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Single nucleotide variants (SNVs), as important components of genetic variation, affect gene expression, function and phenotype. Mining and summarizing the spatial distribution of SNVs in diseased and normal tissues for a better understanding of their characteristics and potential roles in cell-lineage determination, aging, or disease occurrence is significant. Herein, we have developed a comprehensive spatial mutation resource stSNV (http://bio-bigdata.hrbmu.edu.cn/stSNV/index.jsp), which provides an atlas of spatial SNVs in major diseased and normal tissues of human and mouse. stSNV documents 42 202 spatial mutated genes involving 898 908 SNVs called from 730 067 spots within 450 slices from 19 diseased and 28 normal tissues. Importantly, potential characteristics of SNVs are explored and provided by analyzing the perturbation of the SNVs to gene expression, spatial communication, biological function, region-specific mutated genes, spatial mutant signatures, SNV-cell co-localization and mutation core region. All these spatial mutation data and in-depth analyses have been integrated into a user-friendly interface, visualized through intuitive tables and various image formats. Flexible tools are developed to explore co-localization among clusters, genes, cell types and SNVs in the same slice. In summary, stSNV as a valuable resource helps to dissect intra-tissue genetic heterogeneity and lays the groundwork for understanding the SNVs' biological regulatory mechanisms., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

The problem of marine noise pollution has a long history. Strong noise (>120 dB re 1 µPa) will affects the growth, development, physiological responses, and behaviors of fish, and also can induce the stress response, posing a mortal threat. Although many studies have reported that underwater noise may affect the survival of fish by disturbing their nervous system and endocrine system, the underlying causes of death due to noise stimulation remain unknown. Therefore, in this study, we used the underwater noise stress models to conduct underwater strong noise (50-125 dB re 1 µPa, 10-22,000 Hz) stress experiments on small yellow croaker for 10 min (short-term noise stress) and 6 days (long-term noise stress). A total of 150 fishes (body weight: 40-60 g; body length: 12-14 cm) were used in this study. Omics (metabolomics and transcriptomics) studies and quantitative analyses of important genes (HPA (hypothalamic-pituitary-adrenal)-axis functional genes) were performed to reveal genetic and metabolic changes in the important tissues associated with the HPA axis (brain, heart, and adrenal gland). Finally, we found that the strong noise pollution can significantly interfere with the expression of HPA-axis functional genes (including corticotropin releasing hormone (CRH), corticotropin releasing hormone receptor 2 (CRHR2), and arginine vasotocin (AVT)), and long-term stimulation can further induce metabolic disorders of the functional tissues (brain, heart, and adrenal gland), posing a lethal threat. Meanwhile, we also found that there were two kinds of death processes, direct death and chronic death, and both were closely related to the duration of stimulation and the regulation of the HPA axis.

Advances in single-cell transcriptomics provide an unprecedented opportunity to explore complex biological processes. However, computational methods for analyzing single-cell transcriptomics still have room for improvement especially in dimension reduction, cell clustering, and cell-cell communication inference. Herein, we propose a versatile method, named DcjComm, for comprehensive analysis of single-cell transcriptomics. DcjComm detects functional modules to explore expression patterns and performs dimension reduction and clustering to discover cellular identities by the non-negative matrix factorization-based joint learning model. DcjComm then infers cell-cell communication by integrating ligand-receptor pairs, transcription factors, and target genes. DcjComm demonstrates superior performance compared to state-of-the-art methods., (© 2024. The Author(s).)

The inference of cell-cell communication (CCC) is crucial for a better understanding of complex cellular dynamics and regulatory mechanisms in biological systems. However, accurately inferring spatial CCCs at single-cell resolution remains a significant challenge. To address this issue, we present a versatile method, called DeepTalk, to infer spatial CCC at single-cell resolution by integrating single-cell RNA sequencing (scRNA-seq) data and spatial transcriptomics (ST) data. DeepTalk utilizes graph attention network (GAT) to integrate scRNA-seq and ST data, which enables accurate cell-type identification for single-cell ST data and deconvolution for spot-based ST data. Then, DeepTalk can capture the connections among cells at multiple levels using subgraph-based GAT, and further achieve spatially resolved CCC inference at single-cell resolution. DeepTalk achieves excellent performance in discovering meaningful spatial CCCs on multiple cross-platform datasets, which demonstrates its superior ability to dissect cellular behavior within intricate biological processes., (© 2024. The Author(s).)

T cells recognize tumor antigens and initiate an anticancer immune response in the very early stages of tumor development, and the antigen specificity of T cells is determined by the T-cell receptor (TCR). Therefore, monitoring changes in the TCR repertoire in peripheral blood may offer a strategy to detect various cancers at a relatively early stage. Here, we developed the deep learning framework iCanTCR to identify patients with cancer based on the TCR repertoire. The iCanTCR framework uses TCRβ sequences from an individual as an input and outputs the predicted cancer probability. The model was trained on over 2,000 publicly available TCR repertoires from 11 types of cancer and healthy controls. Analysis of several additional publicly available datasets validated the ability of iCanTCR to distinguish patients with cancer from noncancer individuals and demonstrated the capability of iCanTCR for the accurate classification of multiple cancers. Importantly, iCanTCR precisely identified individuals with early-stage cancer with an AUC of 86%. Altogether, this work provides a liquid biopsy approach to capture immune signals from peripheral blood for noninvasive cancer diagnosis., Significance: Development of a deep learning-based method for multicancer detection using the TCR repertoire in the peripheral blood establishes the potential of evaluating circulating immune signals for noninvasive early cancer detection., (©2024 American Association for Cancer Research.)

The coronavirus disease 2019 (COVID-19) has merged as a global health threat since its outbreak in December 2019. Despite widespread recognition, there has been a paucity of studies focusing on the T cell receptor (TCR) bias in adaptive immunity induced by SARS-CoV-2. This research conducted a comparative analysis of the TCR immune repertoire to identify notable αβ TCR bias sequences associated with the SARS-CoV-2 virus antigen. The present study encompassed 73 symptomatic COVID-19 patients, categorized as moderate/mild or severe/critical, along with 9 healthy controls. Our findings revealed specific TCR chains prominently utilized by moderate and severe patients, identified as TRAV30-J34-TRBV3-1-J2-7 and TRAV12-3-J6-TRBV28-J1-1, respectively. Additionally, our research explored critical TCR preferences in the bronchoalveolar lavage fluid (BALF) of COVID-19 patients at various disease stages. Indeed, monitoring the dynamics of immune repertoire changes in COVID-19 patients could serve as a crucial biomarker for predicting disease progression and recovery. Furthermore, the study explored TCR bias in both peripheral blood mononuclear cells (PBMCs) and BALF. The most common αβ VJ pair observed in BALF was TRAV12-3-J18-TRBV7-6-J2-7. In addition, a comparative analysis with the VDJdb database indicated that the HLA-A*02:01 allele exhibited the widest distribution and highest frequency in COVID-19 patients across different periods. This comprehensive examination provided a global characterization of the TCR immune repertoire in COVID-19 patients, contributing significantly to our understanding of TCR bias induced by SARS-CoV-2., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.)

Ethnopharmacological relevance: Murrayae Folium et Cacumen (MFC) is a plant considered to be a traditional Chinese medicine with culinary value as well. The dry leaves and twigs of Murraya paniculata and M. exotica are used to treat stomach aches, rheumatism, toothaches, swelling, and insect and snake bites. They are also used to prepare spicy chicken dishes. Aim of the review: This review comprehensively summarizes the available information on the botanical characterization, phytochemistry, pharmacological activities, pharmacodynamics, pharmacokinetics, and toxicity of MFC. Methods: Relevant scientific literature up to August 2023 was included in the study. Chinese and English studies on MFC were collected from databases, including PubMed, Elsevier, Web of Science, Springer, Science Direct, Wiley, ACS, and CNKI (Chinese). Doctoral and Master's dissertations were also included. Results: In total, 720 compounds have been identified and reported in the literature, including flavonoids, coumarins, alkaloids, sterols, phenylpropenols, organic acids, spirocyclopentenones, and volatile oils. Flavonoids and coumarins are the two most important bioactive compounds responsible for these pharmacological activities. MFC has anti-inflammatory, anti-bacterial, anti-microbial, anti-diabetic, anti-tumor, anti-oxidant, anti-depressant, potential anti-Alzheimer's disease, chondroprotective, and analgesic properties. The pharmacological effects include interrupting the STAT3/NF-κB/COX-2 and EGFR signaling pathways, downregulating EpCAM expression, inhibiting NF-κB and ERK signals, inhibiting the EP/cAMP/PKA signaling pathway and miR-29a/Wnt/β-catenin signaling activity, and upregulating Foxo3a expression. Conclusion: This review demonstrates that the chemical constituents, pharmacological activities, pharmacodynamics, pharmacokinetics, and toxicity of MFC support its use in traditional Chinese botanical medicines. MFC contains a wide range of chemical compounds. Flavonoids and coumarins promote strong pharmacological activity and, are low-toxicity natural phytomedicines that are widely used in medicine, food, ornamentation, and cosmetics, making MFC a promising compound for development and use in the treatment of several medical conditions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Qi, Wang, Wang, Wang, Zhu, Zhao and Jiang.)

