Posttranscriptional regulation of de novo lipogenesis by glucose-induced O-GlcNAcylation.

O-linked ß-N-acetyl glucosamine (O-GlcNAc) is attached to proteins under glucose-replete conditions; this posttranslational modification results in molecular and physiological changes that affect cell fate. Here we show that posttranslational modification of serine/arginine-rich protein kinase 2 (SRPK2) by O-GlcNAc regulates de novo lipogenesis by regulating pre-mRNA splicing. We found that O-GlcNAc transferase O-GlcNAcylated SRPK2 at a nuclear localization signal (NLS), which triggers binding of SRPK2 to importin α. Consequently, O-GlcNAcylated SRPK2 was imported into the nucleus, where it phosphorylated serine/arginine-rich proteins and promoted splicing of lipogenic pre-mRNAs. We determined that protein nuclear import by O-GlcNAcylation-dependent binding of cargo protein to importin α might be a general mechanism in cells. This work reveals a role of O-GlcNAc in posttranscriptional regulation of de novo lipogenesis, and our findings indicate that importin α is a "reader" of an O-GlcNAcylated NLS.

Direct stimulation of de novo nucleotide synthesis by O-GlcNAcylation.

O-linked ß-N-acetyl glucosamine (O-GlcNAc) is at the crossroads of cellular metabolism, including glucose and glutamine; its dysregulation leads to molecular and pathological alterations that cause diseases. Here we report that O-GlcNAc directly regulates de novo nucleotide synthesis and nicotinamide adenine dinucleotide (NAD) production upon abnormal metabolic states. Phosphoribosyl pyrophosphate synthetase 1 (PRPS1), the key enzyme of the de novo nucleotide synthesis pathway, is O-GlcNAcylated by O-GlcNAc transferase (OGT), which triggers PRPS1 hexamer formation and relieves nucleotide product-mediated feedback inhibition, thereby boosting PRPS1 activity. PRPS1 O-GlcNAcylation blocked AMPK binding and inhibited AMPK-mediated PRPS1 phosphorylation. OGT still regulates PRPS1 activity in AMPK-deficient cells. Elevated PRPS1 O-GlcNAcylation promotes tumorigenesis and confers resistance to chemoradiotherapy in lung cancer. Furthermore, Arts-syndrome-associated PRPS1 R196W mutant exhibits decreased PRPS1 O-GlcNAcylation and activity. Together, our findings establish a direct connection among O-GlcNAc signals, de novo nucleotide synthesis and human diseases, including cancer and Arts syndrome.

Neurexin-2 restricts synapse numbers and restrains the presynaptic release probability by an alternative splicing-dependent mechanism.

α- and ß-neurexins are extensively alternatively spliced, presynaptic cell-adhesion molecules that are thought to organize synapse assembly. However, recent data revealed that, in the hippocampus in vivo, the deletion of one neurexin isoform, Nrxn2, surprisingly increased excitatory synapse numbers and enhanced their presynaptic release probability, suggesting that Nrxn2 restricts, instead of enabling, synapse assembly. To delineate the synaptic function and mechanism of action of Nrxn2, we examined cultured hippocampal neurons as a reduced system. In heterologous synapse formation assays, different alternatively spliced Nrxn2ß isoforms robustly promoted synapse assembly similar to Nrxn1ß and Nrxn3ß, consistent with a general synaptogenic function of neurexins. Deletion of Nrxn2 from cultured hippocampal neurons, however, caused a significant increase in synapse density and release probability, replicating the in vivo data that suggested a synapse-restricting function. Rescue experiments revealed that two of the four Nrxn2ß splice variants (Nrxn2ß-SS4+/SS5- and Nrxn2ß-SS4+/SS5+) reversed the increase in synapse density in Nrxn2-deficient neurons, whereas only one of the four Nrxn2ß splice variants (Nrxn2ß-SS4+/SS5+) normalized the increase in release probability in Nrxn2-deficient neurons. Thus, a subset of Nrxn2 splice variants restricts synapse numbers and restrains their release probability in cultured neurons.

