Challenges and perspectives in computational deconvolution of genomics data.

Deciphering cell-type heterogeneity is crucial for systematically understanding tissue homeostasis and its dysregulation in diseases. Computational deconvolution is an efficient approach for estimating cell-type abundances from a variety of omics data. Despite substantial methodological progress in computational deconvolution in recent years, challenges are still outstanding. Here we enlist four important challenges related to computational deconvolution: the quality of the reference data, generation of ground truth data, limitations of computational methodologies, and benchmarking design and implementation. Finally, we make recommendations on reference data generation, new directions of computational methodologies, and strategies to promote rigorous benchmarking.

The marine-derived compound TAG alleviates Parkinson's disease by restoring RUBCN-mediated lipid metabolism homeostasis.

Parkinson's disease (PD) is the second most common neurodegenerative disease, and its prevalence is increasing. Currently, no effective therapies for PD exist. Marine-derived natural compounds are considered important resources for the discovery of new drugs due to their distinctive structures and diverse activities. In this study, tetrahydroauroglaucin (TAG), a polyketide isolated from a marine sponge, was found to have notable neuroprotective effects on MPTP/MPP+-induced neurotoxicity. RNA sequencing analysis and metabolomics revealed that TAG significantly improved lipid metabolism disorder in PD models. Further investigation indicated that TAG markedly decreased the accumulation of lipid droplets (LDs), downregulated the expression of RUBCN, and promoted autophagic flux. Moreover, conditional knockdown of Rubcn notably attenuated PD-like symptoms and the accumulation of LDs, accompanied by blockade of the neuroprotective effect of TAG. Collectively, our results first indicated that TAG, a promising PD therapeutic candidate, could suppress the accumulation of LDs through the RUBCN-autophagy pathway, which highlighted a novel and effective strategy for PD treatment.

Single cell transcriptome research in human placenta.

Human placenta is a complex and heterogeneous organ interfacing between the mother and the fetus that supports fetal development. Alterations to placental structural components are associated with various pregnancy complications. To reveal the heterogeneity among various placenta cell types in normal and diseased placentas, as well as elucidate molecular interactions within a population of placental cells, a new genomics technology called single cell RNA-seq (or scRNA-seq) has been employed in the last couple of years. Here we review the principles of scRNA-seq technology, and summarize the recent human placenta studies at scRNA-seq level across gestational ages as well as in pregnancy complications, such as preterm birth and preeclampsia. We list the computational analysis platforms and resources available for the public use. Lastly, we discuss the future areas of interest for placenta single cell studies, as well as the data analytics needed to accomplish them.

First Report of Cladosporium Blossom Blight Caused by Cladosporium cladosporioides on Calliandra haematocephala in China.

