CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.

Extrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in ∼15% of early-stage cancers and ∼30% of late-stage cancers. ecDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies. Paired-end short-read (Illumina) sequencing and mapping have been utilized to represent ecDNA amplifications using a breakpoint graph, in which the inferred architecture of ecDNA is encoded as a cycle in the graph. Traversals of breakpoint graphs have been used to successfully predict ecDNA presence in cancer samples. However, short-read technologies are intrinsically limited in the identification of breakpoints, phasing together complex rearrangements and internal duplications, and deconvolution of cell-to-cell heterogeneity of ecDNA structures. Long-read technologies, such as from Oxford Nanopore Technologies, have the potential to improve inference as the longer reads are better at mapping structural variants and are more likely to span rearranged or duplicated regions. Here, we propose Complete Reconstruction of Amplifications with Long reads (CoRAL) for reconstructing ecDNA architectures using long-read data. CoRAL reconstructs likely cyclic architectures using quadratic programming that simultaneously optimizes parsimony of reconstruction, explained copy number, and consistency of long-read mapping. CoRAL substantially improves reconstructions in extensive simulations and 10 data sets from previously characterized cell lines compared with previous short- and long-read-based tools. As long-read usage becomes widespread, we anticipate that CoRAL will be a valuable tool for profiling the landscape and evolution of focal amplifications in tumors.

Impact of operative time on textbook outcome after minimally invasive esophagectomy, a risk-adjusted analysis from a high-volume center.

BACKGROUND: We aimed to study the impact of operative time on textbook outcome (TO), especially postoperative complications and length of postoperative stay in minimally invasive esophagectomy. METHODS: Patients undergoing esophagectomy for curative intent within a prospectively maintained database from 2016 to 2022 were retrieved. Relationships between operative time and outcomes were quantified using multivariable mixed-effects models with medical teams random effects. A restricted cubic spline (RCS) plotting was used to characterize correlation between operative time and the odds for achieving TO. RESULTS: Data of 2210 patients were examined. Median operative time was 270 mins (interquartile range, 233-313) for all cases. Overall, 902 patients (40.8%) achieved TO. Among non-TO patients, 226 patients (10.2%) had a major complication (grade ≥ III), 433 patients (19.6%) stayed postoperatively longer than 14 days. Multivariable analysis revealed operative time was associated with higher odds of major complications (odds ratio 1.005, P < 0.001) and prolonged postoperative stay (≥ 14 days) (odds ratio 1.003, P = 0.006). The relationship between operative time and TO exhibited an inverse-U shape, with 298 mins identified as the tipping point for the highest odds of achieving TO. CONCLUSIONS: Longer operative time displayed an adverse influence on postoperative morbidity and increased lengths of postoperative stay. In the present study, the TO displayed an inverse U-shaped correlation with operative time, with a significant peak at 298 mins. Potential factors contributing to prolonged operative time may potentiate targets for quality metrics and risk-adjustment process.

Multistage Filtration Desalination via Ion Self-Rejection Effect in Cation-Controlled Graphene Oxide Membrane under 1 Bar Operating Pressure.

By building a thin graphene oxide membrane with Na+ self-rejection ability, high permeability, and multistage filtration strategy, we obtained fresh water from a saline solution under 1 bar of operating pressure. After five and 11 cycles of the multistage filtration, the Na+ concentration decreased from 0.6 to 0.123 mol/L (below physiological concentration) and 0.015 mol/L (fresh water), respectively. In comparison with the performance of commercial reverse osmosis membranes, energy consumption was only 10% and water flux was higher by a factor of 10. Interestingly, the energy consumption of this multistage filtration strategy is close to the theoretical lowest energy consumption. Theoretical calculations showed that such Na+ self-rejection is attributed to the lower transportation rate of the Na+ than that of water within the graphene oxide membrane for the hydrated cation-π interaction. Our findings present a viable desalination strategy for graphene-based membranes and improve the mechanistic understanding of water/ion transportation behaviors in confined spaces.

