scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets.

Undoubtedly, single-cell RNA sequencing (scRNA-seq) has changed the research landscape by providing insights into heterogeneous, complex and rare cell populations. Given that more such data sets will become available in the near future, their accurate assessment with compatible and robust models for cell type annotation is a prerequisite. Considering this, herein, we developed scAnno (scRNA-seq data annotation), an automated annotation tool for scRNA-seq data sets primarily based on the single-cell cluster levels, using a joint deconvolution strategy and logistic regression. We explicitly constructed a reference profile for human (30 cell types and 50 human tissues) and a reference profile for mouse (26 cell types and 50 mouse tissues) to support this novel methodology (scAnno). scAnno offers a possibility to obtain genes with high expression and specificity in a given cell type as cell type-specific genes (marker genes) by combining co-expression genes with seed genes as a core. Of importance, scAnno can accurately identify cell type-specific genes based on cell type reference expression profiles without any prior information. Particularly, in the peripheral blood mononuclear cell data set, the marker genes identified by scAnno showed cell type-specific expression, and the majority of marker genes matched exactly with those included in the CellMarker database. Besides validating the flexibility and interpretability of scAnno in identifying marker genes, we also proved its superiority in cell type annotation over other cell type annotation tools (SingleR, scPred, CHETAH and scmap-cluster) through internal validation of data sets (average annotation accuracy: 99.05%) and cross-platform data sets (average annotation accuracy: 95.56%). Taken together, we established the first novel methodology that utilizes a deconvolution strategy for automated cell typing and is capable of being a significant application in broader scRNA-seq analysis. scAnno is available at https://github.com/liuhong-jia/scAnno.

DeepSSV: detecting somatic small variants in paired tumor and normal sequencing data with convolutional neural network.

It is of considerable interest to detect somatic mutations in paired tumor and normal sequencing data. A number of callers that are based on statistical or machine learning approaches have been developed to detect somatic small variants. However, they take into consideration only limited information about the reference and potential variant allele in both tumor and normal samples at a candidate somatic site. Also, they differ in how biological and technological noises are addressed. Hence, they are expected to produce divergent outputs. To overcome the drawbacks of existing somatic callers, we develop a deep learning-based tool called DeepSSV, which employs a convolutional neural network (CNN) model to learn increasingly abstract feature representations from the raw data in higher feature layers. DeepSSV creates a spatially oriented representation of read alignments around the candidate somatic sites adapted for the convolutional architecture, which enables it to expand to effectively gather scattered evidence. Moreover, DeepSSV incorporates the mapping information of both reference allele-supporting and variant allele-supporting reads in the tumor and normal samples at a genomic site that are readily available in the pileup format file. Together, the CNN model can process the whole alignment information. Such representational richness allows the model to capture the dependencies in the sequence and identify context-based sequencing artifacts. We fitted the model on ground truth somatic mutations and did benchmarking experiments on simulated and real tumors. The benchmarking results demonstrate that DeepSSV outperforms its state-of-the-art competitors in overall F1 score.

On-chip ytterbium-doped lithium niobate waveguide amplifiers with high net internal gain.

Integrated optical systems based on lithium niobate on insulator (LNOI) have shown great potential in recent years. However, the LNOI platform is facing a shortage of active devices. Considering the significant progress made in rare-earth-doped LNOI lasers and amplifiers, the fabrication of on-chip ytterbium-doped LNOI waveguide amplifiers based on electron-beam lithography and inductively coupled plasma reactive ion etching was investigated. The signal amplification at lower pump power (<1 mW) was achieved by the fabricated waveguide amplifiers. A net internal gain of ∼18 dB/cm in the 1064 nm band was also achieved in the waveguide amplifiers under a pump power of 10 mW at 974 nm. This work proposes a new, to the best of our knowledge, active device for the LNOI integrated optical system. It may become an important basic component for lithium niobate thin-film integrated photonics in the future.

On-chip erbium-ytterbium-co-doped lithium niobate microdisk laser with an ultralow threshold.

