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Background: Psoriasis is a chronic, inflammatory autoimmune skin disease that affects 2–3% of the world’s population. Lesions are mainly found on the limbs, trunk, and scalp, but may also affect other parts of the body, and the cause is not yet known. The chronic and relapsing nature of psoriasis makes it one of the most complex and important diseases in current dermatology research. Methods: The search was conducted using PubMed, Embase, Cochrane Library, Web of Science, China National Knowledge Internet, Wanfang Data, VIP journals database, and Chinese biomedical literature database (CBM). The retrieval time limit was from the establishment of the database to January 2021. The quality of the selected literature was evaluated, and ReView Manager 5.3 was used for meta-analysis after randomized controlled trials were filtered. Results: Finally, 16 randomized controlled trials involving 1,967 patients were included. The total effective rate (OR = 3.68, 95% CI [2.73, 4.95], p < 0.00001), cure rate (OR = 2.01, 95% CI [1.62, 2.49], p < 0.00001), and PASI score (OR = –1.83, 95% CI [–2.39, –1.26], p < 0.00001) of the traditional Chinese medicine (TCM) were superior to the Diyin tablet. Conclusion: In the treatment of psoriasis, TCM shows higher efficacy than the Diyin tablet. However, due to the limitations of the included literature, we still need more double-blind, placebo-controlled trials with large samples and multiple centers to provide high-quality clinical evidence.

CRISPR screens with single-cell transcriptomic readouts are a valuable tool to understand the effect of genetic perturbations, but are currently limited because genotypes are inferred from the guide RNA identity. We have developed a technique that couples single-cell genotyping to transcriptomics of the same cells to enable screening for the effects of single nucleotide variants. Analysis of variants tiling across theJAK1gene demonstrates the importance of determining the precise genetic perturbation and classifies missense variants into three functional categories.

The distribution of precipitation in alpine regions with cold climates, such as Upper Reach of Shule River Basin (URSRB), northeastern edge of the Tibetan Plateau, is notoriously difficult to estimate from conventional measurements. Nine precipitation products, including CMFD, CMORPH, ERA-Interim, GPCC, GPCP V2.3, JRA-55, TRMM 3B43, HAR, and CAPD, were evaluated by six alpine ground-based measurement stations from 2001 to 2013 on yearly, seasonal, and monthly scales, respectively. The precipitation gradients of the nine precipitation products in rainy period were calculated by linear regression and then compared with recently observations during 2013–2016 from numerous total precipitation gauges. CMFD has the best overall performance in both yearly, seasonal, and monthly precipitation because it is primarily based on the merged precipitation product from surface measurements and satellite remote sensing data, followed by GPCC and TRMM 3B43. It is also found that CMORPH shows the worst overall performance due to only derived from remote sensing data. Nine precipitation products all showed obvious precipitation gradients. The absolute precipitation gradient of GPCC exhibited the greatest similarity to observations, followed by JRA-55 and CAPD. Although HAR obviously overestimated precipitation, it had an accurate pattern of monthly distribution and relative precipitation gradients in alpine areas, indicating that it has some advantages for applying on Tibetan Plateau. The evaluation suggested that the uncertainty in estimated alpine precipitation has largely decreased in some precipitation products, which will help to comprehensive understanding the climate change and its impact on hydrology of northeastern basins of the Tibetan Plateau.

CRISPR activation (CRISPRa) is an important tool to perturb transcription, but its effectiveness varies between target genes. We employ human pluripotent stem cells with thousands of randomly integrated barcoded reporters to assess epigenetic features that influence CRISPRa efficacy. Basal expression levels are influenced by genomic context and dramatically change during differentiation to neurons. Gene activation by dCas9-VPR is successful in most genomic contexts, including developmentally repressed regions, and activation level is anti-correlated with basal gene expression, whereas dCas9-p300 is ineffective in stem cells. Certain chromatin states, such as bivalent chromatin, are particularly sensitive to dCas9-VPR, whereas constitutive heterochromatin is less responsive. We validate these rules at endogenous genes and show that activation of certain genes elicits a change in the stem cell transcriptome, sometimes showing features of differentiated cells. Our data provide rules to predict CRISPRa outcome and highlight its utility to screen for factors driving stem cell differentiation.