Underwater noise pollution has become a potential threat to aquatic animals in the natural environment. The main causes of such pollution are frequent human activities creating underwater environmental noise, including commercial shipping, offshore energy platforms, scientific exploration activities, etc. However, in aquaculture environments, underwater noise pollution has also become an unavoidable problem due to background noise created by aquaculture equipment. Some research has shown that certain fish show adaptability to noise over a period of time. This could be due to fish's special auditory organ, i.e., their "inner ear"; meanwhile, otoliths and sensory hair cells are the important components of the inner ear and are also essential for the function of the auditory system. Recently, research in respect of underwater noise pollution has mainly focused on adult fish, and there is a lack of the research on the effects of underwater noise pollution on the development process of the auditory system in the embryonic development period. Thus, in this study, we collected embryo-larval samples of the small yellow croaker ( Larimichthys polyactis ) in four important stages of otic vesicle development through artificial breeding. Then, we used metabonomics and transcriptomics analyses to reveal the development process of the auditory system in the embryonic development period under background noise (indoor and underwater environment sound). Finally, we identified 4026 differentially expressed genes (DEGs) and 672 differential metabolites (DMs), including 37 DEGs associated with the auditory system, and many differences mainly existed in the neurula stage (20 h of post-fertilization/20 HPF). We also inferred the regulatory mode and process of some important DEGs ( Dnmt1 , CPS1 , and endothelin-1) in the early development of the auditory system. In conclusion, we suggest that the auditory system development of L. polyactis begins at least in the neurula stage or earlier; the other three stages (tail bud stage, caudal fin fold stage, and heart pulsation stage, 28-35 HPF) mark the rapid development period. We speculate that the effect of underwater noise pollution on the embryo-larval stage probably begins even earlier.

Circulating tumor cells (CTCs) that undergo epithelial-to-mesenchymal transition (EMT) can provide valuable information regarding metastasis and potential therapies. However, current studies on the EMT overlook alternative splicing. Here, we used single-cell full-length transcriptome data and mRNA sequencing of CTCs to identify stage-specific alternative splicing of partial EMT and mesenchymal states during pancreatic cancer metastasis. We classified definitive tumor and normal epithelial cells via genetic aberrations and demonstrated dynamic changes in the epithelial-mesenchymal continuum in both epithelial cancer cells and CTCs. We provide the landscape of alternative splicing in CTCs at different stages of EMT, uncovering cell-type-specific splicing patterns and splicing events in cell surface proteins suitable for therapies. We show that MBNL1 governs cell fate through alternative splicing independently of changes in gene expression and affects the splicing pattern during EMT. We found a high frequency of events that contained multiple premature termination codons and were enriched with C and G nucleotides in close proximity, which influence the likelihood of stop codon readthrough and expand the range of potential therapeutic targets. Our study provides insights into the EMT transcriptome's dynamic changes and identifies potential diagnostic and therapeutic targets in pancreatic cancer., Competing Interests: The authors declare no competing interests., (© 2024 The Authors.)

Central nervous system (CNS) disease is one of the most important causes of human death. Because of their complex pathogenesis, more and more attention has been paid to them. At present, drug treatment of the CNS is the main means; however, most drugs only relieve symptoms, and some have certain toxicity and side effects. Natural compounds derived from plants can provide safer and more effective alternatives. Alkaloids are common nitrogenous basic organic compounds found in nature, which exist widely in many kinds of plants and have unique application value in modern medicine. For example, Galantamine and Huperzine A from medicinal plants are widely used drugs on the market to treat Alzheimer's disease. Therefore, the main purpose of this review is to provide the available information on natural alkaloids with the activity of treating central nervous system diseases in order to explore the trends and perspectives for the further study of central nervous system drugs. In this paper, 120 alkaloids with the potential effect of treating central nervous system diseases are summarized from the aspects of sources, structure types, mechanism of action and structure-activity relationship., (© 2023 John Wiley & Sons, Ltd.)

Motivation: Cell-cell interactions (CCIs) play critical roles in many biological processes such as cellular differentiation, tissue homeostasis, and immune response. With the rapid development of high throughput single-cell RNA sequencing (scRNA-seq) technologies, it is of high importance to identify CCIs from the ever-increasing scRNA-seq data. However, limited by the algorithmic constraints, current computational methods based on statistical strategies ignore some key latent information contained in scRNA-seq data with high sparsity and heterogeneity., Results: Here, we developed a deep learning framework named DeepCCI to identify meaningful CCIs from scRNA-seq data. Applications of DeepCCI to a wide range of publicly available datasets from diverse technologies and platforms demonstrate its ability to predict significant CCIs accurately and effectively. Powered by the flexible and easy-to-use software, DeepCCI can provide the one-stop solution to discover meaningful intercellular interactions and build CCI networks from scRNA-seq data., Availability and Implementation: The source code of DeepCCI is available online at https://github.com/JiangBioLab/DeepCCI., (© The Author(s) 2023. Published by Oxford University Press.)

Over the past decade, the number of cancer cases has continued to rise, placing a heavy burden on patients' families and healthcare systems. Although innovative treatments and drugs have improved patient outcomes, the financial toxicity (FT) of treatment is a growing concern among oncologists. Previous research have examined the impacts of FT on the HRQOL of cancer patients. However, the extent of the association is unclear, given that previous studies vary in the enrolled population, adjustment of confounding factors, and usage of FT assessment tools. To address this gap, the main purpose of this systematic review is to examine the relationship between FT and HRQOL of cancer survivors, and explore any potential factors that may affect this relationship., (© 2022 John Wiley & Sons Australia, Ltd.)

Cancer has become a grave health crisis that threatens the lives of millions of people worldwide. Because of the drawbacks of the available anticancer drugs, the development of novel and efficient anticancer agents should be encouraged. Epidithiodiketopiperazine (ETP) alkaloids with a 2,5-diketopiperazine (DKP) ring equipped with transannular disulfide or polysulfide bridges or S-methyl moieties constitute a special subclass of fungal natural products. Owing to their privileged sulfur units and intriguing architectural structures, ETP alkaloids exhibit excellent anticancer activities by regulating multiple cancer proteins/signaling pathways, including HIF-1, NF-κB, NOTCH, Wnt, and PI3K/AKT/mTOR, or by inducing cell-cycle arrest, apoptosis, and autophagy. Furthermore, a series of ETP alkaloid derivatives obtained via structural modification showed more potent anticancer activity than natural ETP alkaloids. To solve supply difficulties from natural resources, the total synthetic routes for several ETP alkaloids have been designed. In this review, we summarized several ETP alkaloids with anticancer properties with particular emphasis on their underlying mechanisms of action, structural modifications, and synthetic strategies, which will offer guidance to design and innovate potential anticancer drugs., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Single-cell RNA sequencing (scRNA-seq) detects whole transcriptome signals for large amounts of individual cells and is powerful for determining cell-to-cell differences and investigating the functional characteristics of various cell types. scRNA-seq datasets are usually sparse and highly noisy. Many steps in the scRNA-seq analysis workflow, including reasonable gene selection, cell clustering and annotation, as well as discovering the underlying biological mechanisms from such datasets, are difficult. In this study, we proposed an scRNA-seq analysis method based on the latent Dirichlet allocation (LDA) model. The LDA model estimates a series of latent variables, i.e. putative functions (PFs), from the input raw cell-gene data. Thus, we incorporated the 'cell-function-gene' three-layer framework into scRNA-seq analysis, as this framework is capable of discovering latent and complex gene expression patterns via a built-in model approach and obtaining biologically meaningful results through a data-driven functional interpretation process. We compared our method with four classic methods on seven benchmark scRNA-seq datasets. The LDA-based method performed best in the cell clustering test in terms of both accuracy and purity. By analysing three complex public datasets, we demonstrated that our method could distinguish cell types with multiple levels of functional specialization, and precisely reconstruct cell development trajectories. Moreover, the LDA-based method accurately identified the representative PFs and the representative genes for the cell types/cell stages, enabling data-driven cell cluster annotation and functional interpretation. According to the literature, most of the previously reported marker/functionally relevant genes were recognized., (© The Author(s) 2023. Published by Oxford University Press.)

