HSS2305A 2024 Lecture 14 PDF

HSS2305: Molecular Mechanisms of Disease Lecture 14 – Genetics and Disease Prof. Keir Menzies Today’s Outline Announcements Genetics and Disease Genetics and disease Genetic mutations A permanent change in the DNA sequence General Categories 1. Single base pair or point mutati...

HSS2305: Molecular Mechanisms of Disease Lecture 14 – Genetics and Disease Prof. Keir Menzies Today’s Outline Announcements Genetics and Disease Genetics and disease Genetic mutations A permanent change in the DNA sequence General Categories 1. Single base pair or point mutation (also called substitution) 2. Copy number variations: A. Insertions and deletions, which can lead to frameshifts B. Duplication and repeat expansion 3. Chromosomal abnormalities – duplication, inversion, deletion, insertion, translocation, nondisjunction Genetics and disease Genetic mutations A permanent change in the DNA sequence General Categories 1. Single base pair or point mutation (also called substitution) Missense mutation – results in a change in amino acid Nonsense (stop) mutation – results in a premature stop codon Silent mutation – no change in amino acid  Genetics and disease Genetic mutations 1. Single base pair or point mutation *conservative missense mutation is where there is an amino acid change but the properties of the new amino acid resemble the original (hydrophobicity, hydrophilic) Genetics and disease Genetic mutations 1. Point mutation - missense example – Sickle Cell Anaemia https://www.slideshare.net/ShahabRiaz/genetic-disorders-2  Genetics and disease Genetic mutations 1. Point mutation - nonsense (stop) example – Cystic Fibrosis CF Transmembrane Conductance Regulator (CFTR) gene CFTR protein normally helps to maintain the balance of salt and water in many tissues, like the lung. Cystic Fibrosis: chloride becomes trapped in cells. The result is thick mucus that can lead to persistent lung infections and destruction of the pancreas Genetics and disease Genetic mutations A permanent change in the DNA sequence General Categories 1. Single base pair or point mutation (also called substitution) 2. Copy number variations: A. Insertions and deletions (Indels), which can lead to frameshifts Frameshift: Occurs as if the shift is not a multiple of 3 nucleotides Codons after insertion/deletion altered because of shift in nucleotides Genetics and disease Genetic mutations 2. A. Insertion and deletion (indels) mutations Simple Insertion/Deletion Insertion/Deletion Leading to Frameshift Genetics and disease Genetic mutations A permanent change in the DNA sequence General Categories 1. Single base pair or point mutation (missense, nonsense, silent) 2. Copy number variations: A. Insertions and deletions, which can lead to frameshifts B. Duplication and repeat expansion 3. Chromosomal abnormalities – duplication, inversion, deletion, insertion, translocation, nondisjunction  Genetics and disease Genetic mutations 2. B. Duplication example – MYC (responsible for cell growth and proliferation) and cancer The TF MYC is a master regulator, coordinating cell growth and proliferation duplicated in many primary cancers Tansey, New J of Sci, 2014 (ovarian, breast, prostate, squamous cell lung, colorectal, pancreas, renal,)  Genetics and disease Genetic mutations 2. B. Repeat expansion example – trinucleotide repeat & Huntington’s Disease HHT gene plays a crucial role in nerve cell function and normally contains polyglutamine repeats (CAG repeats). >35 CAG repeats due to repeat expansion then this results in protein aggregate formation (protein bundling called inclusion bodies) – toxic and can cause cell death Liou, 2011, Huntington’s Outreach Project for Education, at Stanford Genetics and disease Genetic mutations A permanent change in the DNA sequence General Categories 1. Single base pair or point mutation (missense, nonsense, silent) 2. Copy number variations: A. Insertions and deletions, which can lead to frameshifts B. Duplication and repeat expansion 3. Chromosomal abnormalities – duplication, inversion, deletion, insertion, translocation, nondisjunction Genetics and disease Genetic mutations 3. Chromosome mutation change the number or structure of the whole chromosome Genetics and disease Genetic mutations 3. Chromosomal abnormality examples Down Syndrome: known as trisomy 21 This extra chromosome occurs due to an error in cell division called nondisjunction, which results in the presence of an additional copy of a whole chromosome Normally, each parent contributes one copy of each chromosome during conception, but in the case of nondisjunction, chromosome 21 fails to separate properly. Karyotype Genetics and disease Genetic mutations 3 timepoints where mutations can happen: 1. Hereditary/germline mutations mutations passed from parent to child present throughout a person’s life in virtually every cell in the body 2. De novo mutations mutations that occur during germline development (egg or sperm cell) or immediately after fertilization affected child has a mutation in every cell, but has no family history of the disorder. 