IntroductionPatients with frequent acute exacerbation phenotype chronic obstructive pulmonary disease (AECOPD) have a higher hospitalisation rate than infrequent exacerbation, the disease progresses quickly and treatment is more difficult. At present, it is impossible to predict patients with COPD with frequent acute exacerbation phenotypes. The composition of the lower respiratory tract flora and the intestinal flora is closely related to AECOPD, but the specific association mechanism between them is not very clear. This study used metagenomic next-generation sequencing (mNGS) technology to explore the microbial characteristics of the intestinal tract and airways of patients with COPD, and analyse the correlation between the sequencing results and inflammatory factors, immune factors and nutritional factors.Methods and analysisThis will be a prospective cohort study. We intend to recruit 152 patients with stable COPD. In the baseline, we will detect the participants’ induced sputum and faecal flora through mNGS, and changes in blood immune levels, and the patient’s condition is evaluated. Every 2 months, we will check the number of acute exacerbation through the phone range. After 12 months, we will check again the changes in the blood immune level, evaluate the patient’s condition and count the number of episodes.Ethics and disseminationThis study has been approved by the ethics committee of Guangdong Provincial Hospital of Traditional Chinese Medicine (approval number ZF2019-219-03). The results of the study will be published in peer-reviewed journals.Trial registration numberClinicalTrials.gov Registry (ChiCTR2000032870).

INSIGHT is a two-stage COVID-19 test, which combines point-of-care diagnosis with NGS, aiming to achieve population-scale testing., We present INSIGHT [isothermal NASBA (nucleic acid sequence–based amplification) sequencing–based high-throughput test], a two-stage coronavirus disease 2019 testing strategy, using a barcoded isothermal NASBA reaction. It combines point-of-care diagnosis with next-generation sequencing, aiming to achieve population-scale testing. Stage 1 allows a quick decentralized readout for early isolation of presymptomatic or asymptomatic patients. It gives results within 1 to 2 hours, using either fluorescence detection or a lateral flow readout, while simultaneously incorporating sample-specific barcodes. The same reaction products from potentially hundreds of thousands of samples can then be pooled and used in a highly multiplexed sequencing–based assay in stage 2. This second stage confirms the near-patient testing results and facilitates centralized data collection. The 95% limit of detection is

SummaryHuman Induced Pluripotent Stem Cells (hiPSC) are an established patient-specific model system where opportunities are emerging for cell-based therapies. We contrast hiPSCs derived from different tissues, skin and blood, in the same individual. We show extensive single-nucleotide mutagenesis in all hiPSC lines, although fibroblast-derived hiPSCs (F-hiPSCs) are particularly heavily mutagenized by ultraviolet(UV)-related damage. We utilize genome sequencing data on 454 F-hiPSCs and 44 blood-derived hiPSCs (B-hiPSCs) to gain further insights. Across 324 whole genome sequenced(WGS) F-hiPSCs derived by the Human Induced Pluripotent Stem Cell Initiative (HipSci), UV-related damage is present in ~72% of cell lines, sometimes causing substantial mutagenesis (range 0.25-15 per Mb). Furthermore, we find remarkable genomic heterogeneity between independent F-hiPSC clones derived from the same reprogramming process in the same donor, due to oligoclonal populations within fibroblasts. Combining WGS and exome-sequencing data of 452 HipSci F-hiPSCs, we identify 272 predicted pathogenic mutations in cancer-related genes, of which 21 genes were hit recurrently three or more times, involving 77 (17%) lines. Notably, 151 of 272 mutations were present in starting fibroblast populations suggesting that more than half of putative driver events in F-hiPSCs were acquired in vivo. In contrast, B-hiPSCs reprogrammed from erythroblasts show lower levels of genome-wide mutations (range 0.28-1.4 per Mb), no UV damage, but a strikingly high prevalence of acquired BCOR mutations of ~57%, indicative of strong selection pressure. All hiPSCs had otherwise stable, diploid genomes on karyotypic pre-screening, highlighting how copy-number-based approaches do not have the required resolution to detect widespread nucleotide mutagenesis. This work strongly suggests that models for cell-based therapies require detailed nucleotide-resolution characterization prior to clinical application.

