Role of frameshift ubiquitin B protein in Alzheimer's disease.

Wiley Interdiscip Rev Syst Biol Med. 2016 May 30;

Authors: Chen X, Petranovic D

Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease and is characterized by accumulation of misfolded and aggregated proteins. Since the ubiquitin-proteasome system (UPS) is the major intracellular protein quality control (PQC) system in eukaryotic cells, it is likely involved in the etiology of AD. The frameshift form of ubiquitin (Ubb(+1) ) accumulates in the neuritic plaques and neurofibrillary tangles in patients with AD. Ubb(+1) accumulates in an age-dependent manner as a result of RNA-polymerase mediated molecular misreading during transcription, which allows the formation of mutant proteins in the absence of gene mutations. The accumulation of the Ubb(+1) protein may act as an endogenous reporter for proteasome dysfunction and a growing number of studies have shown that Ubb(+1) may play more important pathogenic roles in AD etiology than previously hypothesized. The yeast Saccharomyces cerevisiae shares many conserved biological processes with all eukaryotic cells, including human neurons. This organism has been regarded as a model system for investigating the fundamental intracellular mechanisms, including those underlying neurodegeneration. We propose here that yeast systems biology approaches, combined with cell and molecular biology approaches will increase the relevant knowledge needed for advancement and elucidation of mechanisms and complex traits, which could provide new targets for therapeutic intervention in AD. For further resources related to this article, please visit the WIREs website.

PMID: 27240056 [PubMed - as supplied by publisher]

Clearing and Labeling Techniques for Large-Scale Biological Tissues.

Mol Cells. 2016 May 30;

Authors: Seo J, Choe M, Kim SY

Abstract
Clearing and labeling techniques for large-scale biological tissues enable simultaneous extraction of molecular and structural information with minimal disassembly of the sample, facilitating the integration of molecular, cellular and systems biology across different scales. Recent years have witnessed an explosive increase in the number of such methods and their applications, reflecting heightened interest in organ-wide clearing and labeling across many fields of biology and medicine. In this review, we provide an overview and comparison of existing clearing and labeling techniques and discuss challenges and opportunities in the investigations of large-scale biological systems.

PMID: 27239813 [PubMed - as supplied by publisher]

From big data to smart data in Alzheimer's disease. The brain health modeling initiative to foster actionable knowledge.

Alzheimers Dement. 2016 May 26;

Authors: Geerts H, Dacks PA, Devanarayan V, Haas M, Khatchaturian Z, Gordon MF, Maudsley S, Romero K, Stephenson D, Brain Health Modeling Initiative (BHMI)

Abstract
Massive investment and technological advances in the collection of extensive and longitudinal information on thousands of Alzheimer patients results in large amounts of data. These "big-data" databases can potentially advance CNS research and drug development. However, although necessary, they are not sufficient, and we posit that they must be matched with analytical methods that go beyond retrospective data-driven associations with various clinical phenotypes. Although these empirically derived associations can generate novel and useful hypotheses, they need to be organically integrated in a quantitative understanding of the pathology that can be actionable for drug discovery and development. We argue that mechanism-based modeling and simulation approaches, where existing domain knowledge is formally integrated using complexity science and quantitative systems pharmacology can be combined with data-driven analytics to generate predictive actionable knowledge for drug discovery programs, target validation, and optimization of clinical development.

PMID: 27238630 [PubMed - as supplied by publisher]

Comparison and Optimization of Methods for the Simultaneous Extraction of DNA, RNA, Proteins, and Metabolites.

Anal Biochem. 2016 May 26;

Authors: Vorreiter F, Richter S, Peter M, Baumann S, von Bergen M, Tomm JM

Abstract
The challenge of performing a time-resolved comprehensive analysis of molecular systems has led to the quest to optimize extraction methods. When the size of a biological sample is limited, there is demand for the simultaneous extraction of molecules representing the four areas of 'omics,' genomics, transcriptomics, proteomics, and metabolomics. Here,we optimized a protocol for the simultaneous extraction of RNA, proteins, and metabolites and a compared it to tow existing protocols.second for the concurrent recovery of DNA, RNA, and proteins and compared it to two existing protconducted a previouslty described method. Our optimisation comprised the addition of a methanol/chloroform metabolite purification before the separation of DNA/RNA and proteins. Extracted DNA, RNA, proteins, and metabolites were quantitatively and/or qualitatively analyzed. Of the three methods, only the newly developed protocol yielded all biomolecule classes of adequate quantity and quality.

