Fundamentals of Human Genome

What a primary care provider should know about in Genetics

Medical paradigm is changing

Genetic disorders may be treatable

Children w/ genetic disorders often become adults w/ genetic disorders

Clinical decisions will increasingly rely on the results of genetic tests

Family history can be a clue to risk

5 common misconceptions about Genetics

1. Genetics deals w/ only rare disorders

• Deals w/ all types of disorders

2. Children should not be tested for genetic disorders

• Should not be tested for genetic disorders that onset as adults, should be tested for genetic disorders that onset as children

3. Insurance does not pay for genetic testing

• Does pay for genetic testing

4. Genetic testing leads to discrimination

• By law, GINA protects every US citizen of discrimination based on genetic information

5. Genetic disorders are not treatable

• May not be curable, but they are treatable

Mitochondrial genome

Very efficient b/c every gene encodes for something important to the cell’s function

• Know every gene in this and its function

Nuclear genome

• Genes and related sequences: 25% → 5% coding DNA, 95% non-coding DNA

• Other DNA: “junk,” don’t understand it’s function (75%)

  • Has a unique pattern → can be used for paternity test or criminal testing

Gene and related sequences

• Coding DNA: codes for protein

  • Goes through transcription and translation

  • Only mRNA goes through translation (why it’s called coding RNA)

• Non-coding DNA: codes for a functional RNA molecule

  • Does not go through translation

Nucleic acids

• Provide genetic material of cells and viruses

• Sugar + Nitrogenous base + Phosphate group

• 4 types of bases: adenine (A), guanine (G), cytosine, thymine (T) in DNA or uracil (U) in RNA

Genes

DNA segments that carry the genetic information to make proteins or functional RNA molecules within the cells

Genome

Collective term for all the different DNA molecules within a cell or organism, distributed between the nucleus and the mitochondria

• 23,000 to 25,000 protein encoding genes in human genome

  • 100,000 or more proteins

Transcriptome

Total set of transcripts in an organism; expressions of the genes modified by external influences (ex. phosphorylation)

• Collects all the different types of RNAs that come out of DNA, which are the end product of transcription

Proteome

Protein variation & function expressed by a genome, cell, tissue, or organism

Metabolome

Complete set of small molecule metabolites

• Metabolic intermediates, hormones, and other signaling molecules

• Metabolic waste products measured in blood and urine tests: Bilirubin, urea, creatinine

Microbiome (human)

Constellation of viruses, bacteria, and fungi that colonize various human tissues

Deoxyribose sugar

• Does NOT have oxygen at C2

• In DNA

Ribose sugar

• Oxygen at C2

• In RNA

Purines

Double Ring

• Adenine

• Guanine

Pyrimidine

Single ring

• Thymine (in DNA)

• Uracil (in RNA)

• Cytosine

DNA vs. RNA nitrogenous base composition

DNA: contains Thymine

• Thymine is really stable → makes DNA stable

RNA: contains Uracil

• Uracil is really unstable and can make unwanted bonds → makes RNA unstable

Chargaff’s rule

n(G) = n(C)

n(A) = n(T)

Phosphate, deoxyribose sugar, and ribose sugar are connected by ___

Covalent bonds

Phosphate and sugar is connected by a ___

phosphodiester bond

Sugar + nitrogenous base is connected by ___

glycosidic bond

DNA Replication (S phase)

Two strands of the double helix are unwound, and each strand is used to make a new complementary DNA copy

• Semi-conservative b/c, at the end of DNA replication, the newly produced DNA strand has one strand from the parent and one newly synthesized strand

Simple: makes DNA copies that are transmitted from cell to cell and from parent to offspring

Key player in DNA replication

DNA poly III: enzyme that attaches new DNA nucleotides

• High fluidity enzyme that rarely makes a mistake

  • Exonuclease usually fixes any mistakes that occur

  • Failure of exonuclease → DNA repair mechanisms kick in

  • If exonuclease and DNA repair mechanisms fail → apoptosis and cell death → live birth w/ disease

Transcription

Genes are used to make a single-stranded RNA copy that is complimentary in sequence to one of the DNA strands

• Simple: produce RNA copy of a gene

Translation

Coding sequence of mRNA are used to make the polypeptide chain of a protein

• Simple: produces a polypeptide using the information in mRNA

• mRNA: temporary copy of a gene that contains information to make a polypeptide

• Polypeptide: becomes part of a functional protein that contributes to an organism’s traits

Exons

Coding sequences; required for protein coding

• Often contain a small amount of coding DNA

Introns

Noncoding DNA sequences; “useless”

• Have some function but not needed for protein coding → usually gets spliced out b/c they are not wanted part of the code

5’ methylguanosine cap and 3’ poly-A tail function

1. Stability of the primary transcript

• Protect mRNA from degradation by exonucleases

• 5’ methylguanosine cap not added = RNA easily destroyed by the nucleases present in the nucleus

