Evolution of multiple cell clones over a 29-year period of a CLL patient

Chronic lymphocytic leukaemia (CLL) is a frequent B-cell malignancy, characterized by recurrent somatic chromosome alterations and a low level of point mutations. Here we present single-nucleotide polymorphism microarray analyses of a single CLL patient over 29 years of observation and treatment, and transcriptome and whole-genome sequencing at selected time points. We identify chromosome alterations 13q14−, 6q− and 12q+ in early cell clones, elimination of clonal populations following therapy, and subsequent appearance of a clone containing trisomy 12 and chromosome 10 copy-neutral loss of heterogeneity that marks a major population dominant at death. Serial single-cell RNA sequencing reveals an expression pattern with high FOS, JUN and KLF4 at disease acceleration, which resolves following therapy, but reoccurs following relapse and death. Transcriptome evolution indicates complex changes in expression occur over time. In conclusion, CLL can evolve gradually during indolent phases, and undergo rapid changes following therapy

Full-length single-cell RNA-seq applied to a viral human cancer:applications to HPV expression and splicing analysis in HeLa S3 cells

Background: Viral infection causes multiple forms of human cancer, and HPV infection is the primary factor in cervical carcinomas Recent single-cell RNA-seq studies highlight the tumor heterogeneity present in most cancers, but virally induced tumors have not been studied HeLa is a well characterized HPV+ cervical cancer cell line Result: We developed a new high throughput platform to prepare single-cell RNA on a nanoliter scale based on a customized microwell chip Using this method, we successfully amplified full-length transcripts of 669 single HeLa S3 cells and 40 of them were randomly selected to perform single-cell RNA sequencing Based on these data, we obtained a comprehensive understanding of the heterogeneity of HeLa S3 cells in gene expression, alternative splicing and fusions Furthermore, we identified a high diversity of HPV-18 expression and splicing at the single-cell level By co-expression analysis we identified 283 E6, E7 co-regulated genes, including CDC25, PCNA, PLK4, BUB1B and IRF1 known to interact with HPV viral proteins Conclusion: Our results reveal the heterogeneity of a virus-infected cell line It not only provides a transcriptome characterization of HeLa S3 cells at the single cell level, but is a demonstration of the power of single cell RNA-seq analysis of virally infected cells and cancers

Therapeutic Effects of Baicalin on Diseases Related to Gut–Brain Axis Dysfunctions

The gut–brain axis is an active area of research. Several representative diseases, including central nervous system disorders (Alzheimer’s disease, Parkinson’s disease, and depression), metabolic disorders (obesity-related diseases), and intestinal disorders (inflammatory bowel disease and dysbiosis), are associated with the dysfunctional gut–brain axis. Baicalin, a bioactive flavonoid extracted from Scutellaria baicalensis, is reported to exert various pharmacological effects. This narrative review summarizes the molecular mechanisms and potential targets of baicalin in disorders of the gut–brain axis. Baicalin protects the central nervous system through anti-neuroinflammatory and anti-neuronal apoptotic effects, suppresses obesity through anti-inflammatory and antioxidant effects, and alleviates intestinal disorders through regulatory effects on intestinal microorganisms and short-chain fatty acid production. The bioactivities of baicalin are mediated through the gut–brain axis. This review comprehensively summarizes the regulatory role of baicalin in gut–brain axis disorders, laying a foundation for future research, although further confirmatory basic research is required

Effects of different concentrations of methanol on the decomposition of methane hydrate: insights from molecular dynamics simulations

As one of the most promising alternative energy, natural gas hydrate has aroused much attention owing to its controllable exploitation with the aid of chemical injections. Although alcohols are commonly used as promoters for hydrate decomposition, few studies have been carried out to investigate the effect of different concentrations of methanol on methane hydrate decomposition at a molecular level. For the first time, we systematically combined the parameters of angular order parameter (AOP), radial distribution function (RDF), and mean square displacement (MSD) to reveal the role of methanol in the decomposition mechanism of methane hydrates through the molecular dynamics approach. The results demonstrated that methanol concentration had an optimal value for hydrate decomposition, which was 20% methanol solution for the best efficiency for the hydrate decomposition and had been examined by analyzing the parameter of AOP. This can be attributed to the promotion effect of methanol on the deconstruction of the hydrogen bond networks of water molecules and the inhibition effect of methanol on the mass transfer effect of methane diffusion, both of which determined the decomposition of methane hydrates. These effects were further quantitatively evaluated by the structural parameters of RDF and MSD. The obtained results reveal the important influence of methanol concentrations on methane hydrates decomposition on molecular scale, and provide useful guidelines for highly efficient exploitation of natural gas hydrate reservoir