Identifying local associations in biological time series: algorithms, statistical significance, and applications.

Local associations refer to spatial-temporal correlations that emerge from the biological realm, such as time-dependent gene co-expression or seasonal interactions between microbes. One can reveal the intricate dynamics and inherent interactions of biological systems by examining the biological time series data for these associations. To accomplish this goal, local similarity analysis algorithms and statistical methods that facilitate the local alignment of time series and assess the significance of the resulting alignments have been developed. Although these algorithms were initially devised for gene expression analysis from microarrays, they have been adapted and accelerated for multi-omics next generation sequencing datasets, achieving high scientific impact. In this review, we present an overview of the historical developments and recent advances for local similarity analysis algorithms, their statistical properties, and real applications in analyzing biological time series data. The benchmark data and analysis scripts used in this review are freely available at http://github.com/labxscut/lsareview.

CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution.

MOTIVATION: Complex tissues are dynamic ecosystems consisting of molecularly distinct yet interacting cell types. Computational deconvolution aims to dissect bulk tissue data into cell type compositions and cell-specific expressions. With few exceptions, most existing deconvolution tools exploit supervised approaches requiring various types of references that may be unreliable or even unavailable for specific tissue microenvironments. RESULTS: We previously developed a fully unsupervised deconvolution method-Convex Analysis of Mixtures (CAM), that enables estimation of cell type composition and expression from bulk tissues. We now introduce CAM3.0 tool that improves this framework with three new and highly efficient algorithms, namely, radius-fixed clustering to identify reliable markers, linear programming to detect an initial scatter simplex, and a smart floating search for the optimum latent variable model. The comparative experimental results obtained from both realistic simulations and case studies show that the CAM3.0 tool can help biologists more accurately identify known or novel cell markers, determine cell proportions, and estimate cell-specific expressions, complementing the existing tools particularly when study- or datatype-specific references are unreliable or unavailable. AVAILABILITY AND IMPLEMENTATION: The open-source R Scripts of CAM3.0 is freely available at https://github.com/ChiungTingWu/CAM3/(https://github.com/Bioconductor/Contributions/issues/3205). A user's guide and a vignette are provided.

Acetylation stabilizes the signaling protein WISP2 by preventing its degradation to suppress the progression of acute myeloid leukemia.

Acute myeloid leukemia (AML) is challenging to treat due to its heterogeneity, prompting a deep understanding of its pathogenesis mechanisms, diagnosis, and treatment. Here, we found reduced expression and acetylation levels of WISP2 in bone marrow mononuclear cells from AML patients and that AML patients with lower WISP2 expression tended to have reduced survival. At the functional level, overexpression of WISP2 in leukemia cells (HL-60 and Kasumi-1) suppressed cell proliferation, induced cell apoptosis, and exerted antileukemic effects in an in vivo model of AML. Our mechanistic investigation demonstrated that WISP2 deacetylation was regulated by the deacetylase histone deacetylase (HDAC)3. In addition, we determined that crosstalk between acetylation and ubiquitination was involved in the modulation of WISP2 expression in AML. Deacetylation of WISP2 decreased the stability of the WISP2 protein by boosting its ubiquitination mediated by NEDD4 and proteasomal degradation. Moreover, pan-HDAC inhibitors (valproic acid and trichostatin A) and an HDAC3-specific inhibitor (RGFP966) induced WISP2 acetylation at lysine K6 and prevented WISP2 degradation. This regulation led to inhibition of proliferation and induction of apoptosis in AML cells. In summary, our study revealed that WISP2 contributes to tumor suppression in AML, which provided an experimental framework for WISP2 as a candidate for gene therapy of AML.

BGL3 lncRNA mediates retention of the BRCA1/BARD1 complex at DNA damage sites.