3. Acquired/somatic mutations occur in the DNA of individual cells at some time during a person’s life environmental factors (i.e. UV), mistakes during DNA replication Review of Genetics Inheritance Each cell: 2 meters of DNA (6 feet) (3 billion base pairs) 25,000 protein coding genes 46 chromosomes 44 autosomal chromosomes (22 pairs) 2 sex chromosomes (1 pair; X and/or Y)  Review of Genetics Inheritance Ch 15 Ch 15 from father from mother Allele = alternative or variant forms of a gene (B vs. b) Homozygous = two alleles of a given gene are identical (BB or bb) Heterozygous = two alleles of a given gene are different (Bb) Allele for Allele for Dominant allele = always produces eye color eye color its trait when inherited (i.e. B) B- brown b - blue Genotype for eye color = Bb Recessive allele = only produce its → Heterozygous trait when homozygous (i.e. b) → Brown eyes  Genetics and disease Single Gene Disorders Abnormal or missing genes 3 Types of Inherited Single Gene Disorders: 1) Autosomal Dominant 2) Autosomal Recessive 3) Sex-linked inheritance Genetics and disease Single Gene Disorders 1) Autosomal Dominant transmission of a dominant disease causing allele 50% chance of being affected disease appears in every generation males and females equally affected Genetics and disease Single Gene Disorders 1) Autosomal Dominant Case Study: Carl is 25 yrs old and is married to Susan who is pregnant with their first child. Over the past decade Carl’s mother has demonstrated dramatic mood swings and declining dementia-like symptoms, which they attributed to menopause and older age. More recently his mother has had major difficulty in walking. In the past couple months Carl’s brother John, 30, has started showing evidence of paranoia and hallucinations in addition to a generalized lack of coordination. What is happening in this family?  Genetics and disease Single Gene Disorders 1) Autosomal Dominant Huntington’s Disease (HD): Inherited brain disorder Expansion CAG repeat in the HTT gene HTT encodes neuronal huntingtin protein Each child of a parent with HD has a 50% chance of inheriting Symptoms personality disturbances→ depression, apathy, irritability, anxiety, obsessive behaviour cognitive loss → inability to focus, plan, recall or make decisions, impaired insight physical deterioration → weight loss, involuntary movements, diminished coordination, difficulty walking, talking, swallowing leads to complete incapacitation and, eventually, death symptoms usually appear between 30-45yrs no cure ~ 1/7,000 Canadians affected Genetics and disease Single Gene Disorders 1) Autosomal Dominant Case Study: Carl is 25 yrs old and is married to Susan who is pregnant with their first child. Over the past decade Carl’s mother has demonstrated dramatic mood swings and declining dementia- like symptoms, which they attributed to menopause and older age. More recently his mother has had major difficulty in walking. In the past couple months Carl’s brother John, 30, has started showing evidence of paranoia and hallucinations in addition to a generalized lack of coordination. Should Carl be tested? Should his fetus be tested? What are the ethical/moral considerations? Genetics and disease Single Gene Disorders 2) Autosomal Recessive disease manifests when individual is homozygous for the defective allele parents are carriers; they do not have the disease child has a 25% chance of being affected affected children more frequent in close intermarriages (closely related ancestors) males and females equally affected Genetics and disease Single Gene Disorders 2) Autosomal Recessive Cystic Fibrosis: child inherits two defective copies of the gene, one from each parent mutation in cystic fibrosis transmembrane conductance regulator (CFTR) gene protein required to regulate the components of sweat, digestive fluids, and mucus symptoms difficulty breathing wet, rattling cough Severe, chronic lung infections permanent lung damage disease difficulty digesting food → failure to grow 1/3,600 children born in Canada 1/25 Canadians is a CF carrier Genetics and disease Single Gene Disorders 3) Sex-linked X-linked recessive defective gene on X chromosome defective X on male is unmasked and the trait is expressed female is carrier for the disease; heterozygous male transmits the defective allele to