Calliandra haematocephala Hassk., commonly called red powder puff, is widely cultivated as an ornamental plant in Taiwan, Hainan, Guangdong and Fujian in China (CAS, 1988). The flowers are dark crimson with conspicuous stamens, which give them the appearance of powder-puffs. Blossom blight on C. haematocephala was first observed in early January 2019 on plants grown on the university campus as well as in parks in Fuzhou city, with nearly 80% of flowers on individual plants infected. At various locations in the city, disease incidence was 100%. Symptoms appeared as grayish green fungal growth on the stamens with the entire flower eventually turning black and covered with masses of fungal spores. Fifteen single spore isolates obtained from nine necrotic stamen samples were purified and cultured on Potato dextrose agar (PDA) plates at 24 ℃.The resultant fungal colonies were olivaceous-green to olivaceous-brown and had a velvet-like appearance. Conidiophores were smooth-walled, solitary, non-nodulose, and measuring 40 to 340 × 3 to 4 µm (n=50). Ramoconidia were cylindrical-oblong or slightly curved with 0 to 3 septa, and measuring 10 to 25 × 3 to 4 µm (n=50). Conidia were smooth-walled and prolifically produced in long chains. Terminal conidia were aseptate, subglobose, ovoid to limoniform, measuring 3 to 6 × 2 to 2.5 µm (n=50). Intercalary conidia were elliptical to limoniform or subcylindrical, aseptate, measuring 5 to 12 × 2.5 to 3 µm (n=50). On the basis of its morphology, the causal organism was identified as Cladosporium cladosporioides (Bensch et al. 2010). For molecular identification, pure cultures of five single-spore isolates were used for DNA extraction. A fragment in the ITS regions of the fungal rDNA, the ACT and the TEF1-α, was amplified using the primers ITS1/ITS4, ACT-512F/ACT-783R, and EF1728 F/EF1-986R. The DNA sequences obtained from all five isolates were identical. The resulting ITS (MK720012) and ACT (MN013164), and TEFl-α (MK752020) sequences from a representative isolate MRCIM19 were 98-100% identical to the C. cladosporioides accessions (ITS: MH863979, MG228421; ACT: HM148509, JF499878, HM148532; TEFl-α: JF499872). To test pathogenicity, a spore suspension (1×105 conidia/mL) was prepared from a seven- day- old culture of isolate MRCIM19 and 10 mL of the suspension was sprayed onto six flowers on each of three C. haematocephala plants. Sterile distilled water was sprayed onto three flowers of two plants as control. The inoculated flowers were covered with plastic bags which were removed two days post inoculation. Disease symptoms were recorded on each flower at 10 days post inoculation. Based on the morpho-molecular characters, the re-isolated fungus from the inoculated flowers was C. cladosporioides. This fungus was previously reported to cause blossom blight in strawberry in the USA and Korea (Gubler et al. 1999; Nam et al. 2015). Although it has been reported from many plants (Zhang 2003) in China, this is the first report of C. cladosporioides on C. haematocephala worldwide. References Bensch, K. et al. 2010. Stud Mycol. 67:1-94. Chinese Academy of Sciences (CAS), 1988. Flora Republicae Popularis Sinicae Editorial Committee, Beijing Sci. Press., 39: 38. Gubler, W. D. et al. 1999. Plant Dis. 83:400. Nam, M. H. et al. 2015. Microbiol. 43: 354-359. Zhang Z., Ed. 2003. Flora fungorum sinicorum, Vol. 14. Cladosporium, Fusicladium, Pyricularia. Beijing Science Press. 297.

Isoflavone lupiwighteone induces cytotoxic, apoptotic, and antiangiogenic activities in DU-145 prostate cancer cells.

Isoflavones constitute a large series of compounds found in many plants. They make up an important part of the diet and have a broad spectrum of biological activities such as cytotoxic and antitumor effects. Lupiwighteone (Lup) is an isoflavone-type compound. It is distributed widely in wild-growing plants such as Glycyrrhiza glabra, Lupinus, and Lotus pedunculatus. On the basis of existing research, Lup shows antioxidant and antimicrobial effects, but its antitumor activity has not been reported as yet. This study aimed to examine the antitumor activity of Lup, explore its antitumor mechanism in a human prostate carcinoma cell line (DU-145), and evaluate its antiangiogenetic activity in the human umbilical vein endothelial cell line (HUVEC). The results showed that Lup could inhibit the growth of DU-145 and HUVEC cells in a concentration-dependent and time-dependent manner by a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay. Flow cytometry analysis indicated that Lup could induce cell cycle arrest, cells apoptosis, mitochondrial membrane potential loss, and an increase in intracellular reactive oxygen species of DU-145 cells. Upregulation of Bax, cytochrome c, caspase-3, and PARP-1 protein expressions and downregulation of Bcl-2, procaspase-9, and p-Akt protein expressions were observed by western blot after the treatment of Lup. Furthermore, the effects of Lup on the cellular behavior of HUVECs were also investigated. Altogether, our data proved the anticancer and antiangiogenesis potential of Lup.

Chabamide induces cell cycle arrest and apoptosis by the Akt/MAPK pathway and inhibition of P-glycoprotein in K562/ADR cells.