Long non-coding RNAs (lncRNAs) are emerging regulators of genomic stability and human disease. However, the molecular mechanisms by which nuclear lncRNAs directly contribute to DNA damage responses remain largely unknown. Using RNA antisense purification coupled with quantitative mass spectrometry (RAP-qMS), we found that the lncRNA BGL3 binds to PARP1 and BARD1, exhibiting unexpected roles in homologous recombination. Mechanistically, BGL3 is recruited to DNA double-strand breaks (DSBs) by PARP1 at an early time point, which requires its interaction with the DNA-binding domain of PARP1. BGL3 also binds the C-terminal BRCT domain and an internal region (amino acids 127-424) of BARD1, which mediates interaction of the BRCA1/BARD1 complex with its binding partners such as HP1γ and RAD51, resulting in BRCA1/BARD1 retention at DSBs. Cells depleted for BGL3 displayed genomic instability and were sensitive to DNA-damaging reagents. Overall, our findings underscore the biochemical versatility of RNA as a mediator molecule in the DNA damage response pathway, which affects the accumulation of BRCA1/BARD1 at DSBs.

Electromagnetic Field-Assisted Frozen Tissue Planarization Enhances MALDI-MSI in Plant Spatial Omics.

Plant samples with irregular morphology are challenging for longitudinal tissue sectioning. This has restricted the ability to gain insight into some plants using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Herein, we develop a novel technique termed electromagnetic field-assisted frozen tissue planarization (EMFAFTP). This technique involves using a pair of adjustable electromagnets on both sides of a plant tissue. Under an optimized electromagnetic field strength, nondestructive planarization and regularization of the frozen tissue is induced, allowing the longitudinal tissue sectioning that favors subsequent molecular profiling by MALDI-MSI. As a proof of concept, flowers, leaves and roots with irregular morphology from six plant species are chosen to evaluate the performance of EMFAFTP for MALDI-MSI of secondary metabolites, amino acids, lipids, and proteins among others in the plant samples. The significantly enhanced MALDI-MSI capabilities of these endogenous molecules demonstrate the robustness of EMFAFTP and suggest it has the potential to become a standard technique for advancing MALDI-MSI into a new era of plant spatial omics.

2-Hydroxy-5-nitro-3-(trifluoromethyl)pyridine as a Novel Matrix for Enhanced MALDI Imaging of Tissue Metabolites.

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), which is a label-free imaging technique, determines the spatial distribution and relative abundance of versatile endogenous metabolites in tissues. Meanwhile, matrix selection is generally regarded as a pivotal step in MALDI tissue imaging. This study presents the first report of a novel MALDI matrix, 2-hydroxy-5-nitro-3-(trifluoromethyl)pyridine (HNTP), for the in situ detection and imaging of endogenous metabolites in rat liver and brain tissues by MALDI-MS in positive-ion mode. The HNTP matrix exhibits excellent characteristics, including strong ultraviolet absorption, µm-scale matrix crystals, high chemical stability, low background ion interference, and high metabolite ionization efficiency. Notably, the HNTP matrix also shows superior detection capabilities, successfully showing 185 detectable metabolites in rat liver tissue sections. This outperforms the commonly used matrices of 2,5-dihydroxybenzoic acid and 2-mercaptobenzothiazole, which detect 145 and 120 metabolites from the rat liver, respectively. Furthermore, a total of 152 metabolites are effectively detected and imaged in rat brain tissue using the HNTP matrix, and the spatial distribution of these compounds clearly shows the heterogeneity of the rat brain. The results demonstrate that HNTP is a new and powerful positive-ion mode matrix to enhance the analysis of metabolites in biological tissues by MALDI-MSI.

Adenosine kinase inhibits ß-cell proliferation by upregulating DNA methyltransferase 3A expression.

