PRAME induces genomic instability in uveal melanoma

PRAME is a CUL2 ubiquitin ligase subunit that is normally expressed in the testis but becomes aberrantly overexpressed in many cancer types in association with aneuploidy and metastasis. Here, we show that PRAME is expressed predominantly in spermatogonia around the time of meiotic crossing-over in coordination with genes mediating DNA double strand break repair. Expression of PRAME in somatic cells upregulates pathways involved in meiosis, chromosome segregation and DNA repair, and it leads to increased DNA double strand breaks, telomere dysfunction and aneuploidy in neoplastic and non-neoplastic cells. This effect is mediated at least in part by ubiquitination of SMC1A and altered cohesin function. PRAME expression renders cells susceptible to inhibition of PARP1/2, suggesting increased dependence on alternative base excision repair pathways. These findings reveal a distinct oncogenic function of PRAME that can be targeted therapeutically in cancer.

PRAME induces genomic instability in uveal melanoma

PRAME is a CUL2 ubiquitin ligase subunit that is normally expressed in the testis but becomes aberrantly overexpressed in many cancer types in association with aneuploidy and metastasis. Here, we show that PRAME is expressed predominantly in spermatogonia around the time of meiotic crossing-over in coordination with genes mediating DNA double strand break repair. Expression of PRAME in somatic cells upregulates pathways involved in meiosis, chromosome segregation and DNA repair, and it leads to increased DNA double strand breaks, telomere dysfunction and aneuploidy in neoplastic and non-neoplastic cells. This effect is mediated at least in part by ubiquitination of SMC1A and altered cohesin function. PRAME expression renders cells susceptible to inhibition of PARP1/2, suggesting increased dependence on alternative base excision repair pathways. These findings reveal a distinct oncogenic function of PRAME than can be targeted therapeutically in cancer.

Effect of the cold pressor test on coronary flow reserve by cardiac magnetic resonance in patients with hereditary TTR+ amyloidosis

Background

Cold pressor test (CPT) is a potent alpha-adrenergic vasoconstrictor stimulus and evaluates the sympathetic reactivity of the cardiovascular system during the immersion of a hand in cold water, its effect on coronary flow reserve (CFR) in patients with hereditary TTR+ amyloidosis is unknown.

Purpose

To evaluate CFR by CPT in hereditary TTR+ amyloidosis patients with different cardiac involvement regarding the distribution of late gadolinium enhancement (LGE) by cardiac magnetic resonance imaging (CMRI) and compare with healthy volunteers

Methods

It was a cross-sectional study of 22 hereditary TTR+ amyloidosis patients with different patterns of LGE (absence/minimum or extensive involvement), and 4 healthy controls without LGE. CPT was performed with immersion of one hand in four Celsius degrees temperated water. Phase-contrast images were acquired on rest and during stress (after four minutes of a hand immersion). Volume quantification was made in posterior analysis to determine flow differences.

Results

No statistically significant differences were found regarding left ventricular (LV) volumes, LV mass, LV ejection fraction, and atrial volumes comparing the three groups of patients. CFR was abnormal in both groups of TTR+ amyloidosis patients compared with higher values in healthy subjects. Nevertheless, no statistically significant differences were determined.

Conclusions

Hereditary TTR+ amyloidosis subjects presented with abnormal values of CFR even with minimal or non-LGE by CMRI in the setting of infiltration. This response hypothesized small vessel involvement due to early infiltration by amyloid deposits before LGE development.

Funding Acknowledgement

Type of funding sources: None.

Impact of Genetic Ancestry on Prognostic Biomarkers in Uveal Melanoma

Simple Summary

Genomic prognostic biomarkers play an important role in the application of precision medicine in patients with uveal melanoma (UM). In this study, we performed a pilot study to assess the impact of global and local genetic ancestry on the presence of these prognostic biomarkers. We found a trend for correlations between high risk biomarkers and European ancestry. These results highlight the need for a rigorous genetic ancestry methodology to study the role of ancestry in determining prognosis in patients with UM.

