Expression profiling of cerebrospinal fluid identifies dysregulated antiviral mechanisms in multiple sclerosis.

Despite the overwhelming evidence that multiple sclerosis is an autoimmune disease, relatively little is known about the precise nature of the immune dysregulation underlying the development of the disease. Reasoning that the CSF from patients might be enriched for cells relevant in pathogenesis, we have completed a high-resolution single-cell analysis of 96 732 CSF cells collected from 33 patients with multiple sclerosis (n = 48 675) and 48 patients with other neurological diseases (n = 48 057). Completing comprehensive cell type annotation, we identified a rare population of CD8+ T cells, characterized by the upregulation of inhibitory receptors, increased in patients with multiple sclerosis. Applying a Multi-Omics Factor Analysis to these single-cell data further revealed that activity in pathways responsible for controlling inflammatory and type 1 interferon responses are altered in multiple sclerosis in both T cells and myeloid cells. We also undertook a systematic search for expression quantitative trait loci in the CSF cells. Of particular interest were two expression quantitative trait loci in CD8+ T cells that were fine mapped to multiple sclerosis susceptibility variants in the viral control genes ZC3HAV1 (rs10271373) and IFITM2 (rs1059091). Further analysis suggests that these associations likely reflect genetic effects on RNA splicing and cell-type specific gene expression respectively. Collectively, our study suggests that alterations in viral control mechanisms might be important in the development of multiple sclerosis.

Representation learning of RNA velocity reveals robust cell transitions.

RNA velocity is a promising technique for quantifying cellular transitions from single-cell transcriptome experiments and revealing transient cellular dynamics among a heterogeneous cell population. However, the cell transitions estimated from high-dimensional RNA velocity are often unstable or inaccurate, partly due to the high technical noise and less informative projection. Here, we present Velocity Autoencoder (VeloAE), a tailored representation learning method, to learn a low-dimensional representation of RNA velocity on which cellular transitions can be robustly estimated. On various experimental datasets, we show that VeloAE can both accurately identify stimulation dynamics in time-series designs and effectively capture expected cellular differentiation in different biological systems. VeloAE, therefore, enhances the usefulness of RNA velocity for studying a wide range of biological processes.

CsA promotes trophoblast invasion accompanied by changes in leukaemic inhibitory factor and fibroblast growth factor in peri-implantation blastocysts.

During the early stages of human pregnancy, successful implantation of embryonic trophoblast cells into the endometrium depends on good communication between trophoblast cells and the endometrium. Abnormal trophoblast cell function can cause embryo implantation failure. In this study, we added cyclosporine A (CsA) to the culture medium to observe the effect of CsA on embryonic trophoblast cells and the related mechanism. We observed that CsA promoted the migration and invasion of embryonic trophoblast cells. CsA promoted the expression of leukaemic inhibitory factor (LIF) and fibroblast growth factor (FGF). In addition, CsA promoted the secretion and volume increase in vesicles in the CsA-treated group compared with the control group. Therefore, CsA may promote the adhesion and invasion of trophoblast cells through LIF and FGF and promote the vesicle dynamic process, which is conducive to embryo implantation.

Cyclosporine A improves the binding of mouse embryos to fibronectin.

AIM: The binding of integrin αvß3 with endometrial fibronectin (FN) promotes the migration of preimplantation embryos in mice. We have previously shown that cyclosporine A (CsA) improves the adhesion and invasion of mouse preimplantation embryos. In this study, we evaluated the roles of calcium ions and downstream signaling factors in the binding of integrin αvß3 to FN. METHODS: Female Institute of Cancer Research (ICR) mice were superovulated and mated, and two-cell embryos were harvested from the oviducts and cultured to the blastocyst stage The adhesion and stretching growth of hatched embryos in laminin-coated dishes were evaluated, and integrinß3 expression was determined using qPCR. Blastocytes were cultured with 0 or 1 µM $$ \upmu \mathrm{M} $$ cyclosporine A (CsA) and the attachment of embryonic integrin αvß3 to FN120 was observed using a fluorescent bead. To further determine the mechanism, the cells were also incubated with calcium ions and protein kinase C and calmodulin antagonists. The binding of integrin αvß3 to FN120 was examined via confocal laser scanning microscopy. RESULTS: The adhesion and stretching growth of peri-implantation embryos were greater and integrinß3 expression was higher in the 1 µM CsA group than in the 0 µM CsA group (p < 0.05). When incubated with calcium ions and protein kinase C and calmodulin antagonists, the ability of peri-implantation embryos to bind to FN decreased; CsA treatment promoted this binding. CONCLUSION: This study revealed that CsA up - regulates integrinß3 expression in peri - implantation embryos and promotes binding to FN via calcium ions, and protein kinase C, and calmodulin. These findings provide evidence supporting the beneficial effect of CsA on the peri - implantation embryo adhesion.