Phytochemical investigation on the whole plant of Euphorbia wallichii led to the identification of twelve diterpenoids, including nine undescribed ones, in which wallkauranes A-E (1-5) were classified as ent-kaurane diterpenoids and wallatisanes A-D (6-9) were assigned as ent-atisane diterpenoids. The biological evaluation of these isolates against NO production was conducted in the LPS-induced RAW264.7 macrophage cells model, resulting in the identification of a series of potent NO inhibitors, with the most active wallkaurane A showing an IC 50 value of 4.21 μM. The mechanistic study disclosed that wallkaurane A could inhibit pro-inflammatory cytokines generation such as TNF-α, IL-1β, and IL-6, and decrease the expression of iNOS and COX-2. Wallkaurane A could regulate the NF-κB signaling pathways and the JAK2/STAT3 signaling pathway to suppress the inflammatory reaction in LPS-induced RAW264.7 cells. Meanwhile, wallkaurane A could also inhibit the JAK2/STAT3 signaling pathway, thereby suppressing apoptosis in LPS-induced RAW264.7 cells., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Background: Fibroblast activation protein (FAP) is a cell-surface serine protease that has both dipeptidyl peptidase as well as endopeptidase activities and could cleave substrates at post-proline bond. Previous findings showed that FAP was hard to be detected in normal tissues but significantly up-regulated in remodeling sites like fibrosis, atherosclerosis, arthritis and embryonic tissues. Though increasing evidence has demonstrated the importance of FAP in cancer progression, no multifactorial analysis has been developed to investigate its function in gastrointestinal cancers until now., Methods: By comprehensive use of datasets from The Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), scTIME Portal and Human Protein Atlas (HPA), we evaluated the carcinogenesis potential of FAP in gastrointestinal cancers, analyzing the correlation between FAP and poor outcomes, immunology in liver, colon, pancreas as well as stomach cancers. Then liver cancer was selected as example to experimentally validate the pro-tumor and immune regulative role of FAP in gastrointestinal cancers., Results: FAP was abundantly expressed in gastrointestinal cancers, such as LIHC, COAD, PAAD and STAD. Functional analysis indicated that the highly-expressed FAP in these cancers could affect extracellular matrix organization process and interacted with genes like COL1A1, COL1A2, COL3A1 and POSTN. In addition, it was also observed that FAP was positively correlated to M2 macrophages infiltration across these cancers. To verify these findings in vitro , we used LIHC as example and over-expressed FAP in human hepatic stellate LX2 cells, a main cell type that produce FAP in tumor tissues, and then investigate its role on LIHC cells as well as macrophages. Results showed that the medium from FAP-over-expressed LX2 cells could significantly promote the motility of MHCC97H and SK-Hep1 LIHC cells, increase the invasion of THP-1 macrophages and induce them into pro-tumor M2 phenotype., Conclusion: In summary, we employed bioinformatic tools and experiments to perform a comprehensive analysis about FAP. Up-regulation of FAP in gastrointestinal cancers was primarily expressed in fibroblasts and contributes to tumor cells motility, macrophages infiltration and M2 polarization, revealing the multifactorial role of FAP in gastrointestinal cancers progression., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Cai, Yang, Sun, Xiao, Han, Zhang, Zhou, Jiang, Jiang, Li and Nie.)

Parkinson's disease (PD) is characterized by dopaminergic neurons degeneration in the substantia nigra pars compacta. Increasing evidence indicates that peripheral CD4 + T cells, a vital pathological component of PD, have been implicated in systemic inflammation activation, blood-brain barrier (BBB) dysfunction, central nervous system infiltration, and consequent neurons degeneration. However, there is no consensus on CD4 + T cell types' exact phenotypic characteristics in systemic inflammation and the mechanism of CD4 + T cells traffic into the BBB in patients with PD. In this study, we employed single-cell RNA sequencing (scRNA-seq) to elucidate the potential mechanism of T cells on the breakdown of BBB. The PD-associated Cytotoxic CD4 + T cells (CD4 + CTLs) were characterized by a significant increase in proportion as well as enhancement of interferon-gamma (IFNG) response and cell adhesion. Meanwhile, TBX21, IRF1 and NFATC2, identified as the key transcription factors in effector CD4 + T cells differentiation, induced overexpression of target genes-IFNG in CD4 + CTLs. Interestingly, endothelial cells (ECs) in PD patients were discovered to be more responsive to IFNG than other cell types of midbrain. Furthermore, the cell-cell communication analysis between CD4 + T cells and midbrain cells identified IFNG/IFNGR1 and SPP1/ITGB1 as the ligand-receptor pairs to mediate CD4 + CTLs' infiltration into the central nervous system (CNS) through the weakened ECs' tight junction. Together, these results suggested that PD-specific peripheral CD4 + CTLs might influence BBB function by migrating to mesencephalic endothelial cells (ECs) and activating the IFNG response in ECs., Competing Interests: Declaration of competing interest None Declared., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Background: Given their potent antioxidation properties, carotenoids play a role in delaying and preventing dementia and mild cognitive impairment (MCI). However, observational studies have found inconsistent results regarding the associations between blood carotenoid levels and the risk of dementia and MCI. We conducted this systematic review and meta-analysis to investigate the relationship between blood carotenoid levels and the risk of dementia and MCI., Methods: A systematic search was performed in the Web of Science, PubMed, Embase, and Cochrane Library electronic databases to retrieve relevant English articles published from their inception until February 23, 2023. Study quality was assessed by the Newcastle-Ottawa scale. Standardized mean differences (SMDs) and 95% confidence intervals (CIs) were pooled using random-effect meta-analyses. Ultimately, 23 studies (n = 6610) involving 1422 patients with dementia, 435 patients with MCI, and 4753 controls were included., Results: Our meta-analysis showed that patients with dementia had lower blood lycopene (SMD: -0.521; 95%CI: -0.741, -0.301), α-carotene (SMD: -0.489; 95%CI: -0.697, -0.281), β-carotene (SMD: -0.476; 95%CI: -0.784, -0.168), lutein (SMD: -0.516; 95%CI: -0.753, -0.279), zeaxanthin (SMD: -0.571; 95%CI: -0.910, -0.232) and β-cryptoxanthin (SMD: -0.617; 95%CI: -0.953, -0.281) than the controls. Our results indicated that blood carotenoid levels were significantly lower in patients with dementia than in controls, despite high heterogeneity across the studies. Owing to insufficient data, we did not observe a similar and stable relationship between blood carotenoid levels and MCI., Conclusions: Our meta-analysis indicated that lower blood carotenoid levels may be a risk factor for dementia and MCI., (© 2023. The Author(s).)

Tumor-infiltrating T cells are essential players in tumor immunotherapy. Great progress has been achieved in the investigation of T cell heterogeneity. However, little is well known about the shared characteristics of tumor-infiltrating T cells across cancers. In this study, we conduct a pan-cancer analysis of 349,799 T cells across 15 cancers. The results show that the same T cell types had similar expression patterns regulated by specific transcription factor (TF) regulons across cancers. Multiple T cell type transition paths were consistent in cancers. We found that TF regulons associated with CD8 + T cells transitioned to terminally differentiated effector memory (Temra) or exhausted (Tex) states were associated with patient clinical classification. We also observed universal activated cell-cell interaction pathways of tumor-infiltrating T cells in all cancers, some of which specifically mediated crosstalk in certain cell types. Moreover, consistent characteristics of TCRs in the aspect of variable and joining region genes were found across cancers. Overall, our study reveals common features of tumor-infiltrating T cells in different cancers and suggests future avenues for rational, targeted immunotherapies., Competing Interests: The authors declare no competing interests., (© 2023 The Authors.)

