Network integration and protein structural binding analysis of neurodegeneration-related interactome.

Neurodegenerative diseases (NDs) usually connect with aggregation and molecular interactions of pathological proteins. The integration of accumulative data from clinical and biomedical research will allow for the excavation of pathological proteins and related interactors. It is also important to systematically study their interacting proteins in order to find more related proteins and potential therapeutic targets. Understanding binding regions in protein interactions will help functional proteomics and provide an alternative method for predicting novel interactions. This study integrated data from biomedical research to achieve systematic mining and analysis of pathogenic proteins and their interaction network. A workflow has been built as a solution for the collective information of proteins involved in NDs, related protein-protein interactions (PPIs) and interactive visualizations. It also included protein isoforms and mapped them in a disease-related PPI network to illuminate the impact of alternative splicing on protein binding. The interacting proteins enriched by diseases and biological processes (BPs) revealed possible regulatory modules. A high-resolution network with structural affinity information was generated. Finally, Neurodegenerative Disease Atlas (NDAtlas) was constructed with an interactive and intuitive view of protein docking with 3D molecular graphics beyond the traditional 2D network. NDAtlas is available at http://bis.zju.edu.cn/ndatlas.

Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition.

BACKGROUND: The endothelial-to-hematopoietic transition (EHT) process during definitive hematopoiesis is highly conserved in vertebrates. Stage-specific expression of transposable elements (TEs) has been detected during zebrafish EHT and may promote hematopoietic stem cell (HSC) formation by activating inflammatory signaling. However, little is known about how TEs contribute to the EHT process in human and mouse. RESULTS: We reconstructed the single-cell EHT trajectories of human and mouse and resolved the dynamic expression patterns of TEs during EHT. Most TEs presented a transient co-upregulation pattern along the conserved EHT trajectories, coinciding with the temporal relaxation of epigenetic silencing systems. TE products can be sensed by multiple pattern recognition receptors, triggering inflammatory signaling to facilitate HSC emergence. Interestingly, we observed that hypoxia-related signals were enriched in cells with higher TE expression. Furthermore, we constructed the hematopoietic cis-regulatory network of accessible TEs and identified potential TE-derived enhancers that may boost the expression of specific EHT marker genes. CONCLUSIONS: Our study provides a systematic vision of how TEs are dynamically controlled to promote the hematopoietic fate decisions through transcriptional and cis-regulatory networks, and pre-train the immunity of nascent HSCs.

Sequence repetitiveness quantification and de novo repeat detection by weighted k-mer coverage.

DNA repeats are abundant in eukaryotic genomes and have been proved to play a vital role in genome evolution and regulation. A large number of approaches have been proposed to identify various repeats in the genome. Some de novo repeat identification tools can efficiently generate sequence repetitive scores based on k-mer counting for repeat detection. However, we noticed that these tools can still be improved in terms of repetitive score calculation, sensitivity to segmental duplications and detection specificity. Therefore, here, we present a new computational approach named Repeat Locator (RepLoc), which is based on weighted k-mer coverage to quantify the genome sequence repetitiveness and locate the repetitive sequences. According to the repetitiveness map of the human genome generated by RepLoc, we found that there may be relationships between sequence repetitiveness and genome structures. A comprehensive benchmark shows that RepLoc is a more efficient k-mer counting based tool for de novo repeat detection. The RepLoc software is freely available at http://bis.zju.edu.cn/reploc.

Bioinformatics resources facilitate understanding and harnessing clinical research of SARS-CoV-2.

