Reactive intermediates : model substrate studies

The reactions of cinnamyl chloride and crotyl chloride with various aldehydes, RCHO; R=Me, Et, iPr, CH₃(CH₂)₅, PhCH₂, Ph, p-MeOPh, p-NCPh, to form homoallylic alcohols under the control of Sn-Al, Cr(II), Zn and Mg were examined and the stereochemistry of the products determined. Stereoselectivity and regioselectivity of these reactions are compared and explained with reference to cyclic and linear mechanisms and the metal involved, frontier molecular orbital energies and molecular modelling experiments. An attempt was made to extend control of the relative stereochemistry of the Sn-Al reaction to systems with more than two contiguous carbon centers. The aldehydes, RCH(CH₃)CHO; R=Me, Ph, tBu, reacting with cinnamyl chloride under control of Sn-Al resulted in moderate Cram selectivity, this diastereofacial selectivity increasing with the bulk of the aldehydes' R group. Glyceraldehyde gave very poor diastereofacial selectivity. Dialdehydes terephthaldecarboxaldehyde and glyoxal were reacted with cinnamyl chloride mediated by Sn-Al and the relative stereochemistries of the major products deduced. Competition experiments of crotyl bromide and cinnamyl chloride with aryl aldehydes, p-R-C₆H₄CHO; R=H, Me, MeO, NC, O₂N, under the control of tin mediated conditions (Sn-Al) and of crotyl organotin and cinnamyl organotin (allylic-SnL₃; L=Ph, nBu) catalysed by either BF₃.OEt₂ or heat were carried out and the results of these experiments discussed in the light of frontier molecular orbital theory. Molecular mechanics calculations were performed to evaluate the steric stability of rotamers of threo and erythro homoallylic alcohols and these used in association with electronic effects to explain the diastereoselectivity of the linear mechanism. Conformational analysis using MM calculations were undertaken in an attempt to rationalize the stereoselectivity at the cyclic transition state. Synthetic pathways to β,γ-epoxy ketones were explored and the synthesis of 38, 44, and 50 effected by a number of different paths to maximize yields; the diastereoselectivities of the epoxidations of intermediate hydroxy and acetoxy alkenes was investigated

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene

To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 index familial ALS cases and 19,494 controls. Through both approaches, we identified kinesin family member 5A (KIF5A) as a novel gene associated with ALS. Interestingly, mutations predominantly in the N-terminal motor domain of KIF5A are causative for two neurodegenerative diseases: hereditary spastic paraplegia (SPG10) and Charcot-Marie-Tooth type 2 (CMT2). In contrast, ALS-associated mutations are primarily located at the C-terminal cargo-binding tail domain and patients harboring loss-of-function mutations displayed an extended survival relative to typical ALS cases. Taken together, these results broaden the phenotype spectrum resulting from mutations in KIF5A and strengthen the role of cytoskeletal defects in the pathogenesis of ALS.Peer reviewe

Reactive intermediates : model substrate studies

The reactions of cinnamyl chloride and crotyl chloride with various aldehydes, RCHO; R=Me, Et, iPr, CH₃(CH₂)₅, PhCH₂, Ph, p-MeOPh, p-NCPh, to form homoallylic alcohols under the control of Sn-Al, Cr(II), Zn and Mg were examined and the stereochemistry of the products determined. Stereoselectivity and regioselectivity of these reactions are compared and explained with reference to cyclic and linear mechanisms and the metal involved, frontier molecular orbital energies and molecular modelling experiments. An attempt was made to extend control of the relative stereochemistry of the Sn-Al reaction to systems with more than two contiguous carbon centers. The aldehydes, RCH(CH₃)CHO; R=Me, Ph, tBu, reacting with cinnamyl chloride under control of Sn-Al resulted in moderate Cram selectivity, this diastereofacial selectivity increasing with the bulk of the aldehydes' R group. Glyceraldehyde gave very poor diastereofacial selectivity. Dialdehydes terephthaldecarboxaldehyde and glyoxal were reacted with cinnamyl chloride mediated by Sn-Al and the relative stereochemistries of the major products deduced. Competition experiments of crotyl bromide and cinnamyl chloride with aryl aldehydes, p-R-C₆H₄CHO; R=H, Me, MeO, NC, O₂N, under the control of tin mediated conditions (Sn-Al) and of crotyl organotin and cinnamyl organotin (allylic-SnL₃; L=Ph, nBu) catalysed by either BF₃.OEt₂ or heat were carried out and the results of these experiments discussed in the light of frontier molecular orbital theory. Molecular mechanics calculations were performed to evaluate the steric stability of rotamers of threo and erythro homoallylic alcohols and these used in association with electronic effects to explain the diastereoselectivity of the linear mechanism. Conformational analysis using MM calculations were undertaken in an attempt to rationalize the stereoselectivity at the cyclic transition state. Synthetic pathways to β,γ-epoxy ketones were explored and the synthesis of 38, 44, and 50 effected by a number of different paths to maximize yields; the diastereoselectivities of the epoxidations of intermediate hydroxy and acetoxy alkenes was investigated