One of the major mechanisms of multidrug resistance in cancer therapy is the overexpression of P-glycoprotein (P-gp). Chabamide, a dimeric alkaloid isolated from Piper chaba Hunter, shows antimalarial, antituberculosis, and cytotoxic activities. However, its mechanism of action has not been elucidated. In this study, the molecular mechanism underlying the cytotoxicity and downregulation of P-gp expression by chabamide in adriamycin-resistant human leukemia cells (K562/ADR) was clarified. Results show that chabamide inhibited the growth of K562/ADR cells in a dose-dependent and time-dependent manner, and significantly inhibited cell proliferation by cell cycle arrest in the G0/G1 phase, which was associated with an obvious increase in p21 and decrease in cyclin D1 and CDK2/4/6 protein expression. Moreover, chabamide could regulate the changes in the mitochondrial membrane potential, increase the expression of apoptosis-related proteins, such as Bax and cytochrome c, and decrease the protein expression levels of Bcl-2, caspase-9, caspase-3, PARP-1, and p-Akt. In addition, we found that JNK, ERK1/2, and p38 were regulated by chabamide in K562/ADR cells. Further studies indicated that the decrease in the reactive oxygen species level inhibited intrinsic P-gp expression. Therefore, chabamide-induced apoptosis in K562/ADR cells was associated with Akt/MAPK and the inhibition of P-gp. These results provide a biochemical basis for possible clinical applications of chabamide in the treatment of leukemia.

Rescue Blood Contamination in scRNA-Seq Data by Originator, a Computational Deciphering Tool using Genetic and Contextual Information.

Single-cell RNA sequencing (scRNA-Seq) data from complex human tissues have prevalent blood cell contamination due to the sample preparation process and may comprise cells of different genetic makeups. To reveal such complexity and annotate cells appropriately, we propose the first-of-its-kind computational framework, Originator, which deciphers single cells by genetic origin and separates blood cells from tissue-resident cells. We show that blood contamination is widely spread in scRNA-Seq data from a variety of tissues. We warn of the significant biases in downstream analysis without considering blood contamination and genetic contexts using pancreatic ductal adenocarcinoma and placenta data, respectively.

A Comprehensive Assessment of Ultraviolet-Radiation-Induced Mutations in Flammulina filiformis Using Whole-Genome Resequencing.

Nucleotide substitutions have played an important role in molecular evolution, and understanding their dynamics would contribute to genetic studies. Related research with defined DNA sequences lasted for decades until whole-genome sequencing arose. UV radiation (UVR) can generate base changes and other genetic variations in a short period of time, so it would be more meaningful to explore mutations caused by UVR from a genomic perspective. The monokaryon enoki strain WT583 was selected as the experimental material in this study because it can spontaneously produce large amounts of oidia on PDA plates, and the monokaryons originating from oidia have the same genotype as their mother monokaryon. After exposure to UV radiation, 100 randomly selected mutants, with WT583 as the reference genome, were sent for genome sequencing. BWA, samtools, and GATK software were employed for SNP calling, and the R package CMplot was used to visualize the distribution of the SNPs on the contigs of the reference genome. Furthermore, a k-mer-based method was used to detect DNA fragment deletion. Moreover, the non-synonymous genes were functionally annotated. A total of 3707 single-base substitutions and 228 tandem mutations were analyzed. The immediate adjacent bases showed different effects on the mutation frequencies of adenine and cytosine. For adenine, the overall effects of the immediate 5'-side and 3'-side bases were T > A > C > G and A > T > G > C, respectively; for cytosine, the overall effects of the immediate 5'-side and 3'-side bases were T > C > A > G and C > T > A > G, respectively. Regarding tandem mutations, the mutation frequencies of double-transition, double-transversion, 3'-side transition, and 5'-side transition were 131, 8, 72, and 17, respectively. Transitions at the 3'-side with a high mutation frequency shared a common feature, where they held transversions at the 5'-side of A→T or T→A without covalent bond changes, suggesting that the sequence context of tandem motifs might be related to their mutation frequency. In total, 3707 mutation sites were non-randomly distributed on the contigs of the reference genome. In addition, pyrimidines at the 3'-side of adenine promoted its transversion frequency, and UVR generated DNA fragment deletions over 200 bp with a low frequency in the enoki genome. The functional annotation of the genes with non-synonymous mutation indicated that UVR could produce abundant mutations in a short period of time.

MFSD7c functions as a transporter of choline at the blood-brain barrier.