Genome-Wide Analysis of TCP Transcription Factors and Their Expression Pattern Analysis of Rose Plants (Rosa chinensis).

The plant-specific transcription factor TEOSINTE BRANCHED, CYCLOIDEA, AND PROLIFERATING CELL FACTOR (TCP) gene family plays vital roles in various biological processes, including growth and development, hormone signaling, and stress responses. However, there is a limited amount of information regarding the TCP gene family in roses (Rosa sp.). In this study, we identified 18 TCP genes in the rose genome, which were further classified into two subgroups (Group A and Group B) via phylogenetic analysis. Comprehensive characterization of these TCP genes was performed, including gene structure, motif composition, chromosomal location, and expression profiles. Synteny analysis revealed that a few TCP genes are involved in segmental duplication events, indicating that these genes played an important role in the expansion of the TCP gene family in roses. This suggests that segmental duplication events have caused the evolution of the TCP gene family and may have generated new functions. Our study provides an insight into the evolutionary and functional characteristics of the TCP gene family in roses and lays a foundation for the future exploration of the regulatory mechanisms of TCP genes in plant growth and development.

Sketching algorithms for genomic data analysis and querying in a secure enclave.

Genome-wide association studies (GWAS), especially on rare diseases, may necessitate exchange of sensitive genomic data between multiple institutions. Since genomic data sharing is often infeasible due to privacy concerns, cryptographic methods, such as secure multiparty computation (SMC) protocols, have been developed with the aim of offering privacy-preserving collaborative GWAS. Unfortunately, the computational overhead of these methods remain prohibitive for human-genome-scale data. Here we introduce SkSES (https://github.com/ndokmai/sgx-genome-variants-search), a hardware-software hybrid approach for privacy-preserving collaborative GWAS, which improves the running time of the most advanced cryptographic protocols by two orders of magnitude. The SkSES approach is based on trusted execution environments (TEEs) offered by current-generation microprocessors-in particular, Intel's SGX. To overcome the severe memory limitation of the TEEs, SkSES employs novel 'sketching' algorithms that maintain essential statistical information on genomic variants in input VCF files. By additionally incorporating efficient data compression and population stratification reduction methods, SkSES identifies the top k genomic variants in a cohort quickly, accurately and in a privacy-preserving manner.

Algorithms of Electrocardiographic Changes for Quantitative and Localization Analysis of Thrombus Burden in Patients with Acute Pulmonary Thromboembolism.

Background: Various electrocardiographic (ECG) abnormalities are associated with the severity of pulmonary thromboembolism (PTE). The utility of evaluating the clot burden of PTE based on ECG findings alone has yet to be thoroughly investigated in Chinese patients. The aim of this study was therefore to use ECG signs to establish novel models for quantitative and localization analysis of clot burden in patients with acute PTE. Methods: Acute PTE patients from three centers were enrolled between 2015 and 2019 in a retrospective cohort study (NCT03802929). We analyzed the 12-lead ECGs at admission and studied computed tomography pulmonary angiography (CTPA) features to obtain the Qanadli score of clot burden and location of thrombus. Novel risk prediction models were developed and validated using derivation and external validation cohorts, respectively. Results: A total of 341 acute PTE patients were screened, of whom 246 (72.1%) were from Shanghai Tenth People's Hospital, 71 (20.8%) were from Shanghai Pulmonary Hospital and 24 (7.0%) were from Qidong People's Hospital. In the derivation cohort, predictors included in the final models were congestive heart failure, chronic obstructive pulmonary disease, hypertension, coronary heart disease, atrial fibrillation and ECG abnormalities. The CHARIS (COPD/CHF/CHD, HTN, Atrial arrhythmias/AF, RBBB/RAD, Inverted T wave and S1Q3T3/ Sinus tachycardia) I model was established for quantitatively assessing Qanadli score. It had moderate discrimination in both the derivation cohort (concordance index (c-index) of 0.720, 95% CI 0.655-0.780) and the validation cohort (c-index of 0.663, 95% CI 0.559-0.757). The CHARIS II model was used to predict the probability of trunk obstruction. It showed similar discrimination in the derivation cohort (c-index of 0.753, 95% CI 0.691-0.811) and in the validation cohort (c-index of 0.741, 95% CI 0.641-0.827). Calibration curves and Hosmer-Lemeshow test confirmed the accuracy of the risk prediction equations in the external validation dataset. Decision curve analysis showed the CHARIS I and CHARIS II algorithms had positive net benefits in both the derivation and validation cohorts. Conclusions: From quantitative and localization perspectives, the CHARIS algorithms can identify acute PTE patients with heavy thrombus burdens prior to imaging diagnosis. Clinical Trial Registration: NCT03802929, https://www.clinicaltrials.gov/study/NCT03802929.

