Melanoma screening by means of complete skin exams for all patients in a dermatology practice reduces the thickness of primary melanomas at diagnosis.

OBJECTIVE: Previous studies have shown that dermatologists detect thinner melanomas than both non-dermatologists and patients in high incidence areas. The authors report depths of melanomas in a central New York practice where the incidence is low, hypothesizing that incidental melanomas detected by a dermatologist will be thinner than melanomas that are part of the chief complaint. DESIGN: A retrospective chart review examining melanoma depth to determine the importance of universal full skin exams. SETTING: Private dermatology clinic in Auburn, New York, employing one board-certified dermatologist and two physician extenders. PARTICIPANTS: Men and women who attended the clinic between 2003 and 2013 who had 235 biopsy-proven melanomas. Total patient visits in this time period was 50,699. MEASUREMENTS: Office notes were reviewed to determine the chief complaint, patient demographics, and depth of the tumor. The authors noted if the melanoma was discovered by the patient, a referring physician, dermatology physician extender, or the dermatologist. RESULTS: More than 45 percent of melanomas were an incidental finding on full skin exam. The dermatologist detected statistically thinner melanomas than melanomas that presented as the chief complaint. The dermatologist tended to detect thinner melanomas than referring physicians and patients. CONCLUSION: A significant portion of melanomas are incidentally found on full skin exam, and thinner melanomas are detected by dermatologists. Universal skin cancer screening takes little additional time, and appropriate use of physician extenders can greatly increase access to dermatological care. Full skin exams increase melanoma detection, decreases overall thickness at diagnosis, and decreases patient morbidity and mortality.

Candidate glioblastoma development gene identification using concordance between copy number abnormalities and gene expression level changes.

Copy number abnormalities (CNAs) in tumor cells are presumed to affect expression levels of genes located in region of abnormality. To investigate this relationship we have surveyed the losses, gains and amplifications in 30 glioblastomas using array comparative genome hybridization and compared these data with gene expression changes in the same tumors using the Affymetrix U133Plus2.0 oligonucleotide arrays. The two datasets were overlaid using our in-house overlay tool which highlights concordance between CNAs and expression level changes for the same tumors. In this survey we have highlighted genes frequently overexpressed in amplified regions on chromosomes 1, 4, 11, and 12 and have identified novel amplicons on these chromosomes. Deletions of specific regions on chromosomes 9, 10, 11, 14, and 15 have also been correlated with reduced gene expression in the regions of minimal overlap. In addition we describe a novel approach for comparing gene expression levels between tumors based on the presence or absence of chromosome CNAs. This genome wide screen provides an efficient and comprehensive survey of genes which potentially serve as the drivers for the CNAs in GBM.

Defining the expression pattern of the LGI1 gene in BAC transgenic mice.

The LGI1 gene has been implicated in the development of epilepsy and the invasion phenotype of glial cells. Controversy over the specific tissue expression pattern of this gene has stemmed from conflicting reports generated using immunohistochemistry and the polymerase chain reaction. LGI1 is one of a four-member family of secreted proteins with high homology and here we demonstrate, using GFP-tagged constructs from the four LGI1family members, that commonly used antibodies against LGI1 cross-react with different family members. With the uncertainty surrounding the use of commercially available antibodies to truly establish the expression pattern of LGI1, we generated transgenic mice carrying the LGI1-containing BAC, RP23-127G7, which had been modified to express the GFP reporter gene under the control of the endogenous regulatory elements required for LGI1 expression. Three founder mice were generated, and immunohistochemistry was used to determine the tissue-specific pattern of expression. In the brain, distinct regions of glial and neuronal cell expression were identified, as well as the choriod plexus, which is largely pia-derived. In addition, strong expression levels were identified in glandular regions of the prostate, individual tubules in the kidney, sympathetic ganglia in the kidney, sebaceous glands in the skin, the islets of Langerhans, the endometrium, and the ovary and testes. All other major organs analyzed were negative. The pattern of reporter gene expression was identical in three individual founder mice, arguing against a position effect altering expression profile due to the integration site of the BAC.

Duplication of the entire 22.9 Mb human chromosome 21 syntenic region on mouse chromosome 16 causes cardiovascular and gastrointestinal abnormalities.

Down syndrome is caused by a genomic imbalance of human chromosome 21 which is mainly observed as trisomy 21. The regions on human chromosome 21 are syntenically conserved in three regions on mouse chromosomes 10, 16 and 17. Ts65Dn mice, the most widely used model for Down syndrome, are trisomic for approximately 56.5% of the human chromosome 21 syntenic region on mouse chromosome 16. To generate a more complete trisomic mouse model of Down syndrome, we have established a 22.9 Mb duplication spanning the entire human chromosome 21 syntenic region on mouse chromosome 16 in mice using Cre/loxP-mediated long-range chromosome engineering. The presence of the intact duplication in mice was confirmed by fluorescent in situ hybridization and BAC-based array comparative genomic hybridization. The expression levels of the genes within the duplication interval reflect gene-dosage effects in the mutant mice. The cardiovascular and gastrointestinal phenotypes of the mouse model were similar to those of patients with Down syndrome. This new mouse model represents a powerful tool to further understand the molecular and cellular mechanisms of Down syndrome.