AIM: To investigate the effects of adenosine kinase (ADK), a key enzyme in determining intracellular adenosine levels, on ß cells, and their underlying mechanism. METHODS: Genetic animal models and transgenic immortalized cells were applied to study the effect of ADK on islet beta-cell proliferation and function. The beta-cell mass and response to glucose were measured in vivo using mice with beta-cell-specific ADK overexpression, and in vitro using ADK-overexpressed immortalized beta-cell. RESULTS: The expression of ADK in human islets at high abundance, especially in ß cells, was decreased during the process of ß-cell proliferation. Additionally, a transgenic mouse model (ADKtg/tg /Mip-Cre) was generated wherein the mouse Insulin1 gene promoter specifically overexpressed ADK in pancreatic ß cells. The ADKtg/tg /Mip-Cre model exhibited impaired glucose tolerance, decreased fasting plasma insulin, loss of ß-cell mass, and inhibited ß-cell proliferation. Proteomic analysis revealed that ADK overexpression inhibited the expression of several proteins that promote cell proliferation and insulin secretion. Upregulating ADK in the ß-cell line inhibited the expression of ß-cell related regulatory molecules, including FoxO1, Appl1, Pxn, Pdx-1, Creb and Slc16a3. Subsequent in vitro experiments indicated that the inhibition of ß-cell proliferation and the decreased expression of Pdx-1, Creb and Slc16a3 were rescued by DNA methyltransferase 3A (DNMT3A) knockdown in ß cells. CONCLUSION: In this study, we found that the overexpression of ADK decreased the expression of several genes that regulate ß cells, resulting in the inhibition of ß-cell proliferation and dysfunction by upregulating the expression of DNMT3A.

Body size, insulin sensitivity, metabolic health and risk of cardiovascular disease in Chinese adults: Insights from the China Cardiometabolic Disease and Cancer Cohort (4C) study.

AIMS: To assess the excess risk of cardiovascular disease (CVD) associated with different criteria for metabolic health, and the interplay of body size, insulin sensitivity and metabolic health with CVD risk. MATERIALS AND METHODS: We conducted a prospective study involving 115 638 participants from the China Cardiometabolic Disease and Cancer Cohort (4C) Study. Metabolic health was defined using three different definitions: (1) insulin sensitivity defined by homeostatic model assessment of insulin resistance index; (2) absence of metabolic syndrome according to the National Cholesterol Education Program Adult Treatment Panel III criteria; and (3) simultaneous absence of metabolic abnormalities (diabetes, hypertension, dyslipidaemia). The primary endpoint was a composite of incident CVD events comprising the first occurrence of myocardial infarction, stroke, heart failure, or cardiovascular death. RESULTS: During a mean 3.61-year follow-up period, obese individuals with insulin sensitivity (multivariable-adjusted hazard ratio [HR] 1.69, 95% confidence interval [CI] 1.37-2.08), or without metabolic syndrome (HR 1.46, 95% CI 1.13-1.89) still exhibited increased CVD risks, when compared to their normal-weight counterparts. Otherwise, those with obesity but simultaneous absence of metabolic abnormalities demonstrated similar CVD risk compared to normal-weight individuals (HR 0.91, 95% CI 0.53-1.59). CVD risk increased with the number of abnormalities across body mass index categories, regardless of insulin sensitivity. CONCLUSIONS: This study emphasizes the need for refined definitions of metabolic health and advocates for meticulous screening for metabolic abnormalities to reduce cardiovascular risks, even in individuals with normal weight and insulin sensitivity.

Tf2O-Mediated Tandem Reaction of Enaminones for the Synthesis of Functionalized Conjugated-Enals/ß-Naphthalaldehydes.

A highly efficient and regioselective method for constructing functionalized conjugated enals via the Tf2O-mediated tandem reaction of enaminones with thiophenols has been described. Chain products with excellent stereoselectivity could be obtained through substrate regulation. Additionally, a feasible method for synthesizing ß-naphthalaldehydes through PhSO2Na/DABCO promoting hydrogen atom transfer process has also been reported here. Mechanism studies have shown that 2-formyl vinyl triflate 8 and sulfonylated enal 9 were the key intermediates in this process.