Prognostic Value of Combination of Lymphocyte-to-Monocyte-Ratio and CYFRA 21-1 in Esophageal Squamous Cell Carcinoma.

BACKGROUND: This study aimed to investigate the potential of a combined score based on CYFRA 21-1 level and LMR as a prognostic predictor for patients with ESCC. METHODS: A total of 460 patients who underwent esophagectomy were analyzed, and three groups were established based on the CA-LMR score. OS and RFS were evaluated using the Kaplan-Meier analysis, and associated factors were analyzed by univariate and multivariate Cox analysis. A mpStage system was also established based on the CA-LMR score. RESULTS: The allocation of CA-LMR score of 0, 1, and 2 was 107 (23.3%), 280 (60.9%), and 73 (15.9%). There was a significant association between CA-LMR and male gender (P = 0.001), lower BMI (P = 0.035), longer tumor lesions (P = 0.002), and high pT, pN, pStage (P < 0.001, P = 0.011, P = 0.001). The 5-year OS rates for CA-LMR scores of 0, 1, and 2 were 75.4%, 60.2%, and 32.8%, respectively (P < 0.001). Multivariate analysis showed that CA-LMR score (P = 0.011) was an independent prognostic factor for OS. The proposed mpStage system, based on CA-LMR score, demonstrated superior discriminatory ability, monotonicity, homogeneity, and prognosis prediction ability over AJCC 8th pStage system. CONCLUSIONS: The CA-LMR score, combined with tumor marker and inflammatory index, could use as a potential prognostic indicator; moreover, our modified pStage system exhibited superior stratification and prognostic accuracy for patients with ESCC.

AKT inhibitor AZD5363 suppresses stemness and promotes anti-cancer activity of 3,3'-diindolylmethane in human breast cancer cells.

3,3'-diindolylmethane (DIM) is a dimer compound converted from Indoly-3-carbinol that had been studied as promising chemo-preventive agent against breast cancer. In this study, we observed that proportion of CD133+Nanog+ subpopulation in MCF-7 cells was significantly increased after DIM administration with up-regulated AKT activity by using CyTOF assay. SPADE analysis revealed this stem-like subpopulation exhibited apoptosis-resistance property against DIM treatment. By combining with AKT inhibitor AZD5363, DIM induced CD133 expression could be suppressed. In addition, a combination treatment of MCF-7 and MDA-MB-231 breast cancer cells with DIM and AZD5363 showed synergistic decreases in cell proliferation and induced apoptosis. Furthermore, results from imaging flow cytometry suggested that FoxO3a nuclear localization and PUMA expression could be improved by combination of AZD5363 with DIM. Taken together, the above observations suggested that the combination of AZD5363 with DIM could be developed as potential therapy for breast cancer.

VCP/p97 targets the nuclear export and degradation of p27Kip1 during G1 to S phase transition.

