Quality and clinical applicability of recommendations for incontinence-associated dermatitis: A systematic review of guidelines and consensus statements

AIMS AND OBJECTIVES

The aim of this study was to assess methodological quality of all currently available guidelines and consensus statements for IAD using the Appraisal of Guidelines, Research and Evaluation (AGREE) II and the AGREE Recommendation Excellence (AGREE-REX) instruments.

BACKGROUND

Globally, incontinence-associated dermatitis (IAD) is a significant health challenge. IAD is a complex healthcare problem that reduces quality of life of patients, increases healthcare costs and prolongs hospital stays. Several guidelines and consensus statements are available for IAD. However, the quality of these guidelines and consensus statements remains unclear.

DESIGN

A systematic review of guidelines and consensus statements.

METHODS

Our study was undertaken using PRISMA guidelines. We searched seven electronic databases. Guidelines and consensus statements had to be published in English, Chinese or German languages. Five independent reviewers assessed the methodological quality of guidelines and consensus statements using the AGREE II and AGREE-REX instruments. Mean with standard deviation (SD) and median with interquartile range (IQR) were calculated for descriptive analyses. We generated bubble plots to describe the assessment results of each domain of each guideline and consensus statement.

RESULTS

We included ten guidelines and consensus statements. The NICE guidelines, obtained the highest scores, fulfilled 86.11%-98.61% of criteria in AGREE II and 76.67%-91.11% for AGREE-REX. In the domains 'Stakeholder Involvement' (4.39 ± 1.64), 'Rigor of Development' (3.38 ± 1.86), 'Applicability' (3.62 ± 1.64), 'Editorial Independence' (3.91 ± 2.56) and 'Values and Preferences' (2.98 ± 1.41), the remaining guidelines and consensus statements showed deficiencies.

CONCLUSIONS

Altogether, this study demonstrated that the currently available guidelines and consensus statements for IAD have room for methodological improvement. NICE guidelines on faecal incontinence and urinary incontinence have better quality. Remaining guidelines and consensus statements showed substantial methodological weaknesses, especially the domains of 'Stakeholder Involvement', 'Rigor of Development', 'Applicability', 'Editorial independence' and 'Values and Preferences'. This study was registered on INPLASY. (Registration number: INPLASY202190078).

RELEVANCE TO CLINICAL PRACTICE

The currently available guidelines and consensus statements on IAD have room for methodological improvement.

Deep Single-Cell-Type Proteome Profiling of Mouse Brain by Nonsurgical AAV-Mediated Proximity Labeling

Proteome profiling is a powerful tool in biological and biomedical studies, starting with samples at bulk, single-cell, or single-cell-type levels. Reliable methods for extracting specific cell-type proteomes are in need, especially for the cells (e.g., neurons) that cannot be readily isolated. Here, we present an innovative proximity labeling (PL) strategy for single-cell-type proteomics of mouse brain, in which TurboID (an engineered biotin ligase) is used to label almost all proteins in a specific cell type. This strategy bypasses the requirement of cell isolation and includes five major steps: (i) constructing recombinant adeno-associated viruses (AAVs) to express TurboID driven by cell-type-specific promoters, (ii) delivering the AAV to mouse brains by direct intravenous injection, (iii) enhancing PL labeling by biotin administration, (iv) purifying biotinylated proteins, followed by on-bead protein digestion, and (v) quantitative tandem-mass-tag (TMT) labeling. We first confirmed that TurboID can label a wide range of cellular proteins in human HEK293 cells and optimized the single-cell-type proteomic pipeline. To analyze specific brain cell types, we generated recombinant AAVs to coexpress TurboID and mCherry proteins, driven by neuron- or astrocyte-specific promoters and validated the expected cell expression by coimmunostaining of mCherry and cellular markers. Subsequent biotin purification and TMT analysis identified ∼10,000 unique proteins from a few micrograms of protein samples with excellent reproducibility. Comparative and statistical analyses indicated that these PL proteomes contain cell-type-specific cellular pathways. Although PL was originally developed for studying protein-protein interactions and subcellular proteomes, we extended it to efficiently tag the entire proteomes of specific cell types in the mouse brain using TurboID biotin ligase. This simple, effective in vivo approach should be broadly applicable to single-cell-type proteomics.

