GENOMIC DRIVERS OF CUTANEOUS SQUAMOUS CELL CARCINOMA DEVELOPMENT

Skin cancer is the most common malignancy in humans. Annually, in U.S. there are over 3 million cases with an estimated overall economic impact of $2 billion. Cutaneous Squamous Cell Carcinoma (cuSCC) comprises 15-20% of all skin cancers. cuSCC has the best-defined progression from a distinct precancerous lesion, the Actinic Keratosis (AK), to invasive cuSCC. Destructive therapies for AK treatment must be used repetitively, causing significant morbidity. There is a tremendous need for targeted diagnostics and therapy for AKs, representing an important opportunity for secondary skin cancer prevention. Our knowledge of the molecular and cellular events that lead to the transformation of normal skin (NS) to AK and subsequently to cuSCC is very limited, thus representing a fundamental gap in our understanding of this progression. In order to identify novel targets for molecular chemoprevention, we used isogenic human samples throughout cuSCC development and a UV-driven Hairless mouse model of cuSCC to identify genomic drivers of cuSCC by cross-species analysis. RNA-Seq identified 349 transcripts that were differentially expressed across normal skin (NS), AK, and cuSCC. mRNA profiles primarily distinguished NS from other samples, whereas microRNA profiles could segregate the three groups. Using cross-species functional pair analysis (anti-correlated miRNA-mRNA expression) we identified several miRNAs (miR-21,-31,-221) and their targets as major promoters of cuSCC development. TRANSFAC analysis identified ETS2, MAZ, and TCF3 as core transcriptional drivers of progression. Whole exome sequencing demonstrated that UVB signature mutations dominate in AKs and cuSCCs, with frequent mutations in TP53, NOTCH1/2, and CDKN2A, as previously reported. Surprisingly, NS samples adjacent to the cuSCCs had up to 1200 mutations with no significant overlap with cuSCC. Ingenuity Variant Analysis identified NOTCH and its coactivators as the functional modules most perturbed in cuSCCs. Because cuSCC shares commonly mutated genes with lung SCC and head & neck SCC (HNSCC), we assessed the global similarity of gene expression to other cancers. By this measure, cuSCC is most similar to HNSCC and its mRNA signature predicts survival in non-HPV-related HNSCC. cuSCC is also similar to lung SCC as well as basal subtype of breast cancer. Our cross species analysis has identified key genomic drivers of cuSCC development as potential chemoprevention targets and suggests that our model can serve as the basis for validating chemoprevention targets in cuSCC and molecularly similar cancers such as HNSCC and lung SCC. Through our initial analysis of 9 sets of matched samples, we identified miR-181a as a potential molecular target; expression of the miR-181a family gradually increases throughout cuSCC progression. Importantly, miR-181a is significantly upregulated in multiple carcinomas. We have focused on the function of TGFΒR3, which is downregulated by miR-181a and which has a tumor suppressor role in many contexts. We hypothesize that upregulation of miR-181a promotes initiation and progression of keratinocyte transformation by targeting TGFΒR3. Comparison of miR-181a levels in human cuSCCs to normal skin shows that miR-181a has a significantly higher expression (~8.4 folds) in cuSCCs. Our results show that miR-181a overexpression (OE) and TGFΒR3 knockdown (KD) significantly suppresses UV-induced apoptosis in HaCaT keratinocytes and in primary normal human epidermal keratinocytes (NHEKs). In addition, OE of miR-181a or direct KD of TGFΒR3 by shRNA is sufficient for enhanced anchorage-independent survival of HaCaTs. Moreover, miR-181a OE or TGFΒR3 KD enhances cellular motility through increase of migration and invasion and upregulation of EMT markers, such as snail, slug, and vimentin. Luciferase assay results demonstrate that miR-181a directly and specifically targets the 3’UTR of TGFBR3. Rescue experiments show that miR-181a phenotype can be partially rescued by TGFBR3 overexpression. In summary, we show that miR-181a regulates susceptibility to apoptosis as well as cellular adhesion and motility at least in part through TGFΒR3