Abstract

Uveal melanoma (UM) is the most common cancer of the eye and leads to metastatic death in up to half of patients. Genomic prognostic biomarkers play an important role in clinical management in UM. However, research has been conducted almost exclusively in patients of European descent, such that the association between genetic admixture and prognostic biomarkers is unknown. In this study, we compiled 1381 control genomes from West African, European, East Asian, and Native American individuals, assembled a bioinformatic pipeline for assessing global and local ancestry, and performed an initial pilot study of 141 UM patients from our international referral center that manages many admixed individuals. Global and local estimates were associated with genomic prognostic determinants. Expression quantitative trait loci (eQTL) analysis was performed on variants found in segments. Globally, after correction for multiple testing, no prognostic variable was significantly enriched in a given ancestral group. However, there was a trend suggesting an increased proportion of European ancestry associated with expression of the PRAME oncogene (q = 0.06). Locally enriched European haplotypes were associated with the poor prognosis class 2 gene expression profile and with genes involved in immune regulation (q = 4.7 × 10⁻¹¹). These findings reveal potential influences of genetic ancestry on prognostic variables, implicate immune genes in prognostic differences based on ancestry, and provide a basis for future studies of admixed patients with UM using rigorous genetic ancestry methodology.

Abstract 1591: Single cell analysis of uveal melanoma reveals new evolutionary complexity

Uveal melanoma (UM) is a highly metastatic cancer that is largely unresponsive to molecular and immune therapy. We used scRNA-seq and other methods to analyze 59,915 tumor and non-neoplastic cells from 8 primary and 3 metastatic UMs. This analysis confirmed the class 1/class 2 transcriptomic landscape established from bulk analysis and revealed newly identified subclonal genomic complexity and transcriptional states consistent with phenotype plasticity. The immune compartment comprised a previously unappreciated diversity of cell types. There was low expression of CTLA4 and PD1, but strong expression of a different checkpoint molecule. These findings revealed a dynamic ecosystem in which UM and immune cells co-evolve along trajectories associated with specific genomic aberrations, and they may explain the poor response of UM to current immunotherapy regimens. We identified a new promising candidate for immune checkpoint blockade in metastatic UM.

Citation Format: Michael A. Durante, Daniel A. Rodriguez, Stefan Kurtenbach, Jeffim N. Kuznetsoff, Margaret I. Sanchez, Christina L. Decatur, Helen Snyder, Lynn G. Feun, Alan S. Livingstone, J. William Harbour. Single cell analysis of uveal melanoma reveals new evolutionary complexity [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1591.

Cutaneous melanoma mutation pathways and driver mutations as racially biased

e22066

Background: Cutaneous melanoma (CM) demonstrates differences in its clinical prevalence in different racial groups. CM generally exhibits a high tumor mutational burden (TMB) and mutually exclusive driving mutations in NRAS, BRAF or KIT. TMB may be driven by different pathways including ultraviolet radiation (UVR), oxidation and deamination. UVR is the most common mutational signature found in CMs, but deamination and oxidation are also present. Methods: We analyzed 321 CMs exome data from The Cancer Genome Atlas network. BRAF, NRAS, KIT and those without (WT) were used to divide the melanomas. Germline SNPs with racial information (Caucasian, African and Asian) that were enriched in melanomas with a particular driving mutation were identified. Results: We compared the 3 racial groups across the 4 driving mutation types, Asian SNPs were significantly higher in KIT, African in WT and Caucasian in BRAF and NRAS. The melanomas were also evaluated by the type of substitution mutations including CC > TT for UV, G > T for oxidative damage and (G/A)C (G) > (G/A)T(G) for deamination. UV and deamination appeared inversely proportional, while oxidative damage appeared to be independent. UV signal was more prominent in BRAF and NRAS groups. KIT had a greater percentage of deamination while WT revealed more oxidative damage. We further compared UV and non-UV (CC > TT absence) KIT subgroups for racial differences. Asian SNPs were greatly increased in non-UV subgroup whereas Caucasian SNPs were in UV subgroup. Further, the non-UV KIT subgroup was divided into deamination and oxidative damage subgroups to compare racial differences. Deamination was significantly increased in Asians whereas oxidative damage was higher in Caucasians. In the case of the WT group, African SNPs were significantly higher in the non UV subgroup and were primarily correlated with oxidative damage. Conclusions: This study suggests that racial genetic background may predispose the distinctive mutational and genetic environments of melanoma development.