Plasma Metabolomics Predicts Chemotherapy Response in Advanced Pancreatic Cancer.

Pancreatic cancer (PC) is one of the deadliest cancers. Developing biomarkers for chemotherapeutic response prediction is crucial for improving the dismal prognosis of advanced-PC patients (pts). To evaluate the potential of plasma metabolites as predictors of the response to chemotherapy for PC patients, we analyzed plasma metabolites using high-performance liquid chromatography-mass spectrometry from 31 cachectic, advanced-PC subjects enrolled into the PANCAX-1 (NCT02400398) prospective trial to receive a jejunal tube peptide-based diet for 12 weeks and who were planned for palliative chemotherapy. Overall, there were statistically significant differences in the levels of intermediates of multiple metabolic pathways in pts with a partial response (PR)/stable disease (SD) vs. progressive disease (PD) to chemotherapy. When stratified by the chemotherapy regimen, PD after 5-fluorouracil-based chemotherapy (e.g., FOLFIRINOX) was associated with decreased levels of amino acids (AAs). For gemcitabine-based chemotherapy (e.g., gemcitabine/nab-paclitaxel), PD was associated with increased levels of intermediates of glycolysis, the TCA cycle, nucleoside synthesis, and bile acid metabolism. These results demonstrate the feasibility of plasma metabolomics in a prospective cohort of advanced-PC patients for assessing the effect of enteral feeding as their primary source of nutrition. Metabolic signatures unique to FOLFIRINOX or gemcitabine/nab-paclitaxel may be predictive of a patient's response and warrant further study

Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project

The Human Proteome Project (HPP) annually reports on progress made throughout the field in credibly identifying and characterizing the complete human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2019–01–11 contains 17 694 proteins with strong protein-level evidence (PE1), compliant with HPP Guidelines for Interpretation of MS Data v2.1; these represent 89% of all 19 823 neXtProt predicted coding genes (all PE1,2,3,4 proteins), up from 17 470 one year earlier. Conversely, the number of neXtProt PE2,3,4 proteins, termed the “missing proteins” (MPs), has been reduced from 2949 to 2129 since 2016 through efforts throughout the community, including the chromosome-centric HPP. PeptideAtlas is the source of uniformly reanalyzed raw mass spectrometry data for neXtProt; PeptideAtlas added 495 canonical proteins between 2018 and 2019, especially from studies designed to detect hard-to-identify proteins. Meanwhile, the Human Protein Atlas has released version 18.1 with immunohistochemical evidence of expression of 17 000 proteins and survival plots as part of the Pathology Atlas. Many investigators apply multiplexed SRM-targeted proteomics for quantitation of organ-specific popular proteins in studies of various human diseases. The 19 teams of the Biology and Disease-driven B/D-HPP published a total of 160 publications in 2018, bringing proteomics to a broad array of biomedical research.G.S.O. acknowledges grant support from National Institutes of Health grants P30ES017885-01A1 and U24CA210967; E.W.D. from National Institutes of Health grants, R01GM087221, R24GM127667, U54EB020406, and the U19AG023122; L.L. and neXtProt from the SIB Swiss Institute of Bioinformatics; C.M.O. by a Canadian Institutes of Health Research Foundation Grant and a Canada Research Chair in Protease Proteomics and Systems Biology; M.S.B. by NHMRC Project Grant APP1010303; J.M.S. by the Knut and Alice Wallenberg Foundation for the Human Protein Atlas; and Y.-K.P. by grants from the Korean Ministry of Health and Welfare HI13C22098 and HI16C0257