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.

Bulk and single-cell DNA sequencing has enabled reconstructing clonal substructures of somatic tissues from frequency and cooccurrence patterns of somatic variants. However, approaches to characterize phenotypic variations between clones are not established. Here we present cardelino (https://github.com/single-cell-genetics/cardelino), a computational method for inferring the clonal tree configuration and the clone of origin of individual cells assayed using single-cell RNA-seq (scRNA-seq). Cardelino flexibly integrates information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. We apply cardelino to a published cancer dataset and to newly generated matched scRNA-seq and exome-seq data from 32 human dermal fibroblast lines, identifying hundreds of differentially expressed genes between cells from different somatic clones. These genes are frequently enriched for cell cycle and proliferation pathways, indicating a role for cell division genes in somatic evolution in healthy skin.

Comparison of recombinant human FSH biosimilar QL1012 with Gonal-f® for ovarian stimulation: a phase-three trial.

RESEARCH QUESTION: Are QL1012 and Gonal-f® equivalent in women undergoing ovarian stimulation for assisted reproductive technology (ART)? DESIGN: This multicentre, randomized, assessor-blinded, phase-three trial was conducted at 13 centres in China. Eligible patients were infertile women; age 20-39 years; body mass index 18-30 kg/m2; regular menstrual cycles; and indication for ART. After successful pituitary downregulation, patients were randomly assigned (1:1) to receive QL1012 or Gonal-f®, stratified by age (initial dose of 75-150 IU for women younger than 30 years, 150-225 IU for women aged 30-34 years and 225-300 IU for women aged ≥35 years, subcutaneously, once daily). The primary end point was the number of oocytes retrieved. RESULTS: Between October 2018, and June 2019, 341 patients were included in the per-protocol set. The mean numbers of oocytes retrieved were 14.7 ± 7.0 in the QL1012 group (n = 169) and 13.4 ± 6.1 in the Gonal-f® group (n = 172). Adjusted by analysis of covariance model, the least-squares mean difference was 1.3 oocytes (95% CI -0.1 to 2.7; P = 0.0650), within the pre-defined equivalence margins of ±3.0. Similar results were observed in the full analysis set. Additionally, no statistical differences were found in secondary end points except oestradiol concentration (median 3948.0 pg/ml versus 3545.3 pg/ml; P = 0.0015). Ovarian hyperstimulation syndrome (12.4% versus 13.1 %) and other adverse events were similar between the two groups. CONCLUSIONS: Therapeutic equivalence and similar safety profiles were demonstrated between QL1012 and Gonal-f® in women undergoing ovarian stimulation for ART.

Cellsnp-lite: an efficient tool for genotyping single cells.

SUMMARY: Single-cell sequencing is an increasingly used technology and has promising applications in basic research and clinical translations. However, genotyping methods developed for bulk sequencing data have not been well adapted for single-cell data, in terms of both computational parallelization and simplified user interface. Here, we introduce a software, cellsnp-lite, implemented in C/C++ and based on well-supported package htslib, for genotyping in single-cell sequencing data for both droplet and well-based platforms. On various experimental datasets, it shows substantial improvement in computational speed and memory efficiency with retaining highly concordant results compared to existing methods. Cellsnp-lite, therefore, lightens the genetic analysis for increasingly large single-cell data. AVAILABILITY AND IMPLEMENTATION: The source code is freely available at https://github.com/single-cell-genetics/cellsnp-lite. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast.

