Citations

BackgroundAlterations in GFER gene have been associated with progressive mitochondrial myopathy, congenital cataracts, hearing loss, developmental delay, lactic acidosis and respiratory chain deficiency in 3 siblings born to consanguineous Moroccan parents by homozygosity mapping and candidate gene approach (OMIM#613076). Next generation sequencing recently confirmed this association by the finding of compound heterozygous variants in 19‐year‐old girl with a strikingly similar phenotype, but this ultra‐rare entity remains however unknown from most of the scientific community.Materials and MethodsWhole exome sequencing was performed as part of a “diagnostic odyssey” for suspected mitochondrial condition in 2 patients, presenting congenital cataracts, progressive encephalomyopathy and hypotrophy and detected unreported compound heterozygous variants in GFER.ResultsThanks to an international data sharing, we found 2 additional patients carrying compound heterozygous variants in GFER. Reverse phenotyping confirmed the phenotypical similarities between the 4 patients. Together with the first literature reports, the review of these 8 cases from 4 unrelated families enables us to better describe this apparently homogeneous disorder, with the clinical and biological stigmata of mitochondrial disease.ConclusionThis report highlights the clinical utility of whole exome sequencing and reverse phenotyping for the diagnosis of ultra‐rare diseases and underlines the importance of a broad data sharing for accurate clinical delineation of previously unrecognized entities.

Background— Lead-related or valve-related endocarditis can complicate cardiovascular implantable electronic device (CIED) infection in patients with both CIED and prosthetic valves. The objective of this study was to determine the outcomes of transvenous lead extraction for CIED infection in patients with prosthetic valves. Methods and Results— We retrospectively screened 794 transvenous lead extraction procedures, between September 1, 2001 and August 31, 2012, at Mayo Clinic to identify patients with prosthetic valves who underwent lead extraction for infection. Demographic, clinical, and follow-up characteristics were analyzed. In total, 51 patients (6%) met the study inclusion criteria, of whom 20 had pocket infection and 31 had lead-related or valve-related, or both, endocarditis or bloodstream infection (mean age, 67 [18] years). Staphylococcal species were the most common pathogens, including Staphylococcus aureus in 20 cases (39%) and coagulase-negative staphylococci in 19 cases (37%). Overall, 127 transvenous leads (median lead age, 52 months) were extracted. Of these leads, 123 (97%) were removed completely. The in-hospital mortality rate was 9.8%; no deaths were attributable to the extraction procedure. Ninety-five percent of patients who survived had no evidence of recurrent device-related or valve-related infection. Conclusions— Transvenous lead extraction seems safe and curative in patients with CIED infection and prosthetic valves. Cure of infection can be achieved in the majority of patients with complete CIED removal and antimicrobial therapy and without valve surgery.

Objective To assess the feasibility of using MicroFil polymer perfusion to detect concomitant saccular aneurysms in an intracranial arterial dolichoectasia (IADE) model in mice, and to report detailed histomorphometric features of these aneurysms. Materials and methods IADE models were created in C57/BL6 mice via microsurgical injection of 25 mU elastase into the cisterna magna. The cerebral vasculature was perfused with MicroFil polymer and harvested at 1, 3, and 7 days, and 2 and 4 weeks (n=8 for each group). IADE was defined by a tortuosity index >10 combined with a 25% increase in diameter of the A1 segment of the anterior cerebral artery (ACA), internal carotid artery (ICA), or basilar artery compared with the baseline of controls, which received heat-inactivated elastase. Saccular aneurysm occurrence rate, location, and morphological parameters were investigated using macroscopic and microscopic analysis. Results IADE was present in 95% (36/38) of the subjects, with a mortality rate of 5% (2/40). Fifteen concomitant saccular aneurysms were detected in 8 (21%) of the 38 surviving mice, including 6 at the posterior communicating artery, 1 along the ACA, 2 along the anterior communicating artery complex, 3 along the ICA, and 3 along the middle cerebral artery. Rupture was confirmed in two aneurysms. Histological examination indicated that the aneurysms develop via arterial-wall remodelling, which is characterized by internal elastic lamina disruptions and muscular layer discontinuity in the media. Conclusions The proportion of subjects developing saccular aneurysms in addition to IADE in our mouse model is similar to the 15% of patients with IADE who have concomitant saccular aneurysms.