2. Transportation of the primary transcript from the nucleus to the cytoplasm

   1. Transcription happens in nucleus

3. Translation: ribosomes come and bind to start the protein synthesis (translation) process in the cytoplasm

Spicing

Process when introns are cleaved and the exons are tied together; cleaving the RNA transcript at the junctions b/w transcribed exons and introns

• Removes introns, covalently link exons to create mature mRNA

  • Mature mRNA does not contain intron, only contains exons

• Occurs after transcription in the nucleus

Spliceosome

Biomolecule that performs RNA splicing

Alternate splicing

Process of mix-matching exons to make alternate transcripts from the same gene

• Creates multiple variants using different splicing patterns

  • Depending on how exons are attached together, you can make different proteins

• What allows the 25k genes to make more than 100k different proteins

Posttranslational modification: Chemical modification

Additional of functional group to the protein chain

Ex. acetylation, methylation, phosphorylation, etc.

Posttranslational modification: Folding

Proper 3D structure (hydrophilic outside, hydrophobic inside)

• Misfolded protein → increase ER stress → apoptosis

  • No apoptosis → accumulation of misfolded protein, causing cystic fibrosis, Parkinson’s, Alzheimer’s, etc.

Posttranslational modification: Cleavage and transport

• Transport to correct cellular location

  • Intracellular or extracellular locations

• Cleavage: cutting the polypeptide chain after it has been synthesized like tailoring

Posttranslational modification: Binding of multiple polypeptide chains

Ex. Hemoglobin is made of 2 alpha and 2 beta chain, which are produced separately but are bound together b/c Hgb is a polypeptide w/ 4 lobes

Function of Hgb

Carry oxygen

Normal shaped RBCs

Bi-concaved disc → helps RBCs squeeze through tiny vasculature w/o getting clogged

Sickle Cell Disease

RBCs are sickle shape → clog and stop blood supply in the artery, causing painful crisis

Cause of SCD

Point Mutation in beta-globin (glutamate → valine) → Hgb crystallize in low O2 → Pleiotropy (MI, Stoke, Anemia)

• Mutation is in the beta globin chain of the Hgb, NOT RBCs

• Pleiotropy: single gene mutation that can result in a variety of clinical manifestations

SCD protects against ___

falciparum malaria

Rate and degree of sickling depends on 3 things

• Mean cell hemoglobin concentration (MCHC)

  • Higher MCHC = more crowded sickle Hb molecules → more likely to bump into each other and polymerize → faster and more severe sickling

• Intracellular pH

  • High acidity/low pH = more sickling

  • Hgb releases more O2 readily in acidic conditions which makes it in the deoxygenated state for a longer amount of time

• Transit time of RBCs through microvascular beds

  • Longer/slow transit time = more time spent deoxygenated → more sickling

Clinical features of SCD don’t develop until the baby is ___

6 months old

Clinical Features of SCD

• Vasoocclusive crisis → pain crisis (bones, lungs, liver, brain)

  • Pain crisis depends on the blood vessel that is blocked

• Acute chest syndrome, priapism, stroke

• Retinopathy/blindness

• “Autosplenecotomy”: spleen self infarction

  • Sickle cells obstruct blood supply to spleen and it can fall off and be detached

• Chronic hypoxia → generalized impairment of growth and development → organ damage affecting the spleen, heart, kidneys, and lungs

• Altered splenic function → susceptibility to infections

  • Functional splenectomy: spleen is alive but not functioning at all b/c blood supply is partially blocked

    • Spleen not functioning well → prone to infection, specifically w/ capsulated bacteria

SCD Epidemiology

Most prevalent in African countries

1/13 African-descent babies have the sickle cell trait

1/365 African descent babies have sickle cell disease

People w/ SCD typically live ____

A normal lifespan, but it’s difficult to manage as the patient need multiple blood transfusions

Hutchinson-Gilford Progeria Syndrome

Rare, fatal, genetic condition of childhood w/ striking features resembling premature aging

Chances of a child w/ Hutchinson-Gilford Progeria Syndrome

1 in 4-8 million

Only ~100 kids live with this

Cause of Hutchinson-Gilford Progeria Syndrome

Sporadic Autosomal Dominant mutation; LMNA gene mutation

• Appears spontaneously, not inherited from parents

• Happens during the process of embryogenesis

Pathogenesis of Hutchinson-Gilford Progeria Syndrome

Abnormal lamin A (Progerin) → abnormal nuclear envelope → cumulative cellular damage → abnormal aging process

Lamin A (Progerin)

Protein produced in the cytoplasm that is responsible for the proper function of the nuclear envelope

• Farnesyl group is added to guide Lamin A to the nuclear membrane → after reaching the nuclear membrane, the farnesyl group must be cleaved

  • If not cleaved, it causes nuclear envelope instability → disrupt gene transcription → Progeria

Diagnosis of Hutchinson-Gilford Progeria Syndrome happens around ___

2 years old

• At birth, the baby appears normal

People w/ Hutchinson-Gilford Progeria Syndrome typically pass away as a ___ d/t ___ or ____

teen d/t stroke or heart disease

Treatment of Hutchinson-Gilford Progeria Syndrome

Farnesyl inhibitor stopping farnesylation

• NOT ideal

  • May not reach the nuclear envelope b/c farnesylation is required for it to reach the nuclear envelope

