Human Genetics Exam 3

define mosaicism

cells within the same person have different genetic makeups due to errors in cell division resulting from mutations within a single zygote

define chimerism

A person who has genetic information from two different sources resulting from the fusion of two or more zygotes

what are epigenetic mechanisms affected by

• development (in utero/childhood)

• environmental chemicals

• drugs/pharmaceuticals

• aging

• diet

define epigenome

complete set of characteristics of epigenetic pathways in an organism

define epigenetics and what can trigger changes in it

how differentiated cells express only the genes that are necessary for their own survival - can be triggered by environmental signals such as stress and diet

when are epigenetic changes preserved

when cells divide

list some epigenetic mechanisms

• DNA methylation

• histone modification

• nucleosome remodeling

• non-coding RNA-mediated pathways

describe epigenetic memory

patterns of DNA methylation and histone modification that are heritable from one cell generation to next

What enzyme is involved in maintenance methylation and how is it transmitted

DNMT-1 DNA methyltransferase1 - transmitted through mitosis to daughter cells

define genomic imprinting

sex-specific epigenetic marking of genes inherited from parental origins via methylation - mammals and flowering plants - keep tags through reprogramming - monoallelic expression

how is imprinting controlled

ICR - imprinting control region

what do many imprinted genes have roles in

early development - embryonic/placental growth and development

is biallelic expression in imprinting possible

yes

describe uniparental disomy

a genetic condition where an individual inherits two copies of a chromosome from one parent and none from the other, instead of the usual one copy from each parent

describe Prader-Willi Syndrome

• 4Mb deletion inherited from father 70% of the time

• or maternal uniparental disomy 25% of the time

• mental retardation, food compulsion, low muscle tone, small hands/feet, dysmorphic facial features

describe Angelman Syndrome

• 4Mb deletion inherited from mother 70% of the time

• paternal uniparental disomy is rare

• gene defects 10-15% of the time

• mental retardation, lack of motor development, epilepsy, no speech, tongue extension, excessive laughter

what enzymes are involved in epigenetic marks and describe their function

• writers -

• erasers -

• readers -

describe epigenetic inheritance

some tags escape reprogramming and are passed from generation to generation - difficult to prove d/t ruling out the possibility of genetic changes - must show that epigenetic effect can pass through enough generations to rule out possibility of direct exposure

describe what the implications of the Dutch Hunger Winter were?

The Dutch Hunger Winter, a famine in the Netherlands during World War II, has been linked to epigenetic changes in individuals conceived during the famine, potentially impacting their health and that of their descendants.

levels of methylation at IGF2 reduced 60 years later

describe what happened to individuals conceived during the famine when they grew older

• few pounds heavier than average

• higher levels of triglycerides and LDL cholesterol

• high rates of conditions such as obesity, diabetes, and schizophrenia

• 10% increase in mortality after 68 years

what is the paternal trans-generational effect

paternal grandfather’s good mid-childhood food supply linked to increased proband diabetic mortality

describe genome engineering versus editing

• genome engineering - refers to DNA being inserted, deleted, or modified in a living cell or organism

• gene editing - usually refers to engineering that is done in a precise targeted manner by introduction of a double strand break

list applications of genome engineering/editing

• function of protein in cells or organisms

• molecular basis of disease alleles

• treatment of human disease

• modification of crops to improve yields or resistance to droughts and disease

forward genetics versus reverse genetics

• forward - identification of mutant phenotype results in gene identification

• reverse genetics - mutation of a certain gene and examination of its functions

what did traditional genome engineering entail

random integration of transposons and viruses for forward genetic approaches

what is transposon mutagenesis

random mutation of model organisms, common way to examine genome

describe gene targeting prior to 2013

• disruption/replacement of gene in a specific manner

• homologous recombination

• high efficiency model organisms such as yeast

what are commonalities to Zinc Finger and TALEN gene editing approaches

• engineered proteins designed to recognize DNA sequences

• DNA binding domains fused to Fok1 endonuclease

• each site requires engineering two proteins - one to cut each strand

• for every site in genome that needs to be modified, new protein must be engineered