Erbium-ion-doped lithium niobate (LN) microcavity lasers working in the communication band have attracted extensive attention recently. However, their conversion efficiencies and laser thresholds still have significant room to improve. Here, we prepared microdisk cavities based on erbium-ytterbium-co-doped LN thin film by using ultraviolet lithography, argon ion etching, and a chemical-mechanical polishing process. Benefiting from the erbium-ytterbium co-doping-induced gain coefficient improvement, laser emission with an ultralow threshold (∼1 µW) and high conversion efficiency (1.8 × 10-3%) was observed in the fabricated microdisks under a 980-nm-band optical pump. This study provides an effective reference for improving the performance of LN thin-film lasers.

High Peroxidase-Mimicking Metal-Organic Frameworks Decorated with Platinum Nanozymes for the Colorimetric Detection of Acetylcholine Chloride and Organophosphorus Pesticides via Enzyme Cascade Reaction.

The sensitive detection of acetylcholinesterase (AChE) and organophosphorus pesticides (OPs) is very important for the protection of human health. Herein, a hybrid material, Pt NPs/Fe-MOF, consisting of a metal-organic framework (MIL-88B-NH2, Fe-MOF) decorated with platinum nanoparticles (Pt NPs), was prepared first and exhibited remarkably improved and excellent peroxidase-mimicking activity compared to the Fe-MOF material resulting from the synergistic catalysis effect between Fe-MOF and Pt NPs, which can effectively catalyze 3,3',5,5'-tetramethylbenzidine (TMB) oxidation to generate a blue product (oxidized TMB, oxTMB). Interestingly, in the presence of AChE and acetylcholinesterase, the peroxidase-mimicking activity from Pt NPs/Fe-MOF was inhibited obviously, and thus, a colorimetric sensing platform for AChE can be constructed; more importantly, after the addition of OPs, this nanozyme activity can be recovered, inducing the further successful construction of a sensitive colorimetric sensing platform for OPs. The related sensing mechanism and condition optimization were studied, and the as-prepared Pt NPs/Fe-MOF nanozyme-based colorimetric method for AChE and OP detection displayed superior analytical performances with wide linearities and low detection limits. Furthermore, the designed method offers satisfactory real application ability. We expect the as-proposed Pt NPs/Fe-MOF nanozyme-based colorimetric sensing platform for AChE and OPs via the enzyme cascade reaction to show great potential application.

Cytokine-Induced Killer Cells in Combination with Heat Shock Protein 90 Inhibitors Functioning via the Fas/FasL Axis Provides Rationale for a Potential Clinical Benefit in Burkitt's lymphoma.

Constant efforts are being made to develop methods for improving cancer immunotherapy, including cytokine-induced killer (CIK) cell therapy. Numerous heat shock protein (HSP) 90 inhibitors have been assessed for antitumor efficacy in preclinical and clinical trials, highlighting their individual prospects for targeted cancer therapy. Therefore, we tested the compatibility of CIK cells with HSP90 inhibitors using Burkitt's lymphoma (BL) cells. Our analysis revealed that CIK cytotoxicity in BL cells was augmented in combination with independent HSP90 inhibitors 17-DMAG (17-dimethylaminoethylamino-17-demethoxygeldanamycin) and ganetespib. Interestingly, CIK cell cytotoxicity did not diminish after blocking with NKG2D (natural killer group 2, member D), which is a prerequisite for their activation. Subsequent analyses revealed that the increased expression of Fas on the surface of BL cells, which induces caspase 3/7-dependent apoptosis, may account for this effect. Thus, we provide evidence that CIK cells, either alone or in combination with HSP90 inhibitors, target BL cells via the Fas-FasL axis rather than the NKG2D pathway. In the context of clinical relevance, we also found that high expression of HSP90 family genes (HSP90AA1, HSP90AB1, and HSP90B1) was significantly associated with the reduced overall survival of BL patients. In addition to HSP90, genes belonging to the Hsp40, Hsp70, and Hsp110 families have also been found to be clinically significant for BL survival. Taken together, the combinatorial therapy of CIK cells with HSP90 inhibitors has the potential to provide clinical benefits to patients with BL.

On-chip ytterbium-doped lithium niobate microdisk lasers with high conversion efficiency.

