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As an important substrate for cell metabolism, the short-chain fatty acid acetate emerges as a regulator of cell fate and function. However, its role in T cell survival and its underlying mechanisms remain largely unknown. Here, we demonstrate that acetate modulates T cell apoptosis via potentiation of α-tubulin acetylation. We further show that acetate treatment effectively increases the expression of the tumor necrosis factor receptor (TNFR) family member CD30 by enhancing its gene transcription. Moreover, CD30 physically associates with and stabilizes the deacetylase HDAC6, which deacetylates α-tubulin to decrease microtubule stability. Proteomic profiling of Cd30 knockout ( Cd30-/-) T cells reveals elevated expression of anti-apoptotic BCL2 family proteins and thus promotes T cell survival via a microtubule-Bcl-2 axis. Taken together, our results demonstrate that acetate is a regulator of T cell survival by controlling levels of acetylated α-tubulin. This suggests that therapeutic manipulation of acetate metabolism may facilitate optimal T cell responses in pathological conditions.

Severe traumatic injury leads to marked systemic inflammation and multiorgan injury. Endogenous drivers such as extracellular nucleic acid may play a role in mediating innate immune response and the downstream pathogenesis. Here, we explored the role of plasma extracellular RNA (exRNA) and its sensing mechanism in inflammation and organ injury in a murine model of polytrauma. We found that severe polytrauma—bone fracture, muscle crush injury, and bowel ischemia—induced a marked increase in plasma exRNA, systemic inflammation, and multiorgan injury in mice. Plasma RNA profiling with RNA sequencing in mice and humans revealed a dominant presence of miRNAs and marked differential expression of numerous miRNAs after severe trauma. Plasma exRNA isolated from trauma mice induced a dose-dependent cytokine production in macrophages, which was almost abolished in TLR7-deficient cells but unchanged in TLR3-deficient cells. Moreover, RNase or specific miRNA inhibitors against the selected proinflammatory miRNAs (i.e., miR-7a-5p, miR-142, let-7j, miR-802, and miR-146a-5p) abolished or attenuated trauma plasma exRNA-induced cytokine production, respectively. Bioinformatic analyses of a group of miRNAs based on cytokine readouts revealed that high uridine abundance (>40%) is a reliable predictor in miRNA mimic-induced cytokine and complement production. Finally, compared with the wild-type, TLR7-knockout mice had attenuated plasma cytokine storm and reduced lung and hepatic injury after polytrauma. These data suggest that endogenous plasma exRNA of severely injured mice and ex-miRNAs with high uridine abundance prove to be highly proinflammatory. TLR7 sensing of plasma exRNA and ex-miRNAs activates innate immune responses and plays a role in inflammation and organ injury after trauma.

Infectious diseases caused by Streptococcus iniae lead to massive death of fish, compose a serious threat to the global aquaculture industry, and constitute a risk to humans who deal with raw fish. In order to realize the early diagnosis of S. iniae, and control the outbreak and spread of disease, it is of great significance to establish fast, sensitive, and convenient detection methods for S. iniae. In the present study, two methods of real-time MIRA (multienzyme isothermal rapid amplification, MIRA) and MIRA-LFD (combining MIRA with lateral flow dipsticks (LFD)) for the simA gene of S. iniae were established, which could complete amplification at a constant temperature of 42 °C within 20 min. Real-time MIRA and MIRA-LFD assays showed high sensitivity (97 fg/μL or 7.6 × 102 CFU/mL), which were consistent with the sensitivity of real-time PCR and 10 times higher than that of PCR with strong specificity, repeatability simplicity, and rapidity for S. iniae originating from Trachinotus ovatus. In summary, real-time MIRA and MIRA-LFD provide effective ways for early diagnosis of S. iniae in aquaculture, especially for units in poor conditions.

Supplementary Figures S1-S8

Cox regression model of IFNG expression on patients’ survival in TCGA and Available expression data of ICB treatment.