what does CRISPR stand for

Clustered regularly interspaced short palindromic repeats

what is CRISPR’s function

serves as part of defense system against viruses in bacteria (50%) and archaea (90%)

describe CRISPR’s mechanism

copies DNA fragment of invading phage and other mobile genetic elements (plasmids and transposons) and inserts it into CRISPR stretch

describe consequences to CRISPR

bacteria and archaea recognize phages and mobile genetic elements upon reinvasion and attack it by cutting its DNA

what are the two components to CRISPR-mediated gene targeting

• Cas9-nuclease that cuts the DNA

• Guide RNA (gRNA) that has a target sequence, structural RNAs that are recognized by Cas9, crRNA and tracrRNA that can be fused into one RNA

what is PAM in relation to CRISPR

photoadjacent motif - a short DNA sequence required for the CRISPR-Cas9 system to bind and cut DNA

what are archaic hominins

• members of genus Homo - humans are the only surviving member

• unifying characteristics of upright walking (bipedalism) and evidence of tool use

describe Homo erectus

• first hominin to leave Africa

• first hominin to use fire

• lots of technological advances

• often considered as ancestral to humans, neanderthals, Denisovans

describe Homo naledi

• most recent discovery in South African cave system

• lots of debate and drama about whether there were deliberate burials

how many high coverage genomes do we have of neanderthals and Denisovans

3 neanderthal and 1 denisovan

what can we do with archaic human genomes

• understand the history and population structure of archaic humans

• look for evidence of gene flow between hominin populations

• identify and characterize archaic regions in modern human genomes

did neanderthals have small or large population sizes and why do we infer this

small - they were highly inbred

how do we identify archaic gene flow events

• comparing archaic and modern human genomes to identify introgressed tracts

• using statistical tools to look for patterns in the genome consistent with archaic introgression

where is Denisovan ancestry concentrated

Asia/Oceania

why did archaic segments in human populations decrease in size and number over time

• deleterious segments were selected against

• neutral segments were lost due to genetic drift

• segment size decreased due to recombination through generations

Describe Hereditary Transthyretin Amyloidosis (TTR)

• autosomal dominant disorder with variable penetrance

• encoded by TTR gene and has >120 pathogenic mutations

• mutation causes protein misfolding and amyloid deposits, causing damage to nerves and organs

TTR treatment options prior to gene therapy

liver transplant - transplanted organ does not produce abnormal protein

goals for gene therapy approaches for TTR

• find molecule to stabilize TTR, prevent misfolding, and stop abnormal proteins from forming

• silence gene that encodes TTR to block production and halt progression of disease

describe Patisiran gene therapy for TTR

• first ever approved RNA-based therapeutic

• utilitizes RNA interference, siRNA

• siRNAs target TTR mRNA

• cleaves wild type and mutated RNA

• formulated in lipid nanoparticles

• intravenous infusion every 3 weeks

what improvements did Patisiran make to TTR

• improvement of motor strength, disability, gait speed, nutritional status, and autonomic symptoms

• improvement in cardiac structure and function in predefined cardiac subpopulation

describe inotersen gene therapy for TTR

• second-generation antisense oligonucleotide (ASO)

• complementary binding in 3’ UTR - no known mutations here

• inhibits synthesis of TTR in liver

• subcutaneous administration

describe TTR stabilizers

Tafamidis

• stabilizes tetramer

• reduces all-cause mortality, cardiovascular hospitalizations, and slows decline in quality of life

• first approval for cardiomyopathy of TTR

Diflunisal

• stabilizes tetramer

describe spinal muscular atrophy SMA

• weakness and atrophy in skeletal muscles - more severe in proximal muscles - usually worsens with age

• autosomal recessive

• Mutation in survival motor neuron 1 gene SMN1 - deletion/point mutation

which type of SMA is most severe

Type 0 - also most rare

Most common form of SMA

Type 1 - Werdnig-Hoffman disease

symptoms Werdnig-Hoffman disease

limited head control, swallowing problems, breathing problems, bell-shaped chest, respiratory failure causing early childhood death

describe SMA type II

• Dubowitz disease

• muscle weakness that develops in children between ages 6 and 12 months

• sitting without support is initially possible

• cannot stand or walk unaided, involuntary trembling (tremors) in fingers, scoliosis, and respiratory muscle weakness that can be life-threatening