Genomic and microbial factors affect the prognosis of anti-pd-1 immunotherapy in nasopharyngeal carcinoma

Antibodies targeting the programmed cell death protein-1 (PD-1) molecule have been reported to hold promising antitumor activities in patients with nasopharyngeal carcinoma (NPC). However, only a small subset of NPC patients benefits from the anti-PD-1 monotherapy and factors that affect the treatment response need further investigation. This study aimed to examine the impact of multiple genetic and environmental factors on outcome of anti-PD-1 immunotherapy by identifying tumor size, tumor mutation burden (TMB) based on whole exon sequencing, human leukocyte antigen class I (HLA-I) homo-/heterozygosity and supertypes, blood Epstein-Barr virus (EBV) DNA load, T cell proportions, and interferon-γ(IFN-γ) levels in a cohort of 57 NPC patients that received Nivolumab or Camrelizumab treatment. Moreover, we profiled the longitudinal changes in gut microbiota composition using shotgun metagenomics sequencing. We observed that high TMB combined with HLA-I heterozygosity was associated with improved clinical outcomes. In agreement with previous studies, we found that patients with higher plasma EBV DNA load showed worse progression-free survival. We found no evidence for an effect of gut bacterial diversity on the treatment response, but identified a higher abundance of seven specific gut bacteria at baseline of non-responders, including Blautia wexlera and Blautia obeum, as well as four other bacteria belonging to the Clostridiales order, and one Erysipelatoclostridium. Combined, this study provides insight into the influence of several genetic and environmental factors on anti-PD-1 immunotherapy responses in NPC patients

Arbutin alleviates fatty liver by inhibiting ferroptosis via FTO/SLC7A11 pathway

Non-alcoholic fatty liver disease (NAFLD) is a potentially serious disease that affects 30 % of the global population and poses a significant risk to human health. However, to date, no safe, effective and appropriate treatment modalities are available. In recent years, ferroptosis has emerged as a significant mode of cell death and has been found to play a key regulatory role in the development of NAFLD. In this study, we found that arbutin (ARB), a natural antioxidant derived from Arctostaphylos uva-ursi (L.), inhibits the onset of ferroptosis and ameliorates high-fat diet-induced NAFLD in vivo and in vitro. Using reverse docking, we identified the demethylase fat mass and obesity-related protein (FTO) as a potential target of ARB. Subsequent mechanistic studies revealed that ARB plays a role in controlling methylation of the SLC7A11 gene through inhibition of FTO. In addition, we demonstrated that SLC7A11 could alleviate the development of NAFLD in vivo and in vitro. Our findings identify the FTO/SLC7A11 axis as a potential therapeutic target for the treatment of NAFLD. Specifically, we show that ARB alleviates NAFLD by acting on the FTO/SLC7A11 pathway to inhibit ferroptosis

Different doping behaviors of silicon in zinc blende and wurtzite GaAs nanowires : implications for crystal-phase device design

Crystal-phase engineering between zinc blende (ZB) and wurtzite (WZ) structures is becoming an important method in designing unique optoelectronic and electronic semiconductor devices. Doping to engineer their electric properties is thus of critical importance, but a direct experimental comparison in doping these two crystal structures is still missing. Nanowires (NWs) allow the coexistence of both structures due to their special growth mode. The differences in dopant incorporation between the two phases are studied here in GaAs NW shells that are coherently grown around the NWs, hence maintaining the crystal structure of the core. The Si dopant is observed to have a higher incorporation efficiency into the WZ structure due to a 2 times lower incorporation energy compared with that of the ZB structure. Besides, it can also be predicted that Si is more inclined toward Ga sites in both structures. Indeed, the As-site doping energy of the WZ structure is several orders of magnitude higher than that of Ga sites, allowing a lower doping compensation effect. This work provides useful information for doping control and hence designing crystal-phase devices