Molecular characterization of the t(3;9) associated with immortalization in the MCF10A cell line.

The t(3;9)(p14;p21) in the MCF10A human mammary gland epithelial cell line was the single cytogenetic event that accompanied the transition from primary culture to immortalized cell line, suggesting that it is related to the development of the immortalization phenotype. To study the molecular consequences of the breakpoints in this rearrangement, we used a combination of fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (CGH). The 3p14 translocation breakpoint occurs within BAC RP11-795e22, which accommodates only the TAFA1 gene, a novel cysteine-rich secreted protein thought to be involved in cytokine signaling. TAFA1 is expressed in normal breast tissue, not in MCF10A, and shows differential expression in a range of breast cancer cell lines. The 9p translocation breakpoint results in a deletion of approximately 4 megabases on the derivative chromosome 9, which includes the CDKN2A (p16) gene. Array CGH and FISH analysis demonstrated that BAC 149i22, which contains the CDKN2A/B genes, is also deleted specifically on the apparently normal copy of chromosome 9, making MCF10A null for the p16/p15 genes. The exact extent of gains and losses of chromosome regions resulting from rearrangements involving chromosomes 1q, 5q, and 8q have also been characterized using the BAC arrays.

Identification of consistent novel submegabase deletions in low-grade oligodendrogliomas using array-based comparative genomic hybridization.

We have analyzed 18 low-grade gliomas using array comparative genomic hybridization (aCGH) with an average resolution of <500 kb. Because the majority of these tumors showed loss of chromosome arms 1p and 19q, we used custom statistical approaches to define submegabase hemizygous losses throughout the genome that correlated with 19q loss. As a result of this analysis, we have identified a approximately 550-kb region in 11q13 and a approximately 300-kb region in 13q12 that showed hemizygous deletion in virtually all the tumors analyzed regardless of their 1p/19q status. FISH analyses of interphase nuclei from the same tumors used for aCGH analysis confirmed the hemizygous loss. The identification of such specific changes provides a potentially very useful diagnostic marker for this subgroup of low-grade tumors. These regions of the genome define small numbers of candidate genes that are within the deletions. The aCGH analysis also defined the spectrum of gain and loss of genomic regions in low-grade oligodendrogliomas.

Molecular characterization of a consistent 4.5-megabase deletion at 4q28 in prostate cancer cells.

Spectral karyotyping of prostate cell lines LNCaP, DU145, PC3, and 22RV demonstrated structural chromosome rearrangements involving the distal long arm of chromosome 4. In all but 22RV, these are nonreciprocal translocations between chromosomes 4 and 10. In 22RV, an apparently reciprocal t(2q;4q) is seen. Fluorescence in situ hybridization analysis of the chromosome 4 translocation breakpoints demonstrated that deletions were associated with all of the translocations, resulting in a net loss of chromosome material. Overlapping deletions in 4q28 approximately 34 were seen in LNCap, DU145, and 22RV, which defined an approximately 4.5-megabase pair common region of deletion. The deletion in PC3 was more proximal on 4q, involving the 4q21 approximately q26 region. A meta analysis of high-resolution definition of losses of chromosome material from published studies demonstrates that loss of 4q material may occur in at least 50% of primary tumors. This analysis defines a series of genes in the critical 4q region, which is potentially associated with prostate tumor development.

Application of bacterial artificial chromosome array-based comparative genomic hybridization and spectral karyotyping to the analysis of glioblastoma multiforme.

Identification of genetic losses and gains is valuable in analysis of brain tumors. Locus-by-locus analyses have revealed correlations between prognosis and response to chemotherapy and loss or gain of specific genes and loci. These approaches are labor intensive and do not provide a global view of the genetic changes within the tumor cells. Bacterial artificial chromosome (BAC) arrays, which cover the genome with an average resolution of less than 1 MbP, allow defining the sum total of these genetic changes in a single comparative genomic hybridization (CGH) experiment. These changes are directly overlaid on the human genome sequence, thus providing the extent of the amplification or deletion, reflected by a megabase position, and gene content of the abnormal region. Although this array-based CGH approach (CGHa) seems to detect the extent of the genetic changes in tumors reliably, it has not been robustly tested. We compared genetic changes in four newly derived, early-passage glioma cell lines, using spectral karyotyping (SKY) and CGHa. Chromosome changes seen in cell lines under SKY analysis were also detected with CGHa. In addition, CGHa detected cryptic genetic gains and losses and resolved the nature of subtle marker chromosomes that could not be resolved with SKY, thus providing distinct advantages over previous technologies. There was remarkable general concordance between the CGHa results comparing the cell lines to the original tumor, except that the magnitude of the changes seen in the tumor sample was generally suppressed compared with the cell lines, a consequence of normal cells contaminating the tumor sample. CGHa revealed changes in cell lines that were not present in the original tumors and vice versa, even when analyzed at the earliest passage possible, which highlights the adaptation of the cells to in vitro culture. CGHa proved to be highly accurate and efficient for identifying genetic changes in tumor cells. This approach can accurately identify subtle, novel genetic abnormalities in tumors directly linked to the human genome sequence. CGHa far surpasses the resolution and information provided by conventional metaphase CGH, without relying on in vitro culture of tumors for metaphase spreads.