Single-cell analysis reveals new evolutionary complexity in uveal melanoma

Uveal melanoma (UM) is a highly metastatic cancer that, in contrast to cutaneous melanoma, is largely unresponsive to checkpoint immunotherapy. Here, we interrogate the tumor microenvironment at single-cell resolution using scRNA-seq of 59,915 tumor and non-neoplastic cells from 8 primary and 3 metastatic samples. Tumor cells reveal novel subclonal genomic complexity and transcriptional states. Tumor-infiltrating immune cells comprise a previously unrecognized diversity of cell types, including CD8⁺ T cells predominantly expressing the checkpoint marker LAG3, rather than PD1 or CTLA4. V(D)J analysis shows clonally expanded T cells, indicating that they are capable of mounting an immune response. An indolent liver metastasis from a class 1B UM is infiltrated with clonally expanded plasma cells, indicative of antibody-mediated immunity. This complex ecosystem of tumor and immune cells provides new insights into UM biology, and LAG3 is identified as a potential candidate for immune checkpoint blockade in patients with high risk UM.

Uveal melanoma is highly metastatic and unresponsive to checkpoint immunotherapy. Here, the authors present single-cell transcriptomics of 59,915 cells in 8 primary and 3 metastatic samples, highlighting the diversity of the tumour microenvironment.

Genomic evolution of uveal melanoma arising in ocular melanocytosis

Ocular melanocytosis is the most important predisposing condition for the eye cancer uveal melanoma (UM). Here, we present a patient who developed UM arising within ocular melanocytosis who was treated with enucleation (eye removal), which provided an invaluable opportunity to interrogate both the UM and adjacent uveal tissue containing the melanocytosis using whole-exome and deep-targeted sequencing. This analysis revealed a clonal PLCB4 mutation in the melanocytosis, confirming that this is indeed a neoplastic condition and explaining why it predisposes to UM. This mutation was present in 100% of analyzed UM cells, indicating that a PLCB4-mutant cell gave rise to the UM. The earliest aberrations specific to the tumor were loss of Chromosomes 1p, 3, and 9p, which were present in virtually all tumor cells. A mutation in BAP1 arose later on the other copy of Chromosome 3 in a tumor subclone, followed by a gain of Chromosome 8q. These findings provide a mechanistic explanation for the well-known clinical association between ocular melanocytosis and UM by showing that this predisposing condition introduces the first “hit” and thereby increases the stochastic likelihood of acquiring further aberrations leading to UM.

Abstract 2903: Genomic evolution of uveal melanoma arising in ocular melanocytosis

Introduction: Ocular melanocytosis is an congenital condition characterized by the presence of excessive hyperpigmented melanocytes in the uveal tract. Epidemiological studies have shown that this condition is the strongest predisposing risk factor for development of uveal melanoma (UM). In UM patients, the presence of ocular melanocytosis doubles the risk of metastasis. UM has well-characterized driver mutations consisting of two groups. The first group consists of mutually exclusive gain-of-function mutations in members of the Gq signaling pathway (GNAQ, GNA11, CYSLTR2 and PLCB4), and are thought to represent initiating oncogenic events that are insufficient alone to cause full malignant transformation. The second group consists of near-mutually exclusive mutations in BAP1, SF3B1, and EIF1AX, which are thought to occur later in tumor progression. The genomics of ocular melanocytosis and matched UM have not been characterized previously. The purpose of this study was to investigate the genomic evolution of matched ocular melanocytosis and UM tumors.

