Lecture 16 Part II: Smith-Magenis Syndrome

What are the discovery, incidence, and survival facts for SMS?

• 1982: Ann Smith described the 17p11.2 deletion; 1986: Smith + Magenis described the full phenotypic spectrum.

• Incidence: underreported, now estimated 1/15,000.

• Prenatal survival unknown (most diagnoses occur after birth); postnatal life expectancy appears normal.

What is the chromosomal location and why is 17p11.2 prone to deletions?

• Deletion at chromosome 17p11.2 (short arm); autosomal dominant.

• High genomic instability due to LCR elements, Alu repeats, and AT-rich repeats, leading to NAHR and NHEJ.

• Many different deletion sizes all overlap at 17p11.2; smallest region of overlap = critical region = RAI1.

What is the most common genetic cause of SMS?

• ~90%: interstitial deletion at 17p11.2, ranging 1.5 to 9 Mb (size leads to phenotypic variability).

• ~80 genes in the region; was originally considered a contiguous gene syndrome.

• Mostly de novo; rarely inherited via maternal germline mosaicism.

What is the second genetic cause of SMS?

• ~10 to 23% of SMS patients have pathogenic point variants in RAI1 alone (no deletion).

• Mostly nonsense/in-frame mutations in exon 3.

• RAI1 haploinsufficiency alone is sufficient to cause SMS; it is the causative gene.

What is RAI1 and what does it normally do?

• RAI1 = Retinoic Acid-Induced 1; transcriptional regulator highly expressed in hippocampus and cerebellum.

• Contains a PHD domain that binds and remodels chromatin.

• Maintains brain homeostasis by regulating synaptic plasticity: upscales connections when activity is low, downscales when activity is high.

What are the craniofacial and multisystemic phenotypes of SMS?

• Craniofacial: broad forehead, brachycephaly, midface retrusion, short upturned nose, short philtrum, downturned lips with tent-shaped vermilion, upslanting palpebral fissures; micrognathia in infancy can progress to prognathism; features worsen with age.

• Ocular: 50% microcornea, 67% iris abnormalities, myopia.

• Hearing: 79% hearing loss; cardiovascular: 25 to 45% congenital heart defects.

• Immunologic: 60% impaired antibody production; musculoskeletal: scoliosis, brachydactyly, constipation.

What are the neurobehavioral phenotypes of SMS and how do they differ by genotype?

• RAI1 haploinsufficiency causes: self-injurious behaviors (95%), repetitive actions (95%), self-hugging (51%), eating disorders, seizures, inverted melatonin secretion/sleep disruption.

• Cognitive level ~6 to 8 years; emotional level ~1 to 3 years.

• RAI1 variant only: primarily neurobehavioral (obesity, eating disorders, self-hugging, skin picking).

• 17p11.2 deletion: multisystemic on top of neurobehavioral (cardiac/renal anomalies, motor delay, short stature, hearing loss).

What are the stage-specific phenotypes of SMS?

• Infant: hypotonia, lethargy, feeding difficulties, failure to thrive.

• Toddler: speech delay, short stature, brachydactyly.

• Preadolescent: overeating, weight >95th percentile, moderate intellectual disability, hyperactivity.

• Adult: more pronounced facial features, persistence of all cardinal SMS features.

What is the differential diagnosis challenge for SMS?

• Only ~50% of individuals with clinical SMS suspicion actually have the SMS genotype.

• Mimics share: intellectual disability, behavioral delay, circadian disruptions, craniofacial abnormalities.

• Why: all associated loci are part of the RAI1 regulatory network (same neurodevelopmental/circadian pathways).

What is the suggested diagnostic approach for SMS?

• Step 1: Array-CGH to look for 17p11.2 deletion or other pathogenic CNVs.

• If negative: WES filtered for RAI1, MBD5, HDAC4, TCF20.

• If still negative with strong clinical suspicion: RAI1 RT-qPCR to check for regulatory/expression variants.

What is MLPA and why is it used in SMS?

• Multiplex Ligation-Dependent Probe Amplification: detects copy number variants (deletions/duplications).

• Probes hybridize to target DNA; ligation only occurs with perfect base pairing, then PCR, then capillary electrophoresis.

• Multiple sequences run simultaneously ("multiplexing"); powerful tool for detecting 17p11.2 CNVs.

What are the current treatments for SMS?

• No cure; personalized medicine.

• Sleep: melatonin, tasimelteon, good sleep hygiene.

• Behavioral: risperidone (hyperactivity/maladaptive behavior), methylphenidate (hyperactivity), clonidine (ADHD/sleep).

What was the hypothesis and approach of the rAAV-CRISPRa study?

• RAI1 is too large to fit in a standard rAAV, so the gene cannot be replaced directly.

• Instead: dCas9 (no DNA cutting) + transcriptional activator + sgRNA targeting the Rai1 promoter to upregulate the remaining functional allele.

• sg2 selected as most effective guide; injected bilaterally into the PVH of SMS mice.

What were the results of the rAAV-CRISPRa study?

• Normalized excessive repetitive rearing.

• Partially rescued obesity (reduced food intake).

• Did not improve social dominance deficits (requires broader brain targeting beyond PVH).

• Significance: novel approach targeting regulatory elements of a haploinsufficient gene rather than inserting/deleting whole genes.