Integrated optical systems based on lithium niobate on insulator (LNOI) have attracted the interest of researchers. Recently, erbium-doped LNOI lasers have been realized. However, the reported lasers have a relatively lower conversion efficiency and only operate in the 1550 nm band. In this paper, we demonstrate an LNOI laser operating in the 1060 nm band based on a high Q factor ytterbium-doped LNOI microdisk cavity. The threshold and the conversion efficiency of the laser are 21.19 µW and 1.36%, respectively. To our knowledge, the conversion efficiency is the highest among the reported rare-earth-doped LNOI lasers. This research extends the operating band of LNOI lasers and shows the potential in realizing high-power LNOI lasers.

Integrated ytterbium-doped lithium niobate microring lasers.

Integrated and stable microlasers are indispensable building blocks of micro-photonics. Here, we report the realization of an ytterbium-doped lithium niobate microring laser operating in the 1060-nm band under the pump of a 980-nm-band laser. The monolithic laser has a low threshold of 59.32 µW and relatively high output power of 6.44 µW, a state-of-the-art value for rare-earth ions-doped lithium niobate thin-film lasers. The monolithic laser with desirable performance and attractive scalability may find many applications in lithium niobite photonics.

Crosstalk between ß-Catenin and CCL2 Drives Migration of Monocytes towards Glioblastoma Cells.

Isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GBM) is a fast growing and highly heterogeneous tumor, often characterized by the presence of glioblastoma stem cells (GSCs). The plasticity of GSCs results in therapy resistance and impairs anti-tumor immune response by influencing immune cells in the tumor microenvironment (TME). Previously, ß-catenin was associated with stemness in GBM as well as with immune escape mechanisms. Here, we investigated the effect of ß-catenin on attracting monocytes towards GBM cells. In addition, we evaluated whether CCL2 is involved in ß-catenin crosstalk between monocytes and tumor cells. Our analysis revealed that shRNA targeting ß-catenin in GBMs reduces monocytes attraction and impacts CCL2 secretion. The addition of recombinant CCL2 restores peripheral blood mononuclear cells (PBMC) migration towards medium (TCM) conditioned by shß-catenin GBM cells. CCL2 knockdown in GBM cells shows similar effects and reduces monocyte migration to a similar extent as ß-catenin knockdown. When investigating the effect of CCL2 on ß-catenin activity, we found that CCL2 modulates components of the Wnt/ß-catenin pathway and alters the clonogenicity of GBM cells. In addition, the pharmacological ß-catenin inhibitor MSAB reduces active ß-catenin, downregulates the expression of associated genes and alters CCL2 secretion. Taken together, we showed that ß-catenin plays an important role in attracting monocytes towards GBM cells in vitro. We hypothesize that the interactions between ß-catenin and CCL2 contribute to maintenance of GSCs via modulating immune cell interaction and promoting GBM growth and recurrence.

Epigenetic Regulatory Enzymes: mutation Prevalence and Coexistence in Cancers.

Epigenetic regulation is an important layer of transcriptional control with the particularity to affect the broad spectrum of genome. Over the years, largely due to the substantial number of recurrent mutations, there have been hundreds of novel driver genes characterized in various cancers. Additionally, the relative contribution of two dysregulated epigenomic entities (DNA methylation and histone modifications) that gradually drive the cancer phenotype remains in the research focus. However, a complex scenario arises when the disease phenotype does not harbor any relevant mutation or an abnormal transcription level. Although the cancer landscape involves the contribution of multiple genetic and non-genetic factors, herein, we discuss specifically the mutation spectrum of epigenetically-related enzymes in cancer. In addition, we address the coexistence of these two epigenetic entities in malignant human diseases, especially cancer. We suggest that the study of epigenetically-related somatic mutations in the early cellular differentiation stage of embryonic development might help to understand their later-staged footprints in the cancer genome. Furthermore, understanding the co-occurrence and/or inverse association of different disease types and redefining the general definition of "healthy" controls could provide insights into the genome reorganization.

On-chip erbium-doped lithium niobate microring lasers.