Methods: Exome and deep-targeted sequencing data from two matched ocular melanocytosis and primary uveal melanomas were evaluated using a previously developed bioinformatic pipeline optimized to call mutations and CNVs in UM. Data from this analysis were used in downstream mutation subclone detection algorithms to determine genomic evolutionary patterns within these matched samples.

Results: For both cases, the initiating driver mutations that are characteristic of UM occur at the same genomic site in matched ocular melanocytosis and UM samples. This finding suggests that they arose within the melanocytosis and subsequently expanded in the tumor. Monosomy of chromosome 3 was absent from the melanocytosis but present in ~100% of tumor cells, indicating that it arose early during clonal tumor expansion. In Patient 1, the BAP1 mutation was present in a tumor subclone and chromosome 8q gain was present in a smaller subclone, indicating that they arose later during tumor evolution. In Patient 2, the BAP1 mutation and other copy number variations were present in ~100% of tumor cells indicating that tumor evolution was completed in this tumor. Additionally, no Gq signaling pathway driver mutations were found in the germline DNA of these patients indicating that that the mutations in ocular melanocytosis occurred somatically during development.

Conclusions: This study provides the first genomic evidence relating ocular melanocytosis to UM. This data shows that Gq signaling pathway driver mutations are early genomic events that are necessary but not sufficient for UM tumor development.These insights help further refine our genomic model of UM tumor evolution and may help to address persistent challenges in the field such as the failure of targeted therapies aimed at inhibiting the Gq pathway.

Citation Format: Michael A. Durante, Matthew G. Field, Margaret I. Sanchez, Kyle R. Covington, Christina L. Decatur, Sander R. Dubovy, J. William Harbour. Genomic evolution of uveal melanoma arising in ocular melanocytosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2903.

Abstract 4244: Novel expressed long non-coding RNAs in uveal melanoma

Uveal melanoma (UM) is a highly aggressive eye cancer that leads to metastatic death in up to half of patients. UMs can be divided into two prognostic groups based on their gene expression profile (GEP). The class 1 GEP is associated with low metastatic risk and the class 2 GEP with high metastatic risk. Class 1 tumors are associated with EIF1AX or SF3B1 mutations while Class 2 tumors are associated with inactivating mutations in the tumor suppressor BAP1. Class 1 and Class 2 UMs have been shown to differ in their expression of numerous known micro-RNAs and long non-coding RNAs (lncRNA). Here, we sought to identify novel differentially expressed lncRNAs using a publicly available RNA-Seq database. Raw RNA-Seq fastq files from 80 TCGA UM samples were obtained from the Cancer Genomics Hub (CGHub), quality controlled using FastQC (v0.11.3), and trimmed using trim-galor (v0.4.1). Sequences were aligned to the human genome (GRCh38) and accompanying general transfer format file (gtf) (Gencode v28) using STAR (v2.5). Transcript discovery was performed using Cufflinks (v2.2.1). Protein coding probability was calculated using CPC (v2.0), and transcripts predicted to be non-coding with transcript length >200bps were retained. 1671 novel transcripts were added to the gtf file, and fastq files were realigned with the new annotation. Estimated counts for all known and novel transcripts were generated using RSEM (v1.3.0) after STAR alignment. A cutoff of RPKM > 1 in at least 35% of tumors was used as a threshold for transcripts of interest, resulting in 61 novel transcripts, 32 of which were differentially expressed at FDR < 0.05 between Class 1 and Class 2 tumors, including 7 upregulated and 25 downregulated in Class 2 tumors. Further work is underway to elucidate the function of these novel transcripts in UM pathogenesis.

Citation Format: Daniel A. Rodriguez, Jeffim N. Kuznetsov, Margaret I. Sanchez, Stefan Kurtenbach, J. William Harbour. Novel expressed long non-coding RNAs in uveal melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4244.