The functional consequences of alternative splicing on altering the transcription rate have been the subject of intensive study in mammalian cells but less is known about effects of splicing on changing the transcription rate in yeast. We present several lines of evidence showing that slow RNA polymerase II elongation increases both cotranscriptional splicing and splicing efficiency and that faster elongation reduces cotranscriptional splicing and splicing efficiency in budding yeast, suggesting that splicing is more efficient when cotranscriptional. Moreover, we demonstrate that altering the RNA polymerase II elongation rate in either direction compromises splicing fidelity, and we reveal that splicing fidelity depends largely on intron length together with secondary structure and splice site score. These effects are notably stronger for the highly expressed ribosomal protein coding transcripts. We propose that transcription by RNA polymerase II is tuned to optimize the efficiency and accuracy of ribosomal protein gene expression, while allowing flexibility in splice site choice with the nonribosomal protein transcripts.

Cryopreservation of human induced pluripotent stem cells by using a new CryoLogic vitrification method.

Human induced pluripotent stem cells (hiPSCs) have the properties of differentiation potential and unlimited self-renewal. Developing efficient and highly safe methods to preserve hiPSCs is important due to they have demonstrated tremendous promise in disease etiology, drug discovery, and regenerative medicine applications. Traditionally, open systems for cell cryopreservation, such as conventional slow freezing and vitrification methods, were widespread application in the storage and transportation of hiPSCs. However, these two methods have such problems of low recovery rate and the risk of cross-contamination. Recently, closed systems for cell cryopreservation, such as CryoLogic Vitrification Method (CVM), were introduced to store and transport embryos. In this study, we developed a new friendly CVM by loading a small piece of hiPSCs colonies in the vitrification solution to the hook of Fiberplug to increase the cooling rate. To warm them, the CVM Fiberplug was immersed directly in a 37 °C warming solution for 1 min, and hiPSCs were then transferred to mTeSR1 medium. The result revealed that the new CVM had a high recovery rate and maintained the stemness and differentiation potential of hiPSCs. Our new CVM not only provide a safe way for hiPSCs preservation but also has a high survival rate in the storage of hiPSCs.

Down-regulated FOXA1 in early-onset pre-eclampsia induces apoptosis, and inhibits migration and invasion of trophoblast cells.

BACKGROUND: Pre-eclampsia (PE) is a major cause of maternal and neonatal mortality and morbidity. Abnormal invasion of trophoblast cells is a major pathogenesis observed in PE. In the present study, we aimed to explore the association between forkhead box A1 (FOXA1) and early-onset pre-eclampsia (EOPE) and to determine the effects of FOXA1 on trophoblast cell apoptosis, migration and invasion. METHODS: Clinical data and placentas of patients with EOPE and normal pregnant women were collected in the First Affiliated Hospital of Hainan Medical College. The protein expression levels of FOXA1 in the clinical samples were evaluated by western blotting and immunohistochemistry. The effects of FOXA1 knockdown on HTR-8/SVneo cell apoptosis, migration and invasion were evaluated by flow cytometry, wound healing and transwell invasion assays, respectively. RESULTS: The western blot and immunohistochemical analysis showed that FOXA1 protein expression in placenta of EOPE group was significantly lower than that of normal group. The expression of FOXA1 in the placentas of EOPE and normal pregnant women was negatively correlated with systolic pressure and diastolic pressure. The expression of FOXA1 in EOPE and normal pregnant women was positively correlated with gestation weeks at delivery and neonatal birthweight. In vitro functional studies showed that silencing FOXA1 increased apoptosis, and inhibited the migration and invasion of HTR-8/SVneo cells. CONCLUSIONS: Down-regulation of FOXA1 in the placentas may indicate poor prognosis of EOPE. Silencing of FOXA1 induced apoptosis in trophoblast cells, and impaired the migratory and invasive capacity of trophoblast cells. FOXA1 may represent a potential therapeutic target for EOPE.

Effects of cyclosporine A on proliferation, invasion and migration of HTR-8/SVneo human extravillous trophoblasts.