The coronavirus disease 2019 (COVID-19) pandemic, caused by the coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has created an unprecedented threat to public health. The pandemic has been sweeping the globe, impacting more than 200 countries, with more outbreaks still lurking on the horizon. At the time of the writing, no approved drugs or vaccines are available to treat COVID-19 patients, prompting an urgent need to decipher mechanisms underlying the pathogenesis and develop curative treatments. To fight COVID-19, researchers around the world have provided specific tools and molecular information for SARS-CoV-2. These pieces of information can be integrated to aid computational investigations and facilitate clinical research. This paper reviews current knowledge, the current status of drug development and various resources for key steps toward effective treatment of COVID-19, including the phylogenetic characteristics, genomic conservation and interaction data. The final goal of this paper is to provide information that may be utilized in bioinformatics approaches and aid target prioritization and drug repurposing. Several SARS-CoV-2-related tools/databases were reviewed, and a web-portal named OverCOVID (http://bis.zju.edu.cn/overcovid/) is constructed to provide a detailed interpretation of SARS-CoV-2 basics and share a collection of resources that may contribute to therapeutic advances. These information could improve researchers' understanding of SARS-CoV-2 and help to accelerate the development of new antiviral treatments.

Evaluating the behavior and principle of deep eutectic solvent on ephedrine-type alkaloid extraction from Ephedrae Herba.

In this study, deep eutectic solvent (DES), as a new green solvent, was used to extract bioactive alkaloids from Ephedrae Herba using supersonic extraction. In a variety of tested hydrophilic and hydrophobic DESs, DES composed of choline chloride and xylitol was proved to be the most efficient solvent. Factors affecting extraction efficiency, including the mole ratio of hydrogen bond acceptor/hydrogen bond donor, water contention, and solid/liquid ratio, were optimized individually. Under optimal conditions, the yield of ephedrine (EP) and pseudoephedrine obtained using this new method was 14.24 and 4.32 mg/g, respectively, which was higher than that using the traditional solvent (acidified water and methanol). Furthermore, the extraction mechanism of DES and EP was investigated using molecular dynamics simulation study. Structural properties such as radial distribution functions and average number of hydrogen bonds were then computed. The results showed that hydrogen bonds and van der Waals forces are important driving forces of extraction; in addition, the hydrogen bonds between the Cl atom of choline chloride and N atom of EP played a dominant part in the extraction process. Based on the extraction principle, the extraction method using choline chloride as extraction solvent was also discussed.

Evaluation of green and efficient deep eutectic solvents as media for extracting alkaloids from lotus leaf.

Deep eutectic solvents (DESs) were applied as eco-friendly solvents in this study for the extraction of alkaloids from lotus leaf, including O-nornuciferine, N-nornuciferine, nuciferine and roemerine. A series of hydrophilic and hydrophobic DESs with different hydrogen bond donors and a acceptors were synthesized and screened for a suitable DESs for extraction of alkaloids from lotus leaf. The study results showed that the hydrophilic DES with choline chloride and propanediol had the highest extraction yield. The main factors affecting the extraction efficiency-choline chloride-propanediol ratio, water content in deep eutectic solvents, solid-liquid ratio and extraction time-were investigated via a single-factor experiment. The optimized extraction conditions were 30% of water in choline chloride-propanediol (1:4) for heated extraction for 30 min and solid-liquid ratio 1:100 g/ml. Under optimum conditions, the extraction yields of O-nornuciferine, N-nornuciferine, nuciferine and roemerine were 0.069, 0.152, 0.334 and 0.041 g/100 g respectively, which were higher than those of methanol in acidified aqueous solution. This study suggests considerable potential for DESs as promising materials for the green and efficient extraction solvents for bioactive alkaloids from natural sources.

A practical guide for DNase-seq data analysis: from data management to common applications.

Deoxyribonuclease I (DNase I)-hypersensitive site sequencing (DNase-seq) has been widely used to determine chromatin accessibility and its underlying regulatory lexicon. However, exploring DNase-seq data requires sophisticated downstream bioinformatics analyses. In this study, we first review computational methods for all of the major steps in DNase-seq data analysis, including experimental design, quality control, read alignment, peak calling, annotation of cis-regulatory elements, genomic footprinting and visualization. The challenges associated with each step are highlighted. Next, we provide a practical guideline and a computational pipeline for DNase-seq data analysis by integrating some of these tools. We also discuss the competing techniques and the potential applications of this pipeline for the analysis of analogous experimental data. Finally, we discuss the integration of DNase-seq with other functional genomics techniques.