Mutations in the orphan transporter MFSD7c (also known as Flvcr2), are linked to Fowler syndrome. Here, we used Mfsd7c knockout (Mfsd7c-/-) mice and cell-based assays to reveal that MFSD7c is a choline transporter at the blood-brain barrier (BBB). We performed comprehensive metabolomics analysis and detected differential changes of metabolites in the brains and livers of Mfsd7c-/-embryos. Particularly, we found that choline-related metabolites were altered in the brains but not in the livers of Mfsd7c-/- embryos. Thus, we hypothesized that MFSD7c regulates the level of choline in the brain. Indeed, expression of human MFSD7c in cells significantly increased choline uptake. Interestingly, we showed that choline uptake by MFSD7c is greatly increased by choline-metabolizing enzymes, leading us to demonstrate that MFSD7c is a facilitative transporter of choline. Furthermore, single-cell patch clamp analysis showed that the import of choline by MFSD7c is electrogenic. Choline transport function of MFSD7c was shown to be conserved in vertebrates, but not in yeasts. We demonstrated that human MFSD7c is a functional ortholog of HNM1, the yeast choline importer. We also showed that several missense mutations identified in patients exhibiting Fowler syndrome had abolished or reduced choline transport activity. Mice lacking Mfsd7c in endothelial cells of the central nervous system suppressed the import of exogenous choline from blood but unexpectedly had increased choline levels in the brain. Stable-isotope tracing study revealed that MFSD7c was required for exporting choline derived from lysophosphatidylcholine in the brain. Collectively, our work identifies MFSD7c as a choline exporter at the BBB and provides a foundation for future work to reveal the disease mechanisms of Fowler syndrome.

MicroRNAs as promising therapeutic agents: A perspective from acupuncture.

MicroRNAs (miRNAs) are gaining recognition as potential therapeutic agents due to their small size, ability to target a wide range of genes, and significant role in disease progression. However, despite their promising potential, nearly half of the miRNA drugs developed for therapeutic purposes have been discontinued or put on hold, and none have advanced to phase III clinical trials. The development of miRNA therapeutics has faced obstacles such as difficulties in validating miRNA targets, conflicting evidence regarding competition and saturation effects, challenges in miRNA delivery, and determining appropriate dosages. These hurdles primarily arise from the intricate functional complexity of miRNAs. Acupuncture, a distinct, complementary therapy, offers a promising avenue to overcome these barriers, particularly by addressing the fundamental issue of preserving functional complexity through acupuncture regulatory networks. The acupuncture regulatory network consists of three main components: the acupoint network, the neuro-endocrine-immune (NEI) network, and the disease network. These networks represent the processes of information transformation, amplification, and conduction that occur during acupuncture. Notably, miRNAs serve as essential mediators and shared biological language within these interconnected networks. Harnessing the therapeutic potential of acupuncture-derived miRNAs can help reduce the time and economic resources required for miRNA drug development and alleviate the current developmental challenges miRNA therapeutics face. This review provides an interdisciplinary perspective by summarizing the interactions between miRNAs, their targets, and the three acupuncture regulatory networks mentioned earlier. The aim is to illuminate the challenges and opportunities in developing miRNA therapeutics. This review paper presents a comprehensive overview of miRNAs, their interactions with acupuncture regulatory networks, and their potential as therapeutic agents. By bridging the miRNA research and acupuncture fields, we aim to offer valuable insights into the obstacles and prospects of developing miRNA therapeutics.

The interplay between α-Synuclein and NLRP3 inflammasome in Parkinson's disease.

α-Synuclein is a member of a protein of synucleins, which is a presynaptic neuron protein. It is usually highly expressed in the brain and participates in the formation and transmission of nerve synapses. It has been reported that abnormal aggregation of α-Syn can induce the activation of NLRP3 inflammasome in microglia, increase the production of IL-1ß, and aggravate neuroinflammation. Therefore, it is recognized as one of the important factors leading to neuroinflammation in Parkinson's disease. In this paper, we aimed to explore the influence of post-translational modification of α-Syn on its pathological aggregation and summarize various pathways that activate NLRP3 triggered by α-Syn and targeted therapeutic strategies, which provided new insights for further exploring the origin and targeted therapy of Parkinson's disease.

[Advances of structure and mechanisms of bromodomain-containing protein 4 and its related research in tumors].