Nucleus basalis of Meynert (NbM), one of the earliest targets of Alzheimer's disease (AD), may act as a seed for pathological spreading to its connected regions. However, the underlying basis of regional vulnerability to NbM dysconnectivity remains unclear. NbM functional dysconnectivity was assessed using resting-state fMRI data of health controls and mild cognitive impairment (MCI) patients from the Alzheimer's disease Neuroimaging Initiative (ADNI2/GO phase). Transcriptional correlates of NbM dysconnectivity was explored by leveraging public intrinsic and differential post-mortem brain-wide gene expression datasets from Allen Human Brain Atlas (AHBA) and Mount Sinai Brain Bank (MSBB). By constructing an individual-level tissue-specific gene set risk score (TGRS), we evaluated the contribution of NbM dysconnectivity-correlated gene sets to change rate of cerebral spinal fluid (CSF) biomarkers during preclinical stage of AD, as well as to MCI onset age. An independent cohort of health controls and MCI patients from ADNI3 was used to validate our main findings. Between-group comparison revealed significant connectivity reduction between the right NbM and right middle temporal gyrus in MCI. This regional vulnerability to NbM dysconnectivity correlated with intrinsic expression of genes enriched in protein and immune functions, as well as with differential expression of genes enriched in cholinergic receptors, immune, vascular and energy metabolism functions. TGRS of these NbM dysconnectivity-correlated gene sets are associated with longitudinal amyloid-beta change at preclinical stages of AD, and contributed to MCI onset age independent of traditional AD risks. Our findings revealed the transcriptional vulnerability to NbM dysconnectivity and their crucial role in explaining preclinical amyloid-beta change and MCI onset age, which offer new insights into the early AD pathology and encourage more investigation and clinical trials targeting NbM., Competing Interests: Declaration of Competing Interest All authors report no competing interests except the Alzheimer's Disease Neuroimaging Initiative: Dr. Petersen serves on scientific advisory boards for Elan Corporation, Wyeth, and GE Healthcare; receives royalties from the publication of Mild Cognitive Impairment (Oxford University Press, 2003); and receives research support from the NIH/NIA (U01 AG06786 [PI], P50 AG16574 [PI], U01 AG 024904 [Subcontract PI], and R01 AG11378 [Co-I]). Dr. Aisen serves on a scientific advisory board for NeuroPhage; serves as a consultant to Elan Corporation, Wyeth, Eisai Inc., Neurochem Inc., Schering-Plough Corp., Bristol-Myers Squibb, Eli Lilly and Company, NeuroPhage, Merck & Co., Roche, Amgen, Genentech, Inc., Abbott, Pfizer Inc, Novartis, and Medivation, Inc.; receives research support from Pfizer Inc, Baxter International Inc., Neuro-Hitech, Abbott, Martek, and the NIH (NIA U01-AG10483 [PI], NIA U01-AG024904 [Coordinating Center Director], NIA R01-AG030048 [PI], and R01-AG16381 [Co-I]); and has received stock options from Medivation, Inc. and NeuroPhage. Dr. Beckett received funding for travel to attend a conference not funded by industry; and receives research support from the NIH (2 P30 AG10129 [Director of Biostatistics Core], 2 P30 CA93373 [Director of Biostatistics Shared Resource], 1 U01 AG24904 [PI, UC Davis site; Biostatistics Team Leader], 1KL2RR024144-01 [Director of Biostatistics Core], 5R01EB002138-07 [Co-I], and 1RC2AG036535-01 [PI, UC Davis site]). Dr. Donohue receives research support from the NIH (AG010483 [Statistician] and AG024904 [Statistician]), the General Clinical Research Center, UCSD, National Center for Research Resources, and from the United States Public Health Service. Dr. Gamst served on an expert review board for Neurochem Inc; and receives research support as an investigator from the NIH [MH22005, CA104573, AG024904, MH062512, DK075128, AG010483, MH079752AG031224, MH083552, MH083506, HL095089], and the National Science Foundation. Dr. Harvey serves as an Associate Editor of Statistics for Alzheimer Disease and Associated Disorders; and receives research support from the NIH (NIA 2P30AG10129 [Biostatistician], NIA R01AG029672 [Biostatistician], NIA 1U01AG24904 [Member of Biostatistics Core], NRCC RL1NS062412 [Biostatistician], NIA R01AG031252 [Biostatistician], 1RC2AG036535– 01 [Member of Biostatistics Team]) and from the Hillblom Foundation, 2007A005NET (Biostatistician). Dr. Jack served on a scientific advisory board for Elan Corporation; receives research support from Pfizer Inc, the NIH (NIA AG11378 [PI], P50-AG16574 [Co-I], and U01 AG024904 [Co-I]) and from the Mayo U of MN Biotechnology Partnership; and holds stock in GE Healthcare. Dr. Jagust has served on a scientific advisory boards for Genentech, Inc.; has served as a consultant for Synarc, Elan Corporation, Genentech, Inc., Ceregene, Schering Plough, and Merck & Co; and receives research support from the NIH (AG027859 [PI], AG027984 [PI], and AG 024904 [Co-I]) and from the Alzheimer’s Association. Dr. Shaw has received funding for travel and speaker honoraria from Pfizer Inc; serves on the editorial board of Therapeutic Drug Monitoring; may potentially receive revenue for patent pending (application 10/192,193): O-methylated rapamycin derivatives for alleviation and inhibition of lymphoproliferative disorders, licensed by the University of Pennsylvania to Novartis; receives royalties from publication of Applied Pharmacokinetics and Pharmacodynamics: Principles of Therapeutic Drug Monitoring, Wolters Kluwer/Lippincott Williams & Wilkins, 2005; receives research support from the NIH (AG024904 [Co-PI Biomarker Core Laboratory]); and receives board of directors’ compensation and holds stock options in Saladax Biomedical. Dr. Toga received a speaker honorarium from St. Jude Children’s Hospital; serves in an editorial capacity for NeuroImage, InSight, The Cerebellum, Neuroimaging, Neuroinformatics, Anatomy & Embryology, Current Medical Imaging Reviews, Biology Image Library, Biomedical Computation Review, Brain Structure and Function, and Journal of Neural Regeneration Research; has served on scientific and/or external advisory boards for Wellcome Trust, Allen Institute for Brain Science, University of Texas at Austin, Oklahoma IDeA Network for Biomedical Research Excellence, Takeda Global Research & Development Center, and the University of Pittsburgh; and has received/receives research support from the NIH (1R01 HD053893-01 [Co-I], NIBIB 2 R01 LM005639 [Co-I], NCRR 5 P41 RR013642 [PI], R01 HD050735-01 [Co-I], 1 R01 NS049194 [Co-I], 1 R01 EB 006266-01 [Subcontract PI], NIMH/UCI, R24 RR021992 [Subcontract PI], 2P50AG005133 [Consultant: Core-Neuroimaging], NCRR 5 U24 RR021760 [PI], NIMH 2 P50 AG016570 [Co-I], NIMH 1R01MH072641-01A1 [Co-I], NIMH 5 R01 MH071940 [PI], NIMH/NIA 1 U01 AG024904 [Subcontract PI], NIMH/MGH, R24 RR021382 [Subcontract PI], NIBIB/BWH 1 U54 EB05149 [Subcontract PI], 1 R01 DA017830 [Co-I], NCRR 5 U54 RR021813 [PI], R01 MH069259 [Subcontract PI], 1 R01 NS050792 [Subcontract PI], MH069433 [Co-I], NIMH 9 P01 EB 001955-11 [CoPI]), 2005 Equipment Grant, and an Academic Excellence Grant–SUN Microsystems, and from High-Q Foundation and the National Multiple Sclerosis Society. Dr. Trojanowski has received funding for travel and honoraria from Takeda Pharmaceutical Company Ltd. and to attend numerous conferences not funded by industry; serves as an Associate Editor of Alzheimer’s & Dementia; holds 14 patents that may accrue revenue: US Patent 5,281,521, issued 25 Jan 1994: Modified Avidin-Biotin Technique; US Patent 5,580,898, issued 3 Dec 1996: Method of Stabilizing Microtubules to Treat Alzheimer’s Disease; US Patent 5,601,985, issued 11 Feb 1997: Method of Detecting Abnormally Phosphorylated Tau; US Patent 5,733,734, issued 31 Mar 1998: Method of Screening for Alzheimer’s Disease or Disease Associated with the Accumulation of Paired Helical Filaments; US Patent 5,792,900, issued 11 Aug 1998: Compositions and Methods for Producing and Using Homogeneous Neuronal Cell Transplants; US Patent 5,849,988, issued 15 Dec 1998: Rat Comprising Straight Filaments in Its Brain; US Patent 6,214,334, issued 10 Apr 2001: Compositions And Methods for Producing and Using Homogeneous Neuronal Cell Transplants to Treat Neurodegenerative Disorders and Brain and Spinal Cord Injuries; US Patent 6,358,681, issued 19 Mar 2002: Diagnostic Methods for Alzheimer’s Disease by Detection of Multiple MRNAs; US Patent 6,727,075, issued 27 Mar 2004: Methods and Compositions for Determining Lipid Peroxidation Levels in OxidantStress Syndromes and Diseases; US Patent 7,011,827, issued 14 Mar 2006: Compositions and Methods for Producing and Using Homogenous Neuronal Cell Transplants; Penn 0652, K1828, filed 5 Aug 1998: Method of Identifying, Diagnosing and Treating Alpha-synuclein Positive Neurodegenerative Disorders; Penn L1986, Filed 13 Nov 1998: Mutation-specific Functional Impairments in Distinct Tau Isoforms of Hereditary Frontotemporal Dementia and Parkinsonism Linked to Chromosome-17: Genotype Predicts Phenotype; Penn R3868 (UPN-4439), filed 28 Feb 2005: Microtubule Stabilizing Therapies for Neurodegenerative Disorders; and Penn S-4018, DB&R 46406-217282, filed 22 Nov 2005: Treatment of Alzheimer’s and Related Diseases with an Antibody; and receives research support from the NIH (NIA P01 AG 09215-20 [PI], NIA P30 AG 10124-18 [PI], NIA PO1 AG 17586-10 [Project 4 Leader], NIA 1PO1 AG-19724-07 [Core C Leader], NIA 1 U01 AG 024904-05 [Co-PI Biomarker Core Laboratory], NINDS P50 NS053488-02 [PI], NIA UO1 AG029213-01 [Co-I]; RC2NS069368 [PI], RC1AG035427 [PI], and NIA P30AG036468 [PI]), and from the Marian S. Ware Alzheimer Program. Dr. Weiner serves on scientific advisory boards for Bayer Schering Pharma, Eli Lilly and Company, CoMentis, Inc., Neurochem Inc, Eisai Inc., Avid Radiopharmaceuticals Inc., Aegis Therapies, Genentech, Inc., Allergan, Inc., Lippincott Williams & Wilkins, Bristol-Myers Squibb, Forest Laboratories, Inc., Pfizer Inc, McKinsey & Company, Mitsubishi Tanabe Pharma Corporation, and Novartis; has received funding for travel from Nestle´ and Kenes International and to attend conferences not funded by industry; serves on the editorial board of Alzheimer’s & Dementia; has received honoraria from the Rotman Research Institute and BOLT International; serves as a consultant for Elan Corporation; receives research support from Merck & Co., Radiopharmaceuticals Inc., the NIH (U01AG024904 [PI], P41 RR023953 [PI], R01 AG10897 [PI], P01AG19724 [Co-I], P50AG23501 [Co-I], R24 RR021992 [Co-I], R01 NS031966 [Co-I], and P01AG012435 [Co-I]), the US Department of Defense (DAMD17- 01-1-0764 [PI]), the Veterans Administration (MIRECC VISN 21 [Core PI]), and from the State of California; and holds stock in Synarc and Elan Corporation., (Copyright © 2022. Published by Elsevier Inc.)