SETD2 is the sole histone methyltransferase responsible for H3K36me3, with roles in splicing, transcription initiation, and DNA damage response. Homozygous disruption of SETD2 yields a tumor suppressor effect in various cancers. However, SETD2 mutation is typically heterozygous in diffuse large B-cell lymphomas. Here we show that heterozygous Setd2 deficiency results in germinal center (GC) hyperplasia and increased competitive fitness, with reduced DNA damage checkpoint activity and apoptosis, resulting in accelerated lymphomagenesis. Impaired DNA damage sensing in Setd2-haploinsufficient germinal center B (GCB) and lymphoma cells associated with increased AICDA-induced somatic hypermutation, complex structural variants, and increased translocations including those activating MYC. DNA damage was selectively increased on the nontemplate strand, and H3K36me3 loss was associated with greater RNAPII processivity and mutational burden, suggesting that SETD2-mediated H3K36me3 is required for proper sensing of cytosine deamination. Hence, Setd2 haploinsufficiency delineates a novel GCB context–specific oncogenic pathway involving defective epigenetic surveillance of AICDA-mediated effects on transcribed genes.Significance:Our findings define a B cell–specific oncogenic effect of SETD2 heterozygous mutation, which unleashes AICDA mutagenesis of nontemplate strand DNA in the GC reaction, resulting in lymphomas with heavy mutational burden. GC-derived lymphomas did not tolerate SETD2 homozygous deletion, pointing to a novel context-specific therapeutic vulnerability.This article is highlighted in the In This Issue feature, p. 1599

The pleiotropic cytokine interferon-gamma (IFNγ) is associated with cytostatic, antiproliferation, and proapoptotic functions in cancer cells. However, resistance to IFNγ occurs in many cancer cells, and the underlying mechanism is not fully understood. To investigate potential IFNγ-resistance mechanisms, we performed IFNγ-sensitivity screens in more than 40 cancer cell lines and characterized the sensitive and resistant cell lines. By applying CRISPR screening and transcriptomic profiling in both IFNγ-sensitive and IFNγ-resistant cells, we discovered that activation of double-strand break (DSB) repair genes could result in IFNγ resistance in cancer cells. Suppression of single-strand break (SSB) repair genes increased the dependency on DSB repair genes after IFNγ treatment. Furthermore, inhibition of the DSB repair pathway exhibited a synergistic effect with IFNγ treatment both in vitro and in vivo. The relationship between the activation of DSB repair genes and IFNγ resistance was further confirmed in clinical tumor profiles from The Cancer Genome Atlas (TCGA) and immune checkpoint blockade (ICB) cohorts. Our study provides comprehensive resources and evidence to elucidate a mechanism of IFNγ resistance in cancer and has the potential to inform combination therapies to overcome immunotherapy resistance.

Supplementary Figure from SETD2 Haploinsufficiency Enhances Germinal Center–Associated AICDA Somatic Hypermutation to Drive B-cell Lymphomagenesis

RNA-seq and ATAC-seq of TRAF3-normal and -deficient B16F10 cells treated with vehicle control or IFNγ

Supplementary Figures S1-S8

Immune checkpoint blockade (ICB) therapy revolutionized cancer treatment, but many patients with impaired MHC-I expression remain refractory. Here, we combined FACS-based genome-wide CRISPR screens with a data-mining approach to identify drugs that can upregulate MHC-I without inducing PD-L1. CRISPR screening identified TRAF3, a suppressor of the NFκB pathway, as a negative regulator of MHC-I but not PD-L1. The Traf3-knockout gene expression signature is associated with better survival in ICB-naïve patients with cancer and better ICB response. We then screened for drugs with similar transcriptional effects as this signature and identified Second Mitochondria-derived Activator of Caspase (SMAC) mimetics. We experimentally validated that the SMAC mimetic birinapant upregulates MHC-I, sensitizes cancer cells to T cell–dependent killing, and adds to ICB efficacy. Our findings provide preclinical rationale for treating tumors expressing low MHC-I expression with SMAC mimetics to enhance sensitivity to immunotherapy. The approach used in this study can be generalized to identify other drugs that enhance immunotherapy efficacy.Significance:MHC-I loss or downregulation in cancer cells is a major mechanism of resistance to T cell–based immunotherapies. Our study reveals that birinapant may be used for patients with low baseline MHC-I to enhance ICB response. This represents promising immunotherapy opportunities given the biosafety profile of birinapant from multiple clinical trials.This article is highlighted in the In This Issue feature, p. 1307

Sup.Table.S4: Gene sets enriched in Man2a1-null B16F10 tumors vs control tumors treated with IgG isotype control. Pre-ranked gene set enrichment analysis (GSEA) was used to perform the analysis.

