Patho 6: Genone + Genetic Diseases

how many autosomes and sex chromosomes are in the human genome?

22 pairs of autosomes

1 pair of sex chromosomes

______% of the genome is transcribed

_______% of the genome is devoted to the regulation of gene expression

Does the majority of the genome consist of protein-coding genes?

80% transcribed

85% regulate gene expression

NO most of the genome is non-protein coding genes

non-coding protein sequences include…

• promoters + enhancers

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

• non-coding regulatory RNAs that are transcribed but not translated (micro-RNA, long non-coding RNAs)

• transposons (mobile genetic elements)

• telomeres + centromeres (structural regions of DNA)

SEQ Gene Transcription (DNA→ RNA)

what is meant by epigenetic mechanisms?

changing gene expression without changing DNA sequences

What are different ways you can change gene expression without having to change the DNA sequence (epigenetics)?

• covalent modifications of DNA

• post-translational modification of histones

• 3d chromatin structure

• non-coding RNA- mediated regulation of transcription/gene

Micro RNAs (miRNAs):

• how many nucleotides make up microRNA?

• can individual miRNA regulate multiple protein-coding genes?

• _____- transcriptional silening of gene expression

• synthetic _________ can knockdown expression of specific target genes

• 21-30

• YES they can regulate entire programs of gene expression

• post

• small interfering RNAs (siRNA)

how many nucleotides make up long-noncoding RNAs?

more than 200

what are long-noncoding RNAs capable of?

1. gene activation

2. gene suppression

   • XIST (X inactive specific transcript)

3. Promote Chromatin modification (methylation, acetylation)

4. stabilize 3D structure and multisubunit complexes

Gene editing using artificial guide RNAs that target a DNA sequence of interest to introduce mutations

CRISPR

how are we able to modify DNA sequences with CRISPR?

Cas9 nuclease targets transcription factor and breaks apart double stranded DNA so you can insert or delete synthetic DNA

what was CRISPR first used for?

alter DNA sequence that causes sickle cell anemia

the mechanism by which an organism equalizes gene expression when different numbers of sex chromosomes are present

ex. x chromosome that encodes for color can be inactivated in some cells

dosage compensation

the presence of two or more cell lineages with different genotypes arising from a single zygote in a single individual

genetic mosaicism

what are SNPs?

polymorphism where single nucleotide is switched

what effect do SNPs on noncoding proteins have on the body?

change in regulation of gene expression

what effect do SNPs on coding proteins have on the body?

can change protein sequence

what effect do neutral SNPs have on the body?

does not impact gene expression or protein sequence

can a single SNP cause significant damage?

NO it is the accumulation of SNPs on multiple different genes on multiple different chromosomes that causes complex disease (diabetes, heart disease, or cancer)

variation in number of large contiguous stretches of DNA

copy number variations

can CNVs or SNPs impact noncoding or coding proteins ?

CNVs can because they are mutations covering LARGE area and coding doesn’t take up that much of the genome but it is more likely to be effected

SNPs cannot because they only effect a single nucleotide and the chances of that being coding is very rare since most of genome is coding

which type of mutations change when and where the gene is expressed?

epigenetic expression

inactivation of tumor suppressor genes and activation of oncogenes are both possible through which type of mutation?

mutation in epigenetic mechanisms

how are tumor suppressor genes activated?

hypermethylation of promoter

how are oncogenes activated?

demethylation of promoter

substituting a single nucleotide base by a different base

point mutation

which type of point mutation changes the amino acid?

missense

which type of point mutation creates a stop codon?

nosense

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

frameshift mutations

amplification of repeated sequence of 3 bases

trinucleotide repeat mutations

what are the 4 structural variations?