PMID: 27237373 [PubMed - as supplied by publisher]

Characteristics of 419 patients with acquired middle ear cholesteatoma.

Braz J Otorhinolaryngol. 2016 May 3;

Authors: Rosito LP, da Silva MN, Selaimen FA, Jung YP, Pauletti MG, Jung LP, Freitas LA, da Costa SS

Abstract
INTRODUCTION: Cholesteatoma is a destructive lesion that can result in life-threatening complications. Typically, it presents with hypoacusis and continuous otorrhea as symptoms. Because it is a rare disease, there are few studies in Brazil describing the characteristics of patients with the disease.
OBJECTIVE: This study aimed to determine the prevalence of cholesteatoma in patients with chronic otitis media and describe clinical, audiological and surgical characteristics of patients with acquired middle ear cholesteatoma treated at a referral hospital in the public health system.
METHODS: Cross-sectional and prospective cohort study, including 1710 patients with chronic otitis media, treated between August 2000 and June 2015, without prior surgery. Detailed clinical history, videotoscopy, and audiometry were performed, in addition to review of medical records to search for surgical data. Cholesteatomas were classified according to their route of formation.
RESULTS: Of the patients with chronic otitis media, 419 (24.5%) had cholesteatoma; mean age of 34.49 years; 53.5% female and 63.8% adults. Bilateral cholesteatoma was observed in 17.1%. Anterior epitympanic cholesteatoma corresponded to 1.9%; posterior epitympanic, 32.9%; posterior mesotympanic, 33.7%; two routes, 14.8%; and indeterminate, 16.7%. The mean air-bone gap was 29.84dB and did not differ between routes of formation. There were no correlations between gap size and patient age or duration of symptoms. Of the surgical cases, 16.8% underwent closed tympanomastoidectomy and 75.2% open tympanomastoidectomy.
CONCLUSION: The prevalence of cholesteatoma in patients with chronic otitis media was 24.5% and it was more common in adults than in children. Posterior mesotympanic cholesteatoma was more frequent, with no difference in mean air-bone gap between the different routes of formation. In patients undergoing surgery, open tympanomastoidectomy was the procedure most frequently chosen.

PMID: 27236633 [PubMed - as supplied by publisher]

Metastatic malignant pleural mesothelioma masquerading as a case of acute abdomen secondary to small bowel perforation.

Ann Saudi Med. 2016 May-Jun;36(3):229-231

Authors: Alkhayal K

Abstract
Metastatic pleural mesothelioma is a rare disease. The present study aimed to report a rare presentation of metastatic malignant mesothelioma (MM). The patient was an elderly man who presented with small bowel (jejunal) perforation secondary to metastatic pleural mesothelioma deposits. This was a rare presentation of a rare disease and the first reported case in the published studies in which MM masqueraded as bowel perforation prior to the primary diagnosis.
SIMILAR CASES PUBLISHED: 1.

PMID: 27236396 [PubMed - as supplied by publisher]

Non-diabetic clinical applications of insulin.

J Basic Clin Physiol Pharmacol. 2016 May 28;

Authors: Benni JM, Patil PA

Abstract
BACKGROUND: Introducing a new drug to the market is a time-consuming process, is complex, and involves consumption of a lot of resources. Therefore, discovering new uses for the old drugs (i.e. drug repurposing) benefits the patients by providing them time-tested drugs. With developments in insulin therapy still happening, it is worth keeping up to date on trends in the use of this powerful glucose-lowering agent. The aim of this article is to explore the potential non-diabetic clinical applications of insulin.
METHODS: Literature survey was carried out through the various scientific journals publishing experimental and clinical research papers regarding the diverse applications of insulin other than in diabetes mellitus. These applications include both therapeutic as well as diagnostic uses of insulin. The relevant information collected from these publications was paraphrased in the present paper.
RESULTS: On studying the literature, the non-diabetic uses of insulin include the following: wound healing, parenteral nutrition, antiaging, body building, cardioprotection in acute coronary syndromes, insulin tolerance test to test the hypothalamo-pituitary-adrenal axis functioning, cell culture, cancer treatment, organ preservation, and management of septic shock, calcium channel, β blocker overdose and other critical illnesses in intensive care units.
CONCLUSIONS: This review attempts to survey some interesting new applications of insulin other than in diabetes mellitus.