Unfolded protein response (UPR) signaling is activated under endoplasmic reticulum (ER) stress, an emerging cancer hallmark, leading to either adaptive survival or cell death, while the mechanisms underlying adaptation-death switch remain poorly understood. Here, we examined whether oncogene iASPP regulates the switch and how the mechanisms can be used in colon cancer treatment. iASPP is downregulated when cells undergo transition from adaptation to death during therapy-induced ER stress. Blocking iASPP's downregulation attenuates stress-induced cell death. Mechanistically, Hu-antigen R (HuR)-mediated stabilization of iASPP mRNA and subsequent iASPP protein production is significantly impaired with prolonged ER stress, which facilitates the degradation of GRP78, a key regulator of the UPR, in the cytosol. Because iASPP competes with GRP78 in binding the ER-resident E3 ligase RNF185, and tips the balance in favor of cell death. Positive correlation between the levels of HuR, iASPP, and GRP78 are detectable in colon cancer tissues in vivo. Genetic inhibition of iASPP/GRP78 or chemical inhibition of HuR not only inhibits tumor growth, but also sensitizes colon cancer cells' responses to BRAF inhibitor-induced ER stress and cell death. This study provides mechanistic insights into the switch between adaptation and death during ER stress, and also identifies a potential strategy to improve BRAF-inhibitor efficiency in colon cancers., (© 2022. The Author(s), under exclusive licence to ADMC Associazione Differenziamento e Morte Cellulare.)

Background: Similar to the side effects of cancer treatment, financial toxicity (FT) can affect the quality of life of patients, which has attracted increasing attention in the field of oncology. Despite the fact that the estimated prevalence and risk factors of FT are widely reported, these results have not been synthesized., Objectives: This review is aimed to systematically assess the prevalence and risk factors of self-reported FT., Design: Systematic review and meta-analyses., Data Sources: A computer search of English literature was conducted using databases of PubMed, EMBASE, Web of Science, PsycINFO, and CINAHL, and reference lists of the qualified articles were also included between January 2010 and September 2021. Observational studies that reported the prevalence or risk factors of FT using subjective measures were included., Methods: The systematic review was guided by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. The risk of bias was assessed by the NIH observational cohort and cross-sectional study quality assessment tool. The data were extracted by two reviewers and listed in a descriptive table for meta-analyses., Results: In the 22 studies available for meta-analyses of pooled prevalence of FT, the result was estimated to be 45% (95% CI: 38% to 53%, I 2 = 97.3%, P < 0.001) based on a random-effects model. The pooled analysis identified 9 potential risk factors of FT (7 in β and 8 in OR): low income (OR = 2.48, 95% CI: 1.72 to 3.24, I 2 = 3.1%, P < 0.001), greater annual OOP (β = -4.26, 95% CI: -6.95 to -1.57, I 2 = 0%, P = 0.002), younger age (OR = 2.05, 95% CI: 1.56 to 2.54, I 2 = 0%, P < 0.001), no private insurance (OR = 1.69, 95% CI: 1.02 to 2.37, I 2 = 0%, P < 0.001), unmarried (OR = 1.10, 95% CI: 0.95 to 1.25, I 2 = 53,3%, P < 0.001), nonwhite (OR = 1.59, 95% CI: 1.33 to 1.85, I 2 = 0%, P < 0.001), advanced cancer (β = -4.74, 95% CI: -6.90 to -2.57, I 2 = 0%, P < 0.001), unemployed (β = -2.90, 95% CI: -5.71 to -0.63, I 2 = 75,7%, P < 0.001), more recent diagnosis (OR = 1.31, 95% CI: 1.04 to 1.57, I 2 = 0%, P < 0.001)., Conclusion: This systematic review reported a pooled prevalence of self-reported FT of 45%. Low income, greater annual OOP (Out of pocket), younger age, unmarried, unemployed, nonwhite, no private insurance, advanced cancer, and more recent diagnosis constituted risk factors for self-reported FT. The research on risk factors for FT can provide a theoretical basis for medical staff to evaluate and intervene in the FT among cancer survivors.

The Euphorbia plants are the focus of natural product drug discovery because of their fascinating structural diversity and broad biological activities. Here we reported the discovery of eight undescribed diterpenoids, including two ent-trachylobanes, five ent-atisanes, and one ent-abietane, together with 15 known ones from the whole plant of Euphorbia wallichii. Their chemical structures were elucidated by detailed spectrometry data analysis and X-ray crystallography. Among them, wallichane G represents a rare ent-atisane type pentacyclic diterpenoid featuring a tetrahydrofuran moiety. Furthermore, bioassays indicated that jolkinolide B exhibited potent inhibitory activities on the production of NO, with an IC 50 value of 3.84 ± 0.25 μM. Meanwhile, the mechanistic study revealed that jolkinolide B could obviously downregulate the expression of iNOS, COX-2, NF-κB, and phosphorylated IκBα in a dose-dependent manner and strongly upregulate the expression of Nrf2 and HO-1 protein, thereby suppressing the inflammatory process in macrophage cells induced by LPS., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Recent advances in spatial transcriptomics (ST) have brought unprecedented opportunities to understand tissue organization and function in spatial context. However, it is still challenging to precisely dissect spatial domains with similar gene expression and histology in situ. Here, we present DeepST, an accurate and universal deep learning framework to identify spatial domains, which performs better than the existing state-of-the-art methods on benchmarking datasets of the human dorsolateral prefrontal cortex. Further testing on a breast cancer ST dataset, we showed that DeepST can dissect spatial domains in cancer tissue at a finer scale. Moreover, DeepST can achieve not only effective batch integration of ST data generated from multiple batches or different technologies, but also expandable capabilities for processing other spatial omics data. Together, our results demonstrate that DeepST has the exceptional capacity for identifying spatial domains, making it a desirable tool to gain novel insights from ST studies., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Ethnopharmacological Relevance: Eriobotrya japonica Lindl. has been included in "The Plant List" (http://www.theplantlist.org) and is the most widely researched species in its genus. E. japonica is a subtropical evergreen fruit tree belonging to the Rosaceae family. Its dried leaves are widely used in traditional Chinese herbal medicine to treat coughing caused by pulmonary inflammation, dyspnea due to asthma and cough, nausea caused by stomach disorders, restlessness, and thirst. Furthermore, it is used to treat stomach ache, ulcers, chronic bronchitis, cancer, and diabetes mellitus in Japanese folk medicine. However, no systematic reports on E. japonica leaves have been published before., Aim of the Study: This review summarizes the available information on the traditional uses, phytochemistry, pharmacology, toxicity, and quality control of various extracts and phytoconstituents of E. japonica leaves., Materials and Methods: Relevant publications between 1931 and 2022 were considered. Chinese and English studies on E. japonica leaves were collected from databases, including PubMed, Web of Science, Elsevier, ACS Publications, Springer, and CNKI (Chinese). The traditional uses, phytochemistry, pharmacology, toxicity, and quality control of E. japonica leaves were reviewed., Results: Briefly, 164 compounds, including triterpenes, flavonoids, sesquiterpene glycosides, megastigmane derivatives, phenylpropanoids, and organic acids, have been identified from E. japonica leaves, in addition to 169 volatile oils. More than half of these compounds have not yet been reported to have pharmacological activities. Triterpenes and flavonoids are the most important bioactive compounds responsible for pharmacological activities, such as antidiabetic, anti-inflammatory, and antitumor activities. Other beneficial physiological effects such as antioxidant, hepatoprotective, bronchodilatory, antitussive, and expectorant effects and tracheal smooth muscle relaxation, protection against myocardial ischemia injury, and improved cognitive activities have also been reported. High doses of E. japonica leaf extracts have been used in laboratory animals, and no side effects or toxicity-symptoms have been observed., Conclusions: The pharmacological activities of E. japonica leaves support their use in traditional Chinese herbal medicine. However, several aspects, such as the bioavailability, pharmacodynamics, pharmacokinetics, mechanism of action, and structure-activity relationships of the pure compounds isolated from E. japonica leaves, have not been studied yet and warrant further studies., Competing Interests: Declaration of competing interest The authors declare no competing financial interests., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Despite global vaccination efforts, COVID-19 breakthrough infections caused by variant virus continue to occur frequently, long-term sequelae of COVID-19 infection like neuronal dysfunction emerge as a noteworthy issue. Neuroimmune disorder induced by Inflammatory factor storm was considered as a possible reason, however, little was known about the functional factors affecting neuroimmune response to this virus. Here, using medial prefrontal cortex single cell data of COVID-19 patients, expression pattern analysis indicated that some immune-related pathway genes expressed specifically, including genes associated with T cell receptor, TNF signaling in microglia and Cytokine-cytokine receptor interaction and HIF-1 signaling pathway genes in astrocytes. Besides the well-known immune-related cell type microglia, we also observed immune-related factors like IL17D, TNFRSF1A and TLR4 expressed in Astrocytes. Based on the ligand-receptor relationship of immune-related factors, crosstalk landscape among cell clusters were analyzed. The findings indicated that astrocytes collaborated with microglia and affect excitatory neurons, participating in the process of immune response and neuronal dysfunction. Moreover, subset of astrocytes specific immune factors (hinged neuroimmune genes) were proved to correlate with Covid-19 infection and ventilator-associated pneumonia using multi-tissue RNA-seq and scRNA-seq data. Function characterization clarified that hinged neuroimmune genes were involved in activation of inflammation and hypoxia signaling pathways, which could lead to hyper-responses related neurological sequelae. Finally, a risk model was constructed and testified in RNA-seq and scRNA data of peripheral blood., Competing Interests: Declaration of competing interest The authors declare no competing interests., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Objective : Using the Comprehensive Score for Financial Toxicity (COST) tool to measure financial toxicity (FT) among nasopharyngeal cancer (NPC) patients in western China and investigate the association between FT and psychological distress., Methods: We conducted a cross-sectional study of survivors with NPC in a tertiary oncology hospital in China. FT was assessed using the COST (Chinese version), a validated instrument widely used both at home and abroad. The NCCN Distress Thermometer (DT) was used to measure psychological distress. A multivariate logistic regression model was built to determine factors associated with FT, and the Pearson correlation was used to assess the correlation between COST and DT scores., Results: Of 210 patients included in this study, the mean FT score was 16.3 (median: 22.5, SD: 9.7), and the prevalence of FT was 66.2% (mild FT: 37.1%, moderate FT: 50.5%, severe FT: 2.4%). Suggested by the logistic regression model, 5 variables were associated with increased FT: unemployed, no commercial insurance, receiving lower annual income, advanced cancer, and receiving targeted therapy. The Pearson correlation showed a significantly moderate correlation between financial toxicity and psychological distress (r= -0.587, P < 0.001)., Conclusion: Patients with nasopharyngeal carcinoma (NPC) in western China demonstrated higher self-reported financial toxicity (FT) associated with factors including unemployed, no commercial insurance, receiving lower annual income, advanced cancer, and receiving targeted therapy. These predictors will help clinicians identify potential patients with FT in advance and conduct effective psychological interventions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Jiang, Mou, Lyu, Jiang, Liu, Zeng, Hu, Zheng, Jiang and Yang.)

