Human Gene Final Exam PDF

HUMAN GENE FINAL EXAM Chapter 12: - double -stranded break repair: ionizing radiation, oxidative damage - Photoreactivation: UV exposure - Mismatch repair: replication errors - Damage tolerance: small errors ignored - Excision repair: nucleotide excision repair & base excision re...

HUMAN GENE FINAL EXAM Chapter 12: - double -stranded break repair: ionizing radiation, oxidative damage - Photoreactivation: UV exposure - Mismatch repair: replication errors - Damage tolerance: small errors ignored - Excision repair: nucleotide excision repair & base excision repair → caused by UV exposure If damage is too severe, p53 gene promotes apoptosis DNA repair disorders include: trichothiodystrophy, colon cancer, xeroderma pigmentosum, ataxia telangiectasia Xeroderma pigmentosum: autosomal recessive disorder, malfunction of excision repair ○ Thymine dimers remain & block replication, must avoid sunlight CHAPTER 13: Chromosomes Large-scale chromosomal abnormalities present in all cells disrupt/halt prenatal development ○ 0.65% of newborns have chromosomal anomalies Heterochromatin: darkly staining → consists of repetitive DNA Euchromatin: lighter-staining → consists most protein-encoding genes Telomeres: chromosome tips composed of many repeats of TTAGGG → shorten with cell division P = short arm, q = long arm In a cancer cell, the telomere does not shorten with cell division and instead it remains the same. The cell contains those genetic changes and becomes a malignant tumor due to the non-stop cell division (uncontrolled growth) Karyotype: chromosome chart can display disorders such as trisomy 21 (3 y chromosomes on 21) down syndrome. ○ Performed during mitotic metaphase telocentric : centromere at the tip Acrocentric: centromere close to the center Submetacentric: centromere off-center Metacentric: centromere at center Amniocentesis: needle used to remove a small sample of amniotic fluid from the uterus of a pregnant woman. Administered through the abdomen.Used for chromosome testing in prenatal diagnosis. Can detect a wider range of conditions. Chorionic villus sampling: 10-12th week of pregnancy, earlier results than amniocentesis; does not detect metabolic problems→ greater risk of spontaneous abortion (cells of chorion are sampled/ placental tissue). ○ Catheter is inserted through the cervix Maternal age defect: the later a woman waits to have a child, the older they get, the more likely they are to have a child with a disorder/defect. ○ By age 42, about ⅓ identified pregnancies is trisomic. Risk of miscarriage rises with maternal age.  Cell-free fetal DNA testing: done at 10 weeks or later. Called noninvasive prenatal diagnosis/testing. ○ Conducted via maternal blood sample, maternal and fetal cell-free DNA are separated to analyze chromosomes for disorders Polyploidy: an increase in the number of chromosome sets ○ Triploid (3N) cells have 3 sets of chromosomes (fusion of haploid and diploid gametes). Fertilization of one egg by two sperm (17% of abortions) Aneuploidy: an extra/missing chromosome→ only a single chromosome ○ Monosomy (2n-1) ○ Trisomy (2n+1) ○ Due to nondisjunction during meiosis ○ Autosomal monosomy→ lethal before pregnancy is recognized ○ Autosomal trisomy→ 50% observed in miscarriages, most are lethal except for trisomy 21 Nondisjunction: error that occurs due to failure of chromosome separation ○ during meiosis 1 results in copies of both homologs in one secondary oocyte/spermatocyte and none in the other (abnormal separation of homologs). There are gametes with (n+1) and some with (n-1) ○ During meiosis II results in both sister chromatids in one gamete and none in the other (abnormal separation of sister chromatids). There are gametes with extra (n+1), missing (n-1), and then normal (n) Trisomy 21: Down syndrome, 85% survival rate ○ Most common, distinctive facial/physical problems. Trisomy 18: Edwards syndrome 30 cell cycle breaks) Cause cancer when they are deleted or inactivated Effects of mutations are recessive ○ DNA