As shown in our previous study, cyclosporine A (CsA) promotes the proliferation, invasion and migration of villous trophoblasts, thus improving embryo implantation. In addition, the incidence of preeclampsia (PE) is decreased in patients with recurrent spontaneous abortion (RSA) and repeated implantation failure (RIF) treated with CsA during the first trimester. Abnormal function of extravillous trophoblasts (EVTs) in early pregnancy is recognized as the pathogenetic mechanism of PE. EVTs share homology and function with pre-villous trophoblasts and villous trophoblasts; thus, we hypothesized that CsA may have the same regulatory effect on EVTs. In this study, we investigated the effects of CsA on HTR-8/SVneo trophoblasts in the extravillous layer and explored the underlying mechanisms. QPCR and Western blot (WB) analyses were performed to detect expression alterations in relevant proliferation and invasion proteins in response to different concentrations of CsA. We used an Affymetrix IVT expression microarray to examine the target genes of CsA in preeclamptic placentas versus normal placentas. Our results showed that certain concentrations of CsA could promote the proliferation, invasion and migration of HTR8/SVneo cells. CsA was also found to promote the expression of titin, MMP9, EGFR, and PRR15. TRAIL may be a target gene for CsA-mediated regulation of EVTs. CONCLUSIONS: By promoting the expression of related proteins and regulating the functions of HTR8/SVneo cells, CsA can promote vascular recasting and placental function, which may affect the pathogenesis of PE.

Systematic characterization and prediction of post-translational modification cross-talk between proteins.

MOTIVATION: Protein post-translational modifications (PTMs) regulate a wide range of cellular protein functions. Many PTM sites from the same (intra) or different (inter) proteins often cooperate with each other to perform a function, which is defined as PTM cross-talk. PTM cross-talk within proteins attracted great attentions in the past a few years. However, the inter-protein PTM cross-talk is largely under studied due to its large protein pair space and lack of a gold standard dataset, even though the PTM interplay between proteins is a key element in cell signaling and regulatory networks. RESULTS: In this study, 199 inter-protein PTM cross-talk pairs in 82 pairs of human proteins were collected from literature, which to our knowledge is the first effort in compiling such dataset. By comparing with background PTM pairs from the same protein pairs, we found that inter-protein cross-talk PTM pairs have higher sequence co-evolution at both PTM residue and motif levels. Also, we found that cross-talk PTMs have higher co-modification across multiple species and 88 human tissues or conditions. Furthermore, we showed that these features are predictive for PTM cross-talk between proteins, and applied a random forest model to integrate these features with achieving an area under the receiver operating characteristic curve of 0.81 in 10-fold cross-validation, prevailing over using any single feature alone. Therefore, this method would be a valuable tool to identify inter-protein PTM cross-talk at proteome-wide scale. AVAILABILITY AND IMPLEMENTATION: A web server for prioritization of both intra- and inter-protein PTM cross-talk candidates is at http://bioinfo.bjmu.edu.cn/ptm-x/. Python code for local computer is also freely available at https://github.com/huangyh09/PTM-X. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The CSRP2BP histone acetyltransferase drives smooth muscle gene expression.

The expression of nearly all smooth muscle genes are controlled by serum response factor binding sites in their promoter regions. However, SRF alone is not sufficient for regulating smooth muscle cell development. It associates with other cardiovascular specific cofactors to regulate smooth muscle gene expression. Previously, we showed that the transcription co-factor CRP2 was a regulator of smooth muscle gene expression. Here, we report that CSRP2BP, a coactivator for CRP2, is a histone acetyltransferase and a driver of smooth muscle gene expression. CSRP2BP directly interacted with SRF, CRP2 and myocardin. CSRP2BP synergistically activated smooth muscle gene promoters in an SRF-dependent manner. A combination of SRF, GATA6 and CRP2 required CSRP2BP for robust smooth muscle gene promoter activity. Knock-down of Csrp2bp in smooth muscle cells resulted in reduced smooth muscle gene expression. We conclude that the CSRP2BP histone acetyltransferase is a coactivator for CRP2 that works synergistically with SRF and myocardin to regulate smooth muscle gene expression.

Statistical modeling of isoform splicing dynamics from RNA-seq time series data.

