Organocatalytic and Late-Stage CH-Functionalization Enabled Asymmetric Synthesis of Communesin F and Putative Communesins

Herein we report the total syntheses of communesin F and putative members of the communesin family of polycyclic bis-aminal alkaloids. The successful strategy featured a novel organocatalytic reaction between two oxindole subunits to cast, after extensive optimization, the all-carbon vicinal quaternary stereocenters of the target molecule with high enantiocontrol. The resulting bis-oxindole intermediate further underwent a Ti­(O^<i>i</i>Pr)₄-mediated dehydrative skeletal rearrangement to furnish the communesin core structure. Consider the ready availability and low-cost of unsubstituted isatin, and the inferior organocatalytic reaction employing a bromo-substituted substrate, a Pd­(OAc)₂-catalyzed and oxalamide-directed aryl CH-alkenylation reaction was implemented to assemble the complete skeletal backbone of the target molecule. Collectively, the synthetic technologies disclosed herein constitute the first asymmetric organocatalytic approach to the communesins, together with a highly effective late-stage CH-functionalization in stark contrast to the bromoarene substrates employed in all of the past synthetic work

Proteogenomic Study beyond Chromosome 9: New Insight into Expressed Variant Proteome and Transcriptome in Human Lung Adenocarcinoma Tissues

This is a report of a human proteome project (HPP) related to chromosome 9 (Chr 9). To reveal missing proteins and undiscovered features in proteogenomes, both LC–MS/MS analysis and next-generation RNA sequencing (RNA-seq)-based identification and characterization were conducted on five pairs of lung adenocarcinoma tumors and adjacent nontumor tissues. Before our previous Chromosome-Centric Human Proteome Project (C-HPP) special issue, there were 170 remaining missing proteins on Chr 9 (neXtProt 2013.09.26 rel.); 133 remain at present (neXtProt 2015.04.28 rel.). In the proteomics study, we found two missing protein candidates that require follow-up work and one unrevealed protein across all chromosomes. RNA-seq analysis detected RNA expression for four nonsynonymous (NS) single nucleotide polymorphisms (SNPs) (in CDH17, HIST1H1T, SAPCD2, and ZNF695) and three synonymous SNPs (in CDH17, CST1, and HNF1A) in all five tumor tissues but not in any of the adjacent normal tissues. By constructing a cancer patient sample-specific protein database based on individual RNA-seq data and by searching the proteomics data from the same sample, we identified four missense mutations in four genes (LTF, HDLBP, TF, and HBD). Two of these mutations were found in tumor samples but not in paired normal tissues. In summary, our proteogenomic study of human primary lung tumor tissues detected additional and revealed novel missense mutations and synonymous SNP signatures, some of which are specific to lung cancers. Data from mass spectrometry have been deposited in the ProteomeXchange with the identifier PXD002523

Proteomic Analysis of the Aqueous Humor in Age-related Macular Degeneration (AMD) Patients

Age-related macular degeneration (AMD) can lead to irreversible central vision loss in the elderly. Although large number of growth factor pathways, including the vascular endothelial growth factor (VEGF), has been implicated in the pathogenesis of AMD, no study has directly assessed the whole proteomic composition in the aqueous humor (AH) among AMD patients. The AH contains proteins secreted from the anterior segment tissue, and these proteins may play an important role in the pathogenesis of AMD. Thus, comparisons between the AH proteomic profiles of AMD patients and non-AMD controls may lead to the verification of novel pathogenic proteins useful as potential clinical biomarkers. In this study, we used discovery-based proteomics and Multiple Reaction Monitoring Mass Spectrometry (MRM-MS) to analyze AH from AMD patients and AH from controls who underwent cataract surgery. A total of 154 proteins with at least two unique peptides were identified in the AH. Of these 154 proteins identified by discovery-based proteomics, 10 AH proteins were novel identifications. The protein composition in the AH was different between AMD patients and non-AMD controls. Subsequently, a systematic MRM-MS assay was performed in seven highly abundant differentially expressed proteins from these groups. Differential expression of three proteins was observed in the AH of AMD patients compared with that of cataract controls (<i>p</i> < 0.0312). Elucidation of the aqueous proteome will establish a foundation for protein function analysis and identify differentially expressed markers associated with AMD. This study demonstrates that integrated proteomic technologies can yield novel biomarkers to detect exudative AMD

Proteomic Analysis of the Aqueous Humor in Age-related Macular Degeneration (AMD) Patients

Age-related macular degeneration (AMD) can lead to irreversible central vision loss in the elderly. Although large number of growth factor pathways, including the vascular endothelial growth factor (VEGF), has been implicated in the pathogenesis of AMD, no study has directly assessed the whole proteomic composition in the aqueous humor (AH) among AMD patients. The AH contains proteins secreted from the anterior segment tissue, and these proteins may play an important role in the pathogenesis of AMD. Thus, comparisons between the AH proteomic profiles of AMD patients and non-AMD controls may lead to the verification of novel pathogenic proteins useful as potential clinical biomarkers. In this study, we used discovery-based proteomics and Multiple Reaction Monitoring Mass Spectrometry (MRM-MS) to analyze AH from AMD patients and AH from controls who underwent cataract surgery. A total of 154 proteins with at least two unique peptides were identified in the AH. Of these 154 proteins identified by discovery-based proteomics, 10 AH proteins were novel identifications. The protein composition in the AH was different between AMD patients and non-AMD controls. Subsequently, a systematic MRM-MS assay was performed in seven highly abundant differentially expressed proteins from these groups. Differential expression of three proteins was observed in the AH of AMD patients compared with that of cataract controls (<i>p</i> < 0.0312). Elucidation of the aqueous proteome will establish a foundation for protein function analysis and identify differentially expressed markers associated with AMD. This study demonstrates that integrated proteomic technologies can yield novel biomarkers to detect exudative AMD

