Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation

We carried out a trans-ancestry genome-wide association and replication study of blood pressure phenotypes among up to 320,251 individuals of East Asian, European and South Asian ancestry. We find genetic variants at 12 new loci to be associated with blood pressure (P = 3.9 × 10-11 to 5.0 × 10-21). The sentinel blood pressure SNPs are enriched for association with DNA methylation at multiple nearby CpG sites, suggesting that, at some of the loci identified, DNA methylation may lie on the regulatory pathway linking sequence variation to blood pressure. The sentinel SNPs at the 12 new loci point to genes involved in vascular smooth muscle (IGFBP3, KCNK3, PDE3A and PRDM6) and renal (ARHGAP24, OSR1, SLC22A7 and TBX2) function. The new and known genetic variants predict increased left ventricular mass, circulating levels of NT-proBNP, and cardiovascular and all-cause mortality (P = 0.04 to 8.6 × 10-6). Our results provide new evidence for the role of DNA methylation in blood pressure regulation

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Primary plasmacytoma of lymph nodes

Primary plasmacytoma of the lymph nodes is very rare, and there are fewer than 20 reported cases. These cases appeared to have a better prognosis than other extramedullary plasmacytomas, with rare recurrence and no progression to myeloma after treatment. To better characterize the clinicopathological features and the pathogenesis of primary plasmacytoma of the lymph nodes, we reviewed our consultation files and retrieved seven such cases. The age of presentation ranged from 39 to 76 years (median age, 59 years), with three women and four men. The clinical follow-up varied from 1 to 14 years. All patients presented with enlarged lymph nodes and had an indolent clinical course, except for one patient with slow progression and increasing numbers of bone marrow plasma cells. Five patients were treated with excision only and two with excision and chemotherapy. None of the patients had recurrence or developed multiple myeloma. All cases showed immunoglobulin light chain restriction, four with monotypic lambda and three with monotypic kappa. One patient had extensive nodal amyloid deposition. Four cases had monoclonal heavy chain expression, three with monoclonal immunoglobulin (Ig) G and one with monoclonal IgM. All cases were negative for CD20 and CD43, and six cases expressed CD79a. Overexpression of p53 and bcl-2 was not detected by immunostaining in any of the cases. Epstein-Barr vital (EBV) RNA was not detected in all seven cases by in situ hybridization, and no Kaposi\u27s sarcoma-associated herpesvirus (KSHV) DNA sequences were detected by polymerase chain reaction in five cases. Our results confirm a more favorable outcome and rare progression to multiple myeloma in primary nodal plasmacytomas after excision or chemotherapy. The results of oncoprotein and vital studies suggest that the pathogenesis of primary nodal plasmacytoma may not be due to bcl-2- and p53-associated changes or viral- induced changes by EBV and KSHV

Neurofibroma and cellular neurofibroma with atypia: A report of 14 tumors

The clinical significance of nuclear atypia in neurofibromas that lack necrosis or significant mitotic activity has not been systematically studied. We reviewed 14 neurofibromas from six patients with mild to marked nuclear atypia, with low mitotic activity in some tumors. Five tumors also had areas of increased cellularity consistent with cellular neurofibroma. Necrosis was absent. All patients were treated by conservative excision. Clinical follow- up, ranging from 8 months to 6 years, showed that none of the tumors recurred or metastasized. To further characterize these neoplasms, we assessed p53 expression, proliferation rate, and DNA content because these methods have been suggested by others as useful in differentiating benign from malignant nerve sheath tumors. p53 expression was detected by immunostaining in one tumor with 5% positive cells and in two tumors with rare positive cells (\u3c1%). The remaining 11 tumors were negative. Tumor cell proliferation rate as determined by Ki-67 immunostaining showed \u3c5% positive cells in 13 tumors. In one tumor, 10% of the cells were Ki-67 positive. Using flow cytometry methods and paraffin-embedded tissue, all tumors had diploid DNA content with an S phase fraction ranging from 5.2% to 18.2% (mean 9.4%). No significant differences were observed between the neurofibromas and cellular neurofibromas. For comparison, we studied three malignant peripheral nerve sheath tumors (MPNSTs). All MPNSTs had relatively high p53 (range 10-16%; mean 12%) and Ki-67 (range 32-42%; mean 38.0%) staining. One of the MPNSTs was aneuploid. The S phase fraction of the MPNSTs ranged from 8.1% to 51.8% (mean 28.6%). These results suggest that clinically benign neurofibromas, both usual and cellular types, can have significant cytologic atypia that can be accompanied by low mitotic activity. Conservative surgical excision for these tumors is adequate. The results of p53 and Ki-67 immunostaining and DNA content and S-phase analysis by flow cytometry support this interpretation. In addition, in tumors with borderline histologic findings, results of these ancillary studies may be useful in distinguishing benign from malignant nerve sheath tumors