MOTIVATION: Isoform quantification is an important goal of RNA-seq experiments, yet it remains problematic for genes with low expression or several isoforms. These difficulties may in principle be ameliorated by exploiting correlated experimental designs, such as time series or dosage response experiments. Time series RNA-seq experiments, in particular, are becoming increasingly popular, yet there are no methods that explicitly leverage the experimental design to improve isoform quantification. RESULTS: Here, we present DICEseq, the first isoform quantification method tailored to correlated RNA-seq experiments. DICEseq explicitly models the correlations between different RNA-seq experiments to aid the quantification of isoforms across experiments. Numerical experiments on simulated datasets show that DICEseq yields more accurate results than state-of-the-art methods, an advantage that can become considerable at low coverage levels. On real datasets, our results show that DICEseq provides substantially more reproducible and robust quantifications, increasing the correlation of estimates from replicate datasets by up to 10% on genes with low or moderate expression levels (bottom third of all genes). Furthermore, DICEseq permits to quantify the trade-off between temporal sampling of RNA and depth of sequencing, frequently an important choice when planning experiments. Our results have strong implications for the design of RNA-seq experiments, and offer a novel tool for improved analysis of such datasets. AVAILABILITY AND IMPLEMENTATION: Python code is freely available at http://diceseq.sf.net CONTACT: G.Sanguinetti@ed.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Systematic characterization and prediction of post-translational modification cross-talk.

Post-translational modification (PTM)(1) plays an important role in regulating the functions of proteins. PTMs of multiple residues on one protein may work together to determine a functional outcome, which is known as PTM cross-talk. Identification of PTM cross-talks is an emerging theme in proteomics and has elicited great interest, but their properties remain to be systematically characterized. To this end, we collected 193 PTM cross-talk pairs in 77 human proteins from the literature and then tested location preference and co-evolution at the residue and modification levels. We found that cross-talk events preferentially occurred among nearby PTM sites, especially in disordered protein regions, and cross-talk pairs tended to co-evolve. Given the properties of PTM cross-talk pairs, a naïve Bayes classifier integrating different features was built to predict cross-talks for pairwise combination of PTM sites. By using a 10-fold cross-validation, the integrated prediction model showed an area under the receiver operating characteristic (ROC) curve of 0.833, superior to using any individual feature alone. The prediction performance was also demonstrated to be robust to the biases in the collected PTM cross-talk pairs. The integrated approach has the potential for large-scale prioritization of PTM cross-talk candidates for functional validation and was implemented as a web server available at http://bioinfo.bjmu.edu.cn/ptm-x/.

Low dose Cyclosporin A treatment increases live birth rate of unexplained recurrent abortion - initial cohort study.

BACKGROUND AND OBJECTIVE: Pregnancy is similar to allogeneic transplantation. Eighty percent of unexplained recurrent spontaneous abortions (URSA) relate to disturbances of immune regulation. Cyclosporin A (CsA) is a immunosuppressant widely used after organ transplantation and to treat autoimmune disease. Animal studies show that low dose of CsA could induce maternal-fetal immunity tolerance while enhance trophoblast invasion. So far no clinical trial reported on the effect and safety of cyclosporin A treatment for URSA has been published. The objective of this study was to explore the effect, safety, and mechanism of low-dose CsA treatment in human patients in order to find a novel therapy to treat URSA. MATERIALS AND METHODS: Eighty-six patients with eligible URSA treated at the clinic of the present hospital were included in this study from December 2009 to December 2012. The research was approved by the Ethics committee. Through a clinical study with prospective non-randomized controlled trials, the patients were divided into CsA treatment group (n = 66 cases) and in control group (n = 20 cases) based on the patients' choice. Both groups started treatment as soon as the pregnancy test was positive. Patients in the treatment group were treated with oral CsA 100 mg/day for 30 days. Patients in the control group were treated with progesterone 20 mg im per day until 12 weeks of gestation. Cytoimmunology test of CD3, CD4, CD8, CD4/8, CD4/25, CD19/21, and Th/Ts were examined before and after the treatment in both groups. Clinical consequences of mothers and fetuses were followed up and recorded. Live birth rate and cytoimmunology markers and their change before and after the treatment were analyzed and compared between the two groups. RESULTS: The live birth rate was significantly higher in study group (41/66, 62.1%) than in the control group (6/20, 30.0%) (p < 0.001). There was no obvious side effect and adverse consequence in the pregnancy women. No IUGR or birth defect was observed in fetus in this study. After CsA treatment, CD3 level in maternal blood was higher in successful group than abortion group but CD8 level was decreased after CsA treatment. CONCLUSIONS: Low-dose CsA treatment increases live birth rate of unexplained recurrent abortion. No maternal-fetal adverse consequence was observed in this study and it is safe in clinic use. The mechanism of CsA therapy may be related to immune regulation which may favor the success of pregnancy.