PMID: 27235672 [PubMed - as supplied by publisher]

Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery.

BMC Genomics. 2016;17(1):414

Authors: Jia Z, Liu Y, Guan N, Bo X, Luo Z, Barnes MR

Abstract
BACKGROUND: Drug repositioning, finding new indications for existing drugs, has gained much recent attention as a potentially efficient and economical strategy for accelerating new therapies into the clinic. Although improvement in the sensitivity of computational drug repositioning methods has identified numerous credible repositioning opportunities, few have been progressed. Arguably the "black box" nature of drug action in a new indication is one of the main blocks to progression, highlighting the need for methods that inform on the broader target mechanism in the disease context.
RESULTS: We demonstrate that the analysis of co-expressed genes may be a critical first step towards illumination of both disease pathology and mode of drug action. We achieve this using a novel framework, co-expressed gene-set enrichment analysis (cogena) for co-expression analysis of gene expression signatures and gene set enrichment analysis of co-expressed genes. The cogena framework enables simultaneous, pathway driven, disease and drug repositioning analysis. Cogena can be used to illuminate coordinated changes within disease transcriptomes and identify drugs acting mechanistically within this framework. We illustrate this using a psoriatic skin transcriptome, as an exemplar, and recover two widely used Psoriasis drugs (Methotrexate and Ciclosporin) with distinct modes of action. Cogena out-performs the results of Connectivity Map and NFFinder webservers in similar disease transcriptome analyses. Furthermore, we investigated the literature support for the other top-ranked compounds to treat psoriasis and showed how the outputs of cogena analysis can contribute new insight to support the progression of drugs into the clinic. We have made cogena freely available within Bioconductor or https://github.com/zhilongjia/cogena .
CONCLUSIONS: In conclusion, by targeting co-expressed genes within disease transcriptomes, cogena offers novel biological insight, which can be effectively harnessed for drug discovery and repositioning, allowing the grouping and prioritisation of drug repositioning candidates on the basis of putative mode of action.

PMID: 27234029 [PubMed - as supplied by publisher]

The importance of review articles in making the voice of rare diseases heard: OJRD's 10th anniversary.

Orphanet J Rare Dis. 2016;11(1):71

Authors: Aymé S

PMID: 27234175 [PubMed - as supplied by publisher]

Perirenal Involvement of Mantle Cell Lymphoma: Imaging Features.

Urology. 2016 May 24;

Authors: Ufuk F, Karaman E, Karabulut N

Abstract
Perirenal lymphoma is a rare disease and accouning for less than 10% of all malignant lymphomas. Mantle cell lymphoma (MCL) is the rarest but one of the most aggressive non-Hodgkin's lymphoma (NHL) subtype. The perirenal involvement of MCL has not been reported previously. A 69-year-old male, who had been diagnosed as having mantle cell lymphoma (MCL) one year ago, presented with recent-onset right back pain. Herein we present the key imaging findings of perirenal soft tissue manifestation of MCL.

PMID: 27233934 [PubMed - as supplied by publisher]

From frames to OWL2: Converting the Foundational Model of Anatomy.