We present INSIGHT (Isothermal NASBA-Sequencing-based hIGH-througput Test): a two-stage COVID-19 testing strategy, using a barcoded isothermal NASBA reaction that combines point-of-care diagnosis with next generation sequencing, aiming to achieve population-scale COVID-19 testing. INSIGHT combines the advantages of near-patient with centralised testing. Stage 1 allows a quick decentralised readout for early isolation of pre-symptomatic or asymptomatic patients. The same reaction products can then be used in a highly multiplexed sequencing-based assay in Stage 2, confirming the near-patient testing results and facilitating centralised data collection. Based on experiments using commercially acquired human saliva with spiked-in viral RNA as input, the INSIGHT platform gives Stage 1 results within one to two hours, using either fluorescence detection or a lateral flow (dipstick) readout, whilst simultaneously incorporating sample-specific barcodes into the amplification product. INSIGHT Stage 2 can be performed by directly pooling and sequencing all post-amplification barcoded Stage 1 products from hundreds of thousands of samples with minimal sample preparation steps. The 95% limit of detection (LoD-95) for INSIGHT is estimated to be below 50 copies of viral RNA per 20 μl of reaction. Our two-stage testing strategy is suitable for further development into a rapid home-based and point-of-care assay, and is potentially scalable to the population level.

We present here INSIGHT (Isothermal NASBA-Sequencing based hIGH-througput Test): a two-stage COVID-19 testing strategy, using a combination of an isothermal NASBA reaction and next generation sequencing. From commercially acquired human saliva with spiked-in viral RNA as input, the first stage employs isothermal amplification of viral RNA to give a rapid result in one to two hours, using either fluorescence detection or a dipstick readout, whilst simultaneously incorporating sample-specific barcodes into the amplification product. In the first stage, fluorescent viral RNA detection can be consistently achieved at 10-100 copies per 20 µl reaction. The second stage pools post-amplification barcoded products from multiple samples for scalable sequencing that could be centralised, to further improve the accuracy of the test in a massively parallel way. Our two-stage testing strategy is suitable for further development into a home-based or point-of-care assay, and is potentially scalable to population level. IMPORTANT This protocol has not been validated on patient samples and should not be used for clinical diagnosis without further validation and certification. ***This is ongoing research to develop a testing strategy for the SARS-CoV-2 virus. The Wellcome Sanger Institute is not in a position to develop this into a commercial product, but would be open to discussions with third parties about how they could develop this further to achieve the societal benefits of this work.***

Soil moisture (SM) plays an important role in regional runoff variations, energy dynamics, and vegetation productivity. It is also widely used to detecting agricultural drought. Recently, a severe drought occurred in Yunnan Province in southwestern China, so long-term changes in surface SM were of concern. However, there were only 18 SM stations in Yunnan Province, and the longest observation was less than five years; thus, long-term changes in Climate Change Initiative (CCI) SM were investigated. CCI SM and in situ SM had similar trends of temporal variations and a systematic difference. The revised CCI SM was built by a linear regression model based on the relationship between in situ SM at each station and the corresponding grid of CCI SM. The revised CCI SM showed an abnormally low value during the severe drought in 2009, indicating that the monthly revised CCI SM could detect drought in Yunnan Province. SM drought easily occurred during the dry seasons, and the frequency of drought seems to decrease, but the severity of drought increased in the 21st century. The seasonal SM struggled to reflect drought correctly and accurately. CCI SM needs validation before use due to its variable quality. In summary, CCI SM provides a better tool than in situ SM to investigate long-term changes in SM and detect drought, and can be used for climate modeling.