The capacity of ion adsorption and purification for coniferous forests is stronger than that of broad-leaved forests.

In the past few decades, industrialization has caused a large number of pollutants to be released into the atmosphere. Forest ecosystems play an important function in regulating the biogeochemistry and the circulation of metal ions pollutants. Forest ecosystems affect the absorption of pollutants and dissolution of nutrients from the atmosphere and vegetation canopy, thereby influencing the content and composition of forest floor leachate and soil solution. This study examined changes in acid anions (NO3-, SO42-, Cl-) and metal cations (K+, Ca2+, Na2+, Mg2+, Fe3+, Pb2+, Cu2+, Cd2+) in rainfall, throughfall, stemflow, and forest floor leachate for five different forests (Larix principis-rupprechtii, Picea wilsonii, Picea crassifolia, Betula platyphylla and Rhododendron communities). The results showed that the enrichment capacity of acid anions and metal cations in the vegetation canopy of the coniferous forests (L. principis-rupprechtii, P. wilsonii, P. crassifolia) was stronger than that of the broad-leaved forests (B. platyphylla and Rhododendron communities). The content of acid anions and metal cations in stemflow of coniferous forests were 3.7-5.6 times and 0-9.3 times higher than those of broad-leaved forests, respectively. Corresponding values in throughfall were 1-1.4 times and 0.3-2.4 times, respectively. The contents of NO3-, Cl-, K+, Mg2+, Fe3+, Pb2+, Cu2+, and Cd2+ in leachate filtered from the soil layers that are deepening gradually showed consistent decreasing trend for all the forest stands. In addition, NO3-, Cl-, K+, Mg2+, Fe3+, and Pb2+ were also concentrated in the topsoil, except for Cu2+ and Cd2+. Nevertheless, SO42- and Na+ were concentrated in the subsoil, whereas Ca2+ was concentrated in the upper soil layers. Soil organic carbon (SOC) and total nitrogen (TN) contents in coniferous forest stands were 20-37% and 34-63% higher than those in broad-leaved forest stands, respectively. This results also shown that the contents of OC and TN has a strong correlation with the content of partial metal cations in soil and litter, indicating that coniferous forest stands had stronger ion scavenging and adsorption capacity in soil layer and litter layer than broad-leaved forest stands. Therefore, L. principis-rupprechtii, P. wilsonii, P. crassifolia had higher air pollutant adsorption and soil pollution remediation capacities than the other two forests. Thus, we recommend planting coniferous tree species (L. principis-rupprechtii, P. wilsonii and P. crassifolia) for eco-rehabilitation and water purification to improve the ecological service function of forest ecosystems.

Optimization of cell lines as tumour models by integrating multi-omics data.

Cell lines are widely used as in vitro models of tumorigenesis. However, an increasing number of researchers have found that cell lines differ from their sourced tumour samples after long-term cell culture. The application of unsuitable cell lines in experiments will affect the experimental accuracy and the treatment of patients. Therefore, it is imperative to identify optimal cell lines for each cancer type. Here, we review the methods used to evaluate cell lines since 2005. Furthermore, gene expression, copy number and mutation profiles from The Cancer Genome Atlas and the Cancer Cell Line Encyclopedia are used to calculate similarity between tumours and cell lines. Then, the ideal cell lines to use for experiments for eight types of cancers are found by combining the results with Gene Ontology functional similarity. After verification, the optimal cell lines have the same genomic characteristics as their homologous tumour samples. The contaminated cell lines identified in previous research are also determined to be unsuitable in vitro cancer models here. Moreover, our study suggests that some of the commonly used cell lines are not suitable cancer models. In summary, we provide a reference for ideal cell lines to use in in vitro experiments and contribute to improving the accuracy of future cancer research. Furthermore, this research provides a foundation for identifying more effective treatment strategies.