Duodenal membranes: a late diagnosis evidenced by foreign bodies

One of the causes of congenital incomplete duodenal obstruction is the presence of duodenal membranes. This condition requires a high index of suspicion for an early and accurate diagnosis. We present two cases of duodenal obstruction with initial diagnosis of foreign bodies that were surgically intervened and where incomplete duodenal membranes were an incidental finding. The clinical course of these patients had a different pattern than expected and thus, it is imperative to use a multidisciplinary approach in this group of patients and separate them from other subtypes of duodenal obstruction.

Abstract 5369: Epigenetic, transciptomic and ubiquitomic changes associated with BAP1 loss in uveal melanoma

Uveal melanoma (UM) is the most common primary and aggressive ocular cancer. Up to 50% of the patients develop metastasis, which are notoriously resistant to all forms of therapy and despite medical treatment leads to death within a mean time of 5-7 months, with a mortality rate of over 90%. We previously described that gene expression profiling can be used to classy UM tumors into two basic categories, class 1 (low metastatic risk) and class 2 (high metastatic risk). We further described that inactivating mutations in the ubiquitin hydrolase BAP1 are found in over 85% of class 2 tumors. BAP1 is involved in removing ubiquitin from specific proteins to regulate their function, like histone H2A, thereby regulating gene expression.

Building on these findings, we have generated uveal melanoma and melanocyte cell lines that allow for the inducible knockdown of BAP1. First, we performed RNAseq on multiple cell lines before and after BAP1 knockdown and compare the results to gene expression of class 1 and class 2 tumors. We identified significant overlap in key genes linked to metastasis between the primary tumors, uveal melanoma and melanocyte cell lines. Using ChIP-seq to interrogate uveal melanoma cells depleted of BAP1, we identified changes in genome wide histone marks and RNA polymerase localization associated with BAP1. To gain further insight into non-histone deubiquitination targets of BAP1, we performed ubiquitination proteomic profiling using the UbiScan® technology and identified a list of high probability BAP1 substrates.

Taken together, these complementary genome-wide investigations provide a global picture of the cellular functions of BAP1 and they provide novel insights into the metastasis-promoting effect of BAP1 loss in UM.

Citation Format: Stefan Kurtenbach, Jeffim N. Kuznetsov, Matthew G. Field, Rohit Reddy, Margaret I. Sanchez, Christina L. Decatur, J William Harbour. Epigenetic, transciptomic and ubiquitomic changes associated with BAP1 loss in uveal melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5369. doi:10.1158/1538-7445.AM2017-5369

Abstract 4861: The role of PRAME in promoting uveal melanoma metastasis

Uveal melanoma (UM) is the most common primary eye cancer and has a predisposition for fatal metastasis. Our group has shown that UMs can be categorized by gene expression profiling (GEP) into two molecular classes associated with metastatic risk: Class 1 (low metastatic risk) and Class 2 (high metastatic risk). While the majority of Class 2 UMs (71%) metastasize, only 38% of Class 1 UMs metastasize. Our group was the first to identify the cancer-testis antigen PRAME as a biomarker for increased metastatic risk in Class 1 UMs, and sub-categorized these tumors into Class1 PRAME+ (intermediate metastatic risk) and Class1 PRAME- (low metastatic risk) subgroups. Further we identified PRAME+ was associated with shorter time to metastasis and worse prognosis in class 2 patients. We have now shown that this PRAME expression is correlated with hypomethylation in the promoter region of the gene, suggesting a mechanism for its expression. Since we have previously shown that PRAME is associated with early metastasis in Class 1 and Class 2 UMs, we hypothesized that PRAME plays a direct role in UM metastasis. To better understand the role of PRAME in UM, we used Class1PRAME+ (F41) and Class1PRAME– (Mel290) UM cell lines to develop in vitro models to study the role of PRAME. Since F41 cells are PRAME+ and highly metastatic, we constitutively silenced PRAME with a V5 tag (F41 shPRAME-V5). For Mel290 cells, we overexpressed PRAME to see whether this cell line, which does not induce metastatic death, became more malignant. We confirmed the silencing and overexpression of PRAME in our transformed cells with western blot. For cell proliferation, we found a slight increase in the Mel290 PRAME+ cells compared to non-transformed Mel290. Strikingly, in F41 cells, knockdown of PRAME led to complete cell death. In a xenograft animal model, NSG male mice were injected with either Mel290 PRAME-V5, Mel290, F41 shPRAME-V5 or F41 TET-empty vector cells. We found that PRAME overexpressing cell lines (Mel290 PRAME-V5 and F41 TET-empty vector) induced rapid, multiple and aggressive liver metastases that led to death, whereas the non-expressing PRAME cells (Mel290 and F41 shPRAME-V5) did not present macro or micrometastasis in any cases. This data highly suggests that PRAME overexpression is involved in UM metastasis. Thus, PRAME mRNA expression is not only a prognostic biomarker but also could be an important target for treatment.

