4- Cancer genetics

• Development Group Problem

  1. If for the light chain there are 380 different V segments and 2 J segments, how many different light chain combinations are possible?

  • 380 X 2 = 760

  2. If for the heavy chain there are 350 V segments, 3 D segments and 8 J segments, how many different heavy and light chain combinations are possible?

  • 350 X 3 X 8 X 760 = 6,384,000
• Normal cells on petri dish grow and divide until they contact each other in a monolayer- growth checked by contact inhibition, cell to cell communication
• Cancer: disease where eukaryotic cells divide uncontrollably and abnormally
• Clonal evolution


  • Tumor cells accumulate somatic mutations that make them increasingly aggressive in their proliferation
  • Rate of clonal evolution determined by frequency of new mutations
• Metastasize


  Cancerous cells can spread through the lymphatic system or blood to other regions of the body
• Oncogenesis


  Cancerous cells can lead to tissue masses called tumors (aka, neoplasm)
• Malignant tumors


  Can spread to other parts of the body, benign tumors are self-contained and do not spread
• 1 in 3 Americans will die of cancer at current rates
• Most cancers are caused by problems with genetic material of the cell
• Cancer is not one disease- thousands of different types caused by different mutations
• Cyclins and cyclin-dependent kinases


  Regulatory molecules that control cell checkpoints
• Signal transduction


  Process of relaying a growth-stimulatory or growth-inhibitory signal after an extracellular factor binds to a cell
• Neoplastic (cancerous) cells


  Cells that divide uncontrollably because of mutations to genes for cell surface receptors, stimulatory factors or inhibitory factors
• Familial cancers


  Some cancers seem to "run in the family" and thus have a hereditary component BUT most cancers are sporadic
• Viruses


  Some viruses introduce their genes into the host, disrupting cell cycle controls
• Mutagens


  1. x-rays, smoking, and chemicals increase the rate of cancer- thus mutations in genes affect risk of cancer
• Chromosomal mutations


  Can lead to cancer- chromosomal breakage affects gene expression crucial for control of the cell cycle
• Viruses


  • Not alive- cannot make energy for themselves, maintain a steady internal environment (i.e., homeostasis), do independent reproduction
  • Must hijack cellular machinery of host cells to replicate themselves
  • Particles of protein and genetic material (either RNA or DNA) that are programmed to invade cells, replicate themselves, and move on to other hosts
  • 5–8% of human genome is endogenous viral elements
• Oncogene


  A gene that causes unregulated cell proliferation- transmitted by RNA tumor viruses (all are retroviruses) into genome of host
• Retroviruses


  Duplicate their RNA genomes through a DNA intermediate using reverse transcriptase

  • example is HIV: human immunodeficiency virus that can cause AIDS (acquired immunodeficiency syndrome)
• Transducing retroviruses


  • Pick up cellular (DNA) genes (often oncogenes) into their RNA genomes, and transfer them to new host genomes
  • Most transducing retroviruses can not self replicate- they need “helper viruses” if the cell is infected with viruses that have replication genes
• Carcinoma


  Epithelial origin (breast, colon, pancreas, and others)
• Sarcoma


  A cancer of the connective or supportive tissue (bone, cartilage, fat, muscle, blood vessels) and soft tissue
• Provirus genome


  When retroviruses invade a cell, the RNA is released, and reverse transcriptase makes a double-stranded DNA copy of the RNA genome
• Self-replicating retroviruses include 3 protein coding genes


  • gag (proteins of virus particle)
  • pol (reverse transcriptase and integrase)
  • env (envelope glycoproteins)
• • Flanking long terminal repeat (LTR) sections include R (repeat) and U (unique) regions- U3 regions for viral promoters & enhancers, U5 regions for RNA cleavage and polyadenylation signals
  • Long-terminal repeats including R, U5 and U3 sequences are ligated together to form a circular, viral cDNA molecule by reverse transcriptase
• Integrase


  Enzyme that makes staggered nicks in the host and viral genomes, and the viral becomes integrated into the host
• • In RSV, the src oncogene transforms the cells they infect
  • RSV is one of the few transducing retroviruses that can also self replicate
• Nononcogenic retroviruses


  Not all retroviruses cause cancer- they direct their own life cycle but do not change the growth properties of the cells they infect
• HIV