repair genes Allow other mutations to persist Most DNA repair disorders are inherited in a single gene fashion  Proto-oncogenes: genes that promote cell division ○ Expression at the wrong time of development or place in the body leads them to function as oncogenes → abnormal and overexpressed ○ Activated via point mutation, chromosomal translocation, inversion ○ Gain of function, dominant Viruses that cause cancer: ○ HPV ○ HIV ○ Herpesvirus 8 ○ Hepatitis C ○ Epstein-barr virus Cancer can be caused by loss or silencing of a tumor suppressor gene ○ Usually a deletion that causes a loss of function (recessive) ○ Wilms’ tumor Retinoblastoma: RB is a rare childhood eye tumor ○ Inherited requires mutations/deletions in the RB1 gene on both alleles ○ In sporadic, two somatic mutations occur on each copy of chromosome 13 ○ RB1 protein binds transcription factors so they cannot carry out mitosis → halts at G1/S ○ When RB1 gene is mutant/missing, the hold on TF is released and cell division ensues G1 checkpoint is for DNA damage ○ P53 detects any damage ○ Cdk inhibitor binds with cyclin complex to pause at G1 p53 protein is a TF that determines if a cell repairs DNA replication errors or dies by apoptosis ○ Li-Fraumeni syndrome Family members who inherit a mutation in p53 have a very high risk of developing cancer Inherited vs sporadic cancer ○ Cancer is genetic, not inherited 10% of cases result from inheriting a cancer susceptibility allele from a parent ○ Germline mutations Cancer susceptibility passed onto offspring Cancer develops when second somatic mutation occurs Rare and strike earlier in life than sporadic cancers ○ Somatic mutations Accounts for 90% of cancers Occur spontaneously in non-sex cells Results from a single dominant mutation or two recessive mutations in same gene Cancer susceptibility is not passed on to offspring Characteristics of cancer cells  ○ Cancer cells can move → affect the cytoskeleton (actin filaments) ○ Metastasize: move to a new location in the body ○ Induce angiogenesis: formation of new capillary extensions VEGF: vascular endothelial growth factor Cancer by loss of specialization ○ Cancer may begin when cells lose some of their distinguishing characteristics as mutations occur when they divide ○ Cells on the road to cancer may begin to express stemness genes that override signals to remain specialized ○ *differentiation reverses specialization* ○ Uncontrolled tissue repair may also cause cancer Driver mutation provides the selective growth advantage to a cell that defines the cancerous state ○ Oncogenes or tumor suppressor genes can be generated from abnormal chromosomes ○ 200 genes have driver mutations ○ About 2% of our genes are involved in cell cycle or DNA repair Passenger mutation: do not directly contribute to development/progression of cancerous cells (typically neutral) ○ Does not cause or propel the cancers growth or spread ○ Occurs in cancerous and noncancerous cells ○ 1000 of genes harbor these mutations Three strikes of cancer ○ Breakthrough: 1st driver mutation. Cancer begins in a single cell when oncogene is turned on or a TSG is turned off Cancer trigger ○ Expansion: 2nd driver mutation Cancer cells divide more frequently and survive in environments with scarce nutrients ○ Further mutations in multiple pathways (invasion) Cancerous tumor grows and spreads locally and enters bloodstream ○ *metastasis is not given its own strike stage* Breast cancer can be familial (germline → somatic) or sporadic (two somatic mutations in the same cell) ○ BRCA: two major breast cancer susceptibility genes are BRCA1 and BRCA2 ○ BRCA1 encodes a protein that interacts with other proteins that counter DNA damage. Also controls cellular defense mechanisms ○ BRCA2 mutation increases the risk of developing colon, kidney, prostate, pancreas, gallbladder, skin or stomach cancer. Functions in DNA repair mainly double stranded breaks Liquid biopsy: checks DNA pieces in the blood plasma for oncogene or tumor suppressor mutations ○ Cell-free tumor DNA ctDNA is