Citation Format: Margaret I. Sanchez, Matthew G. Field, Jeffim N. Kuznetsov, Stefan Kurtenbach, Dien Pham, James W. Harbour. The role of PRAME in promoting uveal melanoma metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4861. doi:10.1158/1538-7445.AM2017-4861

Abstract 4510: KIT melanomas are developmentally racially biased

KIT is a critical pathway for melanocytic homeostasis and it is often down-regulated in cutaneous melanoma. However, KIT activation plays a critical role in a subpopulation of melanomas especially those in acral locations and melanomas on chronically sun damaged skin. We analyzed exome and RNAseq data from The Cancer Genome Atlas (TCGA) Network (321 cutaneous melanomas in the data set) to identify patterns unique to KIT activation. The melanomas were divided based on known mutually exclusive mutations (BRAF, NRAS and KIT) vs those without (WT). We compared RNA data between each group. KIT group had significantly higher expression of KIT than BRAF, NRAS and WT (p<0.01, FDR<0.01) and isoform 2 expression was higher than 1. KIT melanomas were found to overexpress Wnt pathway, pigmentation and genes involved epithelial-mesenchymal transition. From the exome data, germline SNPs with incidence in ethnic groups (Caucasian, Asian and African) and more likely to be present in a specific melanoma groups were selected. Comparing the 3 ethnicity groups across the 4 tumor groups Asian SNPs were significantly enhanced in KIT tumors, African in WT and Caucasian in BRAF and NRAS melanomas. We evaluated the tumors for the primary type of genetic damage. The three signatures that appeared most divergent were CC>TT for UV, (G/A)C(G)>(G/A)T(G) for deamination, and G>T for oxidative damage. UV and deamination appeared inversely proportional, while oxidative damage appeared to be independent of those other two features. KIT and WT had a greater% of non UV high deamination tumoral environments. A fraction of these tumors also had very high oxidative signatures. We then compared 2 KIT subgroups UV vs non UV (absence of CC>TT mutations) for germline ethnicity differences. Asian SNPs were highly increased in non UV subgroup whereas Caucasian SNPs were in UV subgroup. Further, we divided KIT non UV subgroup into deamination and oxidative damage subgroups and compared ethnicity differences. Deamination was significantly higher in Asians whereas oxidative damage was higher in Caucasians. A similar analysis was done to the WT group, where African SNPs were significantly increased in the non UV subgroup and were primarily associated with oxidative damage. This data implies that KIT mutant melanomas develop in a unique genetic and mutational environments and makes this an ideal system to in which study racial disparities at the molecular level.

Citation Format: Margaret I. Sanchez, James M. Grichnik. KIT melanomas are developmentally racially biased. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4510.