One of the critical regulatory mechanisms for cell cycle progression is the timely degradation of CDK inhibitors, including p21Cip1 and p27Kip1 . VCP/p97, an AAA-ATPase, is reported to be overexpressed in many types of cancers. Here, we found that treatment of MCF-7 human breast cancer cells with DBeQ, a VCP inhibitor, or VCP knockdown in MCF-7 cells arrested cells at G1 phase, accompanied with the blockage of both p21 and p27 degradation. Whereas, double knockdown of p21 and p27 in MCF-7 cells rendered cells refractory to DBeQ-induced G1 arrest. Moreover, inhibition or knockdown of VCP or UFD1, one of VCP's co-factors, in MCF-7, NIH3T3, or HEK293T cells blocked the nuclear export of p27 during earlier G1 phase after mitogen stimulation. We also identified the nuclear localization sequence (NLS) of VCP, and found that adding back wild-type VCP, not the NLS-deleted VCP mutant, restored the nuclear export and degradation of p27 in VCP knockout MCF-7 cells. Importantly, we found that VCP inhibition sensitized breast cancer cells to the treatment of several anticancer therapeutics both in vitro and in vivo. Taken together, our study not only uncovers the mechanisms underlying VCP-mediated cell proliferation control but also provides potential therapeutic option for cancer treatment.

A graph-based approach for proteoform identification and quantification using top-down homogeneous multiplexed tandem mass spectra.

BACKGROUND: Top-down homogeneous multiplexed tandem mass (HomMTM) spectra are generated from modified proteoforms of the same protein with different post-translational modification patterns. They are frequently observed in the analysis of ultramodified proteins, some proteoforms of which have similar molecular weights and cannot be well separated by liquid chromatography in mass spectrometry analysis. RESULTS: We formulate the top-down HomMTM spectral identification problem as the minimum error k-splittable flow problem on graphs and propose a graph-based algorithm for the identification and quantification of proteoforms using top-down HomMTM spectra. CONCLUSIONS: Experiments on a top-down mass spectrometry data set of the histone H4 protein showed that the proposed method identified many proteoform pairs that better explain the query spectra than single proteoforms.

iTRAQ-based quantitative proteomic analysis reveals dynamic changes during daylily flower senescence.

MAIN CONCLUSION: Sugar-related metabolic biological processes and metabolic pathways as well as invertase, protease, and ribosomal proteins may be critical regulators controlling the circadian rhythm and ephemeral properties of daylily flowers. Daylily is a familiar perennial flower. The daylily flower opens at dawn and withers away at night. Flower longevity in almost all daylily varieties from opening to fading is less than 24 h. In the past decades, the physiological changes and genetic responses to senescence in daylily flowers have been reported. However, the main metabolic pathways and biological processes involved in daylily flower senescence and the proteins involved in premature senility of daylily flowers are poorly understood. Herein, we identified differences between the proteomes of four developmental stages (s1-s4) of daylily flowers using iTRAQ-based quantitative proteomic methods. A total of 445 proteins (containing at least two unique peptides) were identified, and differentially expressed proteins (upregulation ≥ 1.5 or downregulation ≤ 0.67, P value ≤ 0.05) were detected between these stages in the following numbers: 58 (s2/s1), 59 (s3/s1), 31 (s3/s2), 64 (s4/s1), 52 (s4/s2), and 29 (s4/s3). Protein functions and classifications were analyzed based on GO, KEGG, and COG, and expressive hierarchical cluster analysis and functional enrichment analysis for differentially expressed proteins were carried out. A comparison of the late stages (s3 and s4) with the early stage (s1) revealed that the sugar (hexose, monosaccharide, and glucose) metabolic process GO category was the most enriched, and sugar (galactose, pentose, starch, and sucrose) metabolism pathways constituted the most enriched KEGG category. Finally, the potential research value of invertase, protease, and ribosomal proteins for revealing the mechanism underlying the circadian rhythm and ephemeral properties of daylily flowers are discussed. These data and analyses provide new insight into the senescence mechanism of daylily flowers.