Sup.Fig.9: The effect of Man2a1 inhibition on the immune cell infiltration.

Supplementary Figure Legend

Purpose:Immune checkpoint blockade has shown remarkable efficacy, but in only a minority of patients with cancer, suggesting the need to develop additional treatment strategies. Aberrant glycosylation in tumors, resulting from the dysregulated expression of key enzymes in glycan biosynthesis, modulates the immune response. However, the role of glycan biosynthesis enzymes in antitumor immunity is poorly understood. We aimed to study the immunomodulatory effects of these enzymes.Experimental Design:We integrated transcriptional profiles of treatment-naïve human tumors and functional CRISPR screens to identify glycometabolism genes with immunomodulatory effects. We further validated our findings using in vitro coculture and in vivo syngeneic tumor growth assays.Results:We identified MAN2A1, encoding an enzyme in N-glycan maturation, as a key immunomodulatory gene. Analyses of public immune checkpoint blockade trial data also suggested a synergy between MAN2A1 inhibition and anti–PD-L1 treatment. Loss of Man2a1 in cancer cells increased their sensitivity to T-cell–mediated killing. Man2a1 knockout enhanced response to anti–PD-L1 treatment and facilitated higher cytotoxic T-cell infiltration in tumors under anti–PD-L1 treatment. Furthermore, a pharmacologic inhibitor of MAN2A1, swainsonine, synergized with anti–PD-L1 in syngeneic melanoma and lung cancer models, whereas each treatment alone had little effect.Conclusions:Man2a1 loss renders cancer cells more susceptible to T-cell–mediated killing. Swainsonine synergizes with anti–PD-L1 in suppressing tumor growth. In light of the limited efficacy of anti–PD-L1 and failed phase II clinical trial on swainsonine, our study reveals a potential therapy combining the two to overcome tumor immune evasion.See related commentary by Bhat and Kabelitz, p. 5778

Resistance to apoptosis in acute myeloid leukemia (AML) cells causes refractory or relapsed disease, associated with dismal clinical outcomes. Ferroptosis, a mode of non-apoptotic cell death triggered by iron-dependent lipid peroxidation, has been investigated as potential therapeutic modality against therapy-resistant cancers, but our knowledge of its role in AML is limited. We investigated ferroptosis in AML cells and identified its mitochondrial regulation as a therapeutic vulnerability. GPX4 inhibition induces ferroptosis in AML cells, accompanied with characteristic mitochondrial lipid peroxidation, exerting anti-AML effects in vitro and in vivo. Electron transport chains (ETC) are primary sources of coenzyme Q10 (CoQ) recycling for its function of anti–lipid peroxidation in mitochondria. We found that the mitochondria-specific CoQ potently inhibited GPX4 inhibition–mediated ferroptosis, suggesting that mitochondrial lipid redox regulates ferroptosis in AML cells. Consistently, Rho0 cells, which lack functional ETC, were more sensitive to GPX4 inhibition–mediated mitochondrial lipid peroxidation and ferroptosis than control cells. Furthermore, degradation of ETC through hyperactivation of a mitochondrial protease, caseinolytic protease P (ClpP), synergistically enhanced the anti-AML effects of GPX4 inhibition. Collectively, our findings indicate that in AML cells, GPX4 inhibition induces ferroptosis, which is regulated by mitochondrial lipid redox and ETC.