Exchange transfusion combined with artesunate (ET-AS) as a safe and effective therapy in severe P. falciparum malaria: a case series.

BACKGROUND: the mortality associated with severe malaria due to Plasmodiun falciparum remains high despite improvements in malaria management. Case prensentation: this case series aims to describe the efficacy and safety of the exchange transfusion combined with artesunate (ET-AS) regimen in severe P. falciparum malaria. Eight patients diagnosed with severe P. falciparum malaria were included. All patients underwent ET using the COBE Spectra system. The aimed for a post-exchange hematocrit of 30%. Half the estimated blood volume was removed and replaced using fresh frozen plasma. The regimen was well-tolerated without complications. The parasite clearance time ranged from 1 ~ 5 days. Five patients with cerebral malaria exhibited full improved consciousness within 3 days, while patient2 with hemolysis improved on day 2. Liver function improved within 1 ~ 6 days, and patient 1 and patient 6 showed improvements renal function on days 18 and 19, respectively. The length of intensive care unit stay range from 2 ~ 10 days, and all patients treated with ET-AS remained in the hospital for 3 ~ 19 days. CONCLUSIONS: these preliminary results suggest that ET-AS regimens are a safe and effective therapy for severe P. falciparum malaria and can benefit patients in clinical settings.

Mechanism of interaction between ascorbic acid and soil iron-containing minerals for peroxydisulfate activation and organophosphorus flame retardant degradation.

Soil constituents may play an important role in peroxydisulfate (PDS)-based oxidation of organic contaminants in soil. Iron-containing minerals (Fe-minerals) have been found to promote PDS activation for organics degradation. Our study found that ascorbic acid (H2A) could enhance PDS activation by soil Fe-minerals for triphenyl phosphate (TPHP) degradation. Determination and characterization analyses of Fe fractions showed that H2A could induce the reductive dissolution of solid Fe-minerals and the increasing of oxygen vacancies/hydroxyl groups content on Fe-minerals surface. The increasing of divalent Fe (Fe(II)) accelerated PDS activation to generate reactive oxygen species (ROS). Electron paramagnetic resonance (EPR) and quenching studies showed that sulfate radicals (SO4•-) and hydroxyl radicals (HO•) contributed significantly to TPHP degradation. The composition and content of Fe-minerals and soil organic matter (SOM) markedly influenced ROS transformations. Surface-bond and structural Fe played the main role in the production of Fe(II) in reaction system. The high-concentration SOM could result in ROS consumption and degradation inhibition. Density functional theory (DFT) studies revealed that H2A is preferentially adsorbed at α-Fe2O3(012) surface through Fe-O-C bridges rather than hydrogen bonds. After absorption, H atoms on H2A may further be migrated to adjacent O atoms on the α-Fe2O3(012) surface. With the transformation of H atoms to the α-Fe2O3(012) surface, the Fe-O-C bridge is broken and one electron is transferred from the O to Fe atom, inducing the reduction of trivalent Fe (Fe(III)) atom. MS/MS2 analysis, HPLC analysis, and toxicity assessment demonstrated that TPHP was transformed to less toxic 4-hydroxyphenyl diphenyl phosphate (OH-TPHP), diphenyl hydrogen phosphate (DPHP), and phenyl phosphate (PHP) through phenol-cleavage and hydroxylation processes, and even be mineralized in reaction system.

Mechanistic insight into the impact of interaction between goethite and humic acid on the photooxidation and photoreduction of bifenthrin.