SMAP is a pipeline for sample matching in proteogenomics

The integration of genomics and proteomics data (proteogenomics) holds the promise of furthering the in-depth understanding of human disease. However, sample mix-up is a pervasive problem in proteogenomics because of the complexity of sample processing. Here, we present a pipeline for Sample Matching in Proteogenomics (SMAP) to verify sample identity and ensure data integrity. SMAP infers sample-dependent protein-coding variants from quantitative mass spectrometry (MS), and aligns the MS-based proteomic samples with genomic samples by two discriminant scores. Theoretical analysis with simulated data indicates that SMAP is capable of uniquely matching proteomic and genomic samples when ≥20% genotypes of individual samples are available. When SMAP was applied to a large-scale dataset generated by the PsychENCODE BrainGVEX project, 54 samples (19%) were corrected. The correction was further confirmed by ribosome profiling and chromatin sequencing (ATAC-seq) data from the same set of samples. Our results demonstrate that SMAP is an effective tool for sample verification in a large-scale MS-based proteogenomics study. SMAP is publicly available at https://github.com/UND-Wanglab/SMAP, and a web-based version can be accessed at https://smap.shinyapps.io/smap/.

Sample mix-up is a potential problem in large-scale omic studies due to the complexity of sample processing. Here, the authors present a pipeline for sample matching in proteogenomics to verify sample identity and ensure data integrity.

Scalp Acupuncture Attenuates Brain Damage After Intracerebral Hemorrhage Through Enhanced Mitophagy and Reduced Apoptosis in Rats

To study the effect of scalp acupuncture (SA) on the mitophagy signaling pathway in the caudate nucleus of Sprague-Dawley rats following intracerebral hemorrhage (ICH). An ICH model was established by injecting autologous arterial blood into the caudate nucleus in 200 male Sprague-Dawley rats, which were divided into five groups: sham, ICH, 3-methyladenine group (3-MA, 30 mg/kg), SA, and SA+3-MA. Animals were analyzed at 6 and 24 h as well as at 3 and 7 days. Composite neurological scale score was significantly higher in the SA group than in the ICH group. Transmission electron microscopy showed less structural damage and more autophagic vacuoles within brain in the SA group than in the ICH group. SA group showed higher levels of Beclin1, Parkin, PINK1, NIX protein, and a lower level of Caspase-9 in brain tissue. These animals consequently showed less neural cell apoptosis. Compared with the SA group, however, the neural function score and levels of mitophagy protein in the SA+3-MA group were decreased, neural cell apoptosis was increased with more severe structural damage, which suggested that 3-MA may antagonize the protective effect of SA on brain in rats with ICH. SA may mitigate the neurologic impairment after ICH by enhancing mitophagy and reducing apoptosis.

Proteomic Profiling of Cerebrospinal Fluid by 16-Plex TMT-Based Mass Spectrometry

Mass spectrometry (MS) has become a mainstream platform for comprehensive profiling of proteome, especially with the improvement of multiplexed tandem mass tag labeling coupled with two-dimensional liquid chromatography and tandem mass spectrometry (TMT-LC/LC-MS/MS). Recently, we have established a robust method for direct profiling of undepleted cerebrospinal fluid (CSF) proteome with the 16-plex TMTpro method, in which we optimized parameters in experimental steps of sample preparation, TMT labeling, LC/LC fractionation, tandem mass spectrometry, and computational data processing. The extensive LC fractionation not only enhances proteome coverage of the CSF but also alleviates ratio distortion of TMT quantification. The crucial quality control steps and improvements specific for the TMT16 analysis are highlighted. More than 3000 proteins can be quantified in a single experiment from 16 different CSF samples. This multiplexed method offers a powerful tool for profiling a variety of complex biofluids samples such as CSF, serum/plasma, and other clinical specimens.

Molecular identification of glucose transporter 4: The responsiveness to starvation, glucose, insulin and glucagon on glucose transporter 4 in common carp (Cyprinus carpio L.)

Glucose transporter 4 (GLUT4) is comprehensively investigated in mammals, while the comparative research of GLUT4 in common carp is deficient. To investigate the function of GLUT4, carp glut4 was first isolated. The open reading frame of carp glut4 was 1518 bp in length, encoding 505 amino acids. A high-sequence homology was identified in carp and teleost, and the phylogenetic tree displayed that the carp GLUT4 was clustered with the teleost. A high level of glut4 mRNA was analysed in fat, red muscle and white muscle. After fasting treatment, glut4 mRNA expression was increased significantly in muscle. In the oral glucose tolerance test experiment, glut4 mRNA was also significantly elevated in muscle, gut and fat. Furthermore, intraperitoneal injection of insulin resulted in the upregulation of glut4 gene expression significantly in white muscle, gut and fat. On the contrary, the glut4 mRNA level in the white muscle, gut and fat was markedly downregulated after glucagon injection. These results suggest that GLUT4 might play important roles in food intake and could be regulated by nutrient condition, insulin and glucagon in common carp. Our study is the first to report on GLUT4 in common carp. These data provide a basis for further study on fish GLUT4.