Dark homogeneous streak dermoscopic pattern correlating with specific KIT mutations in melanoma

IMPORTANCE

Mutations driving melanoma growth have diagnostic, prognostic, and therapeutic implications. Traditional classification systems do not correlate optimally with underlying melanoma growth-promoting mutations. Our objective was to determine whether unique dermoscopic growth patterns directly correlate with driving mutations.

OBSERVATIONS

We evaluated common driving mutations in 4 different dermoscopic patterns (rhomboidal, negative pigmented network, polygonal, and dark homogeneous streaks) of primary cutaneous melanomas; 3 melanomas per pattern were tested. Three of the 4 patterns lacked common mutations in BRAF, NRAS, KIT, GNAQ, and HRAS. One pattern, the dark homogeneous streaks pattern, had unique KIT mutations in the second catalytic domain of KIT in exon 17 for all 3 samples tested. Two tumors with the dark homogeneous streaks pattern turned out to be different primary melanomas from the same patient and had different sequence mutations but had an impact on the same KIT domain.

CONCLUSIONS AND RELEVANCE

While future study is required, these results have multiple implications. (1) The underlying melanoma-driving mutations may give rise to specific dermoscopic growth patterns, (2) BRAF/NRAS mutations in early melanomas may not be as common as previously thought, and (3) patients may be predisposed to developing specific driving mutations giving rise to melanomas or nevi of similar growth patterns.

Melanoma's high C>T mutation rate: is deamination playing a role?

The majority of melanoma mutations are C>T transitions, and most bear UV signatures. However, other process may contribute to the high C>T mutation rate. Okura et al., have demonstrated immunohistochemical evidence of deaminating enzymes, activation-induced cytidine deaminase (AID) and apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3B (APOBEC3B) in melanoma. Both have been implicated in cancer. While further validation is necessary, these findings warrant consideration of a role for deamination in melanomagenesis. Deamination primarily drives C>T transitions. Compared with trunk/extremity melanomas, acral melanomas display a significantly higher percentage of 'spontaneous' and 'AID' mutation signature events suggesting deamination may be particularly important in this subgroup.

Nevus senescence

Melanomas and nevi share many of the same growth-promoting mutations. However, melanomas grow relentlessly while benign nevi eventually undergo growth arrest and stabilize. The difference in their long-term growth potential may be attributed to activation of cellular senescence pathways. The primary mediator of senescence in nevi appears to be p16. Redundant, secondary senescence systems are also present and include the p14-p53-p21 pathway, the IGFBP7 pathway, the FBXO31 pathway, and the PI3K mediated stress induced endoplasmic reticulum unfolded protein response. It is evident that these senescence pathways result in an irreversible arrest in most instances; however, they can clearly be overcome in melanoma. Circumvention of these pathways is most frequently associated with gene deletion or transcriptional repression. Reactivation of senescence mechanisms could serve to inhibit melanoma tumor progression.

Nevogenesis: a benign metastatic process?

It is generally accepted that cutaneous nevogenesis is a localized event that occurs exclusively in the dermis and/or epidermis. However, the discovery of nevocytes circulating in the peripheral blood suggests that other, more systemic, benign metastatic processes could also be involved. The theoretical role of lymphatic and hematogenous dissemination of loosely adherent, immature nevus progenitor cells in the development of nodal nevi and eruptive melanocytic nevi will be reviewed.

Method of measuring the spatial resolution of a photoresist

By analysis of the response of a high-contrast photoresist to sinusoidal illumination, generated interferometrically, one can extract a phenomenological modulation transfer function of the resist material, thereby characterizing its spatial resolution. Deep-ultraviolet interferometric lithography allows the resist response to be quantified at length scales below 100 nm. As an example, the resolution (FWHM) of the commercial resist UVII-HS is found to be approximately 50 nm. This simple method can be applied to materials under development for advanced photolithography with short-wavelength illumination.