detected  ○ Can be checked in the urine, sputum, and feces CHAPTER 21: DNA AND RNA technologies In vivo: within a living organism ○ knockout/knockin, transgenic models, reporter models, and disease models Ex vivo, in vitro: outside the organism, in glass or controlled environment ○ Cell models conducted outside an organism on petri dishes In vitro → controlled ○ Cell free ○ Recombinant proteins, in vitro transcription/translation Recombinant DNA technology: (also known as gene cloning) adds genes from one type of organism to the genome of another ○ Makes copies of a specific DNA sequence ○ Insulin was made via recombinant DNA technology ○ Requires three components Restriction enzymes Cloning vectors Recipient cells Selected DNA is inserted into vectors → delivered into cells Creates a recombinant plasmid Sticky ends: Have overhanging single-stranded bases that are complementary to each other, forming hydrogen bonds as base pairs Blunt ends: have no overhanging bases on either side; both strands are cut at the same location Plasmid is a commonly used vector. Bacteriophages, disabled retroviruses, artificial chromosomes from bacteria and yeast. Gene silencing: techniques block synthesis of, or degrade, mRNA Genome editing: create double-stranded breaks in the DNA double helix, enabling insertion of a desired DNA sequence or removal of a sequence “Knock down” means to diminish, “knock out” means to silence RNA interference (RNAi): is a gene silencing technique based on the fact that RNA molecules can fold into short, double-stranded regions where the base sequence is complementary ○ 1) dicer cuts double-stranded RNAs ○ 2) double-stranded RNAs separate and bind RISC and target mRNA ○ 3) target mRNA cut CHAPTER 22: GENETIC TESTING AND TREATMENT Protein-based therapies ○ Enzyme replacement therapy: recombinant human enzyme infused to compensate for deficient or absent enzyme ○ Substrate reduction therapy: oral drug reduces level of substrate so enzyme can function more effectively  ○ Pharmacological chaperone therapy: oral drug binds misfolded proteins, restoring function Germline gene therapy: gamete/zygote alteration; heritable; not done in humans; creates transgenic organisms Somatic gene therapy: corrects only the cells that a disease affects; not heritable Gene therapy invasiveness ○ Ex vivo gene therapy: is applied to cells outside of body that are then returned Via intravenous infusion or into the spinal fluid (ex amniocentesis) ○ In vivo gene therapy: applied directly to an interior body part Through a catheter inserted and snaked to the appropriate organ → most invasive (ex chorionic villi) Viral vectors are created by removing genes that cause symptoms or alert immune system to infection and adding the corrective gene Germline gene therapy uses CRISPR-Cas9 to edit embryos in order to prevent HIV by disposing of CCR5 ADA deficiency: a form of severe combined immune deficiency disease ○ Absence of enzyme causes buildup of deoxyATP→ destroys T cells, B cells not activated Strimvelis: is a form of gene therapy that uses a patient's own haematopoietic stem cells, precursors cells for blood and immune cells, to correct ADA mutation ○ Combo of gene and stem cell therapy Sickle cell disease: single-base mutation in beta subunit causes sickle cell disease ○ One approach increases expression of fetal heme gene ○ Another modifies DNA of the beta globin gene to more like fetal hemoglobin Gene therapy adds correct DNA sequence Gene editing corrects DNA sequences by adding, deleting, or replacing DNA at mutation site CANCER IMMUNOTHERAPY Coley's toxins: toxins that stimulated an immune response ○ Coley found that injecting patients with toxic bacteria killed cancerous tumors → laid groundwork for modern immunotherapy ○ Used both gram (+) and (-) bacteria, heat-killed them to give a attenuated form of the virus so as to not cause actual infections Immune checkpoint inhibitors: block a stranglehold that cancer cells can have on certain T cells, freeing T cells to attack cancer cells ○ CTLA-4 checkpoint proteins prevent dendritic cells from binding to T cells to recognize tumors. Inhibitor drugs block the checkpoint. Discovered by James Allison ○ PD-1 checkpoint protein prevents T cells from attacking cancer cells. Inhibitor drug allows T cells to act. Discovered by Tasuku Honjo CAR (chimeric antigen receptor) T-cell immunotherapy  ○ CAR T improves upon the ability of the immune system to recognize and destroy cancer cells ○ T cell receptor part is engineered to guide the T cell to a specific target like cancer cells ○ Antibody portion binds to the target, altering immune system to respond and kill cancer cells ○ T cell receptor (TCR) mediates T cell activation→ replaces TCR with CAR First cancer patients cured by CAR-T therapy ○ Bill ludwig: 1st patient to receive CAR T-cell therapy to treat chronic lymphocytic leukemia (CLL) ○ Emily whitehead: 1st pediatric patient to receive CAR-T cell therapy to treat acute lymphocytic leukemia (ALL) FDA has approved 7 CAR-T cell therapies (only need 1 time treatment) ○ Anti-CD19 ○ Anti-BCMA (B cell maturation antigen) CASE STUDY PRESENTATION: INSULIN-DEPENDENT TYPE 1 DIABETES Definition: autoimmune disease that occurs when the body’s immune system destroys the cells in the pancreas that produce insulin Symptoms: excessive thirst, weight loss, frequent urination, fast heart rate, excessive hunger, fatigue, blurred vision Genetics ○ HLA genes: HLA-DR, HLA-DQ, HLA-DP ○ CTLA4 gene ○ PTPN22 gene ○ IL2RA and IFIH1 Diagnostic procedures ○ Fasting blood glucose: measures glucose levels after an overnight fast ○ Random blood glucose: measures blood glucose levels at any time of day ○ Hb1A1c test: provides a measure of average blood glucose levels over past 2-3 months Inheritance and transmission ○ Genetic predisposition: individuals with family history if type 1 diabetes ○ Environmental factors: triggers like viral infections or exposure to toxins ○ Disease development: combo of genetic predisposition and environmental triggers Treatment and management ○ Insulin therapy, blood glucose monitoring, diet and exercise CAR T CELL THERAPY CAR engineered T cells reprogram T cells to kill rogue cells High-dose IL-2 therapy ○ IL-2 is a cytokine that was cloned as a T cell growth factor ○ Binding of IL-2 to receptor causes proliferation of T cells  ○ Response is 15% Immune checkpoint inhibitors: ○ anti-CTLA4 ○ anti-PD1 ○ anti-PD-L1 ○ anti-LAG3 Prostate cancer is resistant to immune checkpoint inhibitors ○ Mutation rates activate T cells. Therefore, more mutations cause more T cell activation ○ The prostate has less than 20-30 mutations therefore there is a less chance to activate the immune system. It produces fewer neoantigens, therefore the immune system can not recognize it as foreign and provide a response. This is also bc the prostate is a specialized organ. Called a low mutational burden Limits number for potential targets for CAR-T cells scFv is derived from full length antibody and retains antigen-binding affinity and specificity ○ “Single chain fragment variable” ○ Binds to PSMA mAb Good target for prostate cancer CAR-T cell therapy ○ Cell surface antigen ○ Selectively expressed in prostate cancer ○ Cant be expressed in vital organs PSMA ○ Type 2 transmembrane protein on the cell surface of prostate cancer cells ○ Expressed in normal prostate. Highly overexpressed in prostate cancer ○ Expression is regulated by androgens. ADT increases amount of PSMA on cell surface 5-10-fold ○ 95% of prostate cancers are PSMA (+) ○ Also expressed in blood vessels of solid tumors; not in normal blood vessels CD19 CAR T cell therapy for SLE (systemic lupus erythematosus) ○ Deep deletion of CD119+ B cells and plasmablasts in the tissues could trigger an immune reset in SLE ○ Major concern is that cytokine storm and neurotoxicity could cause severe adverse events ○ Clinical outcomes Rapid remission of refractory SLE Mild cytokine-release syndrome No neurotoxicity Reappearance of B cells Long term abrogation of autoimmunity in SLE patients