Lithium niobate on insulator (LNOI), regarded as an important candidate platform for optical integration due to its excellent nonlinear, electro-optic, and other physical properties, has become a research hotspot. A light source, as an essential component for an integrated optical system, is urgently needed. In this Letter, we reported the realization of 1550 nm band on-chip LNOI microlasers based on erbium-doped LNOI ring cavities with loaded quality factors higher than 1 million at ∼970nm, which were fabricated by using electron beam lithography and inductively coupled plasma reactive ion etching processes. These microlasers demonstrated a low pump threshold of ∼20µW and stable performance under the pump of a 980 nm band continuous laser. Comb-like laser spectra spanning from 1510 to 1580 nm were observed in a high pump power regime, which lays the foundation of the realization of pulsed laser and frequency combs on a rare-earth ion-doped LNOI platform. This Letter effectively promotes the development of on-chip integrated active LNOI devices.

Single symbiotic cell transcriptome sequencing of coral.

Zooxanthellae and coral can form an intracellular symbiotic system. Yet, little is known about the molecular mechanism underlying this symbiosis. In this study, we characterized the symbiosis based on analyses of gene expression at the single-cell level. Among 9110 single coral cells, we identified 4871 symbiotic cells based on the detection of both coral and zooxanthellae gene transcripts within a single cell. Using the bioinformatics tool Seurat, symbiotic cells were further clustered into five groups, 52 genes exhibited differential expression between groups. We proposed an index called the "symbiosis index", to indicate the degree of gene expression of both species in a single symbiotic cell. Interestingly, the index differed distinctly among the five groups. The symbiosis index was highly correlated with the expression of the coral gene gfas1.m1.6761 (ANKRD40), which encodes ankyrin repeat domain-containing protein 40 and is involved in DNA replication (r = 0.76). Two metabolism-related genes, DAGLA and betaGlu, were highly expressed in cells with a high symbiosis index. Four zooxanthellae genes, PRPF19, ATRN, aAA-ATPases and AK812-SmicGene44833, exhibited substantial changes in expression levels when zooxanthellae lived within coral. A trajectory analysis suggested that cells with a higher symbiosis index may be derived from those with a lower index during coral colony development. Taken together, our results provide evidence for zooxanthellae residing within coral, forming a symbiotic system. The symbiosis index is an effective indicator of different cell groups, with lineage relationships among groups. Additionally, we identified specific genes that exhibit expression changes in the symbiotic system.

Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome.

G-quadruplexes are the non-canonical nucleic acid structures that are preferentially formed in G-rich regions. This structure has been shown to be associated with many biological functions. Regardless of the broad efforts on DNA G-quadruplexes, we still have limited knowledge on RNA G-quadruplexes, especially in a transcriptome-wide manner. Herein, by integrating the DMS-seq and the bioinformatics pipeline, we profiled and depicted the RNA G-quadruplexes in the human transcriptome. The genes that contain RNA G-quadruplexes in their specific regions are significantly related to immune pathways and the COVID-19-related gene sets. Bioinformatics analysis reveals the potential regulatory functions of G-quadruplexes on miRNA targeting at the scale of the whole transcriptome. In addition, the G-quadruplexes are depleted in the putative, not the real, PAS-strong poly(A) sites, which may weaken the possibility of such sites being the real cleaved sites. In brief, our study provides insight into the potential function of RNA G-quadruplexes in post-transcription.

[A review on integration methods for single-cell data].

The emergence of single-cell sequencing technology enables people to observe cells with unprecedented precision. However, it is difficult to capture the information on all cells and genes in one single-cell RNA sequencing (scRNA-seq) experiment. Single-cell data of a single modality cannot explain cell state and system changes in detail. The integrative analysis of single-cell data aims to address these two types of problems. Integrating multiple scRNA-seq data can collect complete cell types and provide a powerful boost for the construction of cell atlases. Integrating single-cell multimodal data can be used to study the causal relationship and gene regulation mechanism across modalities. The development and application of data integration methods helps fully explore the richness and relevance of single-cell data and discover meaningful biological changes. Based on this, this article reviews the basic principles, methods and applications of multiple scRNA-seq data integration and single-cell multimodal data integration. Moreover, the advantages and disadvantages of existing methods are discussed. Finally, the future development is prospected.

A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples.

