Genetic Pearls - Basic Science

Pediatric Dwarfisms

Genetic Pearls of Skeletal Dysplasia
Autosomal Dominant
Achondroplasia	FGFR-3	Inhibition of chondrocytes proliferation
Apert Syndrome	FGFR-2	Inhibition of chondrocytes proliferation
CMT (80-90%)	PMP22	Nerve demyelination
Pseudoachondroplasia	COMP	Abnormal cartilage formation
SED congenita	COL2A1 / Type II collagen	Defect in cartilage matrix formation
Kniest's Syndrome	Type II collagen	Type II collagen
MED - Type I	COMP	Type II collagen
MED - Type II	Type IX collagen
Jansen's metaphyseal chondrodysplasia	PTHrP	Functional defect in parathyroid hormone
Schmid's metaphyseal chondrodysplasia	Type X Collagen	Defect in cartilage matrix formation
Cleidocranial dysplasia	CBFA-1	Impaired intramembranous ossification
Osteogenesis Imperfecta (Type I, IV)	COL1A1/COL1A2	Type I collagen
Autosomal Recessive
Diastophic dysplasia	DTD (Sulfate Transport Protein)	Defect in sulfaction of proteoglycan
Friedreich's Ataxia	Frataxin
Osteo. Imperfecta (Type II, III)	COL1A1/COL1A2	Type I collagen
McKusick metaphyseal	Unknown
X Linked Recessive
SED tarda	COL2A1	Type II collagen
CMT (10-20%)	connexin gene	Nerve demyelination

Epigenetics

Overview
- epigenetic changes include inheritable genetic alteration (developmental or environmental cues) that do NOT involve DNA mutation
- DNA methylation, histone modification, nucleosome location, or noncoding RNA are components of epigenetics
- osteoarthritis is thought to have epigenetic mechanisms that influence the disease process

Translocations

Overview
- translocations allow expression of genes (oncogenes) that are usually not active.
- cytogenetic analysis allows for the detection of gene translocations by evaluating the size and number of chromosomes isolated from the cell nucleus.
Examples
- present in up to 95% of sarcomas.

Disease	Translocation	Gene
Ewing's sarcoma	t (11:22)	Fusion protein (EWS-FLI1)
Rhabdomyosarcoma	t (2:13)	Pax3-FKHR
Myxoid liposarcoma	t (12:16)	TLS-CHOP
Synovial sarcoma	t (X:18)	SYT-SSX1, 2, or 4 fusion protein
Clear cell sarcoma	t (12:22)	Fusion protein EWS-ATF1
Chondrosarcoma (Myxoid Variant)	t (9:22)	Fusion protein EWS-CHN

Tumor Suppressor Genes

Definition
- inhibit cell proliferation
- therefore a mutation interfering with normal function causes leads to uncontrolled cell growth
Examples
- retinoblastoma protein (pRB-1)
  - acts as a regulator of gene expression
  - recessive suppressor
    - both alleles must be mutated to have uncontrolled growth
  - Rb mutation in
    - 100% of retinoblastomas
    - 35% of osteosarcomas
  - abnormal state is phosphorylated and unable to bind to DNA to regulate
- p53
  - normal protein prevents entrance into S-phase of cell cycle when DNA is damaged
  - dominant suppressor
    - single allele must be mutated to have uncontrolled growth
  - mutation in this gene found in
    - 50% of all tumors
    - osteosarcoma (20-65%)
    - chondrosarcoma

Oncogenes

Definition
- induce uncontrolled growth
- normal function causes leads to uncontrolled cell
Examples
- FAK
  - focal adhesion kinase)
- Erb-2
  - epidermal growth factor variant

Tumor Antigens

Definition
- tumor antigens are used in the diagnosis, monitoring of treatment response, and are being researched for treatment options as anti-cancer vaccines
Examples
- carcinoembryonic antigen (CEA)
  - colorectal carcinoma
- carbohydrate antigen 19-9 (CA-19-9)
  - pancreatic cancer
- carbohydrate antigen 125 (CA-125)
  - ovarian cancer
- cancer antigen 15-3 (CA-15-3)
  - breast cancer
- alpha fetoprotein (AFP)
  - can be seen in many cancers, but is most commonly seen in hepatocellular carcinomas

Assays

Western blot
- detects protein
Southern blot
- detects DNA
Northern blot
- detects RNA
Southwestern blot
- detects DNA binding proteins
RT-PCR
- reverse transcription PCR
- highly sensitive, detects low copy number of RNA
- reversed transcribed into complimentary DNA (cDNA)
- may be used together with Northern blot
siRNA
- blocks translation of mRNA
- useful for loss-of-function experiment designs