary were to make its way to the peritoneal lining, it will spread everywhere

  
  

antigen expression in cancer

• produce antigens immunologically different than host

• cancer cells can secrete cytokines that suppress the immune response

production of enzymes, hormones, etc. in cancer

• enzymes, clotting mechanisms, hormones that aid in metastasis

• production of hormones normally produced in other parts of the body (pituitary, etc.)

• can lead to paraneoplastic syndromes

  • when you have a cancer that is producing a substance that is usually produced somewhere else

“unlimited” life span in cancer cells

• shortening of the telomere normally limits life span of a cell

• cancer cells produce telomerase → enzyme that prevents telomere shortening and prolongs cell life

cancer growth

• normal adult cells reach equilibrium between cell production and death

• cancer cells continue to divide until limits in blood supply and nutrients become a factor

benign tumors

• named by adding -oma to the type of parenchymal tissue from which the growth originated

  • adenoma → benign neoplasm of glandular tissue

  • osteoma → benign neoplasm of bone

malignant neoplasm of epithelial tissue

• end in suffix -carcinoma

  • adenocarcinoma → malignant neoplasm of glandular epithelial tissue

malignant neoplasm of mesenchymal origin

• end in suffix -sarcoma

  • osteosarcoma → malignant neoplasm of bone

  • liposarcoma → malignant neoplasm of adipose tissue

• (mesenchymal refers to things that create the structure of the body [like ligaments, bone, etc.])

benign cancer key characteristics

• cells are

  • well differentiated

  • resemble tissue of origin

• rate of growth

  • slow

  • may even stop

• mode of growth

  • grows by expansion

  • usually encapsulated

• no metastasis

• potential for death is low

malignant cancer key characteristics

• cells are

  • poorly differentiated

  • little resemblance to tissue of origin

• rate of growth

  • variable

  • more undifferentiated, more rapid

• mode of growth

  • grows by invasion

• metastasis

  • will spread with access to blood and lymph channels

• potential for death is high

categories of malignant neoplasms: solid tumors

• confined to tissue or organ (ex. lymphoma)

• cells detach from original tumor, invade surrounding tissue, and enter bloodstream/lymphatic system

categories of malignant neoplasms: hematologic cancers

• involve cells already in circulation (ex. leukemia)

categories of malignant neoplasms: carcinoma in situ

• localized, pre-invasion lesion

• has not broken through the basement membrane of the tissue

• more easily targeted

cancer growth: DNA repair defects

• inability of body to repair non-lethal mutations

• proto-oncogenes are repaired and preserved

cancer growth: defects in growth factor signaling pathway

• normally cell proliferation requires signal from growth factor to nucleus

• some cells bypass this

cancer growth: evasion of apoptosis

• normally cells undergo apoptosis to destroy abnormal cells that could lead to malignancy

• cancer cells can avoid apoptosis

• many mechanisms

cancer growth: evasion of cellular senescence

• cancer cells secrete telomerase

• telomerase promotes synthesis of telomere

• prevents the chromosomes from shortening and unraveling

cancer growth: development of sustained angiogenesis

• cancer cells produce vascular endothelial growth factor (VEGF)

• promotes production of new blood vessels

cancer growth: invasion and metastasis

• MET proto-oncogene promotes metastasis

host factors that promote cancer growth: heredity

• genetic predisposition

• BRCA 1 and BRCA2 mutations

• HER2 mutations

host factors that promote cancer growth: hormones

• unclear mechanism

• may be related to stimulation of proliferation of cells with malignant phenotype

host factors that promote cancer growth: immunology

• immune system works to suppress tumors

• white blood cells and antibodies have ability to attack tumor cells and destroy them (NK cells, cytotoxic T cells, etc.)

• cancer survival may be related to impaired ability to suppress tumor growth

  • immunocompromised

  • elderly

environmental factors that promote cancer growth

• chemical carcinogens

  • many due to lifestyle (smoking, diet, alcohol, etc.)