Artif Intell Med. 2016 May;69:12-21

Authors: Detwiler LT, Mejino JL, Brinkley JF

Abstract
OBJECTIVE: The Foundational Model of Anatomy (FMA) [Rosse C, Mejino JLV. A reference ontology for bioinformatics: the Foundational Model of Anatomy. J. Biomed. Inform. 2003;36:478-500] is an ontology that represents canonical anatomy at levels ranging from the entire body to biological macromolecules, and has rapidly become the primary reference ontology for human anatomy, and a template for model organisms. Prior to this work, the FMA was developed in a knowledge modeling language known as Protégé Frames. Frames is an intuitive representational language, but is no longer the industry standard. Recognizing the need for an official version of the FMA in the more modern semantic web language OWL2 (hereafter referred to as OWL), the objective of this work was to create a generalizable Frames-to-OWL conversion tool, to use the tool to convert the FMA to OWL, to "clean up" the converted FMA so that it classifies under an EL reasoner, and then to do all further development in OWL.
METHODS: The conversion tool is a Java application that uses the Protégé knowledge representation API for interacting with the initial Frames ontology, and uses the OWL-API for producing new statements (axioms, etc.) in OWL. The converter is relation centric. The conversion is configurable, on a property-by-property basis, via user-specifiable XML configuration files. The best conversion, for each property, was determined in conjunction with the FMA knowledge author. The convertor is potentially generalizable, which we partially demonstrate by using it to convert our Ontology of Craniofacial Development and Malformation as well as the FMA. Post-conversion cleanup involved using the Explain feature of Protégé to trace classification errors under the ELK reasoner in Protégé, fixing the errors, then re-running the reasoner.
RESULTS: We are currently doing all our development in the converted and cleaned-up version of the FMA. The FMA (updated every 3 months) is available via our FMA web page http://si.washington.edu/projects/fma, which also provides access to mailing lists, an issue tracker, a SPARQL endpoint (updated every week), and an online browser. The converted OCDM is available at http://www.si.washington.edu/projects/ocdm. The conversion code is open source, and available at http://purl.org/sig/software/frames2owl. Prior to the post-conversion cleanup 73% of the more than 100,000 classes were unsatisfiable. After correction of six types of errors no classes remained unsatisfiable.
CONCLUSION: Because our FMA conversion captures all or most of the information in the Frames version, is the only complete OWL version that classifies under an EL reasoner, and is maintained by the FMA authors themselves, we propose that this version should be the only official release version of the FMA in OWL, supplanting all other versions. Although several issues remain to be resolved post-conversion, release of a single, standardized version of the FMA in OWL will greatly facilitate its use in informatics research and in the development of a global knowledge base within the semantic web. Because of the fundamental nature of anatomy in both understanding and organizing biomedical information, and because of the importance of the FMA in particular in representing human anatomy, the FMA in OWL should greatly accelerate the development of an anatomically based structural information framework for organizing and linking a large amount of biomedical information.

PMID: 27235801 [PubMed - as supplied by publisher]

SLCO1B1*5 polymorphism (rs4149056) is associated with chemotherapy-induced amenorrhea in premenopausal women with breast cancer: a prospective cohort study.

BMC Cancer. 2016;16(1):337

Authors: Reimer T, Kempert S, Gerber B, Thiesen HJ, Hartmann S, Koczan D

Abstract
BACKGROUND: Because inheritance is recognized as playing a role in age at menarche and natural menopause, the development of chemotherapy-induced amenorrhea (CIA) might depend on inherited genetic factors; however, studies that explore such a correlation are few and have received scant attention. Given the importance of this topic we conducted a comprehensive genotype study in young women (≤45 years) with early-stage breast cancer.
METHODS: Our approach tested the effect of variant polymorphisms in drug metabolism enzymes (DMEs) using a predesigned pharmacogenomics panel (TaqMan® OpenArray®, Life Technologies GmbH, Darmstadt, Germany) in premenopausal women (n = 50). Patients received contemporary chemotherapy; in all cases a cyclophosphamide-based regimen with a dose of at least 500 mg/m(2) for six cycles. CIA was considered to be present in women with no resumption of menstrual bleeding within 12 months after completion of chemotherapy or goserelin.
RESULTS: Twenty-six patients (52 %) showed CIA during follow-up whereas 24 women (48 %) remained premenopausal. Of all the DMEs studied, only the SLCO1B1*5 (rs4149056) genotype was associated with the development of CIA (P = 0.017). Of the 26 patients who were homozygous for the T/T allele SLCO1B1*5, 18 (69.2 %) developed CIA compared with 8 (30.8 %) of the 22 patients who were heterozygous (C/T allele). The association of heterozygous SLCO1B1*5 allele (OR 0.038; 95%CI: 0.05-0.92) with a lower risk of developing CIA remained significant in a binary logistic regression analysis that include age, SLCO1B1*5 allele variants, and goserelin therapy.
CONCLUSIONS: Patient age and SLCO1B1*5 allele variants predict the likelihood of young women with breast cancer developing CIA.

