{"title":"Mechanism-based disease similarity.","authors":"Mehdi B Hamaneh, Yi-Kuo Yu","doi":"10.29245/2572-9411/2016/3.1044","DOIUrl":"10.29245/2572-9411/2016/3.1044","url":null,"abstract":"<p><p>In recent years several methods have been proposed to assign pairwise mechanism- based similarity scores to human diseases. Despite their differences in approach and performance, these methods work in a somewhat similar manner: first a set of biomolecules (genes, proteins, chemicals, etc.) is associated with each disease, and then a measure is defined to calculate the similarity between the sets assigned to a pair of diseases. Since the similarity score between two diseases is defined based on the underlying molecular processes, a high score may hint at a shared cause, and therefore a similar treatment, for both diseases. This is of great practical importance especially when a rare or newly-discovered disease, for which limited information is available, is found to be related to a disease with a known treatment. Thus, in this mini-review we briefly discuss the recently developed methods for computing mechanism-based disease- disease similarities.</p>","PeriodicalId":91764,"journal":{"name":"Journal of rare diseases research & treatment","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404756/pdf/nihms-1003610.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37041746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Lenz-Majewski syndrome: How a single mutation leads to complex changes in lipid metabolism.","authors":"Mira Sohn, Tamas Balla","doi":"10.29245/2572-9411/2017/1.1080","DOIUrl":"https://doi.org/10.29245/2572-9411/2017/1.1080","url":null,"abstract":"Lenz-Majewski syndrome (LMS) is a rare disease presenting with complex physical and mental abnormalities. Whole exome sequencing performed on five LMS-affected individuals has identified gain-of-function mutations in the PTDSS1 gene encoding phosphatidylserine synthase 1 (PSS1) enzyme. These mutations all rendered PSS1 insensitive to PS-mediated product inhibition. In a recent study we showed that uncontrolled PS production by these mutant PSS1 enzymes lead to the accumulation of PS in the ER where it is not detected in normal cells. This increased PS in the ER in turn, activated the Sac1 phosphatase, which is responsible for the dephosphorylation of the minor lipid, phosphatidylinositol 4-phosphate (PI4P) in the ER. Increased Sac1 activity decreased PI4P levels both in the Golgi and the plasma membrane thereby dissipating the PI4P gradients set up by PI 4-kinase enzymes (PI4Ks) between these membranes and the ER. Such PI4P gradients at membrane contact sites have been shown to support the transports of structural lipids such as cholesterol and PS out of the ER by non-vesicular lipid transfer. Therefore, uncontrolled production of PS not only affects the PS status of cells but also initiates an avalanche of changes in the metabolism of other membrane lipids via affecting PI4P gradients throughout the cell. Recognition of the close metabolic interaction between PS synthesis and PI4P metabolism provided a new clue to better understand the molecular underpinning of this rare and severe disease.","PeriodicalId":91764,"journal":{"name":"Journal of rare diseases research & treatment","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404757/pdf/nihms-1005985.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37041747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Philippa C Fowler, Dwayne J Byrne, Niamh C O'Sullivan
{"title":"Rare disease models provide insight into inherited forms of neurodegeneration.","authors":"Philippa C Fowler, Dwayne J Byrne, Niamh C O'Sullivan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Hereditary spastic paraplegias (HSPs) are a group of inherited neurodegenerative conditions characterised by retrograde degeneration of the longest motor neurons in the corticospinal tract, resulting in muscle weakness and spasticity of the lower limbs. To date more than 70 genetic loci have been associated with HSP, however the majority of cases are caused by mutations that encode proteins responsible for generating and maintaining tubular endoplasmic reticulum (ER) structure. These ER-shaping proteins are vital for the long-term survival of axons, however the mechanisms by which mutations in these proteins give rise to HSP remain poorly understood. To begin to address this we have characterized <i>in vivo</i> loss of function models of two very rare forms of HSP caused by loss of the ER-shaping proteins ARL6IP1 (SPG61) and RTN2 (SPG12). These models display progressive locomotor defects, disrupted organisation of the tubular ER and length-dependant defects in the axonal mitochondrial network. Here we compare our findings with those associated with more common forms HSP including: Spastin, Atlastin-1 and REEP 1 which together account for over half of all cases of autosomal dominant HSP. Furthermore, we discuss recent observations in other HSP models which are directly implicated in mitochondrial function and localization. Overall, we highlight the common features of our rare models of HSP and other models of disease which could indicate shared mechanisms underpinning neurodegeneration in these disorders.</p>","PeriodicalId":91764,"journal":{"name":"Journal of rare diseases research & treatment","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5462091/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35080510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Na Zhang, Xing Gao, Yingchao Zhao, Meenal Datta, Pinan Liu, Lei Xu
{"title":"Rationally combining anti-VEGF therapy with radiation in NF2 schwannoma.","authors":"Na Zhang, Xing Gao, Yingchao Zhao, Meenal Datta, Pinan Liu, Lei Xu","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Neurofibromatosis type 2 is characterized by bilateral vestibular schwannomas, which are benign tumors that originate from the nerve sheath and damage the nerve as they grow, causing neurological dysfunction such as hearing loss. Current standard radiation therapy can further augment hearing loss by inducing local damage to mature nerve tissue. Treatment with bevacizumab, a Vascular Endothelial Growth Factor (VEGF)-specific antibody, is associated with tumor control and hearing improvement in NF2 patients; however, its effect is not durable and its mechanism of action on improving nerve function is unknown. Anti-VEGF treatment can normalize the tumor vasculature, improving vessel perfusion and delivery of oxygen. It is known that oxygen is a potent radiosensitizer; therefore, combining anti-VEGF treatment with radiation therapy can achieve better tumor control and allow for the use of lower radiation doses, thus minimizing treatment-related neurological toxicity.</p>","PeriodicalId":91764,"journal":{"name":"Journal of rare diseases research & treatment","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5300073/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141297547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sumita Choudhury, William E Plautz, Cosette Zacarias, Rinku Majumder
{"title":"Mini-review on \"A novel one-step purification of mouse factor IX\".","authors":"Sumita Choudhury, William E Plautz, Cosette Zacarias, Rinku Majumder","doi":"10.29245/2572-9411/2016/2.1031","DOIUrl":"https://doi.org/10.29245/2572-9411/2016/2.1031","url":null,"abstract":"Factor IX (FIX) is a 70-kDa, single-chain, vitamin K-dependent glycoprotein present in trace amounts (~95 nM) in blood plasma1,2. FIX is synthesized as a zymogen that is converted to a serine protease, FIXa, by the activated form of factor XI3,4. FIXa has a central function in the intrinsic pathway of blood coagulation, in that it acts as an activator of factor X (FX), directly upstream of the common pathway1,5. Upon activation, FXa concomitantly converts prothrombin to thrombin to initiate the formation of the fibrin lattice6,7.","PeriodicalId":91764,"journal":{"name":"Journal of rare diseases research & treatment","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88044399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}