Hydrophobic deep eutectic solvent-based dispersive liquid-liquid microextraction for the simultaneous enantiomeric analysis of five ß-agonists in the environmental samples.

In this study, a simple and effective method was developed for the enantiomeric analysis of five ß-agonists (terbutaline, clorprenaline, tulobuterol, clenbuterol, and salbutamol) in water samples using deep eutectic solvent (DES) based dispersive liquid-liquid microextraction and chiral LC-MS. In such a framework, different kinds of hydrophobic DESs were tailored to examine their extraction ability for five ß-agonists from aqueous sample. After an initial screening, the primary factors affecting the extraction recovery of DES based dispersive liquid-liquid microextraction, such as hydrogen-bond acceptor/hydrogen-bond donor ratio, DES volume, type and volume of disperser solvent and so on, were investigated and optimized. Finally, the established method was validated and found to be linear, precise, and accurate. The method was successfully applied to analyze the five ß-agonists in water samples, which will help better understand the behavior of individual enantiomer and make accurate risk assessment on the ecosystem.

Deep eutectic solvent as a green solvent for enhanced extraction of narirutin, naringin, hesperidin and neohesperidin from Aurantii Fructus.

INTRODUCTION: In the present study, a green and efficient extraction method using deep eutectic solvents as extraction solvent was developed for extracting the four major active compounds narirutin, naringin, hesperidin and neohesperidin from Aurantii Fructus. METHODOLOGY: A series of tunable deep eutectic solvents were prepared and investigated by mixing choline chloride or betaine to different hydrogen-bond donors, and betaine/ethanediol was found to be the most suitable extraction solvent. To achieve the best extraction yield, the primary factors affecting the extraction efficiency, such as hydrogen-bond acceptor/hydrogen-bond donor ratio, water content in deep eutectic solvents, extraction temperature, solid/liquid ratio and extraction time, were investigated. RESULTS: The optimal extraction conditions were 40% of water in betaine/ethanediol (1:4) at 60°C for heated extraction of 30 min and solid/liquid ratio 1:100 g/mL. Under the optimum extraction condition, the extraction yields of narirutin, naringin, hesperidin, and neohesperidin were 8.39 ± 0.61, 83.98 ± 1.92, 3.03 ± 0.35 and 35.94 ± 0.63 mg/g, respectively, which were much higher than those of methanol as extraction solvent (5.5 ± 0.48, 64.23 ± 1.51, 2.16 ± 0.15 and 30.14 ± 0.62 mg/g). CONCLUSION: The present results showed that deep eutectic solvents could be promising green and efficient solvents for extraction of the bioactive ingredients from traditional Chinese medicine.

Dispersive micro-solid-phase extraction combined with online preconcentration by capillary electrophoresis for the determination of glycopyrrolate stereoisomers in rat plasma.

A simple and sensitive analytical method for four isomers of glycopyrrolate in rat plasma was developed using cation-selective exhaustive injection-sweeping cyclodextrin-modified electrokinetic chromatography (CSEI-Sweeping-CDEKC) for online enrichment combined with dispersive micro-solid-phase extraction pretreatment. The CSEI-Sweeping-CDEKC was conducted on an uncoated fused silica capillary (40.2 cm × 75 µm) with an applied voltage of -20 kV. The electrophoretic analysis was carried out in 30 mM phosphate solution at pH 2.0 containing 20 mg/mL sulfated-ß-cyclodextrin and 5% acetonitrile. Under these optimized conditions, the detection limit for racemic glycopyrrolate was found to be 2.0 ng/mL and this method could increase 495-fold detection sensitivity compared with the traditional injection method. Additionally, the parameters that affected the extraction efficiency of dispersive micro-solid-phase extraction were also examined systematically. The glycopyrrolate isomers in rat plasma samples as low as 0.0625 µg/mL were able to be separated and detected by capillary electrophoresis with the aid of CSEI-sweeping. The findings of this study show that the dispersive micro-solid-phase extraction pretreatment coupled with CSEI-Sweeping-CDEKC is a rapid and convenient method for analyzing glycopyrrolate isomers in rat plasma.