The rapid development of single-cel+l RNA sequencing (scRNA-seq) technology provides unprecedented opportunities for exploring biological phenomena at the single-cell level. The discovery of cell types is one of the major applications for researchers to explore the heterogeneity of cells. Some computational methods have been proposed to solve the problem of scRNA-seq data clustering. However, the unavoidable technical noise and notorious dropouts also reduce the accuracy of clustering methods. Here, we propose the cauchy-based bounded constraint low-rank representation (CBLRR), which is a low-rank representation-based method by introducing cauchy loss function (CLF) and bounded nuclear norm regulation, aiming to alleviate the above issue. Specifically, as an effective loss function, the CLF is proven to enhance the robustness of the identification of cell types. Then, we adopt the bounded constraint to ensure the entry values of single-cell data within the restricted interval. Finally, the performance of CBLRR is evaluated on 15 scRNA-seq datasets, and compared with other state-of-the-art methods. The experimental results demonstrate that CBLRR performs accurately and robustly on clustering scRNA-seq data. Furthermore, CBLRR is an effective tool to cluster cells, and provides great potential for downstream analysis of single-cell data. The source code of CBLRR is available online at https://github.com/Ginnay/CBLRR., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Structural variation (SV) is a vital part of biological genetic diversity. The simulation and identification with high efficiency and accuracy are considered to be very important. With the continuous development and wide application of various technologies, computer simulation of genomic data has attracted wide attention due to its intuitive and convenient advantages. Meanwhile, there are several high-quality methods used for structural variation identification based on second-generation (short-read) and third-generation (long-read) data. These methods utilize various strategies and compatible aligners and exhibit specific characteristics. In addition, genomic visualization tools use graphical interfaces to visualize the data, which are convenient for data observation, validation, and even for the manual curation of several questionable data. The present study summarized the methods of simulation, identification, and visualization tools for structural variation in the context of sequencing technology development. Overall, this review aimed to offer a more comprehensive understanding of the impact of SV., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing an outbreak of coronavirus disease 2019 (COVID-19), is a major threat to public health worldwide. Previous studies have shown that the spike protein of SARS-CoV-2 determines viral infectivity and major antigenicity. However, the spike protein has been undergoing various mutations, which bring a great challenge to the prevention and treatment of COVID-19. Here we present the MutCov, a pipeline for evaluating the effect of mutations in spike protein on infectivity and antigenicity of SARS-CoV-2 by calculating the binding free energy between spike protein and angiotensin-converting enzyme 2 (ACE2) or neutralizing monoclonal antibody (mAb). The predicted infectivity and antigenicity were highly consistent with biologically experimental results, and demonstrated that the MutCov achieved good prediction performance. In conclusion, the MutCov is of high importance for systematically evaluating the effect of novel mutations and improving the prevention and treatment of COVID-19. The source code and installation instruction of MutCov are freely available at http://jianglab.org.cn/MutCov., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Clinical practice shows that when single-target drugs treat multi-factor diseases such as tumors, cardiovascular system and endocrine system diseases, it is often difficult to achieve good therapeutic effects, and even serious adverse reactions may occur. Multi-target drugs can simultaneously regulate multiple links of disease, improve efficacy, reduce adverse reactions, and improve drug resistance. They are ideal drugs for treating complex diseases, and therefore have become the main direction of drug development. At present, some multi-target drugs have been successfully used in many major diseases. Entrectinib is an oral small molecule inhibitor that targets TRK, ROS1, and ALK. It is used to treat locally advanced or metastatic solid tumors with NTRK1/2/3, ROS1 and ALK gene fusion mutations. It can pass through the blood-brain barrier and is the only TRK inhibitor clinically proven to be effective against primary and metastatic brain diseases. In 2019, entrectinib was approved by the FDA to treat adult patients with ROS1-positive metastatic non-small cell lung cancer. Case reports showed that continuous administration of entrectinib was effective and tolerable. In this review, we give a brief introduction to TKK, ROS1 and ALK, and on this basis, we give a detailed and comprehensive introduction to the mechanism of action, pharmacokinetics, pharmacodynamics, clinical efficacy, tolerability and drug interactions of entrectinib., (Copyright © 2022 The Authors. Published by Elsevier Masson SAS.. All rights reserved.)

Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental disease. To date, more than 1000 genes have been shown to be associated with ASD, and only a few of these genes account for more than 1% of autism cases. Klf7 is an important transcription factor of cell proliferation and differentiation in the nervous system, but whether klf7 is involved in autism is unclear., Methods: We first performed ChIP-seq analysis of klf7 in N2A cells, then performed behavioral tests and RNA-seq in klf7 +/- mice, and finally restored mice with adeno-associated virus (AAV)-mediated overexpression of klf7 in klf7 +/- mice., Results: Klf7 targeted genes are enriched with ASD genes, and 631 ASD risk genes are also differentially expressed in klf7 +/- mice which exhibited the core symptoms of ASD. When klf7 levels were increased in the central nervous system (CNS) in klf7 +/- adult mice, deficits in social interaction, repetitive behavior and majority of dysregulated ASD genes were rescued in the adults, suggesting transcriptional regulation. Moreover, knockdown of klf7 in human brain organoids caused dysregulation of 517 ASD risk genes, 344 of which were shared with klf7 +/- mice, including some high-confidence ASD genes., Conclusions: Our findings highlight a klf7 regulation of ASD genes and provide new insights into the pathogenesis of ASD and promising targets for further research on mechanisms and treatments.