CRISPR screens unveil signal hubs for nutrient licensing of T cell immunity

Nutrients are emerging regulators of adaptive immunity1. Selective nutrients interplay with immunological signals to activate mechanistic target of rapamycin complex 1 (mTORC1), a key driver of cell metabolism2-4, but how these environmental signals are integrated for immune regulation remains unclear. Here we use genome-wide CRISPR screening combined with protein-protein interaction networks to identify regulatory modules that mediate immune receptor- and nutrient-dependent signalling to mTORC1 in mouse regulatory T (Treg) cells. SEC31A is identified to promote mTORC1 activation by interacting with the GATOR2 component SEC13 to protect it from SKP1-dependent proteasomal degradation. Accordingly, loss of SEC31A impairs T cell priming and Treg suppressive function in mice. In addition, the SWI/SNF complex restricts expression of the amino acid sensor CASTOR1, thereby enhancing mTORC1 activation. Moreover, we reveal that the CCDC101-associated SAGA complex is a potent inhibitor of mTORC1, which limits the expression of glucose and amino acid transporters and maintains T cell quiescence in vivo. Specific deletion of Ccdc101 in mouse Treg cells results in uncontrolled inflammation but improved antitumour immunity. Collectively, our results establish epigenetic and post-translational mechanisms that underpin how nutrient transporters, sensors and transducers interplay with immune signals for three-tiered regulation of mTORC1 activity and identify their pivotal roles in licensing T cell immunity and immune tolerance.

The quality and clinical applicability of recommendations in anxiety disorders guidelines: A systematic review of seventeen guidelines from seven countries

BACKGROUND

Anxiety disorders are the most common mental disorders, for which some countries and organizations have developed guidelines. It is necessary to understand the quality of these guidelines.

METHODS

The relevant guidelines were searched systematically by five reviewers using Appraisal of Guidelines for Research and Evaluation (AGREE) II and AGREE Recommendation Excellence (AGREE-REX) instruments. The scores in each domain were descriptively analyzed, and guidelines from different countries were compared.

RESULTS

Seventeen guidelines were included. The scores in the domains "rigor of development" and "applicability" were the lowest and ranged from 16% to 77% and 25% to 71%, respectively. The scores in the domains "implementability" and "values and preferences" were similar and ranged from 30% to 67% and 25% to 77%. In terms of the comparison among countries, the Canadian guidelines achieved the highest scores in many domains but only scored 43% in the domain of "values and preferences". The Indian guidelines scored less than 50% in many domains but achieved a high score of 83% in the domain "scope and purpose".

LIMITATIONS

Language restrictions may cause selection bias. Besides, insufficient reports may lead to deviation of assessment results.

CONCLUSIONS

There was no obvious advantage in guidelines from different countries. There was still a lot of room for improvement in some domains, especially "applicability", "implementability", "rigor of development" and "values and preferences".

A brain proteomic signature of incipient Alzheimer's disease in young APOE ε4 carriers identifies novel drug targets

Aptamer-based proteomics revealed differentially abundant proteins in Alzheimer’s disease (AD) brains in the Baltimore Longitudinal Study of Aging and Religious Orders Study (mean age, 89 ± 9 years). A subset of these proteins was also differentially abundant in the brains of young APOE ε4 carriers relative to noncarriers (mean age, 39 ± 6 years). Several of these proteins represent targets of approved and experimental drugs for other indications and were validated using orthogonal methods in independent human brain tissue samples as well as in transgenic AD models. Using cell culture–based phenotypic assays, we showed that drugs targeting the cytokine transducer STAT3 and the Src family tyrosine kinases, YES1 and FYN, rescued molecular phenotypes relevant to AD pathogenesis. Our findings may accelerate the development of effective interventions targeting the earliest molecular triggers of AD.

Acute depletion of CTCF rewires genome-wide chromatin accessibility

BACKGROUND

The transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studies. However, acute depletion of CTCF globally reduces chromatin interactions but does not significantly alter transcription.