Erdheim-Chester disease (ECD) and Rosai-Dorfman disease (RDD) are rare non-Langerhans cell histiocytoses (non-LCHs) for which therapeutic options are limited. MAPK pathway activation through BRAFV600E mutation or other genomic alterations is a histiocytosis hallmark and correlates with favorable response to BRAF inhibitors and the MEK inhibitor cobimetinib. However, there has been no systematic evaluation of alternative MEK inhibitors. To assess the efficacy and safety of the MEK inhibitor trametinib, we retrospectively analyzed outcomes of 26 adult patients (17 with ECD, 5 with ECD/RDD, 3 with RDD, and 1 with ECD/LCH) treated with orally administered trametinib at four major US care centers. The most common treatment-related toxicity was rash (27% of patients). For most patients, disease was effectively managed at lower doses (0.5-1.0 mg trametinib daily). The response rate in the 17 evaluable patients was 71% (with 73% (8/11) without a detectable BRAF V600E achieving response). At a median follow-up of 23 months, treatment effects were durable, with a median time-to-treatment failure of 37 months, while median progression-free and overall survival had not been reached (at 3 years, 90.1% of patients were alive). Most patients harbored mutations in BRAF (either classic BRAFV600E or other BRAF alterations); or alterations in other genes involved in the MAPK pathway, e.g., MAP2K1, NF1, GNAS or RAS. Most patients required lower than standard doses of trametinib but were responsive to the lower doses. Our data suggest that the MEK inhibitor trametinib is an effective treatment for ECD and RDD, including those without the BRAFV600E mutation.

Data integrity is one of the most critical security concerns for users when using the cloud storage service. However, it is difficult for users to always stay online and frequently interact with storage service providers to ensure continuous data integrity in practice. The existing Proof of Storage-time schemes, enabling verifiable continuous data integrity checking at cost of performance, fail to provide flexible storage period, reliable measurement of storage time, and resistance to the outsourcing attack. In this paper, we propose EnclavePoSt, the first practical Proof of Storage-time via Intel SGX, where the data integrity checking can be automatically executed in a hardware-driven Trusted Execution Environment (TEE), i.e., the enclave, when users are offline. The checking results can be aggregated and efficiently verified by users. Besides, the elapsed time during isolated data integrity checking can be precisely measured, and the storage period is allowed to flexibly change. Lastly, our EnclavePoSt is resistant to the outsourcing attack. The security analysis and evaluations justify that the EnclavePoSt is more practical than previous works.

Job insecurity has become one of the most prominent job stressors for employees. This study focuses on qualitative job insecurity (QJI) and its spillover effects to the family domain. Despite a positive association between QJI and work-to-family conflict revealed in the literature, research on why and when QJI is related to work-to-family conflict is limited. Drawing from Conservation of Resources theory, this paper empirically examines the mediating role of negative affective process underlying the relationship between QJI and work-to-family conflict as well as the moderating role of core self-evaluations in this process. A four-wave survey study was conducted in a sample of 126 Chinese employees. The results showed that psychological contract violation and job dissatisfaction mediated the relationship between QJI and work-to-family conflict. Unexpectedly, core self-evaluations were found to strengthen (not attenuate) the positive relationships of QJI with employee psychological contract violation and job dissatisfaction.

A compound perspective on hydrological extreme events is of paramount significance as it may lead to damages with larger losses. In this study, an integrated framework, based on downscaled climate variables and hydrological model, i.e. the Soil and Water Assessment Tool, was applied to generate extreme precipitation (Rx1day) and extreme streamflow (Sx1day) series under historical and future climate conditions. Then the potential impacts of climate change for univariate and bivariate joint frequency of extreme precipitation and flood in Xitiaoxi River Basin (XRB), a representative watershed of the Yangtze River Delta, is detected. The compound risk of extreme precipitation and flood under different levels of joint return period for historical and projected periods are estimated by copula‐based two-dimensional approaches. Major findings can be summarized: (1) The Rx1day and Sx1day under future scenarios increased by -0.4 ~ 11.7% and 0.7 ~ 20.4%, respectively, compared to historical period based on univariate frequency analysis, indicating the increasing magnitude of the flood in the future. (2) Climate change with different emission scenarios all have a driving effect on the rising coactivity of extreme precipitation and flood under compound flooding frequency analysis. In addition, the enhancement of climate change to extreme events is more apparent for extremes with higher return period and under the periods of 2080s. (3) Moreover, the flood frequency designs are deduced by bivariate joint distribution are safer than that by univariate distribution. This study may provide actionable insights to formulate the planning scheme of flood control and disaster reduction under the changing environment.