Identifying Glyceraldehyde 3-Phosphate Dehydrogenase as a Cyclic Adenosine Diphosphoribose Binding Protein by Photoaffinity Protein-Ligand Labeling Approach.

Cyclic adenosine diphosphoribose (cADPR), an endogenous nucleotide derived from nicotinamide adenine dinucleotide (NAD+), mobilizes Ca2+ release from endoplasmic reticulum (ER) via ryanodine receptors (RyRs), yet the bridging protein(s) between cADPR and RyRs remain(s) unknown. Here we synthesized a novel photoaffinity labeling (PAL) cADPR agonist, PAL-cIDPRE, and subsequently applied it to purify its binding proteins in human Jurkat T cells. We identified glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as one of the cADPR binding protein(s), characterized the binding affinity between cADPR and GAPDH in vitro by surface plasmon resonance (SPR) assay, and mapped cADPR's binding sites in GAPDH. We further demonstrated that cADPR induces the transient interaction between GAPDH and RyRs in vivo and that GAPDH knockdown abolished cADPR-induced Ca2+ release. However, GAPDH did not catalyze cADPR into any other known or novel compound(s). In summary, our data clearly indicate that GAPDH is the long-sought-after cADPR binding protein and is required for cADPR-mediated Ca2+ mobilization from ER via RyRs.

Mining and expression analysis of candidate genes involved in regulating the chilling requirement fulfillment of Paeonia lactiflora 'Hang Baishao'.

BACKGROUND: The artificial enlargement of the planting area and ecological amplitude of ornamentals for horticultural and landscape applications are significant. Herbaceous peony (Paeonia lactiflora Pall.) is a world-famous ornamental with attractive and fragrant flowers and is mainly planted in temperate and cool areas. Comparatively higher winter temperatures in the subtropical and tropical Northern Hemisphere result in a deficit of chilling accumulation for bud dormancy release, which severely hinders "The southward plantation of herbaceous peony". Studies on the dormancy, chilling requirement (CR) and relevant molecular mechanisms of peony are needed to enhance our ability to extend the range of this valuable horticultural species. RESULTS: Based on natural and artificial chilling experiments, and chilling hour (CH) and chilling unit (CU) evaluation systems, the lowest CR of 'Hang Baishao' was between 504.00 and 672.00 CHs and the optimal CR was 672.00 CHs and 856.08 CUs for achieving strong sprouting, growth and flowering performance. Transcriptome sequencing and gene identification by RNA-Seq were performed on 'Hang Baishao' buds during the dormancy and sprouting periods. Six gene libraries were constructed, and 66 temperature- and photoperiod-associated unigenes were identified as the potential candidate genes that may regulate or possibly determine CR characteristics. The difference in the expression patterns of SUPPRESSPOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) between the winters of 2012-2013 and 2015-2016, and the difference of CR fulfillment periods also between these two winters represented the interesting congruent relationships. This correlation was also observed for WRKY DNA-BINDING PROTEIN 33 (WRKY 33). CONCLUSIONS: Combined with the results acquired from all of experiments, 'Hang Baishao' was confirmed to be a superb peony resource that have significantly low CR characteristics. The two genes of SOC1 and WRKY33 are likely involved in determining the CR amount and fulfillment period of 'Hang Baishao'. HEAT SHOCK PROTEIN, OSMOTIN and TIMING OF CAB EXPRESSION 1 also deserve attention for the CR research. This study could contribute to the knowledge of the deep factors and mechanisms that regulate CR characteristics, and may be beneficial for breeding new germplasms that have low CRs for landscape or horticulture applications in subtropical regions.

Learning-Augmented Sketching Offers Improved Performance for Privacy Preserving and Secure GWAS.