Enantioseparation of ofloxacin and its four related substances with ligand exchange-micellar electrokinetic chromatography using copper(II)-L-isoleucine complex as chiral selector.

A ligand-exchange micellar electrokinetic capillary electrophoresis system with copper(II)-L-isoleucine complexes as the chiral selector incorporated in micelles of sodium dodecyl sulfate (SDS) was developed for the enantioseparation of ofloxacin and its four related substances (impurities A, C, E, and F). The effects of important parameters affecting separation such as buffer pH, SDS concentration, chiral selector concentration, and organic additive were investigated in detail. Under optimum experimental conditions, enantioseparation of ofloxacin, impurities A, C, E, and F enantiomers was accomplished with resolutions of 4.28, 2.83, 3.40, 3.58, and 2.46, respectively. Further, simultaneous separation of impurities A, C, E, and F enantiomers was achieved using 10 mmol/L NH4 OAc as the running buffer containing 4 mmol/L copper sulfate,20 mmol/L L-isoleucine, 20 mmol/L SDS, and 5% methanol at pH 8.5. To the best of our knowledge, the simultaneous enantioseparation of four impurities of ofloxacin has not been reported previously.

Glucose Intake Alters Expression of Neuropeptides Derived from Proopiomelanocortin in the Lateral Hypothalamus and the Nucleus Accumbens in Fructose Preference Rats.

To study the neuroendocrine mechanism of sugar preference, we investigated the role of glucose feeding in the regulation of expression levels of neuropeptides derived from proopiomelanocortin (POMC) in the lateral hypothalamus (LH) and nucleus accumbens (NAc) in fructose preference rats. Fructose preference rats were induced by using the lithium chloride backward conditioning procedure. The fructose preference was confirmed by the two-bottle test. The drinking behavior of rats was assessed by the fructose concentration gradient test. The preference of 10% glucose or 0.1% saccharine was assessed, and the expression levels of neuropeptides derived from POMC in the LH and the NAc in fructose preference rats were measured by Western blot analysis. Fructose preference rats displayed a greater fructose preference than control rats. Furthermore, fructose preference rats preferred glucose solution rather than saccharine solution, while control rats preferred saccharine solution rather than glucose solution. The expression levels of neuropeptides derived from POMC in the LH and the NAc were changed by glucose but not saccharine intake. In summary, the data suggests that glucose intake increases the expression of neuropeptides derived from POMC in the LH and the NAc in fructose preference rats.

Capillary electrophoretic enantioseparation of basic drugs using a new single-isomer cyclodextrin derivative and theoretical study of the chiral recognition mechanism.

A novel single-isomer cyclodextrin derivative, heptakis {2,6-di-O-[3-(1,3-dicarboxyl propylamino)-2-hydroxypropyl]}-ß-cyclodextrin (glutamic acid-ß-cyclodextrin) was synthesized and used as a chiral selector in capillary electrophoresis for the enantioseparation of 12 basic drugs, including terbutaline, clorprenaline, tulobuterol, clenbuterol, procaterol, carvedilol, econazole, miconazole, homatropine methyl bromide, brompheniramine, chlorpheniramine and pheniramine. The primary factors affecting separation efficiency, which include the background electrolyte pH, the concentration of glutamic acid-ß-cyclodextrin and phosphate buffer concentration, were investigated. Satisfactory enantioseparations were obtained using an uncoated fused-silica capillary of 50 cm (effective length 40 cm) × 50 µm id with 120 mM phosphate buffer (pH 2.5-4.0) containing 0.5-4.5 mM glutamic acid-ß-cyclodextrin as background electrolyte. A voltage of 20 kV was applied and the capillary temperature was kept at 20°C. The results proved that glutamic acid-ß-cyclodextrin was an effective chiral selector for studied 12 basic drugs. Moreover, the possible chiral recognition mechanism of brompheniramine, chlorpheniramine and pheniramine on glutamic acid-ß-cyclodextrin was investigated using the semi-empirical Parametric Method 3.