Messenger RNA (mRNA) vaccines have shown great potential for anti-tumor therapy due to the advantages in safety, efficacy and industrial production. However, it remains a challenge to identify suitable cancer neoantigens that can be targeted for mRNA vaccines. Abnormal alternative splicing occurs in a variety of tumors, which may result in the translation of abnormal transcripts into tumor-specific proteins. High-throughput technologies make it possible for systematic characterization of alternative splicing as a source of suitable target neoantigens for mRNA vaccine development. Here, we summarized difficulties and challenges for identifying alternative splicing-derived cancer neoantigens from RNA-seq data and proposed a conceptual framework for designing personalized mRNA vaccines based on alternative splicing-derived cancer neoantigens. In addition, several points were presented to spark further discussion toward improving the identification of alternative splicing-derived cancer neoantigens., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Immune system plays important roles in the pathogenesis of Parkinson's disease (PD). However, the role of B cells in this complex disease are still not fully understood. B cells produce antibodies but can also regulate immune responses. In order to decode the relative contribution of peripheral B cell subtypes to the etiology of PD, we performed single cell RNA and BCR sequencing for 10,466 B cells from 8 PD patients and 6 age-matched healthy controls. We observed significant increased memory B cells and significant decreased naïve B cells in PD patients compared to healthy controls. Notably, we also discovered increased IgG and IgA isotypes and more frequent class switch recombination events in PD patients. Moreover, we identified preferential V and J gene segments of B cell receptors in PD patients as the evidence of convergent selection in PD. Finally, we found a marked clonal expanded memory B cell population in PD patients, up-regulating both MHC II genes (HLA-DRB5, HLA-DQA2 and HLA-DPB1) and transcription factor activator protein 1 (AP-1), suggesting that the antigen presentation capacity of B cells was enhanced and B cells were activated in PD patients. Overall, this study conducted a comprehensive analysis of peripheral B cell characteristics of PD patients, which provided novel insights into the humoral immune response in the pathogenesis of PD., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Wang, Luo, Zhou, Jin, Xu, Yan, Li, Xu, Cheng, Huang, Lin, Yao, Nie and Jiang.)

Background: Genes spanning long chromosomal domains are coordinately regulated in human genome, which contribute to global gene dysregulation and carcinogenesis in cancer. It has been noticed that epigenetic modification and chromatin architecture may participate in the regulation process. However, the regulation patterns and functional elements of long-range gene regulation are unclear., Methods: Based on the clinical transcriptome data from different tumor sets, a novel expressional correlation analysis pipeline was performed to classify the co-regulated regions and subsets of intercorrelated regions. The GLAM2 program was used to predict conserved DNA elements that enriched in regions. Two conserved elements were selected to delete in Ishikawa and HeLa cells by CRISPR-Cas9. SAHA treatment and HDAC knockdown were used to change the histone acetylation status. Using qPCR, MTT, and scratch healing assay, we evaluate the effect on gene expression and cancer cell phenotype. By DNA pull-down and ChIP, the element-binding proteins were testified. 3C and 3D-FISH were performed to depict the alteration in chromatin architecture., Results: In multiple cancer genomes, we classified subsets of coordinately regulated regions (sub-CRRs) that possibly shared the same regulatory mechanisms and exhibited similar expression patterns. A new conserved DNA element (CRE30) was enriched in sub-CRRs and associated with cancer patient survival. CRE30 could restrict gene regulation in sub-CRRs and affect cancer cell phenotypes. DNA pull-down showed that multiple proteins including CTCF were recruited on the CRE30 locus, and ChIP assay confirmed the CTCF-binding signals. Subsequent results uncovered that as an essential element, CRE30 maintained chromatin loops and mediated a compact chromatin architecture. Moreover, we found that blocking global histone deacetylation induced chromatin loop disruption and CTCF dropping in the region containing CRE30, linked to promoted gene regulation. Additionally, similar effects were observed with CRE30 deletion in another locus of chromosome 8., Conclusions: Our research clarified a new functional element that recruits CTCF and collaborates with histone deacetylation to maintain high-order chromatin organizations, linking to long-range gene regulation in cancer genomes. The findings highlight a close relationship among conserved DNA element, epigenetic modification, and chromatin architecture in long-range gene regulation process., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Tang, Li, Han, Li, Lin, Sun, Zhang, Jiang, Nie and Li.)

Since the outbreak of SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, the viral genome has acquired numerous mutations with the potential to alter the viral infectivity and antigenicity. Part of mutations in SARS-CoV-2 spike protein has conferred virus the ability to spread more quickly and escape from the immune response caused by the monoclonal neutralizing antibody or vaccination. Herein, we summarize the spatiotemporal distribution of mutations in spike protein, and present recent efforts and progress in investigating the impacts of those mutations on viral infectivity and antigenicity. As mutations continue to emerge in SARS-CoV-2, we strive to provide systematic evaluation of mutations in spike protein, which is vitally important for the subsequent improvement of vaccine and therapeutic neutralizing antibody strategies., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Six undescribed diterpenoid alkaloids including five C 19 -diterpenoid alkaloids forrestlines A-E, and one C 20 -diterpenoid alkaloid forrestline F, together with nine known alkaloids have been isolated from the whole herbs of Delphinium forrestii var. vride. Their structures were elucidated by spectroscopic data, and their inhibitory activities on NO production stimulated by LPS in RAW264.7 macrophage cells were determined. Then, forrestline F, with the strongest inhibitory activity (IC 50 of 9.57 ± 1.43 μM), was selected to study its possible anti-inflammatory mechanism. ELISA results showed that forrestline F suppressed inflammatory cytokines, including interleukin-1β (IL-1β), tumor necrosisfactor-α (TNF-α), and interleukin-6 (IL-6). Moreover, forrestline F could down-regulate LPS-induced expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) by western blotting assay. It also inhibited expression of phosphorylation of MAPKs (including p-p38, p-ERK and p-JNK), and NF-κB p65, and decreased ROS accumulation by upregulating the expression of HO-1 expression via nuclear translocation of Nrf2. In conclusion, forrestline F showed anti-inflammatory effect by inhibiting NF-κB/MAPK and Nrf2/HO-1 signaling pathway. Therefore, forrestline F could be a promising molecule for the development of anti-inflammatory agents in the future., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Phages have seriously affected the biochemical systems of the world, and not only are phages related to our health, but medical treatments for many cancers and skin infections are related to phages; therefore, this paper sought to identify phage proteins. In this paper, a Pseudo-188D model was established. The digital features of the phage were extracted by PseudoKNC, an appropriate vector was selected by the AdaBoost tool, and features were extracted by 188D. Then, the extracted digital features were combined together, and finally, the viral proteins of the phage were predicted by a stochastic gradient descent algorithm. Our model effect reached 93.4853%. To verify the stability of our model, we randomly selected 80% of the downloaded data to train the model and used the remaining 20% of the data to verify the robustness of our model., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Gu, Guo, Liao and Jiang.)

Accurate prediction of immunogenic peptide recognized by T cell receptor (TCR) can greatly benefit vaccine development and cancer immunotherapy. However, identifying immunogenic peptides accurately is still a huge challenge. Most of the antigen peptides predicted in silico fail to elicit immune responses in vivo without considering TCR as a key factor. This inevitably causes costly and time-consuming experimental validation test for predicted antigens. Therefore, it is necessary to develop novel computational methods for precisely and effectively predicting immunogenic peptide recognized by TCR. Here, we described DLpTCR, a multimodal ensemble deep learning framework for predicting the likelihood of interaction between single/paired chain(s) of TCR and peptide presented by major histocompatibility complex molecules. To investigate the generality and robustness of the proposed model, COVID-19 data and IEDB data were constructed for independent evaluation. The DLpTCR model exhibited high predictive power with area under the curve up to 0.91 on COVID-19 data while predicting the interaction between peptide and single TCR chain. Additionally, the DLpTCR model achieved the overall accuracy of 81.03% on IEDB data while predicting the interaction between peptide and paired TCR chains. The results demonstrate that DLpTCR has the ability to learn general interaction rules and generalize to antigen peptide recognition by TCR. A user-friendly webserver is available at http://jianglab.org.cn/DLpTCR/. Additionally, a stand-alone software package that can be downloaded from https://github.com/jiangBiolab/DLpTCR., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Epigenetic aberrations have played a significant role in affecting the pathophysiological state of colorectal cancer, and global DNA hypomethylation mainly occurs in partial methylation domains (PMDs). However, the distribution of PMDs in individual cells and the heterogeneity between cells are still unclear. In this study, the DNA methylation profiles of colorectal cancer detected by WGBS and scBS-seq were used to depict PMDs in individual cells for the first time. We found that more than half of the entire genome is covered by PMDs. Three subclasses of PMDS have distinct characteristics, and Gain-PMDs cover a higher proportion of protein coding genes. Gain-PMDs have extensive epigenetic heterogeneity between different cells of the same tumor, and the DNA methylation in cells is affected by the tumor microenvironment. In addition, abnormally elevated promoter methylation in Gain-PMDs may further promote the growth, proliferation and metastasis of tumor cells through silent transcription. The PMDs detected in this study have the potential as epigenetic biomarkers and provide a new insight for colorectal cancer research based on single-cell methylation data., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