The introduction of trusted execution environments (TEEs), such as secure enclaves provided by the Intel SGX technology has enabled secure and privacy-preserving computation on the cloud. The stringent resource limitations, such as memory constraints, required by some TEEs necessitates the development of computational approaches with reduced memory usage, such as sketching. One example is the SkSES method for GWAS on a cohort of case and control samples from multiple institutions, which identifies the most significant SNPs in a privacy-preserving manner without disclosing sensitive genotype information to other institutions or the cloud service provider. Here we show how to improve the performance of SkSES on large datasets by augmenting it with a learning-augmented approach. Specifically, we show how individual institutions can perform smaller scale GWAS on their own datasets and identify two sets of variants according to certain criteria, which are then used to guide the sketching process to more accurately identify significant variants over the collective dataset. The new method achieves up to 40% accuracy gain compared to the original SkSES method under the same memory constraints on datasets we tested on. The code is available at https://github.com/alreadydone/sgx-genome-variants-search.

Efficacy of GluN2B-Containing NMDA receptor antagonist for antitumor and antidepressant therapy in non-small cell lung cancer.

Non-small cell lung cancer (NSCLC) is the predominant subtype of lung cancer. Evidence suggests that the ionotropic glutamate receptor N-methyl-D-aspartate (NMDA) receptor, a critical molecule in the central nervous system, is expressed in NSCLC. However, the specific expression patterns, subcellular localization, functional modulation, and pathological implications of NMDA receptor subtypes in NSCLC have not been fully elucidated. In this study, we employed a multi-disciplinary approach, combining biochemical and molecular biology with electrophysiological recordings and behavioral assays, to investigate these aspects. We reveal the expression of GluN2B-containing NMDA receptors in A549 and H460 NSCLC cell lines and the induction of NMDA receptor-mediated currents by glutamate in A549 cells. Furthermore, the GluN2B-specific inhibitors ifenprodil and Ro 25-6981 significantly reduced cell viability and migration, while promoting apoptosis. Importantly, intraperitoneal administration of ifenprodil in nude mice inhibited the growth of subcutaneous tumors derived from A549 and H460 cells and ameliorated depression-like behaviors. These findings underscore the potential antiproliferative effects of ifenprodil and Ro 25-6981 and suggest that GluN2B-containing NMDA receptors may represent novel therapeutic targets for NSCLC, with the added benefit of potential antidepressant action.

A large-aperture, high-power ultrawideband radiation system with beam broadening capacity.

Due to the limited maximum output power of the pulsers based on avalanche transistors, high-power ultrawideband (UWB) radiation systems usually synthesize plenty of modules simultaneously to achieve a high peak effective potential (rEp). However, this would lead to an increased aperture size as well as a narrower beam, which would limit their applications in intentional electromagnetic interference fields. In this paper, a high-power UWB radiation system with beam broadening capacity is developed. To achieve beam broadening in the time domain, a power-law time delay distribution method is proposed and studied by simulation, and then the relative excitation time delays of the modules are optimized to achieve higher rEp and avoid beam splitting in the beam broadening mode. In order to avoid false triggering of the pulser elements when implementing the beam broadening, the mutual coupling effect in the system is analyzed and suppressed by employing onboard high-pass filters, since the mutual coupling effect is much more severe in the low-frequency range. Finally, a radiation system with 36 modules is developed. Measuring results indicate that in the high-rEp mode, the developed system could achieve a maximum effective potential rEp of 313.6 kV and a maximum pulse-repetition-rate of 20 kHz. In the beam broadening mode, its half-peak-power beam width in the H-plane is broadened from the original value of 3.9° to 7.9°, with a maximum rEp of 272.9 kV. The polarization direction of the system could be flexibly adjusted by a built-in motor.

Inhibition of novel human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer.