Body Mass Index and Mortality in Korean Intensive Care Units: A Prospective Multicenter Cohort Study

<div><p>Background</p><p>The level of body mass index (BMI) that is associated with the lowest mortality in critically ill patients in Asian populations is uncertain. We aimed to examine the association of BMI with hospital mortality in critically ill patients in Korea.</p><p>Methods</p><p>We conducted a prospective multicenter cohort study of 3,655 critically ill patients in 22 intensive care units (ICUs) in Korea. BMI was categorized into five groups: <18.5, 18.5 to 22.9, 23.0 to 24.9 (the reference category), 25.0 to 29.9, and ≥30.0 kg/m².</p><p>Results</p><p>The median BMI was 22.6 (IQR 20.3 to 25.1). The percentages of patients with BMI<18.5, 18.5 to 22.9, 23.0 to 24.9, 25.0 to 29.9, and ≥30.0 were 12, 42.3, 19.9, 22.4, and 3.3%, respectively. The Cox-proportional hazard ratios with exact partial likelihood to handle tied failures for hospital mortality comparing the BMI categories <18.5, 18.5 to 22.9, 25.0 to 29.9, and ≥30.0 with the reference category were 1.13 (0.88 to 1.44), 1.03 (0.84 to 1.26), 0.96 (0.76 to 1.22), and 0.68 (0.43 to 1.08), respectively, with a highly significant test for trend (<i>p</i> = 0.02).</p><p>Conclusions</p><p>A graded inverse association between BMI and hospital mortality with a strong significant trend was found in critically ill patients in Korea.</p></div

Severity and outcomes according to body mass index.

<p>Continuous variables are presented as medians (interquartile ranges).</p><p>Categorical variables are presented as frequencies (%).</p><p>SAPS, simplified acute physiology score; PDR, predicted death rate; SOFA, sequential organ failure assessment; ICU, intensive care unit; LOS, length of stay; MV, mechanical ventilation; CRRT, continuous renal replacement therapy.</p

Cox-proportional hazard ratios with exact partial likelihood and 95% confidence intervals for hospital mortality according to body mass index categories.

<p>Categorical variables are presented as frequencies (%).</p><p>HR, hazard ratio; CI, confidence interval.</p><p>*Adjusted for age, sex, SOFA, CPF, DM, cancer, severe sepsis or septic shock at ICU admission, ARDS at ICU admission, admission category, use of CRRT, mechanical ventilation, and use of vasopressors.</p>†<p>Adjusted age, sex, SOFA, DM, cancer, severe sepsis or septic shock at ICU admission, ARDS at ICU admission, admission category, use of CRRT, mechanical ventilation, and use of vasopressors.</p>§<p>Adjusted age, sex, SOFA, cirrhosis, CPF, cancer, severe sepsis or septic shock at ICU admission, ARDS at ICU admission, admission category, use of CRRT, mechanical ventilation, and use of vasopressors.</p>‡<p>Adjusted age, sex, SOFA, cirrhosis, cancer, severe sepsis or septic shock at ICU admission, ARDS at ICU admission, use of CRRT, mechanical ventilation, and use of vasopressors.</p>#<p>Adjusted age, sex, SOFA, cirrhosis, CPF, cancer, severe sepsis or septic shock at ICU admission, ARDS at ICU admission, use of CRRT, mechanical ventilation, and use of vasopressors.</p

Multivariable-adjusted Cox-proportional hazard ratios with exact partial likelihood for hospital mortality comparing body mass index categories.

<p>Multivariable adjusted Cox-proportional hazard ratios with exact partial likelihood and 95% confidence intervals are shown in this figure, illustrating a graded inverse association between BMI and hospital mortality with a strong significant trend (<i>p</i> = 0.02).</p

Characterization of Site-Specific <i>N</i>‑Glycopeptide Isoforms of α‑1-Acid Glycoprotein from an Interlaboratory Study Using LC–MS/MS

Glycoprotein conformations are complex and heterogeneous. Currently, site-specific characterization of glycopeptides is a challenge. We sought to establish an efficient method of <i>N</i>-glycoprotein characterization using mass spectrometry (MS). Using alpha-1-acid glycoprotein (AGP) as a model <i>N</i>-glycoprotein, we identified its tryptic <i>N</i>-glycopeptides and examined the data reproducibility in seven laboratories running different LC–MS/MS platforms. We used three test samples and one blind sample to evaluate instrument performance with entire sample preparation workflow. 165 site-specific <i>N</i>-glycopeptides representative of all <i>N</i>-glycosylation sites were identified from AGP 1 and AGP 2 isoforms. The glycopeptide fragmentations by collision-induced dissociation or higher-energy collisional dissociation (HCD) varied based on the MS analyzer. Orbitrap Elite identified the greatest number of AGP <i>N</i>-glycopeptides, followed by Triple TOF and Q-Exactive Plus. Reproducible generation of oxonium ions, glycan-cleaved glycopeptide fragment ions, and peptide backbone fragment ions was essential for successful identification. Laboratory proficiency affected the number of identified <i>N</i>-glycopeptides. The relative quantities of the 10 major <i>N</i>-glycopeptide isoforms of AGP detected in four laboratories were compared to assess reproducibility. Quantitative analysis showed that the coefficient of variation was <25% for all test samples. Our analytical protocol yielded identification and quantification of site-specific <i>N</i>-glycopeptide isoforms of AGP from control and disease plasma sample