RESULTS

Here, we systematically integrate multi-omics data including ATAC-seq, RNA-seq, WGBS, Hi-C, Cut&Run, and CRISPR-Cas9 survival dropout screens, and time-solved deep proteomic and phosphoproteomic analyses in cells carrying auxin-induced degron at endogenous CTCF locus. Acute CTCF protein degradation markedly rewires genome-wide chromatin accessibility. Increased accessible chromatin regions are frequently located adjacent to CTCF-binding sites at promoter regions and insulator sites associated with enhanced transcription of nearby genes. In addition, we use CTCF-associated multi-omics data to establish a combinatorial data analysis pipeline to discover CTCF co-regulatory partners. We successfully identify 40 candidates, including multiple established partners. Interestingly, many CTCF co-regulators that have alterations of their respective downstream gene expression do not show changes of their own expression levels across the multi-omics measurements upon acute CTCF loss, highlighting the strength of our system to discover hidden co-regulatory partners associated with CTCF-mediated transcription.

CONCLUSIONS

This study highlights that CTCF loss rewires genome-wide chromatin accessibility, which plays a critical role in transcriptional regulation.

Abstract 1543: Mining cancer-specific isoforms as CAR T-cell therapy targets for pediatric solid and brain tumors

Immunotherapy with T-cells expressing chimeric antigen receptors (CARs) holds the promise to improve outcomes for children with solid and brain tumors. However, at present, there is a limited array of targetable antigens. We posit here that targets generated by alternative splicing events (ASEs) in cancer cells present an untapped class of CAR targets since many of these are tumor-specific and overexpressed in malignant cells. Thus, we developed Cancer-Specific Isoform Miner (CSI-Miner), a pipeline to perform a comprehensive ASE analysis of pediatric cancers to discover CSIs as CAR T-cell therapy targets. We analyzed 1,938 solid and brain tumor samples collected from PCGP, TARGET, and St. Jude's real-time clinical sequencing data sets. In addition, 7,527 GTEx RNAseq samples across 31 human tissues were harmonized to prioritize exon candidates with minimal expression in normal tissue. Through CSI-Miner, we identified 40,748 highly expressed exons from the tumor's surfaceome and secretome, of which 185 were unannotated novel exons. Taking advantage of available mass-spectrometry proteome data from the Clinical Proteomic Tumor Analysis Consortium and St. Jude's proteomics facility, we validated the presence of peptides encoded by these novel exons for rhabdomyosarcoma, medulloblastoma, high-grade glioma, low-grade glioma, and ependymoma. Moreover, non-malignant mass-spectrometry data from muscle and brain samples were incorporated as negative controls. Several secretome targets were identified that adhered to the surface of cancer cells, including EDB, an oncofetal splice variant of fibronectin. EDB was expressed in a broad range of pediatric solid and brain tumors, including Ewing sarcoma and high-grade glioma. We generated T-cells expressing a 2nd generation EDB-CAR (EDB-CAR T-cells) by standard retroviral transduction. EDB-CAR T-cells recognized and killed EDB+ cancer cells in vitro and had potent antitumor activity in xenograft models, resulting in improved overall survival compared to control mice. Importantly, EDB-CAR T-cells did not induce ‘on target/off cancer' toxicities in mice, which is encouraging since EDB is identical in mice and humans. c-MET was also identified as a candidate surfaceome CAR target for rhabdomyosarcoma and melanoma. In summary, we developed CSI-Miner, an integrative analysis pipeline to discover CSIs as CAR T-cell therapy targets, comprised of 248 surfaceome and 51 secretome candidates, for pediatric solid and brain tumors. At present we have validated these CSIs by mass-spectrometry and successfully generated CAR T-cells for one of the candidates. Collectively, CSIs present an untapped class of immunotherapy targets that hold the promise to improve current CAR T-cell therapy approaches for a wide range of pediatric solid and brain tumors. A web portal has been developed supporting access and visualization of this data set to the research community.

Citation Format: Timothy I. Shaw, Jessica Wagner, Elizabeth Wickman, Liqing Tian, Dong Li, Suresh Poudel, Elizabeth Stewart, Yuxin Li, Hong Wang, Mingming Niu, Robin Paul, Colleen Reilly, Xin Zhou, Michael Dyer, Suzanne Baker, Junmin Peng, Jiyang Yu, Paulina Velasquez, Chris DeRenzo, Giedre Krenciute, Jinghui Zhang, Stephen Gottschalk. Mining cancer-specific isoforms as CAR T-cell therapy targets for pediatric solid and brain tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1543.

Prespecification of subgroup analyses and examination of treatment-subgroup interactions in cancer individual participant data meta-analyses are suboptimal

OBJECTIVES

This study aimed to explore the prespecification and conduct of subgroup analyses in cancer individual participant data meta-analyses (IPDMAs).