Sperm development, age and sex chromosome meiotic drive in the stalk-eyed fly, Cyrtodiopsis whitei

The cytological basis of X chromosome meiotic drive or sex ratio (SR) has been reported for several species of Drosophila but not for other species. Here we describe how sperm development in the stalk-eyed fly, Cyrtodiopsis whitei, influences progeny sex proportion, in order to determine if a common developmental mechanism could cause meiotic drive in these distantly related taxa. Because age has been found to affect the degree of segregation distortion in some Drosophila, we tested flies from six to 26 weeks of age. We find that spermatocyst bundles in SR males frequently contain incompletely elongated spermatid nuclei independently of male age. Older males have, however, more spermatocyst bundles in their testes than younger males. Abnormal spermatid elongation affects male fertility since SR males produce 74% as many progeny per week as ST males. The proportion of spermatocyst bundles with improperly elongated spermatid nuclei explains 71% of the variation in progeny sex proportion. After reviewing the literature on sperm development and meiotic drive, we conclude that the cytological basis of meiotic drive in diopsids closely resembles Drosophila. Across species in both groups, the production of fertile males is associated with less than half of all spermatids not elongating normally in a spermatocyst bundle. We discuss the possibility that frequency-dependent selection on male fertility could stabilize the drive polymorphism in these unusual flies.

A new classification for renal defects in net acid excretion

The traditional classification of the group of disorders called renal tubular acidosis (RTA) into proximal and distal subclasses is based on which nephron segment is thought to have an abnormal function. Nevertheless, such a distinction may not be correct and also does not characterize the pathophysiology of the renal acidosis in each patient. In this article, we propose an alternative classification, one that is based on the component of net acid excretion that is abnormal. We also suggest expanding the definition of net acid excretion to include a term that describes the renal handling of metabolizable organic anions because their loss in the urine represents the loss of "potential bicarbonate." Because a low rate of excretion of ammonium (NH4+) is present in patients with both distal and isolated proximal RTA, our initial clinical step in patients with hyperchloremic metabolic acidosis (HCMA) is to evaluate the rate of excretion of NH4+. The basis for a low rate of excretion of NH4+ is shown by examining the urine pH. If the urine pH is low, further studies are performed to determine why the availability of NH3 is low; if the urine pH is high, further investigations are initiated to examine if the defect in H+ secretion involves the proximal or the distal nephron. Conversely, if the rate of excretion of NH4+ is high in a patient with HCMA, a component of the degree of acidosis could be attributable to a high rate of excretion of metabolizable organic anions. Case examples are provided to illustrate the approach and its implications for future molecular studies.

Impaired urinary ammonium excretion in patients with isolated proximal renal tubular acidosis

During previous studies in patients with isolated proximal renal tubular acidosis (pRTA), the rates of urinary ammonium excretion were considered inappropriately low for their state of chronic metabolic acidosis. These observations were made while the patients were on a normal diet as well as when they were undergoing a short ammonium chloride test. Because these findings suggested an impaired ability to excrete maximal amounts of ammonium, the response to the 3-day acid loading test was evaluated in eight patients with isolated pRTA and in 10 normal control subjects. Plasma creatinine, acid-base, and electrolyte values were analyzed before and after 3 days of ingesting 2 mmol/kg.24 h of ammonium chloride. Twenty-four-hour urine specimens were collected the day before and on the third day of acid loading to determine urine pH, as well as the rate of excretion of NH4+ and titratable acid in milliequivalents per 24 h per 1.73 m2. During the basal state, all patients with pRTA had hyperchloremic metabolic acidosis and they excreted urine of lower pH (5.51 +/- 0.18 versus 6.00 +/- 0.13; P < 0.05) and greater titratable acid (29.1 +/- 4.3 versus 21.8 +/- 1.4; P < 0.05); however, they had rates of NH4+ excretion similar to those of controls. On the third day of acid loading, they excreted urine of lower pH (4.66 +/- 0.03 versus 5.00 +/- 0.03; P < 0.05) and equivalent amounts of titratable acid, whereas their NH4+ excretion was significantly less than that of controls (47.7 +/- 4.4 versus 76.3 +/- 5.7; P < 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)