PMID: 27234217 [PubMed - as supplied by publisher]

Genetic polymorphisms of pharmacogenomic VIP variants in the Mongol of Northwestern China.

BMC Genet. 2016;17(1):70

Authors: Jin T, Shi X, Wang L, Wang H, Feng T, Kang L

Abstract
BACKGROUND: Within a population, the differences of pharmacogenomic variant frequencies may produce diversities in drug efficacy, safety, and the risk associated with adverse drug reactions. With the development of pharmacogenomics, widespread genetic research on drug metabolism has been conducted on major populations, but less is known about minorities.
RESULTS: In this study, we recruited 100 unrelated, healthy Mongol adults from Xinjiang and genotyped 85 VIP variants from the PharmGKB database. We compared our data with eleven populations listed in 1000 genomes project and HapMap database. We used χ(2) tests to identify significantly different loci between these populations. We downloaded SNP allele frequencies from the ALlele FREquency Database to observe the global genetic variation distribution for these specific loci. And then we used Structure software to perform the genetic structure analysis of 12 populations.
CONCLUSIONS: Our results demonstrated that different polymorphic allele frequencies exist between different nationalities,and indicated Mongol is most similar to Chinese populations, followed by JPT. This information on the Mongol population complements the existing pharmacogenomic data and provides a theoretical basis for screening and therapy in the different ethnic groups within Xinjiang.

PMID: 27233804 [PubMed - as supplied by publisher]

FGFR2 risk SNPs confer breast cancer risk by augmenting estrogen responsiveness.

Carcinogenesis. 2016 May 28;

Authors: Campbell TM, Castro MA, de Santiago I, Fletcher MN, Halim S, Prathalingam R, Ponder BA, Meyer KB

Abstract
The fibroblast growth factor receptor 2 (FGFR2) locus is consistently the top hit in genome-wide association studies (GWAS) for estrogen receptor-positive (ER(+)) breast cancer. Yet, its mode of action continues to be controversial. Here we employ a systems biology approach to demonstrate that signalling via FGFR2 counteracts cell activation by estrogen. In the presence of estrogen, the estrogen receptor (ESR1) regulon (set of ESR1 target genes) is in an active state. However, signalling by FGFR2 is able to reverse the activity of the ESR1 regulon. This effect is seen in multiple distinct FGFR2 signalling model systems, across multiple cells lines and is dependent on the presence of FGFR2. Increased estrogen exposure has long been associated with an increased risk of breast cancer. We therefore hypothesised that risk variants should reduce FGFR2 expression and subsequent signalling. Indeed, transient transfection experiments assaying the three independent variants of the FGFR2 risk locus (rs2981578, rs35054928 and rs45631563) in their normal chromosomal context show that these single nucleotide polymorphisms (SNPs) map to transcriptional silencer elements and that, compared to wild type, the risk alleles augment silencer activity. The presence of risk variants results in lower FGFR2 expression and increased estrogen responsiveness. We thus propose a molecular mechanism by which FGFR2 can confer increased breast cancer risk that is consistent with estrogen exposure as a major driver of breast cancer risk. Our findings may have implications for the clinical use of FGFR2 inhibitors.

PMID: 27236187 [PubMed - as supplied by publisher]

Identification of associations between small molecule drugs and miRNAs based on functional similarity.

Oncotarget. 2016 May 24;

Authors: Wang J, Meng F, Dai E, Yang F, Wang S, Chen X, Yang L, Wang Y, Jiang W

Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that regulate gene expression at post-transcriptional level. Increasing evidences show aberrant expression of miRNAs in varieties of diseases. Targeting the dysregulated miRNAs with small molecule drugs has become a novel therapy for many human diseases, especially cancer. Here, we proposed a novel computational approach to identify associations between small molecules and miRNAs based on functional similarity of differentially expressed genes. At the significance level of p < 0.01, we constructed the small molecule and miRNA functional similarity network involving 111 small molecules and 20 miRNAs. Moreover, we also predicted associations between drugs and diseases through integrating our identified small molecule-miRNA associations with experimentally validated disease related miRNAs. As a result, we identified 2265 associations between FDA approved drugs and diseases, in which ~35% associations have been validated by comprehensive literature reviews. For breast cancer, we identified 19 potential drugs, in which 12 drugs were supported by previous studies. In addition, we performed survival analysis for the patients from TCGA and GEO database, which indicated that the associated miRNAs of 4 drugs might be good prognosis markers in breast cancer. Collectively, this study proposed a novel approach to predict small molecule and miRNA associations based on functional similarity, which may pave a new way for miRNA-targeted therapy and drug repositioning.

