Gene expression analysis has identified biologically relevant subclasses of breast cancer. However, most classification schemes do not robustly cluster all HER2+ breast cancers, in part due to limitations and bias of clustering techniques used. In this article, we propose an alternative approach that first separates the HER2+ tumors using a gene amplification signal for Her2/neu amplicon genes and then applies consensus ensemble clustering separately to the HER2+ and HER2À clusters to look for further substructure. We applied this procedure to a microarray data set of 286 early-stage breast cancers treated only with surgery and radiation and identified two basal and four luminal subtypes in the HER2À tumors, as well as two novel and robust HER2+ subtypes. HER2+ subtypes had median distant metastasis-free survival of 99 months [95% confidence interval (95% CI), 83-118 months] and 33 months (95% CI, 11-54 months), respectively, and recurrence rates of 11% and 58%, respectively. The low recurrence subtype had a strong relative overexpression of lymphocyte-associated genes and was also associated with a prominent lymphocytic infiltration on histologic analysis. These data suggest that early-stage HER2+ cancers associated with lymphocytic infiltration are a biologically distinct subtype with an improved natural history. [Cancer Res 2007;67(22):10669-76]

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Preeclampsia, a common pregnancy disorder associated with an increase in systemic inflammation, is the leading cause of maternal and fetal morbidity and mortality throughout the world. It is associated with shallow extravillous trophoblast invasion of the decidua, leading to uteroplacental blood flow that is inadequate for the developing fetal-placental unit. In preeclamptic women, interleukin-6 (IL-6) levels in plasma, but not placenta, are elevated, prompting evaluation of the decidua as a potential source of this excess, circulating IL-6. The current study found significantly higher immunohistochemical staining for IL-6 in decidual cells from preeclamptic versus preterm, gestational age-matched control placentas. Proinflammatory cytokines associated with the genesis of preeclampsia (i.e., tumor necrosis factor-␣ and interleukin-1␤) enhanced IL-6 mRNA levels and increased secreted IL-6 levels in first trimester leukocytefree decidual cell incubations, as measured by real time quantitative RT-PCR , ELISA , and Western blotting. Therefore , decidual cell-derived IL-6 may contribute to excess circulating IL-6 levels that can promote both endothelial cell dysfunction (and subsequent vascular dysfunction) and the pathogenesis of preeclampsia whereas locally elevated IL-6 levels may contribute to an excess of decidual macrophages implicated in shallow extravillous trophoblast invasion of the decidua. Maternal-fetal interactions create a mild systemic inflammatory state exemplified by activation of both vascular endothelium and leukocytes that is most apparent in the third trimester of uncomplicated human pregnancies.

Human papillomavirus (HPV) gene expression is dramatically altered during cervical carcinogenesis. Because dysregulated genes frequently show abnormal patterns of DNA methylation, we hypothesized that comprehensive mapping of the HPV methylomes in cervical samples at different stages of progression would reveal patterns of clinical significance. To test this hypothesis, thirteen HPV16-positive samples were obtained from women undergoing routine cervical cancer screening. Complete methylation data were obtained for 98.7% of the HPV16 CpGs in all samples by bisulfite-sequencing. Most HPV16 CpGs were unmethylated or methylated in only one sample. The other CpGs were methylated at levels ranging from 11% to 100% of the HPV16 copies per sample. The results showed three major patterns and two variants of one pattern. The patterns showed minimal or no methylation (A), low level methylation in the E1 and E6 genes (B), and high level methylation at many CpGs in the E5/L2/L1 region (C). Generally, pattern A was associated with negative cytology, pattern B with low-grade lesions, and pattern C with high-grade lesions. The severity of the cervical lesions was then ranked by the HPV16 DNA methylation patterns and, independently, by the pathologic diagnoses. Statistical analysis of the two rating methods showed highly significant agreement. In conclusion, analysis of the HPV16 DNA methylomes in clinical samples of cervical cells led to the identification of distinct methylation patterns which, after validation in larger studies, could have potential utility as biomarkers of neoplastic cervical progression.

Twenty-five cases of a morphologically distinctive vascular lesion of the spleen are described. The patients were 17 women and 8 men, ranging in age from 22 to 74 years (mean, 48.4 years; median, 56 years). The most common presentations were incidental finding of an asymptomatic splenic mass (13 patients), abdominal pain or discomfort (6 patients), and splenomegaly (4 patients). None of the patients had evidence of recurrent disease after splenectomy. The splenic lesion was solitary, measuring 3 to 17 cm, and sharply demarcated from the surrounding parenchyma. The cut surface revealed a mass of coalescing red-brown nodules embedded in a dense fibrous stroma. All cases showed a remarkably consistent multinodular appearance at low-power examination. The individual nodules had an angiomatoid appearance, in the sense that they were composed of slit-like, round or irregular-shaped vascular spaces lined by plump endothelial cells and interspersed by a population of spindly or ovoid cells. Some of the nodules (particularly the smaller ones) were surrounded by concentric rings of collagen fibers. Numerous red blood cells were present, as well as scattered inflammatory cells. Nuclear atypia was minimal, mitotic figures were extremely rare, and necrosis was consistently absent. The internodular stroma consisted of variably myxoid to dense fibrous tissue with scattered plump myofibroblasts, plasma cells, lymphocytes, and siderophages. Immunostaining revealed 3 distinct types of vessels in the angiomatoid nodules: CD34+/CD8-/CD31+ capillaries, CD34-/CD8+/CD31+ sinusoids, and CD34-/CD8-/CD31+ small veins, recapitulating the composition of the normal splenic red pulp. These features are therefore different from those of littoral cell angioma, conventional hemangioma, and hemangioendothelioma of the spleen. We interpret these angiomatoid nodules as altered red pulp tissue that had been entrapped by a nonneoplastic stromal proliferative process. The characteristic morphologic appearance, immunophenotype, and benign clinical course suggest that this is a distinctive nonneoplastic vascular lesion of the spleen that we propose to designate as sclerosing angiomatoid nodular transformation (SANT).