Glacier changes in the Upper Reach of the Shule River Basin (URSRB) serve as a good indicator of climate change in the western part of the Qilian Mountains, located on the northeastern edge of the Tibetan Plateau. However, information on recent glacier changes in the URSRB is limited. In this study, the changes in ice surface elevation were determined using geodetic methods based on digital elevation models (DEMs) derived from the Shuttle Radar Topography Mission (SRTM) (2000), and from pairs of Third Resources Satellite (ZY-3) of China (taken around 2013). In addition, glacier area changes from 2000&ndash, 2015, were derived from Landsat TM/ETM+/OLI images. The results suggest that 478 glaciers with an area of 375.1 &plusmn, 2.68 km2 remained in the URSRB in 2015. Ice cover diminished by 57.5 &plusmn, 2.68 km2 (11.9 &plusmn, 0.60%), or 0.79 &plusmn, 0.04% a&minus, 1 and 35 small glaciers disappeared from 2000 to 2015 in the URSRB. The most pronounced glacier shrinkage occurred during 2004 to 2009. The average ice surface elevation of the URSRB from 1999 to 2013 reduced by about 4.98 &plusmn, 0.6 m, which is equal to a mass loss of 0.383 &plusmn, 0.046 m&middot, a&minus, 1. This reduction indicates that the ice storage loss has accelerated since 1999, compared to a mass loss of 0.21 &plusmn, 0.04 m&middot, 1 around Tuanjiefeng from 1966 to 1999, as reported by Xu et al. (2013).

Background/Objectives: Bariatric surgery offers sustained marked weight loss and often remission of type 2 diabetes, yet the mechanisms of establishment of these health benefits are not clear. Subjects/Methods: We mapped the coordinated systemic responses of gut hormones, the circulating miRNAome and the metabolome in a rat model of Roux-en-Y gastric bypass (RYGB) surgery. Results: The response of circulating microRNAs (miRNAs) to RYGB was striking and selective. Analysis of 14 significantly altered circulating miRNAs within a pathway context was suggestive of modulation of signaling pathways including G protein signaling, neurodegeneration, inflammation, and growth and apoptosis responses. Concomitant alterations in the metabolome indicated increased glucose transport, accelerated glycolysis and inhibited gluconeogenesis in the liver. Of particular significance, we show significantly decreased circulating miRNA-122 levels and a more modest decline in hepatic levels, following surgery. In mechanistic studies, manipulation of miRNA-122 levels in a cell model induced changes in the activity of key enzymes involved in hepatic energy metabolism, glucose transport, glycolysis, tricarboxylic acid cycle, pentose phosphate shunt, fatty-acid oxidation and gluconeogenesis, consistent with the findings of the in vivo surgery-mediated responses, indicating the powerful homeostatic activity of the miRNAs. Conclusions: The close association between energy metabolism, neuronal signaling and gut microbial metabolites derived from the circulating miRNA, plasma, urine and liver metabolite and gut hormone correlations further supports an enhanced gut-brain signaling, which we suggest is hormonally mediated by both traditional gut hormones and miRNAs. This transomic approach to map the crosstalk between the circulating miRNAome and metabolome offers opportunities to understand complex systems biology within a disease and interventional treatment setting.

Post-transcriptional silencing by microRNAs (miRNAs) is a critical constituent of eukaryotic gene regulation. miRNAs are short (~22nt) noncoding RNAs capable of specifically targeting the miRNA-induced-silencing-complex (miRISC) to transcripts bearing a complementary miRNA response element (MRE). Although recent methodological advances have greatly improved our understanding of miRNA biogenesis and the mechanisms by which miRNAs repress their cognate targets, exploring the physiological relevance of direct miRNA-target interactions in vivo has remained an outstanding challenge. Here we describe the experimental protocol underlying a novel approach, which allows direct interrogation of specific miRNA-MRE interactions by CRISPR/Cas9-mediated genome engineering. In this instance, the CRISPR/Cas9 system is first used to catalyze homology-directed replacement of candidate MREs with molecular barcodes at endogenous loci. Subsequently, the effect of MRE mutation on transcript abundance (i.e., MRE activity) can be rapidly evaluated by routine quantitative PCR. This strategy enables functional investigation of a putative miRNA-target pair in a pool of transiently transfected cells, obviating the need for generation of clonal cell lines or transgenic animals. This protocol can be implemented in any cell line in less than 2 weeks, and can readily be scaled up for multiplex studies. To facilitate the conceptual workflow underlying this strategy, we also describe a genome-wide resource for automated design and computational evaluation of CRISPR/Cas9 guide RNAs targeting all predicted MREs in various species (miR-CRISPR).