The world is facing a pandemic of Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Adaptive immune responses are essential for SARS-CoV-2 virus clearance. Although a large body of studies have been conducted to investigate the immune mechanism in COVID-19 patients, we still lack a comprehensive understanding of the BCR repertoire in patients. In this study, we used the single-cell V(D)J sequencing to characterize the BCR repertoire across convalescent COVID-19 patients. We observed that the BCR diversity was significantly reduced in disease compared with healthy controls. And BCRs tend to skew toward different V gene segments in COVID-19 and healthy controls. The CDR3 sequences of heavy chain in clonal BCRs in patients were more convergent than that in healthy controls. In addition, we discovered increased IgG and IgA isotypes in the disease, including IgG1, IgG3 and IgA1. In all clonal BCRs, IgG isotypes had the most frequent class switch recombination events and the highest somatic hypermutation rate, especially IgG3. Moreover, we found that an IgG3 cluster from different clonal groups had the same IGHV, IGHJ and CDR3 sequences (IGHV4-4-CARLANTNQFYDSSSYLNAMDVW-IGHJ6). Overall, our study provides a comprehensive characterization of the BCR repertoire in COVID-19 patients, which contributes to the understanding of the mechanism for the immune response to SARS-CoV-2 infection., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Two previously undescribed compounds, moranigrine A ( 1 ) and morusamine ( 2 ), along with 18 known compounds were isolated from the fruits of Morus nigra Linn. and structurally characterized using spectroscopic data and electronic circular dichroism analyses. All isolates were evaluated for their inhibitory effects on the 3-phosphoglycerate dehydrogenase (PHGDH) enzyme, which catalyzes the first committed step for the synthesis of glucose-derived serine and is associated with many kinds of cancers. Among these compounds, methyl caffeate ( 3 ) exhibited effective inhibition against PHGDH and was directly bound to PHGDH based on the microscale thermophoresis method and the cellular thermal shift assay. Further biochemical assays revealed that 3 was a noncompetitive inhibitor with respect to the substrate of 3-phosphoglycerate and exhibited a concentration-dependent inhibition. Molecular docking demonstrated that 3 coordinated in an allosteric site of PHGDH with low binding energy. Meanwhile, 3 was selectively toxic to high PHGDH-expressing cancer cell lines and could cause apoptosis of cervical cancer cells in micromolar concentrations and could obviously inhibit tumor growth in the HeLa xenograft mouse model with low toxicities. Therefore, 3 could be developed as a potential inhibitor of PHGDH for the treatment of cancers. Our present study provides information about M. nigra as a functional food or pharmaceutical supplement in the application of cancer prevention and treatment.

Background: Small interfering RNA (siRNA) has emerged as a kind of promising therapeutic agents for cancer therapy. However, the off-target effect and degradation are the main challenges for siRNAs delivery. Herein, an enzyme-free DNA amplification strategy initiated by a specific endogenous microRNA has been developed for in situ generation of siRNAs with enhanced gene therapy effect on cervical carcinoma., Methods: This strategy contains three DNA hairpins (H1, H2/PS and H3) which can be triggered by microRNA-21 (miR-21) for self-assembly of DNA nanowheels (DNWs). Notably, this system is consistent with the operation of a DNA logic circuitry containing cascaded "AND" gates with feedback mechanism. Accordingly, a versatile biosensing and bioimaging platform is fabricated for sensitive and specific analysis of miR-21 in HeLa cells via fluorescence resonance energy transfer (FRET). Meanwhile, since the vascular endothelial growth factor (VEGF) antisense and sense sequences are encoded in hairpin reactants, the performance of this DNA circuit leads to in situ assembly of VEGF siRNAs in DNWs, which can be specifically recognized and cleaved by Dicer for gene therapy of cervical carcinoma., Results: The proposed isothermal amplification approach exhibits high sensitivity for miR-21 with a detection limit of 0.25 pM and indicates excellent specificity to discriminate target miR-21 from the single-base mismatched sequence. Furthermore, this strategy achieves accurate and sensitive imaging analysis of the expression and distribution of miR-21 in different living cells. To note, compared to naked siRNAs alone, in situ siRNA generation shows a significantly enhanced gene silencing and anti-tumor effect due to the high reaction efficiency of DNA circuit and improved delivery stability of siRNAs., Conclusions: The endogenous miRNA-activated DNA circuit provides an exciting opportunity to construct a general nanoplatform for precise cancer diagnosis and efficient gene therapy, which has an important significance in clinical translation., (© 2021. The Author(s).)

Great progress has been made in the investigation on mutation and expression of splicing factor. However, little is known on the role of alternative splicing of splicing factors across cancers. Here, we reported a pan-cancer analysis of alternative splicing of splicing factors spanning 6904 patients across 16 cancer types, and identified 167 splicing factors with implications regulating cancer-specific splicing patterns through alternative splicing. Furthermore, we found that abnormal splicing events of splicing factors could serve as potential common regulators for alternative splicing in different cancers. In addition, we developed a splicing-derived neoepitopes database (ASPNs), which provided the corresponding putative alternative splicing-derived neoepitopes of 16 cancer types. Our results suggested that alternative splicing of splicing factors involved in the pre-RNA splicing process was common across cancer types and may represent an underestimated hallmark of tumorigenesis., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing an outbreak of coronavirus disease 2019 (COVID-19), has been undergoing various mutations. The analysis of the structural and energetic effects of mutations on protein-protein interactions between the receptor binding domain (RBD) of SARS-CoV-2 and angiotensin converting enzyme 2 (ACE2) or neutralizing monoclonal antibodies will be beneficial for epidemic surveillance, diagnosis, and optimization of neutralizing agents. According to the molecular dynamics simulation, a key mutation N439K in the SARS-CoV-2 RBD region created a new salt bridge with Glu329 of hACE2, which resulted in greater electrostatic complementarity, and created a weak salt bridge with Asp442 of RBD. Furthermore, the N439K-mutated RBD bound hACE2 with a higher affinity than wild-type, which may lead to more infectious. In addition, the N439K-mutated RBD was markedly resistant to the SARS-CoV-2 neutralizing antibody REGN10987, which may lead to the failure of neutralization. The results show consistent with the previous experimental conclusion and clarify the structural mechanism under affinity changes. Our methods will offer guidance on the assessment of the infection efficiency and antigenicity effect of continuing mutations in SARS-CoV-2., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Zhou, Xu, Wang, Luo, Xu, Cheng, Jin, Guo, Xue, Juan, Anashkina, Nie and Jiang.)

Given the chronic inflammatory nature of Parkinson's disease (PD), T cell immunity may be important for disease onset. Here, we performed single-cell transcriptome and TCR sequencing, and conducted integrative analyses to decode composition, function and lineage relationship of T cells in the blood and cerebrospinal fluid of PD. Combined expression and TCR-based lineage tracking, we discovered a large population of CD8 + T cells showing continuous progression from central memory to terminal effector T cells in PD patients. Additionally, we identified a group of cytotoxic CD4 + T cells (CD4 CTLs) remarkably expanded in PD patients, which derived from Th1 cells by TCR-based fate decision. Finally, we screened putative TCR-antigen pairs that existed in both blood and cerebrospinal fluid of PD patients to provide potential evidence for peripheral T cells to participate in neuronal degeneration. Our study provides valuable insights and rich resources for understanding the adaptive immune response in PD., (© 2021. The Author(s).)

Backgroud: Cancer stemness is associated with metastases in kidney renal clear cell carcinoma (KIRC) and negatively correlates with immune infiltrates. Recent stemness evaluation methods based on the absolute expression have been proposed to reveal the relationship between stemness and cancer. However, we found that existing methods do not perform well in assessing the stemness of KIRC patients, and they overlooked the impact of alternative splicing. Alternative splicing not only progresses during the differentiation of stem cells, but also changes during the acquisition of the stemness features of cancer stem cells. There is an urgent need for a new method to predict KIRC-specific stemness more accurately, so as to provide help in selecting treatment options., Methods: The corresponding RNA-Seq data were obtained from the The Cancer Genome Atlas (TCGA) data portal. We also downloaded stem cell RNA sequence data from the Progenitor Cell Biology Consortium (PCBC) Synapse Portal. Independent validation sets with large sample size and common clinic pathological characteristics were obtained from the Gene Expression Omnibus (GEO) database. we constructed a KIRC-specific stemness prediction model using an algorithm called one-class logistic regression based on the expression and alternative splicing data to predict stemness indices of KIRC patients, and the model was externally validated. We identify stemness-associated alternative splicing events (SASEs) by analyzing different alternative splicing event between high- and low- stemness groups. Univariate Cox and multivariable logistic regression analysisw as carried out to detect the prognosis-related SASEs respectively. The area under curve (AUC) of receiver operating characteristic (ROC) was performed to evaluate the predictive values of our model., Results: Here, we constructed a KIRC-specific stemness prediction model with an AUC of 0.968,and to provide a user-friendly interface of our model for KIRC stemness analysis, we have developed KIRC Stemness Calculator and Visualization (KSCV), hosted on the Shiny server, can most easily be accessed via web browser and the url https://jiang-lab.shinyapps.io/kscv/ . When applied to 605 KIRC patients, our stemness indices had a higher correlation with the gender, smoking history and metastasis of the patients than the previous stemness indices, and revealed intratumor heterogeneity at the stemness level. We identified 77 novel SASEs by dividing patients into high- and low- stemness groups with significantly different outcome and they had significant correlations with expression of 17 experimentally validated splicing factors. Both univariate and multivariate survival analysis demonstrated that SASEs closely correlated with the overall survival of patients., Conclusions: Basing on the stemness indices, we found that not only immune infiltration but also alternative splicing events showed significant different at the stemness level. More importantly, we highlight the critical role of these differential alternative splicing events in poor prognosis, and we believe in the potential for their further translation into targets for immunotherapy.