Mutations in PRRT2 and 16p11.2 microdeletion including PRRT2 have been identified as the pathogenic cause of paroxysmal kinesigenic dyskinesia (PKD).The objective was to investigate the clinical and genetic features of PKD and to analyze the genotype-phenotype correlation.We recruited PKD patients, recorded clinical manifestations, and performed PRRT2 screening in 150 PKD patients by unified PKD registration forms. Genotype-phenotype correlation analyses were conducted in probands. High-knee-exercise (HKE) tests were applied in one hundred and six patients.Eight PRRT2 mutations were detected, accounting for 22.76% of the probands. Three mutations (c.649dupC, c.649delC, and c.510_513delTCTG) were already reported, while four mutations (c.252_264delCACAGACCTCAGC, c.503_504delCT, c.679C T, and c.804C A) were first reported. One heterozygous microdeletion of 606 kb in 16p11.2 was detected in one patient. Compared with non-PRRT2 mutation carriers, the PRRT2 mutation carriers were younger at onset, experienced longer attacks, and tended to present with complicated PKD, combined phenotypes of dystonia and chorea. 57.01% of patients could effectively induce movement disorders through the HKE test. A good response was shown in 81.93% of the patients prescribed with antiepileptic drugs. 13.54% (13/96) had abnormal EEG results.PRRT2 mutations are common in patients with PKD and are significantly associated with an earlier age at onset, longer duration of attacks, a complicated form of PKD, combined phenotypes of dystonia and chorea. Patients with microdeletion of 16p11.2 may have more severe manifestations. The HKE test could contribute to the diagnosis of PKD. Carbamazepine is still the first choice for PKD patients, but individualized treatment should be formulated.

Motivation Single-cell RNA sequencing (scRNA-seq) has revolutionized biological research by enabling the measurement of transcriptomic profiles at the single-cell level. With the increasing application of scRNA-seq in larger-scale studies, the problem of appropriately clustering cells emerges when the scRNA-seq data are from multiple subjects. One challenge is the subject-specific variation; systematic heterogeneity from multiple subjects may have a significant impact on clustering accuracy. Existing methods seeking to address such effects suffer from several limitations. Results We develop a novel statistical method, EDClust, for multi-subject scRNA-seq cell clustering. EDClust models the sequence read counts by a mixture of Dirichlet-multinomial distributions and explicitly accounts for cell-type heterogeneity, subject heterogeneity and clustering uncertainty. An EM-MM hybrid algorithm is derived for maximizing the data likelihood and clustering the cells. We perform a series of simulation studies to evaluate the proposed method and demonstrate the outstanding performance of EDClust. Comprehensive benchmarking on four real scRNA-seq datasets with various tissue types and species demonstrates the substantial accuracy improvement of EDClust compared to existing methods. Availability and implementation The R package is freely available at https://github.com/weix21/EDClust. Supplementary information Supplementary data are available at Bioinformatics online.

Myelodysplastic syndromes (MDS) are heterogeneous neoplastic disorders of hematopoietic stem cells (HSCs). The current standard of care for patients with MDS is hypomethylating agent (HMA)-based therapy; however, almost 50% of MDS patients fail HMA therapy and progress to acute myeloid leukemia, facing a dismal prognosis due to lack of approved second-line treatment options. As cancer stem cells are the seeds of disease progression, we investigated the biological properties of the MDS HSCs that drive disease evolution, seeking to uncover vulnerabilities that could be therapeutically exploited. Through integrative molecular profiling of HSCs and progenitor cells in large patient cohorts, we found that MDS HSCs in two distinct differentiation states are maintained throughout the clinical course of the disease, and expand at progression, depending on recurrent activation of the anti-apoptotic regulator BCL-2 or nuclear factor-kappa B-mediated survival pathways. Pharmacologically inhibiting these pathways depleted MDS HSCs and reduced tumor burden in experimental systems. Further, patients with MDS who progressed after failure to frontline HMA therapy and whose HSCs upregulated BCL-2 achieved improved clinical responses to venetoclax-based therapy in the clinical setting. Overall, our study uncovers that HSC architectures in MDS are potential predictive biomarkers to guide second-line treatments after HMA failure. These findings warrant further investigation of HSC-specific survival pathways to identify new therapeutic targets of clinical potential in MDS.