• radiation

  • ionizing

  • ultraviolet (UVA penetrates deeper)

• bacteria

  • helicobacter pylori

• viruses

  • HPV, EBV, HBV

clinical manifestation of cancer

• initial manifestations often associated with disruption of normal parenchymal (functional) tissue

  • cancer of the lung associated with impairment of respiratory function initially

• tumors compress and erode blood vessels

  • may lead to frank bleeding or hemorrhage

• tumors may produce enzymes and toxins that destroy surrounding tissue

• development of effusions (fluid) in peritonea/pleural/pericardial space

anorexia cachexia syndrome and cancer

• an energy imbalance disorder in which energy intake is decreased and energy usage is increased

• loss of appetite and impaired taste associated with cancer (mostly solid tumors)

• hypermetabolic state, protein breakdown and apoptosis of muscle cells

• visualized as muscle wasting

fatigue and cancer

• early sign of malignancy

• multifactorial

• poor sleep quality

anemia and cancer

• multifactorial

• nutritional deficiency

• bone marrow failure

• inflammatory cytokines

• response to chemotherapy

• blood loss or hemolysis

other clinical manifestations of cancer

• GI disturbances

  • diarrhea and stomatitis - due to chemo therapy destroying highly proliferative cells

• alopecia

  • due to chemotherapy destroying highly proliferative cells in hair follicles

• lymphedema

  • accumulation of fluid in tissue 2^o disruptions in lymphatic system due to surgery, radiation or metastasis

• pain

  • intensifies with disease progression - 2^o direct pressure, obstruction, stretching, inflammation

paraneoplastic syndromes and cancer

• cancer can produce manifestations in sites not affected by the primary cancer

• most commonly the result of hormones secreted by the tumor

• most common in lung, breast, and hematologic cancers

screening and diagnosis of cancer

• screening is secondary prevention

• observation, palpation, and lab tests (pap smear, colonoscopy, mammography, PSA testing, etc.)

• had lead to early detection of many cancers

  • identified at earlier stages

  • more easily treated

screening and diagnosis of cancer: tumor markers

types of screening for cancer

• Papanicolaou test

  • microscopic examination for abnormal cells

  • used for cervical cancer and for evaluating body secretions (nipple drainage, pleural/peritoneal fluid) for cancer

• tissue biopsy

  • removal of tissue sample for microscopic evaluation

• immunohistochemistry

  • use of antibodies to detect cell products or surface markers on cancer cells

three factors in cancer staging

• used to determine how advanced cancer is

  • size of tumor (T)

  • degree of local spread to lymph nodes (N)

  • extent of metastases (M)

• this info is usually combined with other factors (tumor marker data, etc) to establish a staging in the four stage system

four stage system in cancer

• stage 0: carcinoma in situ

• stage 1: cancer confined to organ or origin

• stage 2: cancer that is starting to show signs of local spread within local tissue

• stage 3: cancer that has spread to regional nodes

• stage 4: cancer that has spread to distal organs (liver, brain, bone, etc.)

methods of cancer spread

• direct invasion

  • direct extension

  • seeding → one cell breaks free and implants itself somewhere else

• metastasis

  • cancer cell breaks loose and gains access to blood or lymph channel

    • blood → venous system

    • lymph → sentinel node and then adjacent nodes

cancer spread: sites of metastasis

• venous and lymphatic drainage of primary tumor often determines location of metastasis

• not always true

modes of cancer treatment

• surgery

  • often first treatment for solid tumors

• radiation

  • destroy or damage cancer cells by creating free radicals

  • rapidly proliferating cancer cells more susceptible

• chemotherapy

  • prevent cell growth, inhibit DNA, RNA, protein synthesis

• hormone therapy

  • disrupt hormonal environment of cancer cells (antiestrogens, androgen blockers, etc.)

• biotherapy

  • change person’s immune response to cancer