Pathogenic copy number variants that affect gene expression contribute to genomic burden in cerebral palsy

Cerebral palsy (CP) is the most frequent movement disorder of childhood affecting 1 in 500 live births in developed countries. We previously identified likely pathogenic de novo or inherited single nucleotide variants (SNV) in 14% (14/98) of trios by exome sequencing and a further 5% (9/182) from evidence of outlier gene expression using RNA sequencing. Here, we detected copy number variants (CNV) from exomes of 186 unrelated individuals with CP (including our original 98 trios) using the CoNIFER algorithm. CNV were validated with Illumina 850 K SNP arrays and compared with RNA-Seq outlier gene expression analysis from lymphoblastoid cell lines (LCL). Gene expression was highly correlated with gene dosage effect. We resolved an additional 3.7% (7/186) of this cohort with pathogenic or likely pathogenic CNV while a further 7.7% (14/186) had CNV of uncertain significance. We identified recurrent genomic rearrangements previously associated with CP due to 2p25.3 deletion, 22q11.2 deletions and duplications and Xp monosomy. We also discovered a deletion of a single gene, PDCD6IP, and performed additional zebrafish model studies to support its single allele loss in CP aetiology. Combined SNV and CNV analysis revealed pathogenic and likely pathogenic variants in 22.7% of unselected individuals with CP

Progress on identifying and characterizing the human proteome: 2019 metrics from the HUPO human proteome project

The Human Proteome Project (HPP) annually reports on progress made throughout the field in credibly identifying and characterizing the complete human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2019-01-11 contains 17 694 proteins with strong protein-level evidence (PE1), compliant with HPP Guidelines for Interpretation of MS Data v2.1; these represent 89% of all 19 823 neXtProt predicted coding genes (all PE1,2,3,4 proteins), up from 17 470 one year earlier. Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), has been reduced from 2949 to 2129 since 2016 through efforts throughout the community, including the chromosome-centric HPP. PeptideAtlas is the source of uniformly reanalyzed raw mass spectrometry data for neXtProt; PeptideAtlas added 495 canonical proteins between 2018 and 2019, especially from studies designed to detect hard-to-identify proteins. Meanwhile, the Human Protein Atlas has released version 18.1 with immunohistochemical evidence of expression of 17 000 proteins and survival plots as part of the Pathology Atlas. Many investigators apply multiplexed SRM-targeted proteomics for quantitation of organ-specific popular proteins in studies of various human diseases. The 19 teams of the Biology and Disease-driven B/D-HPP published a total of 160 publications in 2018, bringing proteomics to a broad array of biomedical research

Research on The Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, according to the HUPO Human Proteome Project

According to the 2020 Metrics of the HUPO Human Proteome Project (HPP), expression has now been detected at the protein level for >90% of the 19,773 predicted proteins coded in the human genome. The HPP annually reports on progress made throughout the world toward credibly identifying and characterizing the complete human protein parts list and promoting proteomics as an integral part of multi-omics studies in medicine and the life sciences. NeXtProt release 2020-01 classified 17,874 proteins as PE1, having strong protein-level evidence, up 180 from 17,694 one year earlier. These represent 90.4% of the 19,773 predicted coding genes (all PE1,2,3,4 proteins in neXtProt). Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), was reduced by 230 from 2129 to 1899 since the neXtProt 2019-01 release. PeptideAtlas is the primary source of uniform re-analysis of raw mass spectrometry data for neXtProt, supplemented this year with extensive data from MassIVE. PeptideAtlas 2020-01 added 362 canonical proteins between 2019 and 2020 and MassIVE contributed 84 more, many of which converted PE1 entries based on non-MS evidence to the MS-based subgroup. The 19 Biology and Disease-driven B/D-HPP teams continue to pursue the identification of driver proteins that underlie disease states, the characterization of regulatory mechanisms controlling the functions of these proteins, their proteoforms, and their interactions, and the progression of transitions from correlation to co-expression to causal networks after system perturbations. And the Human Protein Atlas published Blood, Brain, and Metabolic Atlases