1. deletion

2. tandem duplication

3. translocation (move gene)

4. mobile-element insertion

5. inversion (take out DNA and put it back backwards)

which type of genetic disorder is due to a mutation in a single gene?

mendelian

which type of disease arises from changes in the chromosomal number or structure?

cytogenic

which types of diseases arise from single gene mutations with atypical patterns of expression?

non-mendelian genetic disease

which mutations are disease-causing

• mendelian

• cytogenic

• non-mendelian

which mutations are disease-associated

complex disorders

what causes complex disorders (diabetes, heart disease, cancer) ?

multiple gene mutations and environmental influences

one copy of the gene is sufficient to cause disease

autosomal dominant

which type of disease manifests in a heterozygous state?

autosomal dominant

which type of disease manifests in a homozygous state?

autosomal recessive

which disease requires two copies of the gene?

autosomal recessive

are males or females more impacted by sex-linked genetic disorders?

males because females need the gene to be expressed on both of their X chromosomes, males only need the one X chromosome they have to express the gene

can males transmit x-linked diseases to their sons?

NO because fathers give their sons their Y chromosome NOT X

can males or females be carriers of x-linked disorders without having the disease

females

Autosomal Dominant Disorders:

• do these disorders skip generations?

• do affected offspring have affected parents?

• is one gender more likely to get the disease?

• NO

• yes

• no, equally likely

Autosomal Recessive Disorders:

• are generations typically skipped?

• are the parents of the offspring with the disease also affected?

• is there a gender that is more likely to be affected?

• yes

• NO (Both parents may have Aa, but the offspring gets aa)

• no

X-linked recessive disorders:

• do these disorders skip generations?

• do parents also have to have the disease?

• yes

• affected daughters must have a mom AND a dad that are affected to get aa

• affected sons can have an unaffected mother (mother may have Aa and not have disease)

mom gives X dad gives X or Y

if son, that means X is from mom and Y is from dad

if daughter, that means X if from mom X is from dad

how does this relate to x-linked disorders

for daughter needs mom and dad effected so they have BOTH Xs affected

sons cant get from dad because they get their Y chromome from dad NOT mutated X

if sons get the bad X from their mom THATS it becuase they only need one X to be effected

a single gene mutation that has many phenotype differences

pleiotropy

multiple genes cause the same trait

genetic heterogeneity

the proportion of individuals with the mutation that exhibit CLINICAL symptoms AMONG all individuals with such mutations

penetrance

the degree to which a phenotype is expressed by individuals having a particular genotype

expressivity

penentrance is high for which type of disorder?

mendelian (majority of patients experience clinical symptoms)

• Ether Danlos Syndrome

• Hunnington’s Disease

are both examples of which type of inheritance?

generic heterogeneity (many genes cause 1 phenotype)

Ether Danlos Syndrome is caused by a mutation in which protein? How does this protein normally function?

• collagen

• provides structural support in the extracellular matrix

Hunnington’s disease is caused by a mutation in which protein? specifically, what type of mutation is present? how does the protein normally function?

hunington

trinucleotide repeat

function unknown

• Cystic Fibrosis

• alpha and beta thalassemias

• sickle cell disease

involve which type of genetic inheritance?

autosomal recessive

what is an example of an x-linked recessive inheritance?

Fragile X Syndrome

which protein is mutated in cystic fibrosis patients? what does the protein normally do?

cystic fibrosis transmembrane regulator

takes Cl- out of the cell

which protein is mutated in a-b- thalassemias? what does this protein noramlly do?

• hemoglobin

• oxygen transport

whcih protein is mutated in sickle cell disease? what does this protein normally do?

• hemoglobin

• oxygen transport

the traits of cystic fibrosis is accounted for by multiple sets of genes. What is this called?

gene heterogeneity

fragile X syndrome is a mutation in what protein? how does that protein function normally?

FMRP

RNA translation

fragile X syndrome features genetic anticipation. What does this mean?

most likely to impact future generation

how does CTFR normally function?

Na+ and Cl- leave the epithelial tissue

water then arrives to the site of Na+Cl-

outside mucus is less thick due to water

CTFR takes Cl- out of epithelial cell and makes sure Na+ doesn’t leave the airway so they can form NaCl together

What happens in cystic fibrosis?

Cl- unable to leave epithelial cells, cause

how many mutations are identified in CTFR?

more than 2000

what are the five classes of mutations in the CTFR?

