Background Histopathologic examination is sometimes inadequate for accurate and reproducible diagnosis of certain melanocytic neoplasms. As a result, more sophisticated and objective methods have been sought. The goal of this study was to identify a gene expression signature that reliably differentiated benign and malignant melanocytic lesions and evaluate its potential clinical applicability. Herein, we describe the development of a gene expression signature and its clinical validation using multiple independent cohorts of melanocytic lesions representing a broad spectrum of histopathologic subtypes. Methods Using quantitative reverse‐transcription polymerase chain reaction ( PCR ) on a selected set of 23 differentially expressed genes, and by applying a threshold value and weighting algorithm, we developed a gene expression signature that produced a score that differentiated benign nevi from malignant melanomas. Results The gene expression signature classified melanocytic lesions as benign or malignant with a sensitivity of 89% and a specificity of 93% in a training cohort of 464 samples. The signature was validated in an independent clinical cohort of 437 samples, with a sensitivity of 90% and specificity of 91%. Conclusions The performance, objectivity, reliability and minimal tissue requirements of this test suggest that it could have clinical application as an adjunct to histopathology in the diagnosis of melanocytic neoplasms.
The innate response interferon-inducible transmembrane (Ifitm) proteins have been characterized as influencing proliferation, signaling complexes and restricting virus infections. Treatment of cells lacking these proteins (IfitmDel) with IFN-β resulted in the loss of clathrin from membrane compartments and the inhibition of clathrin-mediated phagocytosis, suggesting a molecular interaction between clathrin and Ifitm proteins. The pH of endosomes of IfitmDel cells, with or without IFN activation, was neutralized, suggesting the function of the vacular ATPase proton pumps in such cells was compromised. Co-immunoprecipitation of Ifitm3 with Atp6v0b demonstrated a direct interaction between the Ifitm proteins and the v-ATPase. These data suggest that the Ifitm proteins help stabilize v-ATPase complexes in cellular membranes which, in turn, facilitates the appropriate subcellular localization of clathrin.
The cell cycle progression test has a significant impact in assisting physicians and patients reach personalized treatment decisions.
The expression of the CD21 and CD23 genes is coincident with differentiation from transition 1 B cells (T1) to transition 2 B cells (T2). To define constituents controlling CD21 and CD23 expression, we conducted chromatin immunoprecipitation analyses for candidate transcription factors. We found constitutive binding of Oct-1, NFAT species, YY1, NF-κB-p52, Pax5, E2A, and RBP-Jκ to CD21 sequences and NF-κB-p52, Pax5, NFAT species, E2A, and RBP-Jκ to CD23 promoter sequences. Splenic T and B cell subsets displayed constitutive binding of YY1, NF-κB-p52, Pax5, and Oct-1 proteins to CD21 sequences in B cells but no specific binding of NFATc3 or Pax5 in T cells. Similarly, CD23 sequences demonstrated constitutive binding of NF-κB-p52 in splenic T and B cells but only Pax5 in B cells. Of the various NFAT species, only a subset were found forming constitutive DNA/protein complexes with the CD21, CD23, and IL-2 gene sequences. Maturing B cells in the marrow possess stable Pax5 complexes on CD19, CD21, and CD23 gene promoters in the nuclei of such cells, even though only CD19 is expressed. The similarity of genetic controlling elements between the CD21 and CD23 genes does not suggest a mechanism for alternative regulation of these genes; however, separation of splenic B cell subsets into T1, T2, marginal zone (MZ), and mature follicular B cells, followed by quantitative RT-PCR, demonstrated the lack of appreciable CD23 transcripts in CD21+ MZ cells. We propose an alternative derivation of MZ cells as maturing directly from T1 cells, leaving CD23 transcriptionally inactive in that lineage of cells.
The TNF family member BAFF serves to promote the survival and differentiation of maturing splenic B cells. The major receptor for BAFF (BAFF-R) is expressed by the transition 2, marginal zone and follicular, mature conventional B-2 cell populations; functional BAFF/BAFF-R signaling is required for T1 to T2 cell B cell maturation. Induced expression of CD23 and CD21 is also coincident with the T1 to T2 maturation stage. A key question we address in this report is if BAFF signaling directly induces CD21 and CD23 gene transcription and expression at this B cell transition point, or if their expression is simply coincident with B cell maturation and differentiation. We present data that supports the contention that BAFF does not preferentially induce the expression of CD23 or CD21 at the T1 to T2 transition, nor does exogenous BAFF lead to preferential increased expression of these proteins/genes in mature B cell populations. The analysis of LPS-induced splenic B cells from BAFF-R defective (A/WySnJ) mice did not show the preferential induction of expression of CD21 or CD23 that might have been expected if NF-κB-p52 protein was lacking due to insufficient BAFF-R signaling in cells bearing this mutation. Indeed, chromatin immunoprecipitation analysis demonstrated stable NF-κB-p52 complexes on CD21 and CD23 genes obtained from both wild type and A/WySnJ B cells. FACS analysis of splenic B cells from 1, 2, 3 and 6 wk old A/WySnJ mice demonstrated a block in differentiation (thus reducing overall B cell numbers) resulting in a failure of such cells to express CD21 but allowing for the expression level of CD23 per cell to reach levels approaching wild type. We have dubbed this CD23 HI CD21 LO subset as the T1b transition B cell. These data support the recognized role of BAFF as promoting the survival and differentiation of splenic B cells but do not support a model of BAFF signaling directly inducing the expression of the CD21 and CD23 proteins via translocation of NF-κB-p52 species.
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