PMID: 27232942 [PubMed - as supplied by publisher]

What We Know About the Pathogenesis of Idiopathic Pulmonary Fibrosis.

Semin Respir Crit Care Med. 2016 Jun;37(3):358-367

Authors: Puglisi S, Torrisi SE, Giuliano R, Vindigni V, Vancheri C

Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease of unknown cause, occurring in adults, limited to the lungs and associated with the pathologic and radiologic pattern of usual interstitial pneumonia. Prognosis is poor, and most patients die of respiratory failure within 3 to 6 years from the onset of symptoms. Although our understanding of the pathogenesis of IPF has improved over the past two decades, the mechanisms responsible for this disorder have not been clearly defined. Aging is the single most important risk factor, but genetic, environmental, and diverse exogenous factors such as smoking, viral infections, chronic tissue injury (i.e., gastroesophageal reflux disease, traction injury) play contributory roles. In this review, we focus on pathogenetic mechanisms that we think are crucial for the initiation of the fibrotic process and for its progressive evolution. In the early stage of the disease, in the context of the permissive genetic background combined with the presence of specific risk factors, alveolar epithelial cells play a leading role. Subsequent evolution of the fibrotic process and its lethal progression is likely due to the abnormal tissue repair process that takes place in the lung and to the inability to counteract this process. In this phase of the disease, fibroblasts assume a crucial role. Current pharmacological treatment strategies for IPF have only modest value, principally by slowing the course of disease progression. Unfortunately, improvement or cure has not yet been achieved with pharmacological agents. The challenge for the future is to improve the comprehension of the mechanisms involved in the inception and evolution of IPF and their articulated interactions. This is fundamental not only to conceive and develop new drugs against this dreadful disease but also to apply different therapeutic approaches such as drug repositioning and personalized therapies in the management of IPF.

PMID: 27231860 [PubMed - as supplied by publisher]

Data integration to prioritize drugs using genomics and curated data.

BioData Min. 2016;9:21

Authors: Louhimo R, Laakso M, Belitskin D, Klefström J, Lehtonen R, Hautaniemi S

Abstract
BACKGROUND: Genomic alterations affecting drug target proteins occur in several tumor types and are prime candidates for patient-specific tailored treatments. Increasingly, patients likely to benefit from targeted cancer therapy are selected based on molecular alterations. The selection of a precision therapy benefiting most patients is challenging but can be enhanced with integration of multiple types of molecular data. Data integration approaches for drug prioritization have successfully integrated diverse molecular data but do not take full advantage of existing data and literature.
RESULTS: We have built a knowledge-base which connects data from public databases with molecular results from over 2200 tumors, signaling pathways and drug-target databases. Moreover, we have developed a data mining algorithm to effectively utilize this heterogeneous knowledge-base. Our algorithm is designed to facilitate retargeting of existing drugs by stratifying samples and prioritizing drug targets. We analyzed 797 primary tumors from The Cancer Genome Atlas breast and ovarian cancer cohorts using our framework. FGFR, CDK and HER2 inhibitors were prioritized in breast and ovarian data sets. Estrogen receptor positive breast tumors showed potential sensitivity to targeted inhibitors of FGFR due to activation of FGFR3.
CONCLUSIONS: Our results suggest that computational sample stratification selects potentially sensitive samples for targeted therapies and can aid in precision medicine drug repositioning. Source code is available from http://csblcanges.fimm.fi/GOPredict/.

PMID: 27231484 [PubMed]

GM3 synthase deficiency due to ST3GAL5 variants in two Korean female siblings: Masquerading as Rett syndrome-like phenotype.