Background: Statins have proven cardioprotective effects, but higher doses are accompanied by various concerns and may not lead to superior clinical outcomes in Chinese/Asian populations. Objective: We designed a trial to test the efficacy of high-intensity statin therapy for the reduction of periprocedural myocardial infarction (MI) and 1-year major adverse cardiovascular events (MACEs, including cardiovascular death, spontaneous MI, unplanned revascularization) in an Asian population. Methods: A total of 798 Chinese patients with stable angina or acute coronary syndrome (ACS) were randomized to high-intensity atorvastatin (80 mg/d before percutaneous coronary intervention [PCI] and 40 mg/d thereafter for 1 year, n = 400) or moderate-intensity atorvastatin (20 mg/d for 1 year, n = 398). The primary end point was 1-year incidence of MACEs. Result: In patients with stable angina, 1-year MACE rates were not significantly different between moderate- and high-intensity groups (7.6% vs 5.7%, P = 0.53). In contrast, in patients with ACS, the 1-year MACE rate was significantly higher in the moderate- than in the high-intensity atorvastatin group (16.8% vs 10.1%, P = 0.021; adjusted hazard ratio = 1.71, 95% CI = 1.08 to 2.77, P = 0.021). Conclusions: Whereas stable angina patients derive similar benefit from moderate- and high-intensity atorvastatin therapy over the duration of 1 year after PCI, high-intensity statin therapy is superior in ACS patients.

Abstract Motivation: Prediction and prioritization of human non-coding regulatory variants is critical for understanding the regulatory mechanisms of disease pathogenesis and promoting personalized medicine. Existing tools utilize functional genomics data and evolutionary information to evaluate the pathogenicity or regulatory functions of non-coding variants. However, different algorithms lead to inconsistent and even conflicting predictions. Combining multiple methods may increase accuracy in regulatory variant prediction. Results: Here, we compiled an integrative resource for predictions from eight different tools on functional annotation of non-coding variants. We further developed a composite strategy to integrate multiple predictions and computed the composite likelihood of a given variant being regulatory variant. Benchmarked by multiple independent causal variants datasets, we demonstrated that our composite model significantly improves the prediction performance. Availability and Implementation: We implemented our model and scoring procedure as a tool, named PRVCS, which is freely available to academic and non-profit usage at http://jjwanglab.org/PRVCS. Contact: wang.junwen@mayo.edu, jliu@stat.harvard.edu, or limx54@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.

Abstract Background A subset of triple negative breast cancers (TNBC) has somatic amplification of chromosome 9p24.1, encoding PD-L1, PD-L2, and JAK2 (the "PDJ" amplicon). The JAK/STAT pathway promotes malignant transformation and proliferation, and the JAK1/JAK2 inhibitor ruxolitinib is being evaluated in early phase clinical trials in breast cancer. This study was designed to measure the frequency of PDJ copy number gain in existing TNBC cell lines, and determine the impact of targeted JAK2 inhibition on cellular proliferation. Methods: Copy number alterations were measured in nine TNBC cell lines (MDA-MB-453, MDA-MB-436, BT549, MDA-MB231, MFM-223, MDA-MB-468, H5578T, MDA-MB-157, HCC1937) by array comparative genomic hybridization (aCGH). JAK2 and pSTAT3 expression was measured by immunoblot in four of the TNBC lines (HCC1937, MDA-MB-468, MDA-MB-231, MDA-MB-436) and compared with MCF10A, SK-BR3, and T47D. To selectively inhibit JAK2, lentiviral vectors encoding five different shRNA targeting JAK2 were generated. Ruxolitinib treatment was performed at 25 uM for 48 hrs and 72 hrs. Cell proliferation was measured by CellTiter-Glo. Results: All TNBC cell lines had an elevated level of baseline protein expression of JAK2 and pSTAT3 compared to SK-BR3, T47D, and MCF10A. Of the nine TNBC cell lines, only MDA-MB-436 and BT549 had copy number gain of 9p24.1 (log2ratio<1). Four independent shRNA efficiently silenced over 90% of JAK2 expression in MDA-MB-231. The inhibition of JAK2 in MDA-MB-231 was associated with a decrease in both JAK2 and pSTAT3 protein expression and reduction in cell proliferation compared to control shRNA after 96 hrs (p<0.0001). Inhibition of proliferation was also observed for both MDA-MB-231 and MDA-MB-436 after ruxolitinib treatment. Conclusion These results demonstrate that existing TNBC cell lines have varying copy number alterations of chromosome 9p24.1 encoding JAK2, and targeted JAK2 inhibition in TNBC inhibits cell proliferation. Citation Format: Chen M, Andreozzi M, Gonzalez-Malerva L, Eaton S, Pockaj B, Barrett MT, Anderson KS. JAK2 copy number and targeted JAK2 inhibition of TNBC cell lines. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-04-19.

AbstractThe recent announcement of the Precision Medicine Initiative by President Obama has brought precision medicine (PM) to the forefront for healthcare providers, researchers, regulators, innovators, and funders alike. As technologies continue to evolve and datasets grow in magnitude, a strong computational infrastructure will be essential to realize PM’s vision of improved healthcare derived from personal data. In addition, informatics research and innovation affords a tremendous opportunity to drive the science underlying PM. The informatics community must lead the development of technologies and methodologies that will increase the discovery and application of biomedical knowledge through close collaboration between researchers, clinicians, and patients. This perspective highlights seven key areas that are in need of further informatics research and innovation to support the realization of PM.