STUDY DESIGN AND SETTING

We searched PubMed, Embase.com, Cochrane Library, and Web of Science to identify IPDMAs of randomized controlled trials evaluating intervention effects for cancer. We evaluated how often cancer IPDMAs prespecify subgroup analyses and statistical approaches for examining treatment-subgroup interactions and handling continuous subgroup variables.

RESULTS

We included 89 IPDMAs, of which 41 (46.1%) reported a statistically significant treatment-subgroup interaction (P < 0.05) in at least one subgroup analysis. 47 (52.8%) IPDMAs prespecified methods for conducting subgroup analyses and the remaining 42 (47.2%) did not prespecify subgroup analyses. Of the 47 IPDMAs prespecified subgroup analyses, 19 performed the planned subgroup analyses, 21 added subgroup analyses, 7 reduced subgroup analyses. Eighty IPDMAs examined treatment-subgroup interactions, but 72 IPDMAs did not provide enough information to determine whether an appropriate approach that avoided aggregation bias was used. 85 IPDMAs that used continuous variables in subgroup analyses categorized continuous variables and only 1 IPDMA examined non-linear relationships.

CONCLUSION

Many cancer IPDMAs did not prespecify subgroup analyses, nor did they fully perform planned subgroup analyses. Lack of details for the test of treatment-subgroup interactions and examination of non-linear interactions was suboptimal.

Global Profiling of Lysine Accessibility to Evaluate Protein Structure Changes in Alzheimer's Disease

The linear sequence of amino acids in a protein folds into a 3D structure to execute protein activity and function, but it is still challenging to profile the 3D structure at the proteome scale. Here, we present a method of native protein tandem mass tag (TMT) profiling of Lys accessibility and its application to investigate structural alterations in human brain specimens of Alzheimer's disease (AD). In this method, proteins are extracted under a native condition, labeled by TMT reagents, followed by trypsin digestion and peptide analysis using two-dimensional liquid chromatography and tandem mass spectrometry (LC/LC-MS/MS). The method quantifies Lys labeling efficiency to evaluate its accessibility on the protein surface, which may be affected by protein conformations, protein modifications, and/or other molecular interactions. We systematically optimized the amount of TMT reagents, reaction time, and temperature and then analyzed protein samples under multiple conditions, including different labeling time (5 and 30 min), heat treatment, AD and normal human cases. The experiment profiled 15370 TMT-labeled peptides in 4475 proteins. As expected, the heat treatment led to extensive changes in protein conformations, with 17% of the detected proteome displaying differential labeling. Compared to the normal controls, AD brain showed different Lys accessibility of tau and RNA splicing complexes, which are the hallmarks of AD pathology, as well as proteins involved in transcription, mitochondrial, and synaptic functions. To eliminate the possibility that the observed differential Lys labeling was caused by protein level change, the whole proteome was quantified with standard TMT-LC/LC-MS/MS for normalization. Thus, this native protein TMT method enables the proteome-wide measurement of Lys accessibility, representing a straightforward strategy to explore protein structure in any biological system.

Removing leakage-induced correlated errors in superconducting quantum error correction

Quantum computing can become scalable through error correction, but logical error rates only decrease with system size when physical errors are sufficiently uncorrelated. During computation, unused high energy levels of the qubits can become excited, creating leakage states that are long-lived and mobile. Particularly for superconducting transmon qubits, this leakage opens a path to errors that are correlated in space and time. Here, we report a reset protocol that returns a qubit to the ground state from all relevant higher level states. We test its performance with the bit-flip stabilizer code, a simplified version of the surface code for quantum error correction. We investigate the accumulation and dynamics of leakage during error correction. Using this protocol, we find lower rates of logical errors and an improved scaling and stability of error suppression with increasing qubit number. This demonstration provides a key step on the path towards scalable quantum computing.

Associating the risk of three urinary cancers with obesity and overweight: an overview with evidence mapping of systematic reviews

BACKGROUND

The relationship between cancer with overweight and obesity has been extensively reported. However, the association between urinary cancers with these risk factors remains unclear, with existing reports showing conflicting findings. The current review, therefore, sought to clarify the latter association by assessing the methodological and reporting quality of existing systematic reviews on the subject.

METHODS

We first screened PubMed, EMBASE, and Cochrane Library databases for relevant literature and subjected the resulting articles to meta-analysis. We adopted the AMSTAR-2 and PRISMA checklists for assessing methodological and reporting quality, respectively, then performed meta-analyses to determine the relationship between incidence and mortality of three types of urinary cancers with obesity and overweight. Indirect comparisons were also done across subgroups.