1. protein production

2. protein processing (F508del)

3. gating

4. conduction

5. insufficient protein

which class mutation is present in CTFR? what is it called?

protein processing mutation

F508del

cystic fibrosis effects fluid secretion in the lining of the _____________, __________. and _________________ tracts

• respritory

• GI

• reproductive

cystic fibrosis involves recurrent and chronic _________________ infections

_____________________ insufficiency

______________ in males

and high _________in the sweat

pulmonary

pancreatic

infertility

NaCl salt

what are the three parts of Trikafta? what does each do?

1. elexacaftor (CFTR modulator)

2. ivacaftor (chloride channel opener)

3. tezacaftor (CFTR modulator)

Which drug was approved in 2019 for carriers of cystic fibrosis including those with CF2 with F508del and 177 other mutations?

Trikafta

benefits of Trikafta

• increased drug adherance (patient has less drugs to worry about)

• dramatically increased life span of patients from 26-66

what are the five different types of cytogenetic disorders? what is meant by cytogenetic?

1. translocations

2. isochromosomes

3. deletions

4. inversions

5. ring chromosomes

change in chromosome number or structure

What are 4 cytogenetic disorders?

1. trisomy 21 (down syndrome)

2. Philadelphia chromosome

3. Fragile X Syndrome

4. Hunnington’s Disease

explain what down syndrome is? which disease is seen in 40% of down syndrome cases?

a third copy of the 21st chromosome

congenital heart disease

which chromosme includes the genes that encode alzehimers? what does this mean for patients with down syndrome?

21

patients with Down syndrome have an extra 21 chromosome so their chances of getting alzheimer’s are significantly increased

which disease is visible of a karyotype? what is a karyotype?

karyotpe= layout of all of your chromosmes, you can make a karytope by cutting up one cell and gathering all of the chromosomes

if you have trisomy 21 you can see all three chromosomes

the Philadelphia chromosome is a translocation event between which two genes? Where do the two genes come from?

BCR (chromosome 22)

ABL (chromosome 9)

what is the philadelphia chromosome?

combination of ABL which was cut from chromosome 9 and BCR on chromosome 22

together these two segments create the Philadelphia gene in a translocation event

in which diseases do you see the presence of a Philadelphia gene? which drug has increased 10-year survival rates?

• chronic myeloid leukemia

• acute lymphocytic leukemia

• acute myelogenous leukemia

GLEEVEC

trinucleotide (CGG) expansion mutation in the familial mental retardation 1 gene

fragile X sydrome

Fragile X syndrome:

• __________________ expansion mutation in the mamilial mental retardation gene (_________)

• which diseases are associated with the fragile x mutation?

• is there a certain gender that is more likely to be affected?

• what does it mean to be genetically anticipating?

• trinucleotide (CGG) ‘FMR1

• tremor/ataxia and primary ovarian sufficiency

• males

• each generation experiences symptoms earlier

what is the result of 6-55 repeated gene segments of CGG?

what is the result of 55-200 repeated gene segments of CGG?

what is the result of more than 200 repeated gene segments of CGG?

• 6-55 = healthy

• 55-200 reduced protein expression (FTAS)

• >200 = protein expression fully blocked

hunningtons disease is a trinucleotide cytogenetic disease? which three nucleotides are repeated? what does this lead to?

CAG

neurodegenerative movement disorders

how many repeated units of CAG for patients to experience full penetrance?

greater than or equal to 40

what are some examples of multigenic disorders? (accumulation of multiple mutations)

• cancer

• diabetes

• hypertension/ heart disease

• autoimmune disease

• parkinson’s disease

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

what causes complex multigenetic disorders

can polymorphisms on their own lead to complex multigenetic disorders?

many disease-associated polymorphisms are in coding/noncoding regions. can they effect epigenetics?

1. genetic variatiants

2. environmental factors

3. interactions between mutated genes

   • NO

   • noncoding

   • yes polymorphism in noncoding regions can effect gene expression without changing their sequence

complex diseases arise when many _______ each with small effect and low ___________ occur together

polymorphisms

penetrance

a genetic variant that occurs in at least 1% of the population

polymorphism