The Syndrome Of Perisylvian Polymicrogyria With Congenital Arthrogryposis

Background: Bilateral perisylvian polymicrogyria (BPP) is a well-recognized malformation of cortical development commonly associated with epilepsy, cognitive impairment, and oromotor apraxia. Reports have suggested the association of BPP with arthrogryposis multiplex congenita. We sought to investigate the clinical, electrophysiological, and neuroradiological features of this combined syndrome to determine if there are unique features that distinguish BPP with arthrogryposis from BPP alone. Methods: Cases of BPP with congenital arthrogryposis were identified from a large research database of individuals with polymicrogyria. Clinical features (including oromotor function, seizures, and joint contractures), MR brain imagine, and results of neuromuscular testing were reviewed. Results: Ten cases of BPP with congenital arthrogryposis were identified. Most cases had some degree of oromotor apraxia. Only a few had seizures, but a majority of cases were still young children. Electrophysiological studies provided evidence for lower motor neuron or peripheral nervous system involvement. On brain imaging, bilateral polymicrogyria (PMG) centered along the Sylvian fissures was seen, with variable extension frontally or parietally; no other cortical malformations were present. We did not identify obvious neuroimaging features that distinguish this syndrome from that of BPP without arthrogryposis. Conclusions: The clinical and neuroimaging features of the syndrome of BPP with congenital arthrogryposis appear similar to those seen in cases of isolated BPP without joint contractures, but electrophysiological studies often demonstrate coexistent lower motor neuron or peripheral nervous system pathology. These findings suggest that BPP with arthrogryposis may have a genetic etiology with effects at two levels of the neuraxis. (C) 2009 Elsevier B.V. All rights reserved.Wo

SLC25A22 is a novel gene for migrating partial seizures in infancy

ObjectiveTo identify a genetic cause for migrating partial seizures in infancy (MPSI).MethodsWe characterized a consanguineous pedigree with MPSI and obtained DNA from affected and unaffected family members. We analyzed single nucleotide polymorphism 500K data to identify regions with evidence of linkage. We performed whole exome sequencing and analyzed homozygous variants in regions of linkage to identify a candidate gene and performed functional studies of the candidate gene SLC25A22.ResultsIn a consanguineous pedigree with 2 individuals with MPSI, we identified 2 regions of linkage, chromosome 4p16.1-p16.3 and chromosome 11p15.4-pter. Using whole exome sequencing, we identified 8 novel homozygous variants in genes in these regions. Only 1 variant, SLC25A22 c.G328C, results in a change of a highly conserved amino acid (p.G110R) and was not present in control samples. SLC25A22 encodes a glutamate transporter with strong expression in the developing brain. We show that the specific G110R mutation, located in a transmembrane domain of the protein, disrupts mitochondrial glutamate transport.InterpretationWe have shown that MPSI can be inherited and have identified a novel homozygous mutation in SLC25A22 in the affected individuals. Our data strongly suggest that SLC25A22 is responsible for MPSI, a severe condition with few known etiologies. We have demonstrated that a combination of linkage analysis and whole exome sequencing can be used for disease gene discovery. Finally, as SLC25A22 had been implicated in the distinct syndrome of neonatal epilepsy with suppression bursts on electroencephalogram, we have expanded the phenotypic spectrum associated with SLC25A22

Genomewide Clonal Analysis of Lethal Mutations in the Drosophila melanogaster Eye: Comparison of the X Chromosome and Autosomes

Using a large consortium of undergraduate students in an organized program at the University of California, Los Angeles (UCLA), we have undertaken a functional genomic screen in the Drosophila eye. In addition to the educational value of discovery-based learning, this article presents the first comprehensive genomewide analysis of essential genes involved in eye development. The data reveal the surprising result that the X chromosome has almost twice the frequency of essential genes involved in eye development as that found on the autosomes