RESULTS

All systematic reviews (SRs) were of critically low methodological quality. Seventeen SRs had minimal reporting flaws, and 11 SRs had minor reporting flaws. We found an association between obesity with an incidence of kidney (RR = 1.68, 95% CI 1.47-1.92), bladder (RR = 1.1, 95% CI 1.07-1.13), and prostate (RR = 1.02, 95% CI 0.91, 1.13) cancers. Similarly, overweight was associated with the incidence of the three types of cancer, recording RR values of 1.37 (95% CI 1.26-1.48), 1.07 (95% CI 1.03-1.1), and 1 (95% CI 0.93, 1.07) for kidney, bladder, and prostate cancers, respectively. With regard to the dose analysis, the RR of BMI (per 5 kg/m2 increase) was associated with kidney (RR = 1.24, 95% CI 1.2-1.28), bladder (RR = 1.03, 95% CI 1.02-1.05), and prostate (RR = 1.02, 95% CI 1.01, 1.03) cancers.

CONCLUSIONS

This comprehensive quantitative analysis provides an affirmation that overweight and obesity are strong risk factors for kidney cancer, owing to a strong association between them. Conversely, a weak association between overweight and obesity with bladder and prostate cancers confirms their status as mild risk factors for the 2 types of cancer. But due to the low quality of included SRs, the results need to be interpreted with caution.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO CRD42019119459.

Molecular identification of FNDC5 and effect of irisin on the glucose metabolism in common carp (Cyprinus carpio L.)

Irisin, encoded by fibronectin type III domain-containing protein 5 (FNDC5) gene, plays a role in energy expenditure and insulin sensitivity in mice. In fish, the function of irisin related to glucose metabolism is less reported. It may increase glucose utilization in fish. The aim of the present study was to characterize the regulatory role of irisin in glucose metabolism in common carp (Cyprinus carpio L.). In this study, FNDC5a and FNDC5b were isolated from common carp. The cDNA of FNDC5a and FNDC5b were 722 bp and 714 bp, encoding 221 and 207 amino acids, respectively. FNDC5a was abundantly expressed in the brain and gonad. FNDC5b was mainly expressed in brain. Different expression pattern of FNDC5a and FNDC5b under fasting/refeeding and OGTT experiment were identified. The recombinant common carp irisinA and irisinB were prepared by prokaryotic expression system. Glucose concentration was decreased in treatment with irisinA or irisinB in the in vitro and in vivo experiments. The mRNA expression levels of gluconeogenesis-related genes were significantly down-regulated, while the mRNA expression of glycolysis-related genes were significantly up-regulated after treatment with recombinant irisinA or irisinB in liver in vivo and in primary hepatocytes in vitro. Our research shows that irisin inhibits hepatic gluconeogenesis and promotes hepatic glycolysis. Taken together, this study for the first time revealed the two subtypes of FNDC5 and explored the function and mechanisms of irisinA and irisinB in fish glucose homeostasis.

Diffusion-tensor imaging for differentiating uterine sarcoma from degenerative uterine fibroids

AIM

To explore the applicability of diffusion-tensor imaging (DTI) sequence quantitative parameters in differentiating uterine sarcoma (USr) from degenerative uterine fibroids (DUF).

MATERIALS AND METHODS

Fourteen cases of USr and 30 cases of DUF were analysed retrospectively. The diffusion-weighted imaging (DWI) and DTI images were analysed by two observers using Functool software on a ADW4.6 workstation. The images were post-processed to generate an apparent diffusion coefficient (ADC) map of DWI, ADC map of DTI (ADC^T map), and fractional anisotropy (FA) map. Three regions of interest (ROI) were selected from the ADC, ADC^T, and FA maps to obtain the ADC, ADC^T, and FA values. The receiver operating characteristic (ROC) curves of all parameters were used to analyse and compare the diagnostic value of USr and DUF.

RESULTS

The ADC value, ADC^T value, and FA value of USr (1.190 ± 0.262 × 10^-3mm²/s, 1.165 ± 0.270 × 10^-9mm²/s, 0.168 ± 0.063) were significantly lower compared to the values for DUF (1.525 ± 0.314 × 10^-3mm²/s, 1.650 ± 0.332 × 10^-9mm²/s, 0.254 ± 0.111; all p<0.001). The diagnostic threshold values for USr were: ADC ≤1.290 × 10^-3mm²/s, ADC^T ≤1.322 × 10^-9mm²/s and FA ≤0.192. The corresponding sensitivities and specificities were 78.6%/90%, 96.7%/92.9%, and 86.7%/85.7%, respectively. The areas under the curve (AUC) were 0.875, 0.974, and 0.831, respectively.