Post-transcriptional silencing by microRNAs (miRNAs) is a critical constituent of eukaryotic gene regulation. miRNAs are short (~22nt) noncoding RNAs capable of specifically targeting the miRNA-induced-silencing-complex (miRISC) to transcripts bearing a complementary miRNA response element (MRE). Although recent methodological advances have greatly improved our understanding of miRNA biogenesis and the mechanisms by which miRNAs repress their cognate targets, exploring the physiological relevance of direct miRNA–target interactions in vivo has remained an outstanding challenge. Here we describe the experimental protocol underlying a novel approach, which allows direct interrogation of specific miRNA–MRE interactions by CRISPR/Cas9-mediated genome engineering. In this instance, the CRISPR/Cas9 system is first used to catalyze homology-directed replacement of candidate MREs with molecular barcodes at endogenous loci. Subsequently, the effect of MRE mutation on transcript abundance (i.e., MRE activity) can be rapidly evaluated by routine quantitative PCR. This strategy enables functional investigation of a putative miRNA–target pair in a pool of transiently transfected cells, obviating the need for generation of clonal cell lines or transgenic animals. This protocol can be implemented in any cell line in less than 2 weeks, and can readily be scaled up for multiplex studies. To facilitate the conceptual workflow underlying this strategy, we also describe a genome-wide resource for automated design and computational evaluation of CRISPR/Cas9 guide RNAs targeting all predicted MREs in various species (miR-CRISPR).

Bariatric surgery, also known as metabolic surgery, is an effective treatment for morbid obesity which also offers pronounced metabolic effects including the resolution of type 2 diabetes and a decrease in cardiovascular disease and long-term cancer risk. However, the mechanisms of surgical weight loss and the long term consequences of bariatric surgery remain unclear. Bariatric surgery has been demonstrated to alter the composition of both the microbiome and the metabolic phenotype. We observed a marked shift towards Gammaproteobacteria, particularly Enterobacter hormaechei, following Roux-en-Y gastric bypass (RYGB) surgery in a rat model compared with sham operated controls. Fecal water from RYGB surgery rats was highly cytotoxic to rodent cells (mouse lymphoma cell line), although In contrast, fecal water from sham operated animals showed no/very low cytotoxicity. This shift in the gross structure of the microbiome correlated with greatly increased cytotoxicity in a regulatory acceptable mouse lymphoma assay. Urinary phenylacetylglycine and indoxyl sulfate and fecal GABA, putrescine, tyramine and uracil were found to be inversely correlated with cell survival rate. This profound co-dependent response of mammalian and microbial metabolism to RYGB surgery and the impact on the cytotoxicity of the gut luminal environment suggests that RYGB exerts local and global metabolic effects which may have an influence on long term cancer risk and cytotoxic load.

Obesity is a worldwide public health issue which can lead to cardiovascular disease, type 2 diabetes, and cancers. Bariatric surgery can provide sustained weight loss and a significant reduction of cancer risk. MicroRNAs are approximately 22 nucleotide long post transcription regulators. MicroRNAs are suggested to play important roles in obesity and metabolic syndrome related biological processes, but also are involved in different types of cancer. Recently microRNAs have been shown to be present in blood, and it is proposed that circulating microRNAs may be biomarker of tissue biochemistry and pathology. The aim of this study is to investigate if the circulation microRNA profile is changed by bariatric surgery and whether the altered microRNA expression could contribute to the long term reduced predisposition cancer risk associated with such surgery. Total plasma RNA from 53 days post bariatric surgery and sham operated rats were isolated and then examined using Taqman Rodent MicroRNA A+B Cards which have the capacity to evaluate expression levels of 373 rat microRNAs. Four different normalization methods (Global, cel-miR-39 spiked in, U6 endogenous and five endogenous microRNAs normalization) were tested. Five endogenous microRNAs normalization was found to be optimal and selected for all downstream analysis. Our preliminary data showed that 113 microRNAs were expressed in the plasma of bariatric surgical rats and 92 in sham operated rats. Furthermore, an OPLS-DA model clearly showed that bariatric surgery changed the circulating microRNA expression profile. Among nineteen of the most significantly changed microRNAs, nine of them are relevant to cancer. In summary, our data suggest that bariatric surgery fundamentally changed circulating microRNA expression. Understanding the significance of these changes in circulating microRNA may give clues to the mechanisms whereby bariatric surgery affords health benefits to individual undergoing such surgery, including a reduced predisposition to disease such as cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4130. doi:1538-7445.AM2012-4130