Extrachromosomal circular DNA (ecDNA) have been found in most types of human cancers, and ecDNA incorporating viral genomes has recently been described, specifically in human papillomavirus (HPV)-mediated oropharyngeal cancer (OPC). However, the molecular mechanisms of human-viral hybrid ecDNA (hybrid ecDNA) for carcinogenesis remains elusive. We characterized the epigenetic status of hybrid ecDNA using HPVOPC cell lines and patient-derived tumor xenografts, identifying HPV oncogenes E6/E7 in hybrid ecDNA were flanked by novel somatic DNA enhancers and HPV L1 enhancers, with strong cis-interaction. Targeting of these enhancers by clustered regularly interspaced short palindromic repeats interference or hybrid ecDNA by bromodomain and extra-terminal inhibitor reduced E6/E7 expression, and significantly inhibited in vitro and/or in vivo growth only in ecDNA(+) models. HPV DNA in hybrid ecDNA structures are associated with novel somatic and HPV enhancers in hybrid ecDNA that drive HPV ongogene expression and carcinogenesis, and can be targeted with ecDNA disrupting therapeutics.

CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.

Extrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in approximately 15% of early stage cancers and 30% of late-stage cancers. EcDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy-number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies. Paired-end short-read (Illumina) sequencing and mapping have been utilized to represent ecDNA amplifications using a breakpoint graph, where the inferred architecture of ecDNA is encoded as a cycle in the graph. Traversals of breakpoint graph have been used to successfully predict ecDNA presence in cancer samples. However, short-read technologies are intrinsically limited in the identification of breakpoints, phasing together of complex rearrangements and internal duplications, and deconvolution of cell-to-cell heterogeneity of ecDNA structures. Long-read technologies, such as from Oxford Nanopore Technologies, have the potential to improve inference as the longer reads are better at mapping structural variants and are more likely to span rearranged or duplicated regions. Here, we propose CoRAL (Complete Reconstruction of Amplifications with Long reads), for reconstructing ecDNA architectures using long-read data. CoRAL reconstructs likely cyclic architectures using quadratic programming that simultaneously optimizes parsimony of reconstruction, explained copy number, and consistency of long-read mapping. CoRAL substantially improves reconstructions in extensive simulations and 9 datasets from previously-characterized cell-lines as compared to previous short-read-based tools. As long-read usage becomes wide-spread, we anticipate that CoRAL will be a valuable tool for profiling the landscape and evolution of focal amplifications in tumors.

Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes.

The study of the tumor microbiome has been garnering increased attention. We developed a computational pipeline (CSI-Microbes) for identifying microbial reads from single-cell RNA sequencing (scRNA-seq) data and for analyzing differential abundance of taxa. Using a series of controlled experiments and analyses, we performed the first systematic evaluation of the efficacy of recovering microbial unique molecular identifiers by multiple scRNA-seq technologies, which identified the newer 10x chemistries (3' v3 and 5') as the best suited approach. We analyzed patient esophageal and colorectal carcinomas and found that reads from distinct genera tend to co-occur in the same host cells, testifying to possible intracellular polymicrobial interactions. Microbial reads are disproportionately abundant within myeloid cells that up-regulate proinflammatory cytokines like IL1Β and CXCL8, while infected tumor cells up-regulate antigen processing and presentation pathways. These results show that myeloid cells with bacteria engulfed are a major source of bacterial RNA within the tumor microenvironment (TME) and may inflame the TME and influence immunotherapy response.

Cold atmospheric plasma: Novel opportunities for tumor microenvironment targeting.

With mounting preclinical and clinical evidences on the prominent roles of the tumor microenvironment (TME) played during carcinogenesis, the TME has been recognized and used as an important onco-therapeutic target during the past decade. Delineating our current knowledge on TME components and their functionalities can help us recognize novel onco-therapeutic opportunities and establish treatment modalities towards desirable anti-cancer outcome. By identifying and focusing on primary cellular components in the TME, that is, tumor-infiltrating lymphocytes, tumor-associated macrophages, cancer-associated fibroblasts and mesenchymal stem cells, we decomposed their primary functionalities during carcinogenesis, categorized current therapeutic approaches utilizing traits of these components, and forecasted possible benefits that cold atmospheric plasma, a redox modulating tool with selectivity against cancer cells, may convey by targeting the TME. Our insights may open a novel therapeutic avenue for cancer control taking advantages of redox homeostasis and immunostasis.