Comparison of the outcome of conventional in vitro fertilization and intracytoplasmic sperm injection in moderate male infertility from ejaculate.

OBJECTIVE: To evaluate whether couples with moderate male infertility should be treated with conventional in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI). PATIENTS AND METHODS: A total of 249 couples with moderate male infertility undergoing their first IVF/ICSI cycle were enrolled in the study. The couples were divided into two groups according to the results of semen analysis: moderate oligozoospermia (O group) and moderate oligoasthenozoospermia (OA group). Sibling oocytes were randomized into groups to be inseminated either by conventional IVF or ICSI. Fertilization rate, embryo quality, implantation rate, and clinical pregnancy rate were examined. RESULTS: There was no difference in the fertilization, implantation, and pregnancy rates between conventional IVF and ICSI in either the O group or OA group (p > 0.05). Additionally, in the OA group, the good quality embryo rate was similar after IVF or ICSI (p > 0.05). However, in the O group, the good quality embryo rate was significantly higher after ICSI than after IVF (p < 0.05). CONCLUSIONS: Couples with moderate oligozoospermia or moderate oligoasthenozoospermia did not influence the major indices of IVF. Because of the uncertainties concerning the safety of ICSI, couples with moderate oligozoospermia or moderate oligoasthenozoospermia need not be subjected to this procedure.

Generation of site-specific mutant mice using the CRISPR/Cas9 system.

The CRISPR/Cas9 system is a recently developed important technology for genome editing in cellular and animal models. Here we established a CRISPR/Cas9-based system of generating site-specific mutant mice using DNA double-strand breaks (DSBs) induced homologous recombination (HR)-dependent or independent repair mechanism. Through co-microinjection of Cas9 mRNA and single-guide RNA (sgRNA) targeting genomic DNA sequence corresponding to enzyme activity of lysine (K)-specific demethylase 2b (Kdm2b), both a frame-shifted Kdm2b null mutant and a Kdm2b enzyme activity disrupted mouse strain were obtained simultaneously. Moreover, sgRNA targeting flavin containing monooxygenases3 (Fmo3) gene and the corresponding single strand oligonucleotides (ssODN) donor template with point mutation were co-injected into the male pronucleus of one-cell mouse embryos stimulated HR-mediated repair mechanism. Genomic sequence analysis of F0 mice showed that frame-shifted Fmo3 knockout mouse and site-specific Fmo3 knock-in mouse with single base substitution were successfully generated, and these mutations could be stably transmitted to the next generation. Therefore, we successfully generated mouse strains containing site-specific mutations through HR-dependent and -independent DSB repair using the CRISPR/Cas9 system.

Reliable imputation of spatial transcriptomes with uncertainty estimation and spatial regularization.

Imputation of missing features in spatial transcriptomics is urgently needed due to technological limitations. However, most existing computational methods suffer from moderate accuracy and cannot estimate the reliability of the imputation. To fill this research gap, we introduce a computational model, TransImpute, that imputes the missing feature modality in spatial transcriptomics by mapping it from single-cell reference data. We derive a set of attributes that can accurately predict imputation uncertainty, enabling us to select reliably imputed genes. In addition, we introduce a spatial autocorrelation metric as a regularization to avoid overestimating spatial patterns. Multiple datasets from various platforms demonstrate that our approach significantly improves the reliability of downstream analyses in detecting spatial variable genes and interacting ligand-receptor pairs. Therefore, TransImpute offers a reliable approach to spatial analysis of missing features for both matched and unseen modalities, such as nascent RNAs.