Am J Med Genet A. 2016 May 27;

Authors: Lee JS, Yoo Y, Lim BC, Kim KJ, Song J, Choi M, Chae JH

Abstract
There have been a few reports of GM3 synthase deficiency since the disease of the ganglioside biosynthetic pathway was first reported in 2004. It is characterized by infantile-onset epilepsy with severe intellectual disability, blindness, cutaneous dyspigmentation, and choreoathetosis. Here we report the cases of two Korean female siblings with ST3GAL5 variants, who presented with a Rett-like phenotype. They had delayed speech, hand stereotypies with a loss of purposeful hand movements, and choreoathetosis, but no clinical seizures. One of them had microcephaly, while the other had small head circumference less than 10th centile. There were no abnormal laboratory findings with the exception of a high lactate level. MECP2/CDKL5/FOXG1 genetic tests with an array comparative genomic hybridization revealed no molecular defects. Through whole-exome sequencing of the proband, we found compound heterozygous ST3GAL5 variants (p.Gly201Arg and p.Cys195Ser), both of which were novel. The siblings were the same compound heterozygotes and their unaffected parents were heterozygous carriers of each variant. Liquid chromatography-mass spectrometry analysis confirmed a low level of GM3 and its downstream metabolites, indicating GM3 synthase deficiency. These cases expanded the clinical and genetic spectrum of the ultra-rare disease, GM3 synthase deficiency with ST3GAL5 variants. © 2016 Wiley Periodicals, Inc.

PMID: 27232954 [PubMed - as supplied by publisher]

Research advances on medical genetics in China in 2015.

Yi Chuan. 2016 May 20;38(5):363-390

Authors: Yuanfeng L, Yubo H, Pengbo C, Jinfeng M, Haibei L, Geng Q, Feng Z, Guangfu J, Yong Y, Lingqian W, Jie P, Gangqiao Z

Abstract
Steady progress has been achieved in the medical genetics in China in 2015, as numerous original researches were published in the world's leading journals. Chinese scientists have made significant contributions to various fields of medical genetics, such as pathogenicity of rare diseases, predisposition of common diseases, somatic mutations of cancer, new technologies and methods, disease-related microRNAs (miRNAs), disease-related long non-coding RNAs (lncRNAs), disease-related competing endogenous RNAs (ceRNAs), disease-related RNA splicing and molecular evolution. In these fields, Chinese scientists have gradually formed the tendency, from common variants to rare variants, from single omic analyses to multipleomics integration analyses, from genetic discovery to functional confirmation, from basic research to clinical application. Meanwhile, the findings of Chinese scientists have been drawn great attentions of international peers. This review aims to provide an overall picture of the front in Chinese medical genetics, and highlights the important findings and their research strategy.

PMID: 27232486 [PubMed - as supplied by publisher]

Mutations in SLC39A14 disrupt manganese homeostasis and cause childhood-onset parkinsonism-dystonia.

Nat Commun. 2016;7:11601

Authors: Tuschl K, Meyer E, Valdivia LE, Zhao N, Dadswell C, Abdul-Sada A, Hung CY, Simpson MA, Chong WK, Jacques TS, Woltjer RL, Eaton S, Gregory A, Sanford L, Kara E, Houlden H, Cuno SM, Prokisch H, Valletta L, Tiranti V, Younis R, Maher ER, Spencer J, Straatman-Iwanowska A, Gissen P, Selim LA, Pintos-Morell G, Coroleu-Lletget W, Mohammad SS, Yoganathan S, Dale RC, Thomas M, Rihel J, Bodamer OA, Enns CA, Hayflick SJ, Clayton PT, Mills PB, Kurian MA, Wilson SW

Abstract
Although manganese is an essential trace metal, little is known about its transport and homeostatic regulation. Here we have identified a cohort of patients with a novel autosomal recessive manganese transporter defect caused by mutations in SLC39A14. Excessive accumulation of manganese in these patients results in rapidly progressive childhood-onset parkinsonism-dystonia with distinctive brain magnetic resonance imaging appearances and neurodegenerative features on post-mortem examination. We show that mutations in SLC39A14 impair manganese transport in vitro and lead to manganese dyshomeostasis and altered locomotor activity in zebrafish with CRISPR-induced slc39a14 null mutations. Chelation with disodium calcium edetate lowers blood manganese levels in patients and can lead to striking clinical improvement. Our results demonstrate that SLC39A14 functions as a pivotal manganese transporter in vertebrates.

PMID: 27231142 [PubMed - in process]