CONCLUSIONS

DTI quantitative parameters can be used to differentiate USr from DUF. The ADC^T value had the highest diagnostic efficacy.

Demonstrating a Continuous Set of Two-Qubit Gates for Near-Term Quantum Algorithms

Quantum algorithms offer a dramatic speedup for computational problems in material science and chemistry. However, any near-term realizations of these algorithms will need to be optimized to fit within the finite resources offered by existing noisy hardware. Here, taking advantage of the adjustable coupling of gmon qubits, we demonstrate a continuous two-qubit gate set that can provide a threefold reduction in circuit depth as compared to a standard decomposition. We implement two gate families: an imaginary swap-like (iSWAP-like) gate to attain an arbitrary swap angle, θ, and a controlled-phase gate that generates an arbitrary conditional phase, ϕ. Using one of each of these gates, we can perform an arbitrary two-qubit gate within the excitation-preserving subspace allowing for a complete implementation of the so-called Fermionic simulation (fSim) gate set. We benchmark the fidelity of the iSWAP-like and controlled-phase gate families as well as 525 other fSim gates spread evenly across the entire fSim(θ,ϕ) parameter space, achieving a purity-limited average two-qubit Pauli error of 3.8×10^{-3} per fSim gate.

Brevibacillus migulae sp. nov., isolated from a Yellow River sediment sample

Strain CFH S0501^T, a novel Gram-stain-positive, aerobic, rod-shaped, endospore-forming and motile micro-organism with peritrichous flagella, was isolated from a sediment sample collected from the Yellow River in Henan Province, PR China. Optimum growth was observed at 28 °C, pH 7.0 and without NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the strain belonged to the genus Brevibacillus and was closely related to Brevibacillus centrosporus DSM 8445^T and Brevibacillus ginsengisoli Gsoil 3088^T (with 96.8 and 96.7 % sequence similarity, respectively). The predominant menaquinone was MK-7. Major cellular fatty acids were anteiso-C_15 : 0 and iso-C_15 : 0. Polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, two unidentified phospholipids and an unidentified polar lipid. The cell-wall peptidoglycan was found to contain meso-diaminopimelic acid. The genome size was 5.26 Mbp with a G+C content of 49.7 mol%. The average nucleotide identity (ANI) and in silico DNA-DNAhybridization (DDH) values between CFH S0501^T and the other species of the genus Brevibacillus were found to be low (ANIm <86.11 %, ANIb <70.30 % and DDH <25.00 %). Based on physiological properties, chemotaxonomic characteristics and low ANI and DDH results, strain CFH S0501^T is considered to represent a novel species, for which the name Brevibacillus migulae sp. nov. is proposed. The type strain is CFH S0501^T (=DSM 29940^T=BCRC 80809^T).

High-throughput and Deep-proteome Profiling by 16-plex Tandem Mass Tag Labeling Coupled with Two-dimensional Chromatography and Mass Spectrometry

Isobaric tandem mass tag (TMT) labeling is widely used in proteomics because of its high multiplexing capacity and deep proteome coverage. Recently, an expanded 16-plex TMT method has been introduced, which further increases the throughput of proteomic studies. In this manuscript, we present an optimized protocol for 16-plex TMT-based deep-proteome profiling, including protein sample preparation, enzymatic digestion, TMT labeling reaction, two-dimensional reverse-phase liquid chromatography (LC/LC) fractionation, tandem mass spectrometry (MS/MS), and computational data processing. The crucial quality control steps and improvements in the process specific for the 16-plex TMT analysis are highlighted. This multiplexed process offers a powerful tool for profiling a variety of complex samples such as cells, tissues, and clinical specimens. More than 10,000 proteins and posttranslational modifications such as phosphorylation, methylation, acetylation, and ubiquitination in highly complex biological samples from up to 16 different samples can be quantified in a single experiment, providing a potent tool for basic and clinical research.

Integrated analysis of ultra-deep proteomes in cortex, cerebrospinal fluid and serum reveals a mitochondrial signature in Alzheimer's disease

BACKGROUND

Based on amyloid cascade and tau hypotheses, protein biomarkers of different Aβ and tau species in cerebrospinal fluid (CSF) and blood/plasma/serum have been examined to correlate with brain pathology. Recently, unbiased proteomic profiling of these human samples has been initiated to identify a large number of novel AD biomarker candidates, but it is challenging to define reliable candidates for subsequent large-scale validation.