  • Nononcogenic retrovirus- the synthesis of DNA from reverse transcriptase is very error prone, which causes many mutations, allowing drug resistance to evolve quickly
  • During viral replication HIV kills the cells it infects (including immune system cells), releasing more virions to infect other cells
  • When immune system cell counts are low, AIDS can develop- can lead to cancer indirectly
• DNA Tumor Viruses


  • Can cause cancer but they do not carry oncogenes like RNA tumor viruses
  • Normally don't induce cancer- virus makes a protein that causes host's cell to replicate DNA virus genome, causing cell lysis
  • If DNA virus genome is not replicated but is incorporated into host genome by mistake- host expresses viral gene for protein that causes DNA replication and cell cannot stop replicating
  • Examples: papovaviruses (HPV), hepatitis B, herpes, adenoviruses, and pox viruses
• Proto-oncogenes


  • In 1975 Michael Bishop & Harold Varmus found some normal animal genes are similar to viral oncogenes- called them proto-oncogenes
  • When proto-oncogenes undergo mutation, they can become oncogenes that induce cancer in normal cells
  • Only one proto-oncogene on a homologous pair of chromosomes is necessary to induce cancer- so the mutations are dominant
  • Proto-oncogene proteins are involved in cell growth and division
• Proto-Oncogene Proteins


  *All involved in positive control of cell growth and division*

  • Growth Factors: causes cells to grow and divide
  • Protein Kinase: enzymes that add phosphate groups to target proteins, thus altering their function (known to affect signaling pathways of cells that are involved with growth factors)
  • Membrane-Associated G Proteins: activated by growth factors to cell membrane receptors- involved in signaling cascade that activates transcription factors for specific genes
• Tumor suppressor genes


  • 1960’s Henry Harris fused normal rodent cells with cancer cells- some of the hybrids did not form tumors and were normal!
  • Found the normal cells had tumor suppressor genes, that can suppress uncontrolled growth of cancerous cells
  • Mutations of tumor suppressor genes are recessive, so both mutant alleles must be present to deactivate uncontrolled growth
  • Inactivation of tumor suppressor genes can lead to cancer of breast, colon, and lung
• TP53 mutations


  • Involved in @50% of all cancers
  • TP53 codes for the p53 transcription factor that interacts with a negative regulator Mdm2- Mdm2 degrades p53 and keeps p53 levels low in normal cells
  • In mutations, the p53/Mdm2 molecules become phosphorylated and cannot bind
  • Too much p53 can activate the WAF1 gene to make p21, which blocks a cyclin needed to move cells from the G1 to S stages
  • p53 also involved in cell apoptosis- or programmed cell death
  • If BOTH TP53 genes are mutated, no p53 is made, WAF1 is not activated, and the cell proceeds to the S stage too soon- also heavily damaged cells cannot undergo apoptosis
• HPV


  Produces proteins called E6 & E7, which bind to p53, leading to tumors in form of warts
• Because every cell has the potential to become transformed, bigger animals with more cells have a higher risk of getting cancer (in theory) BUT elephants are 5X less likely to get cancer than humans

  • Most mammals have 2 alleles of the p53 gene, but elephants have 40- some with slightly varied structures that interact with Mdm2 differently
• Retinoblastoma


  • Retinoblastoma: childhood cancer of the eye before 4 years… 90% treatable
  • Sporadic: (60%) cancer develops with no family history- one eye only; heriditary: (40%) cancer develops because of heredity- often two eyes
  • Herditary form is worse- cancer appears earlier and usually involves BOTH eyes
• Alfred Knudson and Retinoblastoma


  • Alfred Knudson (died July 2016) cancer genetics researcher
  • 1971: proposed a hypothesis (two-hit mutational model) to explain 2 forms of retinoblastoma
  • In sporadic form, two mutations occur in eye cell- rare so it only happens in one eye
  • In hereditary form- one mutation is passed on by heredity- but 2nd mutation occurs in eye cell
  • Developing eye retinas include many cells, and with average mutation rate- it is likely for some heterozygotes to become homozygous recessive

  **Most cancers involve more than one gene**
• Breast Cancer Tumor Suppressor Genes


  • Breast cancer kills 46,000 women a year, but can aflict men too
  • Only 5% of breast cancer is hereditary
  • In hereditary form- mutation of BRCA1 gene can also lead to increased risks of breast and ovarian cancer
  • BRCA1 & BRCA2 involved in DNA repair mechanisms