Ultrasonic extraction and purification of scutellarin from Erigerontis Herba using deep eutectic solvent.

Nowadays, deep eutectic solvent (DES) was widely used in the extraction of bioactive in traditional Chinese medicine (TCM) as an alternative to organic solvents. While as, it is still a challenge for the removal of DES solvents and recovery of the extracted product. In this study, a simple, efficient and green technique of preparing scutellarin from Erigerontis Herba(EH) was proposed, combining ultrasonic assisted-DES extraction with anti-solvent purification. Firstly, different types of DES were prepared and studied for their abilities to extract scutellarin from EH. DES composed of choline chloride and acetamide (1:4 mol/mol) with 30% water obtained the highest extraction yield. Anti-solvent was proved as an efficient method to recover scutellarin from the DES extract with a content of purification up to 71.2%. Moreover, microscopic structural analysis was carried out to investigate the extract process and explain the extraction principle. Furthermore, the antioxidative activities of the DES extracts were evaluated, indicated that the bioactive property of scutellarin were still remained by using DES as the extraction solvent. In conclusion, the proposed simple and green ultrasonic assisted DES extraction method will serve as an effective alternative strategy to extract bioactive compounds from TCM.

Nacre-mimetic Strategy to Fabricate Waterborne FrGO/Zn/Epoxy Coatings with Dual Corrosion Protection.

The service life of metal and other infrastructure requires extending through eco-friendly, low-carbon technology. Here, a nacre-mimetic γ-Fe2O3/reduced graphene oxide (FrGO)/zinc-containing epoxy coating (FrGO/Zn/epoxy coating) was fabricated by spraying a mixture of waterborne epoxy resin, zinc flakes, and magnetic conductive FrGO under a magnetic field. The FrGO, which was synthesized by in situ redox and precipitation, was aligned in the zinc-containing coatings (ZCC), and it oriented the zinc flakes in the direction of the magnetic field to mimic the lamellar structure of nacre. The obtained anti-corrosion coating showed enhanced barrier protection and cathodic protection, which was confirmed by the electrochemical tests and salt spray test results. The waterborne coatings less than 50 µm thick with parallelly aligned FrGO and 30 wt % zinc flakes exhibited a long cathodic period lasting more than 99 days and excellent barrier performance with a high initial coating resistance of 5.31 × 109 Ω·cm2, which was superior to that of the conventional zinc-rich coating containing 80 wt % zinc (80 days, 3.74 × 103 Ω·cm2). The dual anti-corrosion mechanism of the waterborne FrGO/Zn/epoxy coating was investigated. The integrity and long-term cathodic protection of the coatings were derived from the compactness achieved by the nacre-mimetic structure and the interface chemical and hydrogen bonding crosslinking interactions and the high, uniform zinc utilization achieved by the aligned FrGO-Zn charge transmission network. This work provides a feasible nacre-inspired strategy to fabricate a lightweight anti-corrosion waterborne ZCC that is resource-efficient and promising in creating compact materials with other functional properties, such as electromagnetic shielding and conductive networks.

A global study for acute myeloid leukemia with RARG rearrangement.