METHODS

We present a comprehensive strategy to identify biomarker candidates of high confidence by integrating multiple proteomes in AD, including cortex, CSF and serum. The proteomes were analyzed by the multiplexed tandem-mass-tag (TMT) method, extensive liquid chromatography (LC) fractionation and high-resolution tandem mass spectrometry (MS/MS) for ultra-deep coverage. A systems biology approach was used to prioritize the most promising AD signature proteins from all proteomic datasets. Finally, candidate biomarkers identified by the MS discovery were validated by the enzyme-linked immunosorbent (ELISA) and TOMAHAQ targeted MS assays.

RESULTS

We quantified 13,833, 5941, and 4826 proteins from human cortex, CSF and serum, respectively. Compared to other studies, we analyzed a total of 10 proteomic datasets, covering 17,541 proteins (13,216 genes) in 365 AD, mild cognitive impairment (MCI) and control cases. Our ultra-deep CSF profiling of 20 cases uncovered the majority of previously reported AD biomarker candidates, most of which, however, displayed no statistical significance except SMOC1 and TGFB2. Interestingly, the AD CSF showed evident decrease of a large number of mitochondria proteins that were only detectable in our ultra-deep analysis. Further integration of 4 cortex and 4 CSF cohort proteomes highlighted 6 CSF biomarkers (SMOC1, C1QTNF5, OLFML3, SLIT2, SPON1, and GPNMB) that were consistently identified in at least 2 independent datasets. We also profiled CSF in the 5xFAD mouse model to validate amyloidosis-induced changes, and found consistent mitochondrial decreases (SOD2, PRDX3, ALDH6A1, ETFB, HADHA, and CYB5R3) in both human and mouse samples. In addition, comparison of cortex and serum led to an AD-correlated protein panel of CTHRC1, GFAP and OLFM3. In summary, 37 proteins emerged as potential AD signatures across cortex, CSF and serum, and strikingly, 59% of these were mitochondria proteins, emphasizing mitochondrial dysfunction in AD. Selected biomarker candidates were further validated by ELISA and TOMAHAQ assays. Finally, we prioritized the most promising AD signature proteins including SMOC1, TAU, GFAP, SUCLG2, PRDX3, and NTN1 by integrating all proteomic datasets.

CONCLUSIONS

Our results demonstrate that novel AD biomarker candidates are identified and confirmed by proteomic studies of brain tissue and biofluids, providing a rich resource for large-scale biomarker validation for the AD community.

A longitudinal study on α-synuclein in plasma neuronal exosomes as a biomarker for Parkinson's disease development and progression

BACKGROUND AND PURPOSE

The identification of reliable diagnostic and prognostic biomarkers for Parkinson's disease (PD) is urgently needed. Here, we explored the potential use of α-synuclein (α-syn) in plasma neuronal exosomes as a biomarker for early PD diagnosis and disease progression.

METHODS

This study included both cross-sectional and longitudinal designs. The subjects included 36 patients with early-stage PD, 17 patients with advanced PD, 20 patients with idiopathic rapid eye movement sleep behavior disorder and 21 healthy controls (HCs). α-syn levels were measured by electrochemiluminescence immunoassay. A subgroup of patients with early-stage PD (n = 18) participated in a follow-up examination with repeated blood collection and clinical assessments after an average of 22 months.

RESULTS

The α-syn levels in plasma neuronal exosomes were significantly higher in patients with early-stage PD compared with HCs (P = 0.007). Differences in α-syn levels between patients with idiopathic rapid eye movement sleep behavior disorder and HCs did not reach statistical significance (P = 0.08). In addition, Spearman correlation analysis revealed that neuronal exosomal α-syn concentrations were correlated with Movement Disorders Society Unified Parkinson's Disease Rating Scale III/(I + II + III) scores, Non-Motor Symptom Questionnaire scores and Sniffin' Sticks 16-item test scores of patients with PD (P < 0.05). After a mean follow-up of 22 months in patients with early-stage PD, a Cox regression analysis adjusted for age and gender showed that longitudinally increased α-syn rather than baseline α-syn levels were associated with higher risk for motor symptom progression in PD (P = 0.039).

CONCLUSIONS

Our results suggested that α-syn in plasma neuronal exosomes may serve as a biomarker to aid early diagnosis of PD and also as a prognostic marker for PD progression.