The bromodomain and extraterminal domain (Bet) family are the regulators of the epigenome and also the pivotal driving factors for the expression of tumor related genes that tumor cells depend on for survival and proliferation. Bromodomain-containing protein 4 (Brd4) is a member of the Bet protein family. Generally, Brd4 identifies acetylated histones and binds to the promoter or enhancer region of target genes to initiate and maintain expression of tumor related genes. Brd4 is closely related to the regulation of multiple transcription factors and chromatin modification and is involved in DNA damage repair and maintenance of telomere function, thus maintaining the survival of tumor cells. This review summarizes the structure and function of Brd4 protein and the application of its inhibitors in tumor research.

The protective effects of electroacupuncture on intestinal barrier lesions in IBS and UC model.

Irritable bowel syndrome (IBS) and ulcerative colitis (UC) are two intestinal diseases with different pathological changes. Electroacupuncture (EA) at Zusanli (ST36) on both IBS and UC is widely used in clinic practice. But it is unclear whether acupuncture at one acupoint can treat two different intestinal diseases at different layers of intestinal barrier. To address this question, we explored three intestinal barrier lesions in IBS and UC mice with the aid of transcriptome data analysis and studied the efficacy of EA at ST36 on them. The transcriptome data analysis showed that both UC and IBS had disrupted intestinal barrier in various layers. And both UC and IBS had epithelial barrier lesions with reduction of ZO-1, Occludin and Claudin-1, while UC rather than IBS had the destruction of the mucus barrier with less MUC2 expression. As to the vascular barrier, UC showed a higher CD31 level and mesenteric blood flow reduction, while IBS showed a lower PV-1 level. EA at ST36 can significantly improve the above lesions of intestinal barrier of IBS and UC. Our results gave more details about the comprehensive protective effect of EA for UC and IBS. We guess the effect of acupuncture may be a kind of homeostasis regulation.

ASGARD is A Single-cell Guided Pipeline to Aid Repurposing of Drugs.

Single-cell RNA sequencing technology has enabled in-depth analysis of intercellular heterogeneity in various diseases. However, its full potential for precision medicine has yet to be reached. Towards this, we propose A Single-cell Guided Pipeline to Aid Repurposing of Drugs (ASGARD) that defines a drug score to recommend drugs by considering all cell clusters to address the intercellular heterogeneity within each patient. ASGARD shows significantly better average accuracy on single-drug therapy compared to two bulk-cell-based drug repurposing methods. We also demonstrated that it performs considerably better than other cell cluster-level predicting methods. In addition, we validate ASGARD using the drug response prediction method TRANSACT with Triple-Negative-Breast-Cancer patient samples. We find that many top-ranked drugs are either approved by the Food and Drug Administration or in clinical trials treating corresponding diseases. In conclusion, ASGARD is a promising drug repurposing recommendation tool guided by single-cell RNA-seq for personalized medicine. ASGARD is free for educational use at https://github.com/lanagarmire/ASGARD .

A homolog of AtCBFs, SmDREB A1-4, positively regulates salt stress tolerance in Arabidopsis thaliana and Salix matsudana.

CBFs (C-repeat binding factors) have multiple functions in abiotic stress adaption; functional research of these genes will provide precious gene resources for plant genetic improvement. In this study, a homolog of AtCBFs, SmDREB A1-4 was cloned and its role in salt tolerance was explored. SmDREB A1-4 is a member of DREB A1 subgroup with 10 members. SmDREB A1-4 localized in nuclei and cytoplasm and expressed ubiquitously in different tissue and organs. The expression level of SmDREB A1-4 could be induced by NaCl treatment and the TC-rich repeat and DREB motif on the SmDREB A1-4 gene promoter may mediate the NaCl-induced expression pattern. Overexpression of the SmDREB A1-4 gene in Arabidopsis enhanced the salt tolerance of transgenic Arabidopsis lines, while down-regulated the expression level in Salix plantlets by Virus induce gene silencing decreased the salt tolerance capacity in VIGS Salix plantlets. Experiments data from both sides confirmed that SmDREB A1-4 is a positive regulatory factor in salt stress tolerance. qRT-PCR and luciferase reporter assays revealed that SOS1 and DREB2A are downstream genes of SmDREB A1-4. Through upregulating the expression of SOS1 and DREB2A, SmDREB A1-4 enhanced plant tolerance to salinity by regulating ion homeostasis, reduction of Na+/K+ ratio, and improvement of proline biosynthesis. This research offers a potentially valuable gene resource for the stress-resistant varieties breeding of Salix matsudana in the future.