Numerous application of pyrethroid insecticides has led to their accumulation in the environment, threatening ecological environment and human health. Its fate in the presence of iron-bearing minerals and natural organic matter under light irradiation is still unknown. We found that goethite (Gt) and humic acid (HA) could improve the photodegradation of bifenthrin (BF) in proper concentration under light irradiation. The interaction between Gt and HA may further enhance BF degradation. On one hand, the adsorption of HA on Gt may decrease the photocatalytic activity of HA through decreasing HA content in solution and sequestering the functional groups related with the production of reactive species. On the other hand, HA could improve the photocatalytic activity of Gt through extending light absorption, lowing of bandgap energy, hindering the recombination of photo-generated charges, and promoting the oxidation and reduction reaction on Gt surface. The increased oxygen vacancies on Gt surface along with the reduction of trivalent iron and the nucleophilic attack of hole to surface hydroxyl group contributed to the increasing photocatalytic activity of Gt. Electron paramagnetic resonance and quenching studies demonstrated that both oxidation species, such as hydroxyl radical (•OH) and singlet oxygen (1O2), and reducing species, such as hydrogen atoms (H•) and superoxide anion radical (O2•-), contributed to BF degradation in UV-Gt-HA system. Mass spectrometry, ion chromatography, and toxicity assessment indicated that less toxic C23H22ClF3O3 (OH-BF), C9H10ClF3O (TFP), C14H14O2 (OH-MBP), C14H12O2 (MBP acid), C14H12O3 (OH-MBP acid), and chloride ions were the main degradation products. The production of OH-BF, MPB, and TFP acid through oxidation and the production of MPB and TFP via reduction were the two primary pathways of BF degradation.

AHR signaling pathway mediates mitochondrial oxidative phosphorylation which leads to cytarabine resistance.

The aryl hydrocarbon receptor (AHR) has been identified as a significant driver of tumorigenesis. However, its clinical significance in acute myeloid leukemia (AML) remains largely unclear. In this study, RNA-Seq data from AML patients (bone marrow samples from 173 newly diagnosed AML patients) obtained from the TCGA database, and normal human RNA-Seq data (bone marrow samples from 70 healthy individuals) obtained from the GTEX database are downloaded for external validation and complementarity. The data analysis reveals that the AHR signaling pathway is activated in AML patients. Furthermore, there is a correlation between the expressions of AHR and mitochondrial oxidative phosphorylation genes. In vitro experiments show that enhancing AHR expression in AML cells increases mitochondrial oxidative phosphorylation and induces resistance to cytarabine. Conversely, reducing AHR expression in AML cells decreases cytarabine resistance. These findings deepen our understanding of the AHR signaling pathway's involvement in AML.

Targeting Proteins in Nucleus through Dual-Regulatory Pathways Acting in Cytoplasm.

Nuclear proteins have been regarded as attractive targets for exploiting therapeutic agents. However, those agents cannot efficiently pass through nuclear pores and it is also difficult to overcome the crowded nuclear environment to react with proteins. Herein, we propose a novel strategy acting in the cytoplasm to regulate nuclear proteins based on their signaling pathways, instead of directly entering into nuclei. A multifunctional complex PKK-TTP/hs carries human telomerase reverse transcriptase (hTERT) small interfering RNA (defined as hs) for gene silencing in the cytoplasm, which reduced the import of nuclear protein. At the same time, it could generate reactive oxygen species (ROS) under light irradiation, which raised the export of nuclear proteins by promoting proteins translocation. Through this dual-regulatory pathway, we successfully reduced nuclear protein (hTERT proteins) in vivo (42.3%). This work bypasses the challenge of directly entering into the nucleus and provides an effective strategy for regulating nuclear proteins.

High-throughput MALDI-MSI metabolite analysis of plant tissue microarrays.