BACKGROUND: The identification of cell type-specific genes (markers) is an essential step for the deconvolution of the cellular fractions, primarily, from the gene expression data of a bulk sample. However, the genes with significant changes identified by pair-wise comparisons cannot indeed represent the specificity of gene expression across multiple conditions. In addition, the knowledge about the identification of gene expression markers across multiple conditions is still paucity. RESULTS: Herein, we developed a hybrid tool, LinDeconSeq, which consists of 1) identifying marker genes using specificity scoring and mutual linearity strategies across any number of cell types, and 2) predicting cellular fractions of bulk samples using weighted robust linear regression with the marker genes identified in the first stage. On multiple publicly available datasets, the marker genes identified by LinDeconSeq demonstrated better accuracy and reproducibility compared to MGFM and RNentropy. Among deconvolution methods, LinDeconSeq showed low average deviations (≤0.0958) and high average Pearson correlations (≥0.8792) between the predicted and actual fractions on the benchmark datasets. Importantly, the cellular fractions predicted by LinDeconSeq appear to be relevant in the diagnosis of acute myeloid leukemia (AML). The distinct cellular fractions in granulocyte-monocyte progenitor (GMP), lymphoid-primed multipotent progenitor (LMPP) and monocytes (MONO) were found to be closely associated with AML compared to the healthy samples. Moreover, the heterogeneity of cellular fractions in AML patients divided these patients into two subgroups, differing in both prognosis and mutation patterns. GMP fraction was the most pronounced between these two subgroups, particularly, in SubgroupA, which was strongly associated with the better AML prognosis and the younger population. Totally, the identification of marker genes by LinDeconSeq represents the improved feature for deconvolution. The data processing strategy with regard to the cellular fractions used in this study also showed potential for the diagnosis and prognosis of diseases. CONCLUSIONS: Taken together, we developed a freely-available and open-source tool LinDeconSeq ( https://github.com/lihuamei/LinDeconSeq ), which includes marker identification and deconvolution procedures. LinDeconSeq is comparable to other current methods in terms of accuracy when applied to benchmark datasets and has broad application in clinical outcome and disease-specific molecular mechanisms.

Genome organization in proximity to the BAP1 locus appears to play a pivotal role in a variety of cancers.

Cancer studies primarily focus on the characterization of the key driver genes and the underlying pathways. However, the contribution of other cancer-associated genes located in the genomic neighborhood of the driver genes could help to understand further aspects of cancer progression. Given the frequent involvement of chromosome 3 in multiple human cancers, in particular in the form of the prognostically highly relevant monosomy 3 in uveal melanoma (UM), we investigated the cumulative impact of cancer-associated genes on chromosome 3. Our analysis showed that these genes are enriched with repetitive elements with genes surrounded by distinctive repeats (MIR, hAT-Charlie, ERVL-MaLR, LINE-2, and simple/low complexity) in the promoter being more precisely associated with cancer-related pathways than the ones with major transposable elements (SINE/Alu and LINE-1). Additionally, these genes showed strong intrachromosomal chromatin interactions in 3D nuclear organization. Further investigations revealed a genomic hotspot in the vicinity of BAP1 locus, which is affected in 27 types of different cancers and contains abundant noncoding RNAs that are often expressed in a tissue-specific manner. The cross-species comparison of these cancer-associated genes revealed mostly a shared synteny in closer primates. However, near to the BAP1 locus signs of chromosomal inversions were observed during the course of evolution. To our knowledge, this is the first study to characterize the entire genomic neighborhood of cancer-associated genes located on any single chromosome. Based on our results, we hypothesize that monosomy of chromosome 3 will have important clinical and molecular consequences in the respective diseases and in particular in UM.

Correction: p-Type conductivity mechanism and defect structure of nitrogen-doped LiNbO3 from first-principles calculations.

Correction for 'p-Type conductivity mechanism and defect structure of nitrogen-doped LiNbO3 from first-principles calculations' by Weiwei Wang et al., Phys. Chem. Chem. Phys., 2020, 22, 20-27.

Ubiquitin Carboxyl-Terminal Hydrolases (UCHs): Potential Mediators for Cancer and Neurodegeneration.