Genome-wide characterization and identification of Trihelix transcription factors and expression profiling in response to abiotic stresses in Chinese Willow (Salix matsudana Koidz).

Trihelix transcription factors (TTF) are a class of light-responsive proteins with a typical triple-helix structure (helix-loop-helix-loop-helix). Members of this gene family play an important role in plant growth and development, especially in various abiotic stress responses. Salix matsudana Koidz is an allotetraploid ornamental forest tree that is widely planted for its excellent resistance to stress, but no studies on its Trihelix gene family have been reported. In this study, the Trihelix gene family was analyzed at the genome-wide level in S. matsudana. A total of 78 S. matsudana Trihelix transcription factors (SmTTFs) were identified, distributed on 29 chromosomes, and classified into four subfamilies (GT-1, GT-2, SH4, SIP1) based on their structural features. The gene structures and conserved functional domains of these Trihelix genes are similar in the same subfamily and differ between subfamilies. The presence of multiple stress-responsive cis-elements on the promoter of the S. matsudana Trihelix gene suggests that the S. matsudana Trihelix gene may respond to abiotic stresses. Expression pattern analysis revealed that Trihelix genes have different functions during flooding stress, salt stress, drought stress and low temperature stress in S. matsudana. Given that SmTTF30, as a differentially expressed gene, has a faster response to flooding stress, we selected SmTTF30 for functional studies. Overexpression of SmTTF30 in Arabidopsis thaliana (Arabidopsis) enhances its tolerance to flooding stress. Under flooding stress, the leaf cell activity and peroxidase activity (POD) of the overexpression strain were significantly higher than the leaf cell activity and POD of the wild type, and the malondialdehyde (MDA) content was significantly lower than the MDA content of the wild type. Thus, these results suggest that SmTTF30 enhances plant flooding tolerance and plays a positive regulatory role in plant flooding tolerance.

Cystathionine Gamma-Lyase Regulate Psilocybin Biosynthesis in Gymnopilus dilepis Mushroom via Amino Acid Metabolism Pathways.

As a potential medicine for the treatment of depression, psilocybin has gradually attracted attention. To elucidate the molecular mechanism regulating psilocybin synthesis in Gymnopilus dilepis, ultra-performance liquid chromatography (UPLC) was used to detect the changes in psilocybin content after S-adenosyl-l-homocysteine (SAH) treatment and the changes of psilocybin content in different parts (stipe and pileus), and RNA-Seq was used to explore the mechanism of psilocybin content changes. In this study, the psilocybin content in G. dilepis mycelia treated with SAH was significantly lower than that in the control group, and the content of psilocybin in the stipe was significantly higher than that in the pileus. Transcriptome analysis revealed that differential expression genes (DEGs) were associated with cysteine and methionine metabolism. In particular, the transcription levels of genes encoding Cystathionine gamma-lyase (CTH) in different treatments and different parts were positively correlated with psilocybin content. In addition, we found that the exogenous addition of CTH activity inhibitor (DL-propargylglycine, PAG) could reduce the content of psilocybin and L-serine, and the content of psilocybin and L-serine returned to normal levels after L-cysteine supplementation, suggesting that psilocybin synthesis may be positively correlated with L-cysteine or CTH, and L-cysteine regulates the synthesis of psilocybin by affecting L-serine and 4-hydroxy-L-tryptophan. In conclusion, this study revealed a new molecular mechanism that affects psilocybin biosynthesis, which can provide a theoretical basis for improving psilocybin synthesis and the possibility for the development of biomedicine.

A Dual-Filtration System for Single-Cell Sequencing of Circulating Tumor Cells and Clusters in HCC.