A novel metabolomics analysis technique, termed matrix-assisted laser desorption/ionization mass spectrometry imaging-based plant tissue microarray (MALDI-MSI-PTMA), was successfully developed for high-throughput metabolite detection and imaging from plant tissues. This technique completely overcomes the disadvantage that metabolites cannot be accessible on an intact plant tissue due to the limitations of the special structures of plant cells (e.g. epicuticular wax, cuticle and cell wall) through homogenization of plant tissues, preparation of PTMA moulds and matrix spraying of PTMA sections. Our study shows several properties of MALDI-MSI-PTMA, including no need of sample separation and enrichment, high-throughput metabolite detection and imaging (>1000 samples per day), high-stability mass spectrometry data acquisition and imaging reconstruction and high reproducibility of data. This novel technique was successfully used to quickly evaluate the effects of two plant growth regulator treatments (i.e. 6-benzylaminopurine and N-phenyl-N'-1,2,3-thiadiazol-5-ylurea) on endogenous metabolite expression in plant tissue culture specimens of Dracocephalum rupestre Hance (D. rupestre). Intra-day and inter-day evaluations indicated that the metabolite data detected on PTMA sections had good reproducibility and stability. A total of 312 metabolite ion signals in leaves tissues of D. rupestre were detected, of which 228 metabolite ion signals were identified, they were composed of 122 primary metabolites, 90 secondary metabolites and 16 identified metabolites of unknown classification. The results demonstrated the advantages of MALDI-MSI-PTMA technique for enhancing the overall detection ability of metabolites in plant tissues, indicating that MALDI-MSI-PTMA has the potential to become a powerful routine practice for high-throughput metabolite study in plant science.

swCAM: estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution.

MOTIVATION: Complex biological tissues are often a heterogeneous mixture of several molecularly distinct cell subtypes. Both subtype compositions and subtype-specific (STS) expressions can vary across biological conditions. Computational deconvolution aims to dissect patterns of bulk tissue data into subtype compositions and STS expressions. Existing deconvolution methods can only estimate averaged STS expressions in a population, while many downstream analyses such as inferring co-expression networks in particular subtypes require subtype expression estimates in individual samples. However, individual-level deconvolution is a mathematically underdetermined problem because there are more variables than observations. RESULTS: We report a sample-wise Convex Analysis of Mixtures (swCAM) method that can estimate subtype proportions and STS expressions in individual samples from bulk tissue transcriptomes. We extend our previous CAM framework to include a new term accounting for between-sample variations and formulate swCAM as a nuclear-norm and ℓ2,1-norm regularized matrix factorization problem. We determine hyperparameter values using cross-validation with random entry exclusion and obtain a swCAM solution using an efficient alternating direction method of multipliers. Experimental results on realistic simulation data show that swCAM can accurately estimate STS expressions in individual samples and successfully extract co-expression networks in particular subtypes that are otherwise unobtainable using bulk data. In two real-world applications, swCAM analysis of bulk RNASeq data from brain tissue of cases and controls with bipolar disorder or Alzheimer's disease identified significant changes in cell proportion, expression pattern and co-expression module in patient neurons. Comparative evaluation of swCAM versus peer methods is also provided. AVAILABILITY AND IMPLEMENTATION: The R Scripts of swCAM are freely available at https://github.com/Lululuella/swCAM. A user's guide and a vignette are provided. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Base-Promoted Decarboxylative Annulation of Methyl 2-(2-Bromophenyl)acetates and Ynones to Access Benzoxepines.

A simple and efficient base-mediated decarboxylative annulation of ynones with methyl 2-(2-bromophenyl)acetates has been developed. A broad range of benzoxepines were prepared with a broad substrate scope and high regioselectivity in moderate to excellent yields under transition-metal-free conditions. This method proceeds through a tandem [2 + 4] annulation, ring-opening decarboxylative reaction, and the intramolecular nucleophilic aromatic substitution reaction. Additionally, the key intermediates were successfully obtained and characterized unambiguously by single-crystal X-ray crystallography, which could favorably support a decarboxylative annulation mechanism. Furthermore, gram-scale reaction and synthetic applications for the further functionalization are also studied.