Emerging evidence suggests an inverse association between cancer and neurodegenerative diseases (NDD). Although phenotypically different, both diseases display a significant imbalance in the ubiquitination/deubiquitination processes. Therefore, we particularly investigated the expression of ubiquitin C-terminal hydrolases (UCHs: UCH-L1, UCH-L3, UCH-L5 and BAP1), a subfamily of deubiquitinating enzymes (DUBs), using publically available datasets (GTEx, TCGA) and observed altered expression of UCH-L1, UCH-L3, UCH-L5 in 17 cancer types. Interestingly, UCH-L1 (known to be enriched in neurons and interacting with the Parkinson's disease-associated protein α-synuclein) appeared to be a prognostic indicator of unfavorable outcome in endometrial and urothelial cancer, while increased expression of UCH-L3 and UCH-L5 was associated with poor survival in liver and thyroid cancer, respectively. In normal tissues, UCH-L1 was found to be strongly expressed in the cerebral cortex and hypothalamus, while UCH-L3 expression was somewhat higher in the testis. The occurrence of mutation rates in UCHs also suggests that BAP1 and UCH-L5 may play a more dominant role in cancers than UCH-L1 and UCH-L3. We also characterized the functional context and configuration of the repeat elements in the promoter of DUBs genes and found that UCHs are highly discriminatory for catabolic function and are mainly enriched with LINE/CR1 repeats. Regarding the thesis of an inverse association between cancer and NDD, we observed that among all DUBs, UCHs are the one most involved in both entities. Considering a putative therapeutic potential based on presumed common mechanisms, it will be useful to determine whether other DUBs can compensate for the loss of UCH activity under physiological conditions. However, experimental evidence is required to substantiate this argument.

p-Type conductivity mechanism and defect structure of nitrogen-doped LiNbO3 from first-principles calculations.

Most metal-doped lithium niobates (LiNbO3, LN) exhibit n-type conductivity. The absence of p-type conductive LiNbO3 limits its application. Based on the finding that p-type conductive LiNbO3 can be realized by doping with a non-metallic element N, we investigate the most stable defect configurations and formation energies of LiNbO3 doped with non-metal nitrogen (LN:N) by first-principles calculations. Nitrogen substitution, interstitial and quasi-substitution point defects in different sites and their effects were explored. The results show that N prefers to occupy the oxygen site with only little lattice distortion. Ab initio molecular dynamics (AIMD) simulations confirm the structural stability of an N ion occupying the O site. The charge-state transition level ε(0/-1) slightly above the valence band maximum (VBM) indicates that N point defects would contribute to p-type conductivity of LiNbO3. The analysis of the band structure reveals that the partially filled impurity levels can accommodate electrons that jump from valence bands and result in holes to become the main charge carriers. The calculation not only explains the occurrence of p-type conductivity in LN:N but also provides a simple and efficient way to discover p-type conductive candidates in numerous doped LiNbO3 crystals.

An approach of identifying differential nucleosome regions in multiple samples.

BACKGROUND: Nucleosome plays a role in transcriptional regulation through occluding the binding of proteins to DNA sites. Nucleosome occupancy varies among different cell types. Identification of such variation will help to understand regulation mechanism. The previous researches focused on the methods for two-sample comparison. However, a multiple-sample comparison (n ≥ 3) is necessary, especially in studying development and cancer. METHODS: Here, we proposed a Chi-squared test-based approach, named as Dimnp, to identify differential nucleosome regions (DNRs) in multiple samples. Dimnp is designed for sequenced reads data and includes the modules of both calling nucleosome occupancy and identifying DNRs. RESULTS: We validated Dimnp on dataset of the mutant strains in which the modifiable histone residues are mutated into alanine in Saccharomyces cerevisiae. Dimnp shows a good capacity (area under the curve > 0.87) compared with the manually identified DNRs. Just by one time, Dimnp is able to identify all the DNRs identified by two-sample method Danpos. Under a deviation of 40 bp, the matched DNRs are above 60% between Dimnp and Danpos. With Dimnp, we found that promoters and telomeres are highly dynamic upon mutating the modifiable histone residues. CONCLUSIONS: We developed a tool of identifying the DNRs in multiple samples and cell types. The tool can be applied in studying nucleosome variation in gradual change in development and cancer.