• life expectancy varies; many people live into their twenties or thirties

Describe SMA type III

• Kugelberg-Welander disease

• typically causes muscle weakness after early childhood

• can stand and walk unaided, but over time, walking and climbing stairs may become increasingly difficult; often require wheelchair assistance later in life

• often normal life expectancy

describe SMA type IV

• rare, often beings in early adulthood

• mild to moderate muscle weakness, tremors, and mild breathing problems

• normal life expectancy

describe the 2 SMN genes

• nearly identical genes on 5q13

• telomeric copy - SMN1, survival motor neuron

• centromeric copy - SMN2

describe Spinraza treatment for SMA

• antisense oligonucleotide (ASO) - 18 letter string of DNA

• modifies alternative splicing of SMN2 gene

• intrathecal injection

• multiple doses throughout life

describe Zolgensma treatment for SMA

• gene therapy treatment - delivers SMN1 transgene

• intravenous formulation for children <24 months

• one time treatment

describe Evrysdi SMA treatment

• oral medication

• pyridazine derivative

• increases amount of functional survivor motor neuron protein produced by SMN2 gene through splice pattern modification

describe CAR T-cell therapy

• remove blood to get T cells

• make CAR T cells in lab

• grow millions of CAR T cells

• infuse into patient

• CAR T cells bind to cancer cells and kill them

how is CAR T cell therapy used to treat cancer

T cells are genetically altered to have special receptors called chimeric antigen receptors

Describe Elevidys as DMD gene therapy

• uses adeno-associated viral vector for delivery

• shortened, but functional, version of the dystrophin gene to muscle cells

• does not work with certain deletions

describe Casgevy as gene therapy for sickle cell anemia

• also treats beta-thalassemia

• first approved CRISPR-based gene therapy

• deletes DNA to reactivate fetal hemoglobin expression

describe Lyfgenia to treat Sickle Cell Anemia

• uses lentivirus

• insertion of an enhanced B-globin into the patient’s hematopoietic stem cells - this hemoglobin has anti-sickling properties

• black label - blood cancer

1 in ___ humans will develop cancer

3

examples how cancer thrives

• evading apoptosis

• self-sufficiency in growth signals

• insensitivity to antigrowth signals

• sustained angiogenesis

• limitless replicative potential

• tissue invasion and metastasis

>__% of all human genes are implicated via mutation in cancer

1

______ mutated in 50% of all cancers

Tp53

what is senescence

cells cannot divide anymore

fetal cells reach senescence after ___-___ divisions in culture

40-60

how do cancer cells bypass senescence

suppressing tumor suppressors such as p53 and RB1 retinoblastoma protein

how do cancer cells acquire immortality

• divide indefinitely

• expression of telomerase in cancer cells maintains the length of chromosome ends

why are there higher mutation rates of cancer cells

enzymatic systems that repair DNA damage or mistake during replication are often defective

10 acquired properties or hallmarks of cancer

• self-sufficiency in growth signaling

• insensitivity to signals suppressing growth

• ability to avoid apoptosis

• replicative immortality

• genome instability

• induction of angiogenesis

• tissue invasion and metastasis

• ability to avoid immune destruction

• induction of tumor-promoting inflammation

• reprogramming energy metabolism

properties of cancer cells

• readjust their metabolism

• derive energy from glycolysis

• epigenetic programming

• driver and passenger mutations

• development of counter-attacking measures to escape destruction by the immune system

• recruitment of normal cells for support

• metastasis

• angiogenesis

describe how cancer cells readjust their metabolism

• increased flux through pentose phosphate pathway

• elevated rates of lipid biosynthesis

• utilization of high rates of glucose

describe oncogenes

• dominantly acting cancer-susceptibility genes

• often have role in growth signaling pathways to promote cell proliferation or inhibit apoptosis (proto-oncogenes)