his daughters male never transmits to son since only Y chromosome goes to son Genetics and disease Single Gene Disorders 4) Sex-linked Colour blindness: inability/decreased ability to see color, or perceive color differences red/green discrimination mutations in genes that produce photopigments → located on X-chromosome 1 in 10 males affected by some form of color blindness uncommon in females → second X chromosome Genetics and disease Multi-Gene Disorders Familial inheritance: diseases run in families but means of inheritance are not completely understood effects of several genes working together with environmental Male Deceased Affected influences Female Example: pedigree chart: diagram that shows the Diabetes relationships within a family, and it is used to Allergies track the inheritance of specific genetic traits or disorders over multiple generations Review of Genetics Inheritance Each cell: 2 meters of DNA 25,000 genes → code for proteins 46 chromosomes 44 autosomal chromosomes (22 pairs) 2 sex chromosomes (1 pair; X and/or Y) Karyotype = characterization of the chromosome complement → shape, size, number Genetics Karyotype Karyotyping is done to determine whether: parental chromosomes have an abnormality that can be inherited a chromosome defect is preventing a woman from becoming pregnant a chromosome defect is present in a fetus a chromosome defect is the cause of a baby's birth defects identify the sex of a person by determining the presence of the Y chromosome  Genetics Karyotype biological sample → blood, amniotic fluid, placenta Trypsin degrades proteins like histones or anything bound to DNA: Mitogen: Loosens chromosome Encourages structure cells to divide Then G-banding is shown following Giemsa staining – exhibiting light and dark banding of chromosome (fewer A-T Cohchicine arrests cells in bands will be lighter) metaphase (poisons the mitotic spindle) Nuclei swelling, bursting of cells Genetics Karyotype G-banding -allows each chromosome to be identified by its characteristic banding pattern Autosomal chromasomes: numbered from 1 to 22, in descending order by size 46,XX Genetics and disease chromosomal abnormalities 4. Chromosome abnormality missing, extra, or irregular portion of chromosomal DNA can cause problems with a person's growth, development, and body functions Chromosomal diseases disease that results from a chromosome abnormality 1. numerical anomalies → aneuploidy (i.e. monosomy, trisomy) Aneuploidy Presence/absence of 1 or more chromosomes 2. structural anomalies → deletions, duplications, translocations, inversions, insertions error in cell division following meiosis or mitosis germ cells → all cells of body affected somatic cells → mosaicism  Genetics and disease chromosomal abnormalities Review of mitosis – cell duplication cell division occurs in almost all eukaryotic cells division of mother cell into 2 genetically identical daughter cells diploid → n= 46 chromosomes ( 22 pairs; XY)  Genetics and disease chromosomal abnormalities Review of meiosis – reproduction reductive division necessary for sexual reproduction produce gametes → sperm or oocytes haploid → n = 23 chromosomes (one copy of each); males can have X or Y recombination often occurs in meiosis I → genetic shuffle, unique genetic combinations in each gamete https://www.youtube.com/watch?v=zrKdz93W lVk Genetics and disease chromosomal abnormalities Types of Chromosomal Abnormalities: 1. Gamete Nondisjunction In sex cell during meiosis I or II Autosomal chromosomes numerical Sex chromosomes 2. Zygote Nondisjunction After fertilization 3. Chromosome deletions structural 4. Chromosome duplications 5. Chromosome translocations  Genetics and disease chromosomal abnormalities 1. Gamete Nondisjunction: homologous chromosomes in germ cells fail to separate from one another in either 1st or 2nd meiotic division anaphase I/II (of Meiosis I or II) disturbance in spindle structure germ cell can have extra or missing chromosome following fertilization, resulting embryo: Often trisomy lethal monosomy  Genetics and disease chromosomal abnormalities Meiosis I and Meiosis II homologous chromosomes don't separate M1 50% 50% Anaphase I Anaphase II Sister chromatids don't separate n M2 50% n n -1 25% n +1 25% Genetics and disease chromosomal abnormalities Gamete nondisjunction of autosomal chromosomes: autosomal chromosomes (1-22) ~0.2-0.5% of living newborns most are incompatible with fetal survival monosomy generally not compatible with fetal survival trisomies for all chromosomes have been reported only 3 types reported to result in live births ~ 30-50% of spontaneous abortions (miscarriages) result of aneuploidy nondisjunction in oocyte germ cell at least 