The G2028R glycine substitution mutation in COL7A1 leads to marked inter-familiar clinical heterogeneity in dominant dystrophic epidermolysis bullosa.

BACKGROUND: Glycine substitution mutations in COL7A1 not only cause dominant dystrophic epidermolysis bullosa (DDEB), but can also be silent mutations which lead to recessive dystrophic epidermolysis bullosa (RDEB) in combination with additional mutations in the other allele. OBJECTIVE: In this study, we have examined a large American Caucasian pedigree in which 10 family members from four generations presented with simple toenail dystrophy without skin fragility in autosomal dominant manner. METHOD: We sequenced COL7A1 of this pedigree. RESULTS: Mutational analysis indeed detected a heterozygous G-to-A transition at nucleotide position 6082 leading to G2028R in all the affected members. Surprisingly, mutation database revealed that this G2028R mutation had been previously identified in two distinct Asian families with DDEB showing apparent skin fragility and blister formation. One case was a 17-month-old Chinese female with classical phenotype of DDEB and the other was a 27-year-old Japanese female with typical epidermolysis bullosa (EB) pruriginosa. To better understand the molecular mechanisms of this marked inter-familiar clinical heterogeneity, we examined the entire sequence of all the exons and exon-intron borders as well as the promoter region of COL7A1 in all the three families. Sequence results demonstrated no significant nucleotide difference in COL7A1 among the three pedigrees. CONCLUSION: This paper has demonstrated for the first time that identical COL7A1 glycine substitutions can cause remarkably heterogeneous clinical phenotypes extending from simple toe nail dystrophy without skin fragility to typical DDEB and EB pruriginosa. In addition, the fact of inter-familiar, not intra-familiar clinical heterogeneity associated with G2028R suggest that the other molecular mechanisms not controlled by COL7A1 coding sequence might be responsible for the clinical heterogeneity.

Nonsteroidal antiinflammatory drug-induced pseudoporphyria: a case series.

BACKGROUND: Pseudoporphyria is a diagnosis that is used when porphyria-like clinical lesions arise in the setting of normal porphyrin levels. This condition was first described in the 1960s and was initially related to the use of certain antibiotic drugs. In 1985, pseudoporphyria was first attributed to the use of nonsteroidal antiinflammatory drugs (NSAIDs). Subsequently, a host of NSAIDs and other drugs have been found to elicit the same clinical entity. The exact mechanism by which certain drugs create clinical lesions resembling porphyria cutanea tarda or erythropoietic protoporphyria is still unknown. A phototoxic mechanism is hypothesized. OBJECTIVE: We describe six patients diagnosed with pseudoporphyria and detail the diagnostic tests leading to the eventual diagnosis. RESULTS: The patients ranged in age from 27 to 59 years and had a female:male predominance of 2:1. The offending NSAID was DayPro (oxaprozin) for three of the patients, Relafen (nabumetone) for two of the patients, and Aleve (naproxen) for one patient. For each patient, histology and immunofluorescence was either consistent with the diagnosis of porphyria cutanea tarda or nonspecific, while serum, stool, and urine porphyrins did not support that diagnosis. Withdrawal of the offending agent provided relief from the clinical symptoms for each patient. None of our patients were rechallenged with the putative offending drug. However, prolonged avoidance has provided a sustained remission from symptoms in all six patients. CONCLUSIONS: Pseudoporphyria is a relatively rarely reported condition. Clinical suspicion with appropriate laboratory and histopathologic findings help to make this diagnosis, and exclude true porphyrias. Rechallenge with the offending drug to produce symptom relapse has been proposed to be helpful in confirming this diagnosis of exclusion. Since all 6 patients with drug-induced pseudoporphyria experienced resolution of their symptoms after discontinuing the offending agent, we propose that this clinical correlation alone is sufficient to confirm this diagnosis. Our observation of six new cases of NSAID-induced pseudoporphyria over a two-year interval suggests that this is not a rare entity.