Salvianolic acid B (SAB) is a widely used cardioprotective agent, while its clinical application was limited by poor intestinal absorption and low oral bioavailability. In this study, SAB phospholipid (SP) complex was first prepared to improve the lipophilicity of SAB and then combined with d-glucose to further enhance intestinal absorption. Compared with free SAB, SP or the mixture of SAB and d-glucose, combination of SP and d-glucose showed higher intestinal absorption evidenced by increased effective permeation coefficient (

Maturation of oocytes and early embryo development are regulated precisely by numerous factors at transcriptional and posttranslational levels through precise mechanisms. N6-methyladenosine (m6A) is the most common modification in mRNA which regulates RNA metabolism and gene expression. However, the role of RNA m6A on porcine oocyte maturation and early embryogenesis is largely unknown. Here, we found that oocytes treated with cycloleucine (CL), an RNA m6A inhibitor, express impaired cumulus expansion, increased production of reactive oxygen species (ROS) in the mitochondria, and delayed maturation of oocytes by disrupting spindle organization and chromosome alignment. Also, CL halted the development of embryos at the 4-cell stage and resulted in low-quality blastocysts. Furthermore, CL treatment decreased the RNA m6A, H3K4me3, and H3K9me3 levels, but increased the acetylation level of H4K16 during parthenogenetic embryonic development in pigs. Single-cell RNA-seq (scRNA-seq) analysis further revealed that CL treatment dramatically up-regulated the expression of metabolism-related genes (SLC16A1, and MAIG3 etc.) and maternal related genes, including BTG4, WEE2, and BMP15 among others, at the blastocyst stage. Taken together, inhibition of RNA m6A by CL impaired meiosis of oocytes and early embryonic development of porcine via RNA m6A methylation, histone modifications, and altering the expression of metabolism-related genes in blastocysts.

Resveratrol is a polyphenol with antiaging and anticancer effects. Most previous studies used a single analysis to determine the key functions of resveratrol in inhibiting cancer progression. However, most of the signal transmission pathways in biological processes are multilevel. We used bioinformatics to elucidate the mechanism of resveratrol inhibition of breast cancer development. The mRNA expression profile of GSE25412 from the National Center for Biotechnology Information (NCBI) and the microRNA (miRNA) expression profile of PubMed identifier (PMID) 26890143 were integrated. De novo motifs were used to obtain predicted transcription factor (TF) motifs for differentially expressed genes. The regulatory effect of resveratrol on key nodes in the comprehensive analysis results was verified. The TF–miRNA–mRNA interaction network based on the STITCH and miRDB databases showed that resveratrol exerted a dual inhibitory effect by activating inhibitory TFs to block the cell cycle and inhibit miRNAs from upregulating apoptosis. However, these two processes did not work completely independently. TP53 is the dominant hub gene associated with the cell cycle and apoptosis throughout the TF–miRNA network. Kaplan–Meier plotter analysis found that resveratrol‐induced expression changes in key RNAs, such as E2F2, JUN, FOS, BRCA1, CDK1, CDKN1A, TNF, and hsa‐miR‐34a‐5p, significantly improved the prognosis of breast cancer patients, which was further verified using real‐time quantitative PCR (qPCR) and western blotting. This study constructed a TF–miRNA regulatory network with TP53 and E2F as the main central genes to elucidate the molecular mechanism of resveratrol in the treatment of breast cancer., Resveratrol is a polyphenol with anti‐aging and anti‐cancer effects, which can significantly inhibit cell proliferation in MCF‐7 cells. Here, we found that resveratrol induces cell cycle arrest and promotes apoptosis by regulating transcription factors and microRNA networks. In addition, TP53 and E2F2 are hub proteins in the regulation network.

In this work, two types of Ni phyllosilicates (2 : 1 and 1 : 1 Ni phyllosilicates) are prepared for the one-pot selective conversion of levulinic acid (LA) to 2-methyltetrahydrofuran (2-MTHF).

An all-solid Z-scheme heterojunction TiO2–TiC/g-C3N4 was proposed and synthesized successfully by a facile calcination method and used for photocatalytic CO2 reduction in the presence of CH4.

SVCV P protein plays an essential role in the virus replication and viral immune evasion process. Here, we identify maoc1 as a novel SVCV-inducible gene and demonstrate its antiviral capacity through attenuating SVCV replication, by directly binding to P protein and mediating its degradation via the autophagy-lysosomal pathway.