2X more common than sperm germ cell Genetics and disease chromosomal abnormalities Gamete nondisjunction of autosomal chromosomes: 100,000 PREGNANCIES 15,000 spontaneous abortions (15%) 85,000 live births (85%) Trisomy 1 0 0 2 159 0 3 53 0 4 95 0 5 0 0 6–12 561 0 128 13 17 (~10%) 14 275 0 15 318 0 16 1229 0 17 10 0 223 18 13 (~10%) 19–20 52 0 350 21 113 (~80%) 22 424 0 Genetics and disease chromosomal abnormalities Gamete nondisjunction of autosomal chromosomes: Trisomy 13 - Patau syndrome cleft palate, close-set eyes, decreased muscle tone, severe intellectual disability, seizures, skeletal abnormalities, microcephaly (head size is significantly smaller-brain not fully developed) , congenital heart defects more than 80% of children die in the first year of life 47,XX,+13 Genetics and disease chromosomal abnormalities Gamete nondisjunction of autosomal chromosomes: Trisomy 18 – Edwards syndrome 3X more common in girls low birth weight, mental delay, microcephaly, congenital heart abnormalities, kidney defects more than 50% of children die in the first week of life 47,XX,+18 Genetics and disease chromosomal abnormalities Gamete nondisjunction of autosomal chromosomes: Trisomy 21 – Downs syndrome most common trisomy positively correlated to maternal age distinctive facial features, developmental and social delays, eye problems, congenital heart anomalies can live independent and productive lives well into adulthood 47,XX,+21 Genetics and disease chromosomal abnormalities Gamete nondisjunction of sex chromosomes: failure of proper separation of sex chromosomes (X, Y) in germ cells ~0.2-0.3% of living newborns Phenotype is less severe than autosomal nondisjunction since: X chromosome inactivation in females Y chromosomes have low gene content common signs/symptoms: delay in onset of puberty primary or secondary amenorrhea (absence of menstruation) infertility ambiguous genitalia Genetics and disease chromosomal abnormalities Gamete nondisjunction of sex chromosomes: Klinefelter's Syndrome (XXY): Paternal nondisjunction Maternal nondisjunction ~ 50% ~ 50% Genetics and disease chromosomal abnormalities Gamete nondisjunction of sex chromosomes: Klinefelter's Syndrome (XXY): external genitalia = male, but testicles are atrophic no sperm production → sterile body configuration somewhat female, possible breast hypertrophy intelligence is normal Decreases with > 2 Xs ~1/500-1000 males born in Canada 47,XXY Genetics and disease chromosomal abnormalities Gamete nondisjunction of sex chromosomes: Turner's Syndrome (X0): Paternal nondisjunction Maternal nondisjunction ~ 80% ~ 20% Genetics and disease chromosomal abnormalities Gamete nondisjunction of sex chromosomes: Turner's Syndrome (X0): ~ 50% result from nondisjunction incomplete X chromosome (20%) or mosaic expression (30%) external genitalia = female uterus is small, ovaries contain only fibrous tissue → sterile secondary sex characteristics underdeveloped short stature, broad neck and chest cardiovascular malformations ~1/2,000 females born in Canada 45,X0 Genetics and disease chromosomal abnormalities Gamete nondisjunction of sex chromosomes: Triple X Syndrome (Super-female): Paternal nondisjunction Maternal nondisjunction ~10% ~ 90% Genetics and disease chromosomal abnormalities Gamete nondisjunction of sex chromosomes: Triple X Syndrome (Super-female): ~ 70% of the cases result from nondisjunction at the gamete stage If it happens in a zygote rather than a gamete then it causes mosaic expression (30% of the cases) (some cells affected others are not) phenotype is subtle and can be variable tall stature at adolescence, normal sexual development/puberty, are fertile, no/minor mental deficiencies, may have learning disabilities and or problems with motor coordination associated with advanced maternal age 1/1,400 females born in Canada 47,XXX Genetics and disease chromosomal abnormalities Gamete nondisjunction of sex chromosomes: XYY Syndrome (Super-male): Paternal nondisjunction 100% Genetics and disease chromosomal abnormalities Gamete nondisjunction of sex chromosomes: XYY Syndrome (Super-male): phenotype is usually normal, many males do not know increased growth velocity from early childhood, severe acne in some cases, some learning disabilities, normal sexual development, normal fertility associated with advanced maternal age ~1/1,000 males born in Canada 47,XYY Genetics and disease chromosomal abnormalities 2) Zygote nondisjunction (mitotic nondisjunction) normal, haploid gametes → normal diploid embryo sister chromatids in somatic cell fail to separate during mitosis anaphase with subsequent rounds of mitosis end up with populations of cells with different karyotype → mosaicism examples: Downs syndrome Turners syndrome Triple X syndrome Genetics and disease chromosomal abnormalities 3) Chromosome deletions a part of a chromosome has been deleted during meiosis (often during cross-over) can occur on any chromosome, at any allele, and can be any size (large or small) results of deletion depends on where the deletion is and what genes are missing embryos with significant deletions do not develop to term Genetics and disease chromosomal abnormalities 3) Chromosome deletions Cri Du Chat Syndrome: deletion on short arm of chromosome 5 defect in larynx →high-pitched “cat-cry” intellectual disability, delayed development, microcephaly, low birth weight, and hypotonia in infancy (“floppy”/ reduced strength) distinctive facial features → widely set eyes, low-set ears, small jaw, rounded face some children are born with a heart defect can lead to death in childhood Genetics and disease chromosomal abnormalities 4) Chromosome duplications a part of a chromosome is duplicated during meiosis phenotype results from altered gene dosage genes present in 3 copies → partial trisomy phenotype usually less severe than deletion tandem duplication → duplicated section is adjacent to the original displaced duplication → duplicated sections are separated by non-duplicated regions Genetics and disease chromosomal abnormalities 4) Chromosome duplications Charcot-Marie-Tooth Disease (CMT): It was named after the physicians who discovered it in 1886: Jean-Martin Charcot, Pierre Marie, and Howard Henry Tooth. 70-80% CMT cases → duplication of large region on short arm of chromosome 17 multiple copies of peripheral myelin protein 22 (PMP22) abnormal myelin production causes demyelinating neuropathy – causes nerve damage progressive loss of muscle tissue and touch sensation across various parts of the body. breathing, hearing and vision can be affected in some individuals onset → late childhood/early adulthood symptoms and progression of the disease can vary Genetics and disease chromosomal abnormalities 5) Chromosome translocations piece of one chromosome becomes attached to another chromosome and vice-versa Balanced translocation in somatic cells: no loss or gain of genetic material therefore little effect on function a gene fusion protein may be created when the translocation joins two otherwise separated genes increases likelihood of malignancy process not entirely clear may occur following breakage of chromosomal DNA during normal process of transcription Genetics and disease chromosomal abnormalities 5) Chromosome translocations Unbalanced translocation in gametes: Aberrant meiosis can result in a gain or loss of chromosomal material significant impact on phenotype miscarriages or severe birth defects Genetics and disease chromosomal abnormalities 5) Chromosome translocations Chronic Myelogenous leukemia (CML): Philadelphia Chromosome → portion of chromosome 22 is translocate to chromosome 9 fusion of a protein kinase gene (ABL; Ch9) with a portion of a BCR gene (Ch22) novel fusion protein retains catalytic properties involved in cell proliferation of protein kinase but no longer properly regulated by cell → malignancy Balanced translocation  Diagnosis of Genetic Diseases Early diagnosis is critical to detection and treatment of genetic diseases in some cases, prevention Ex. Phenylketonuria (PKU) autosomal recessive disease managed with dietary adjustment -a rare inherited disorder that causes the amino acid phenylalanine to build up in the body Pre-natal Diagnosis o Amniocentesis (small amount of amniotic fluid) o Chorionic Villous Sampling (small sample of cells taken from placenta) Post-natal Diagnosis o Newborn Blood Sampling o 28 conditions can be identified → metabolic disorder, endocrine disorders, blood disorders, cystic fibrosis  Diagnosis of Genetic Diseases Amniocentesis amniotic fluid withdrawn (14th – 18th week) can detect ~ 200 genetic diseases Chorionic villous sampling removing chorionic villi cells from placental (8th-10th week) Advantage: gives results earlier in the pregnancy Diagnosis of Genetic Diseases (altered levels of AFP (alpha fetoprotein), hCG (human chronic gonadotropin), and Estriol (an estrogen produced by both the fetus and the placenta)  Gene Therapy Gene therapy (genetic engineering) = insertion, alteration, or removal of gene within an individual's cells or tissues to treat disease Limitations: longevity of new gene integration multiple copies of gene insertion immune response to viral vectors multi-gene disorders mutagenesis long term outcomes unclear http://www.youtube.com/watch?v=Ez560GnkSrE&feature=s hare&list=TLjSkTSUlmwTk Next Lecture Genetics and Disease cont. Cell Signalling and G-Coupled Receptors