Absence of Kaposi\u27s sarcoma-associated herpesvirus-like DNA sequences in malignant vascular tumors of the serous membranes

Reports connect Kaposi\u27s sarcoma-associated herpesvirus (KSHV) with various types of Kaposi\u27s sarcoma (KS) and body-cavity-based lymphomas (primary effusion lymphomas). KSHV DNA sequences have also been detected in a few non-KS malignant vascular tumors. To determine whether KSHV is associated with malignant vascular tumors involving the body cavities, 11 primary vascular tumors of the serous membranes (4 angiosarcomas, 7 hemangioendotheliomas) were tested for KSHV sequences by polymerase chain reaction and Southern blot hybridization. The tumors were from patients who were not known to be immunocompromised. KSHV sequences were detected in the penile KS control but were absent in all 11 specimens studied. Our results were consistent with previous reports that KSHV sequences were rarely detected in non-KS vascular lesions. The results also suggested that although KSHV sequences might be present in primary effusion tumors such as primary effusion lymphoma, they might not be found in other tumors related to body cavities or to serous membranes

Oncocytic adrenocortical neoplasms: A report of seven cases and review of the literature

Oncocytic neoplasms of the adrenal gland are rare. We describe the clinicopathologic and immunohistochemical findings of seven oncocytic adrenocortical neoplasms, five oncocytomas, and two oncocytic neoplasms of uncertain malignant potential. Three tumors were studied using electron microscopy. These neoplasms occurred in five women and two men (median age, 55 years) with no clinical evidence that the neoplasms were functional. The size of the neoplasms varied from 5.0 cm to 13.5 cm. Histologically, each neoplasm was composed exclusively of oncocytes. The oncocytomas had very low or absent mitotic activity and no evidence of necrosis. The two oncocytic neoplasms of uncertain malignant potential had increased mitotic activity and necrosis but no evidence of invasion or metastases. Nuclear atypia, either focal or generalized, was found in all neoplasms. Immunohistochemical studies performed using fixed, paraffin-embedded sections showed strong reactivity with the mitochondrial antibody mES-13 in all neoplasms. Four of five oncocytomas and one oncocytic neoplasm of uncertain malignant potential expressed keratin, predominantly keratin 18, as shown using the CAM 5.2 and AE3 antibodies. Two neuroendocrine-associated markers, neuron specific enolase and synaptophysin, were positive in seven and five neoplasms, respectively. However, all neoplasms were negative for the other neuroendocrine markers tested, including chromogranin A, tyrosine hydroxylase, and dopamine β-hydroxylase, as well as for epithelial membrane antigen, S 100, and p53. Using the MIB-1 (Ki-67) antibody, proliferative activity was increased in both oncocytic neoplasms of uncertain malignant potential. All six patients with available clinical follow-up data are alive without evidence disease, although the follow-up interval is relatively short (\u3c 2 years) for the two patients with oncocytic neoplasms of uncertain malignant potential. We conclude that oncocytic adrenocortical neoplasms are nonfunctional tumors that can become large before they are detected by radiologic studies. The majority of neoplasms are benign and should not be misdiagnosed as carcinoma

Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation

We carried out a trans-ancestry genome-wide association and replication study of blood pressure phenotypes among up to 320,251 individuals of East Asian, European and South Asian ancestry. We find genetic variants at 12 new loci to be associated with blood pressure (P = 3.9 × 10 -11 to 5.0 × 10 -21). The sentinel blood pressure SNPs are enriched for association with DNA methylation at multiple nearby CpG sites, suggesting that, at some of the loci identified, DNA methylation may lie on the regulatory pathway linking sequence variation to blood pressure. The sentinel SNPs at the 12 new loci point to genes involved in vascular smooth muscle (IGFBP3, KCNK3, PDE3A and PRDM6) and renal (ARHGAP24, OSR1, SLC22A7 and TBX2) function. The new and known genetic variants predict increased left ventricular mass, circulating levels of NT-proBNP, and cardiovascular and all-cause mortality (P = 0.04 to 8.6 × 10 -6). Our results provide new evidence for the role of DNA methylation in blood pressure regulation