Functional loss of TDP-43, an RNA-binding protein genetically and pathologically linked to ALS and FTD, leads to inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. However, the possibility ofde novoprotein synthesis from cryptic exon transcripts has not been explored. Here, we show that mRNA transcripts harboring cryptic exons generatede novoproteins both in TDP-43 deficient cellular models and in disease. Using coordinated transcriptomic and proteomic studies of TDP-43 depleted iPSC-derived neurons, we identified numerous peptides that mapped to cryptic exons. Cryptic exons identified in iPSC models were highly predictive of cryptic exons expressed in brains of patients with TDP-43 proteinopathy, including cryptic transcripts that generatedde novoproteins. We discovered that inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Finally, we showed that thesede novopeptides were present in CSF from patients with ALS. The demonstration of cryptic exon translation suggests new mechanisms for ALS pathophysiology downstream of TDP-43 dysfunction and may provide a strategy for novel biomarker development.One Sentence SummaryLoss of TDP-43 function results in the expression ofde novoproteins from mis-spliced mRNA transcripts.

In recent years, single-cell or low-input multi-omics techniques have brought a revolution in the study of pre-implantation embryo development. However, single-cell or low-input proteome research in this field is relatively underdeveloped, due to the limited source of mammalian embryo samples, the objective reality of high abundance zona pellucida proteins, and the lack of hypersensitive proteome technology. Here, a comprehensive solution of ultrasensitive proteome technology was developed for single-cell or low-input mouse embryos. Both deep coverage route and high-throughput route could significantly reduce the starting material and enhance the proteomic depth without any customized instrument. Using the deep coverage route, an average of 2,665 or 4,585 protein groups can be identified from 1 or 20 mouse zygotes respectively. Using the high-throughput route, 300 single mouse zygotes can be analysis in 8 days with an average of 2,371 proteins identified. With its popularization, we believe researchers can choose deep coverage or high-throughput technology routes according to their own conditions.

Motivation Cell label annotation is a challenging step in the analysis of single-cell RNA sequencing (scRNA-seq) data, especially for tissue types that are less commonly studied. The accumulation of scRNA-seq studies and biological knowledge leads to several well-maintained cell marker databases. Manually examining the cell marker lists against these databases can be difficult due to the large amount of available information. Additionally, simply overlapping the two lists without considering gene ranking might lead to unreliable results. Thus, an automated method with careful statistical testing is needed to facilitate the usage of these databases. Results We develop a user-friendly computational tool, EasyCellType, which automatically checks an input marker list obtained by differential expression analysis against the databases and provides annotation recommendations in graphical outcomes. The package provides two statistical tests, gene set enrichment analysis and a modified version of Fisher’s exact test, as well as customized database and tissue type choices. We also provide an interactive shiny application to annotate cells in a user-friendly graphical user interface. The simulation study and real-data applications demonstrate favorable results by the proposed method. Availability and implementation https://biostatistics.mdanderson.org/shinyapps/EasyCellType/; https://bioconductor.org/packages/devel/bioc/html/EasyCellType.html. Supplementary information Supplementary data are available at Bioinformatics Advances online.

Continuous biomarkers are common for disease screening and diagnosis. To reach a dichotomous clinical decision, a threshold would be imposed to distinguish subjects with disease from non-diseased individuals. Among various performance metrics for a continuous biomarker, specificity at a controlled sensitivity level (or vice versa) is often desirable for clinical utility since it directly targets where the clinical test is intended to operate. Covariates, such as age, race, and sample collection, could impact the controlled sensitivity level in subpopulations and may also confound the association between biomarker and disease status. Therefore, covariate adjustment is important in such biomarker evaluation. In this paper, we suggest to adopt a parsimonious quantile regression model for the diseased population, locally at the controlled sensitivity level, and assess specificity with covariate-specific control of the sensitivity. Variance estimates are obtained from a sample-based approach and bootstrap. Furthermore, our proposed local model extends readily to a global one for covariate adjustment for the receiver operating characteristic (ROC) curve over the sensitivity continuum. We demonstrate computational efficiency of this proposed method and restore the inherent monotonicity in the estimated covariate-adjusted ROC curve. The asymptotic properties of the proposed estimators are established. Simulation studies show favorable performance of the proposal. Finally, we illustrate our method in biomarker evaluation for aggressive prostate cancer., 28 pages, 2 figures