  • growth factor

  • receptor

  • transcription factor

  • regulatory protein

  • suppression of apoptosis

• activating mutation in single allele (gain-of-function)

how does a proto-oncogene become an oncogene

gene amplification

how are proto-oncogenes activated

• point mutations - missense mutation

• gain of function mutations

describe epidermal growth factor receptor as it relates to proto-oncogenes → oncogenes

• EGFR or ERBB1

• receptor kinase

• mutation in ATP-binding pocket is common and enhances signal

• mutation promotes uncontrolled growth

describe the ras (rat sarkoma) oncogene family

• human three genes (HRAS, KRAS, NRAS) by working as GTPases and mediating growth signaling

• 1 in 6 human cancers have activating mutation in one of the RAS genes (mostly commonly KRAS

describe enhancer capture in relation to proto-oncogenes → oncogenes

genes located in close proximity to a regulatory sequence

describe microRNAs as oncogenes

• aberrant miRNA expression is very common

• one miRNA can target many mRNA species and single mRNA can be regulated by many miRNAs - difficult to identify specific miRNAs as key players in cancer

________ + _________ results in uncontrolled growth

impairment of DNA damage response plus oncogene proliferation activation

describe tumor suppressor genes

restrain cell proliferation (opposite to oncogenes)

describe gatekeeper genes

tumor suppressor genes that direct control through:

• regulation of cell cycle and induction of cell cycle arrest

• role in upstream growth signaling pathways

• promote apoptosis

describe caretaker genes

tumor suppressor genes that help maintain integrity of the genome

describe landscaper genes

tumor suppressor genes that control stromal environment in which the cells grow

faulty tumor suppressor genes are commonly _________ cancer-susceptibility genes

recessive

describe retinoblastoma

• caused by mutations in RB gene

• inheritance of one RB- copy predisposes to cancer of retina

• often tumors in both eyes

• during proliferation of retinal cells, RB+ allele is lost or mutated

• tumors develop as clone of RB-/RB- cells

how does tumor suppressor gene silencing work

• through mutation

• often silenced epigenetically through methylation

which is more common: microRNA as oncogenes or microRNA as tumor suppressor genes

tumor suppressor genes

why is the two-hit hypothesis not always true for all cancers

• some familial cancers have different mutations than the majority of sporadic cancers (e.g., breast cancer)

• haploinsufficiency leading to one hit being enough

• gain of function mutation

• partial loss of tumor suppressors can make a considerable contribution to tumorgenesis

describe p53

• guardian of the genome

• determines if a cell repairs DNA replication/damage errors or dies by apoptosis

• more than 50% of human cancers involved an abnormal p53 gene

• expressed in virtually all cells

• self-limiting regulation

• non-classical tumor suppressor gene

• Li-Fraumeni syndrome

describe Li-Fraumeni Syndrome

• mutation in Tp53 gene

• causes sarcomas (soft tissue and osteo)

• pediatric leukemias, adrenocortical carcinoma

• breast cancer, brain cancer

• cancer at an earlier age than expected

• diagnosis of more than one cancer over lifetime

• autosomal dominant

• 80% have mutation in T

describe Peutz Jeghers Syndrome

• benign polyps called haramtomas on mucous lining of GI system

• dark blue/brown skin freckling around the mouth, eyes, nostrils, fingers, oral mucosa

• highly increased (up to 93%) risk of developing GI and other cancers

• most patients develop cancer by 5th decade

describe the genetics behind Peutz Jeghers Syndrome

• autosomal dominant

• caused by mutations in STK11/LKB1 gene

• >200 disease-causing mutations reported

• 100% penetrance

• women at higher risk than men

describe Familial Adenomatous Polypsis (FAP)

• multiple colonic polyps, 100% risk colon cancer

• pancreas, thyroid, brain, hepatoblastoma

• autosomal dominant

• caused by mutations in the APC gene

• congenital hypertrophy of the retinal pigment epithelium (CHRPE)

• Gardner syndrome (osteomas)