Hepatocellular carcinoma (HCC) is a leading cause of cancer death worldwide. Identification and sequencing of circulating tumor (CT) cells and clusters may allow for noninvasive molecular characterization of HCC, which is an unmet need, as many patients with HCC do not undergo biopsy. We evaluated CT cells and clusters, collected using a dual-filtration system in patients with HCC. We collected and filtered whole blood from patients with HCC and selected individual CT cells and clusters with a micropipette. Reverse transcription, polymerase chain reaction, and library preparation were performed using a SmartSeq2 protocol, followed by single-cell RNA sequencing (scRNAseq) on an Illumina MiSeq V3 platform. Of the 8 patients recruited, 6 had identifiable CT cells or clusters. Median age was 64 years old; 7 of 8 were male; and 7 of 8 had and Barcelona Clinic Liver Cancer stage C. We performed scRNAseq of 38 CT cells and 33 clusters from these patients. These CT cells and clusters formed two distinct groups. Group 1 had significantly higher expression than group 2 of markers associated with epithelial phenotypes (CDH1 [Cadherin 1], EPCAM [epithelial cell adhesion molecule], ASGR2 [asialoglycoprotein receptor 2], and KRT8 [Keratin 8]), epithelial-mesenchymal transition (VIM [Vimentin]), and stemness (PROM1 [CD133], POU5F1 [POU domain, class 5, transcription factor 1], NOTCH1, STAT3 [signal transducer and activator of transcription 3]) (P < 0.05 for all). Patients with identifiable group 1 cells or clusters had poorer prognosis than those without them (median overall survival 39 vs. 384 days; P = 0.048 by log-rank test). Conclusion: A simple dual-filtration system allows for isolation and sequencing of CT cells and clusters in HCC and may identify cells expressing candidate genes known to be involved in cancer biology. Presence of CT cells/clusters expressing candidate genes is associated with poorer prognosis in advanced-stage HCC.

Evaluation of Cell Type Annotation R Packages on Single-cell RNA-seq Data.

Annotating cell types is a critical step in single-cell RNA sequencing (scRNA-seq) data analysis. Some supervised or semi-supervised classification methods have recently emerged to enable automated cell type identification. However, comprehensive evaluations of these methods are lacking. Moreover, it is not clear whether some classification methods originally designed for analyzing other bulk omics data are adaptable to scRNA-seq analysis. In this study, we evaluated ten cell type annotation methods publicly available as R packages. Eight of them are popular methods developed specifically for single-cell research, including Seurat, scmap, SingleR, CHETAH, SingleCellNet, scID, Garnett, and SCINA. The other two methods were repurposed from deconvoluting DNA methylation data, i.e., linear constrained projection (CP) and robust partial correlations (RPC). We conducted systematic comparisons on a wide variety of public scRNA-seq datasets as well as simulation data. We assessed the accuracy through intra-dataset and inter-dataset predictions; the robustness over practical challenges such as gene filtering, high similarity among cell types, and increased cell type classes; as well as the detection of rare and unknown cell types. Overall, methods such as Seurat, SingleR, CP, RPC, and SingleCellNet performed well, with Seurat being the best at annotating major cell types. Additionally, Seurat, SingleR, CP, and RPC were more robust against downsampling. However, Seurat did have a major drawback at predicting rare cell populations, and it was suboptimal at differentiating cell types highly similar to each other, compared to SingleR and RPC. All the code and data are available from https://github.com/qianhuiSenn/scRNA_cell_deconv_benchmark.

Lilikoi V2.0: a deep learning-enabled, personalized pathway-based R package for diagnosis and prognosis predictions using metabolomics data.

BACKGROUND: previously we developed Lilikoi, a personalized pathway-based method to classify diseases using metabolomics data. Given the new trends of computation in the metabolomics field, it is important to update Lilikoi software. RESULTS: here we report the next version of Lilikoi as a significant upgrade. The new Lilikoi v2.0 R package has implemented a deep learning method for classification, in addition to popular machine learning methods. It also has several new modules, including the most significant addition of prognosis prediction, implemented by Cox-proportional hazards model and the deep learning-based Cox-nnet model. Additionally, Lilikoi v2.0 supports data preprocessing, exploratory analysis, pathway visualization, and metabolite pathway regression. CONCULSION: Lilikoi v2.0 is a modern, comprehensive package to enable metabolomics analysis in R programming environment.