• Extends lifespan anywhere from 3 months-2 years

Clinical Features of Hutchinson-Gilford Progeria Syndrome

• Progressive atherosclerosis and associated cardiovascular abnormalities → life-threatening complications

• Old people symptoms: bald, cataract (clouding of eyes), lose elasticity of skin, osteoporosis, arthritis

Other Conditions w/ Lamin A Mutations:

• Emery-Dreifuss MD/Skeletal myopathy

• Progressive AV block and atrial arrhythmias

• Worst prognosis when you have a LMNA mutation and DCM (dilated cardiomyopathy)

  • LMNA mutation w/ DCM is worse than just DCM by itself

Cystic Fibrosis (CF)

Most common lethal inherited disease in Caucasians

Cause of CF

Defect in the CFTR gene leading to misfolded proteins, causing abnormalities of cAMP-regulated chloride transport across epithelial cells on mucosal surfaces

• Inability to conduct chloride properly

Importance of Chloride Channels

Required to maintain the fluid nature of your secretions → flowing freely, liquidy = no obstruction

• Defective → secretions become thick → obstructions → does not reach place it needs to do its function

  • Chloride ions not getting into secretion → sodium and water is also not getting into the secretion → secretions become thick

• In all tissues, the chloride channel conducts the chloride from inside the cell to the outside (lumen) of the cell

  • Except sweat glands are the opposite

Inheritance of CF

Autosomal recessive

Organs affected in CF

Lungs (primary), pancreas, liver, kidneys, and intestines

Effect on Lungs: ↓Cl- transport, ↑Na2+ absorption, ↑H2O absorption, ↓ciliary clearance

GI Symptoms of CF

1. Abdominal distention and Intestinal obstruction

• Not enough water content → abdominal distention, intestinal obstruction, paste-like feces

2. Increased frequency of stools

3. Failure to thrive

4. Flatulence or foul-smelling flatus, steatorrhea (lipid in the poop)

• Lipase stuck in pancreas → lipid not metabolized → steatorrhea

5. Recurrent abdominal pain

6. Jaundice

• Gallbladder is not able to secrete bile → bile accumulation, backing up into the blood → hyperbilirubinemia (jaundice)

7. GI bleeding

• Pancreatic secretions are required to neutralize the acid

  • Acid not neutralized → erode the membrane → GI bleeding

Genitourinary symptoms of CF

1. Undescended testicles or hydrocele

2. Delayed secondary sexual development

3. Amenorrhea (absence of menstrual cycle) in females

4. Infertility in males

• Super thick mucus stops sperm motility

Respiratory Symptoms in CF

Major cause of death in CF → respiratory infection leading to respiratory failure (lung has a lot of secretions that can invite infections)

1. Cough

2. Recurrent wheezing

3. Recurrent pneumonia

4. Atypical asthma

5. Dyspnea on exertion

6. Chest pain

Epidemiology of CF

40-50k Americans live w/ CF

1/2500 live births in North America have the disease

Typically die around 30-40s d/t respiratory depression

MODY (maturity onset diabetes of the young)

Mutation in HNF4A gene –defective transcription→ degradation of mutated transcripts → defective pancreas and beta-cell function → MODY

Inheritance of MODY

Autosomal dominant, Monogenic

Cause of MODY

HNF4A gene mutation → quantity of beta cells and ability to secrete insulin affected

• HNF4A: maintains the pancreatic beta cell mass and function; maintains the proper quantity of beta cells and secrete insulin

MODY is typically suspected in patients ____ years old w/ ___

<30 years old w/ diabetes

Prevalence of MODY

2-5% d/t it being largely undiagnosed d/t not much clinical practitioners knowledge of MODY

T2D

Mutation in PPARa/ABCC8/KCNJ11 gene → defective insulin secretion/sensitivity → Type II DM

• PPARa: transcription factor required for maintaining insulin sensitivity

• ABCC8/KCNJ11: potassium channels required for insulin secretion

Onset of T2D

>40 years old in Caucasians

Inheritance of T2D

Polygenic

T1D

Autoimmune, lack of insulin

Onset of T1D

20s (<30 years old)

Young onset, No autoimmune antibodies in blood test = ___

MODY

Inheritance of T1D

Polygenic

Metformin

Reduce gluconeogenesis, increase insulin sensitivity, reduce insulin resistance

• Metformin, which improves insulin sensitivity, is less effective in MODY as the primary problem is insufficient insulin secretion

Treatment of MODY

Most MODY patients have issues with insulin release rather than insulin resistance, making sulfonylureas more effective

• Use sulfonylureas to start production of insulin before starting use of insulin in their 20s

• Give insulin = chance of hypoglycemia

  • Prevented through giving an oral meds like sulfonylureas as long as they do not have a sulfur allergy