Acute myeloid leukemia (AML) with retinoic acid receptor γ (RARG) rearrangement has clinical, morphologic, and immunophenotypic features similar to classic acute promyelocytic leukemia. However, AML with RARG rearrangement is insensitive to alltrans retinoic acid (ATRA) and arsenic trioxide (ATO) and carries a poor prognosis. We initiated a global cooperative study to define the clinicopathological features, genomic and transcriptomic landscape, and outcomes of AML with RARG rearrangements collected from 29 study groups/institutions worldwide. Thirty-four patients with AML with RARG rearrangements were identified. Bleeding or ecchymosis was present in 18 (54.5%) patients. Morphology diagnosed as M3 and M3v accounted for 73.5% and 26.5% of the cases, respectively. Immunophenotyping showed the following characteristics: positive for CD33, CD13, and MPO but negative for CD38, CD11b, CD34, and HLA-DR. Cytogenetics showed normal karyotype in 38% and t(11;12) in 26% of patients. The partner genes of RARG were diverse and included CPSF6, NUP98, HNRNPc, HNRNPm, PML, and NPM1. WT1- and NRAS/KRAS-mutations were common comutations. None of the 34 patients responded to ATRA and/or ATO. Death within 45 days from diagnosis occurred in 10 patients (∼29%). At the last follow-up, 23 patients had died, and the estimated 2-year cumulative incidence of relapse, event-free survival, and overall survival were 68.7%, 26.7%, and 33.5%, respectively. Unsupervised hierarchical clustering using RNA sequencing data from 201 patients with AML showed that 81.8% of the RARG fusion samples clustered together, suggesting a new molecular subtype. RARG rearrangement is a novel entity of AML that confers a poor prognosis. This study is registered with the Chinese Clinical Trial Registry (ChiCTR2200055810).

Reassessment of Reliability and Reproducibility for Triple-Negative Breast Cancer Subtyping.

Triple-negative breast cancer (TNBC) is a heterogeneous disease with diverse, often poor prognoses and treatment responses. In order to identify targetable biomarkers and guide personalized care, scientists have developed multiple molecular classification systems for TNBC based on transcriptomic profiling. However, there is no consensus on the molecular subtypes of TNBC, likely due to discrepancies in technical and computational methods used by different research groups. Here, we reassessed the major steps for TNBC subtyping, validated the reproducibility of established TNBC subtypes, and identified two more subtypes with a larger sample size. By comparing results from different workflows, we demonstrated the limitations of formalin-fixed, paraffin-embedded samples, as well as batch effect removal across microarray platforms. We also refined the usage of computational tools for TNBC subtyping. Furthermore, we integrated high-quality multi-institutional TNBC datasets (discovery set: n = 457; validation set: n = 165). Performing unsupervised clustering on the discovery and validation sets independently, we validated four previously discovered subtypes: luminal androgen receptor, mesenchymal, immunomodulatory, and basal-like immunosuppressed. Additionally, we identified two potential intermediate states of TNBC tumors based on their resemblance with more than one well-characterized subtype. In summary, we addressed the issues and limitations of previous TNBC subtyping through comprehensive analyses. Our results promote the rational design of future subtyping studies and provide new insights into TNBC patient stratification.

Simulating the Dynamic Intra-Tumor Heterogeneity and Therapeutic Responses.

A tumor is a complex tissue comprised of heterogeneous cell subpopulations which exhibit substantial diversity at morphological, genetic and epigenetic levels. Under the selective pressure of cancer therapies, a minor treatment-resistant subpopulation could survive and repopulate. Therefore, the intra-tumor heterogeneity is recognized as a major obstacle to effective treatment. In this paper, we propose a stochastic clonal expansion model to simulate the dynamic evolution of tumor subpopulations and the therapeutic effect at different times during tumor progression. The model is incorporated in the CES webserver, for the convenience of simulation according to initial user input. Based on this model, we investigate the influence of various factors on tumor progression and treatment consequences and present conclusions drawn from observations, highlighting the importance of treatment timing. The model provides an intuitive illustration to deepen the understanding of temporal intra-tumor heterogeneity dynamics and treatment responses, thus helping the improvement of personalized diagnostic and therapeutic strategies.