The human genome and genetic diseases

human genome

- 3.3 B DNA base pairs

- 22 pairs autosomes and 1 pair sex chromosomes (X or Y)

- 1.5% of genome codes for proteins

- 85% genome transcribed into RNA

- 80% genome devoted to regulation of gene expression

non-protein coding sequences

- promoters and enhancers

- noncoding regulatory RNAs (transcribed genes that aren't translated including mircoRNAs and long non-coding RNAs)

- transposons: mobile genetic elements

- telomeres and centromeres: structural regions of DNA

promoters and enhancers

- bind transcription factors

- binding sites for DNA-binding proteins that organize and maintain chromatin structure

epigenetic mechanisms

- covalent modifications of DNA (5-methylcytosine and 5-hydroxylmethylcytosine)

- Post-translational modifications of histones

- 3D chromatin structure

single nucleotide polymorphisms (SNPs)

- variants at single nucleotide positions

- in coding and non-coding regions

- non-coding SNPs may alter the regulation of gene expression

- coding SNPs may change protein sequence

- neutral SNPS have no effect on gene function or phenotype

- effect of individual SNPs on disease susceptibility is weak particularly for complex diseases such as diabetes, heart disease, or cancer

copy number variations (CNVs)

- variation in number of large contiguous stretches of DNA (about 50% CNVs involve coding sequences)

- duplications, triplications, deletions, inversions

mutations in protein-coding genes

mutations are changes in DNA sequence

point mutations (substitution of a single nucleotide base by a different base)

- missense: changes an amino acid

- nonsense: creates stop codon

frameshift mutations: insertion or deletion of 1-2 base pairs alters reading frame of the DNA strand

trinucleotide repeat mutation: amplification of repeated sequence of 3 bases

- repeat expansion/amplification: number of repeats increases during gametogenesis

Other alterations in protein-coding genes

structural variations: genomic rearrangement leads to amplifications, deletions, or translocations of chromosomal segments

- single genes to entire chromosomes

- Intra- or inter- chromosomal

gene editing (CRISPR)

- CRISPRs: clustered regularly interspaced short palindromic repeats

- form of bacterial immunity

- gene editing using artificial guide RNAs that target DNA sequence of interest to introduce mutations

- 1st therapy approved in Dec 2023 to treat sickle cell disease (Casgevy)

epimutations

- changes in epigenetic mechanisms that change gene expression

- can have functional outcomes on gene expression and phenotype/disease

- epigenetic and genetic mechanisms in cancer: inactivation of tumor suppressor genes(promoter hypermethylation) and activation of oncogenes(promoter demethylation)

autosomal dominant: mendelian disorder

- doesn't skip generation

- affected offspring have affected parents

- male and female offspring are equally likely to be affected

- Ehler-Danlos syndrome has abnormal collagen, which is supposed to support structure and extracellular matrix --> dominant or recessive; genetic heterogeneity

- Huntington's disease has Huntingtin (trinucleotide repeat) --> genetic anticipation

autosomal recessive: mendelian disorder

- typically skips generation

- affected offspring may have unaffected parents

- male and female offspring equally likely to be affected

- cystic fibrosis (CFTR-1 abnormal) --> genetic heterogeneity

- sickle cell diseases (abnormal hemoglobin involved in oxygen transport)

x-linked recessive: mendelian disorder

- typically skips generation

- affected sons may have unaffected mothers (carrier)

- affected daughters must have affected father AND affected or unaffected mother

- cannot be passed from father to son

- male offspring more likely to be affected

- fragile X syndrome (FMRP is a trinucleotide repeat and a problem in RNA translation) --> genetic anticipation

Mendelian Disorders: patterns of inheritance

- pleiotropy (1 gene mutation = many phenotype effects)

- genetic heterogeneity ( multiple genes = same trait)

- penetrance (proportion of individuals with the mutation that exhibit clinical symptoms among all individual with such mutation; BRCA1 mutations lead to incomplete penetrance)

- expressivity (degree to which a phenotype is expressed by individuals having particular genotype, like sickle cell anemia)

Cystic Fibrosis

- most common life limiting disease in US that is the disorder of epithelial CFTR (Cl- transporter) in respiratory, GI and reproductive tracts

- recurrent and chronic pulmonary infections

- pancreatic insufficiency

- male infertility

- High NaCl in sweat

- >2000 identified mutations in CFTR: protein production, processing, gating, conduction, and insufficient protein

- F508del: most common CF mutation, ~90% of CF population, protein processing mutation

- 2010: all 50 states adopt universal newborn screening

Trikafta

- approved in 2019 for carriers of the most common variant; expanded to people with CF 2 and older with F508del and 177 other mutations

- treats the defective CFTR in a majority of the CF population

- combinations of ivacafactor (chloride channel opener), and tezacaftor, elexacaftor (CFTR modulators)

- impact: median age of death went from 26 years to 66 years between 2008 and 2022

- 1/5 CF patients died before age 40 in 2022 vs almost 1/2 in 2016

- patients take no additional enzymes, no postural drainage, less inhalations from inhalers, no nebulizers, or ensure when on Trikafta vs not

translocation

Change to a chromosome in which a fragment of one chromosome attaches to a nonhomologous chromosome.

isochromosomes

Chromosomes with identical arms

Form when centromeres divide along the incorrect plane during meiosis

deletions

Mutation involving the removal of one or more nucleotide pairs from a gene

inversions

paracentric and pericentric

ring chromosomes

when telomeres break, becoming sticky and the chromosome connects at each ends with each other. Can cause symptoms

Down syndrome: trisomy 21

- extra copy of chromosome 21; visible on karyotype

- multiple genes disrupted, leading to intellectual disability and other symptoms (40% have congenital heart disease, 10-20 fold increased risk of acute leukemia, predisposed to serious lung infection and thyroid autoimmunity, nearly all down syndrome patients older than 40 have Alzheimer's pathology)

- median age 25 (1983) and is 60 due to improved medical care

Philadelphia chromosome

An abnormal chromosome produced by translocation of parts of the long arms of chromosomes 9 (BCR gene) and 22 (ABL gene)

- almost all people with chronic myeloid leukemia and some people with acute lymphocytic leukemia or acute myelogenous leukemia

- Gleevec: 10 year survival rates increased from <20% to 85%

Fragile X syndrome

- Trinucleotide Repeat (CGG)

- X-linked Dominant

- FMR1 (Fragile X Mental Retardation 1)

Inheritance:

- X-Linked Dominant

- Fragile X-associated tremor/ataxia syndrome and fragile X-associated primary ovarian insufficiency- primarily affects males

- genetic anticipation

genetic anticipation

- clinical features worsen or begin earlier with each successive generation

complex multigenetic disorders

- hypertension/heart disease

- diabetes

- cancer

- autoimmune diseases

- parkinson's disease

- non-disease (hair, eye, skin color, height, intelligence)

- genetic variants, environmental factors and the interaction between them

- polymorphism (genetic variant that occurs in at least 1% of the population)

Common disease-common variant hypothesis

Complex diseases arise when many polymorphisms, each with a small effect and low penetrance, occur together

- different polymorphisms vary in significance

- polymorphisms can be disease-specific or shared by related diseases

- many disease-associated polymorphisms are in noncoding regions, so they may affect epigenetics and regulation of gene expression