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• Infection in intensive care unit (ICU) patients with severe pneumonia links to skin microbiota • Microbiome diversity of ICU patients with severe pneumonia is less than the diversity observed in controls • Gram-negative bacteria of ICU patients with severe pneumonia is more than controls Patients with severe pneumonia admitted to the intensive care unit (ICU) have a high risk of mortality, and the microbiome is likely to affect the outcome of such patients. However, the composition of the skin microbiota of ICU patients with severe pneumonia remains unclear. In this study, on the basis of 16S ribosomal ribonucleic acid sequencing, we explored the difference in skin bacterial richness and diversity between the ICU patient group (PG) with severe pneumonia and the healthy control group (CG). The diversity index and taxonomic distribution of skin bacteria were analyzed using the Quantitative Insights Into Microbial Ecology (QIIME) bioinformatics pipeline. Blood, endotracheal aspirate, and bronchoalveolar lavage fluid samples were collected from the same PG subjects for culture. Compared with the CG, the diversity of skin bacteria in the PG decreased significantly. Staphylococcus, Acinetobacter, Stenotrophomonas, Enterococcus, Halomonas , and Brevibacillus were differentially abundant in the PG, and most of these bacteria were also identified in the cultures of upper respiratory tract samples of the same PG. We provide evidence that healthcare-associated infection in ICU patients with severe pneumonia is strongly associated with skin microbiota, which necessitates the prevention and control of skin bacterial pathogens for these patients. [ABSTRACT FROM AUTHOR]

Previous studies indicate that ion channels are mediators of bioelectricity promoting wound closure/regeneration in nonmammalian, lower vertebrate systems. The role of ion channels however in regeneration of wounds in mammalian systems that do not regenerate as adults is not yet defined. Using a mammalian model system that allows us to determine differentially expressed genes when skin regenerates and when skin does not regenerate after wound induction, we identified two potassium channels, kcnh2 and kcnj8, to be (1) differentially expressed between the two states and (2) highly expressed after wound induction at the nonregenerative state. We also found that kcnh2 small molecule inhibitor enhanced wound healing while kcnj8 small molecule inhibitor did not. In contrast, kcnj8 activator accelerated wound healing and even augmented the effect of kcnh2 inhibition. These results provide evidence for the first time that potassium channels may mediate skin wound healing and regeneration interactively. [ABSTRACT FROM AUTHOR]

BRAFV600E/K is a frequent mutationally active tumor-specific kinase in melanomas that is currently targeted for therapy by the specific inhibitor PLX4032. Our studies with melanoma tumor cells that are BRAFV600E/K and BRAFWT showed that, paradoxically, while PLX4032 inhibited ERK1/2 in the highly sensitive BRAFV600E/K, it activated the pathway in the resistant BRAFWT cells, via RAF1 activation, regardless of the status of mutations in NRAS or PTEN. The persistently active ERK1/2 triggered downstream effectors in BRAFWT melanoma cells and induced changes in the expression of a wide-spectrum of genes associated with cell cycle control. Furthermore, PLX4032 increased the rate of proliferation of growth factor-dependent NRAS Q61L mutant primary melanoma cells, reduced cell adherence and increased mobility of cells from advanced lesions. The results suggest that the drug can confer an advantage to BRAFWT primary and metastatic tumor cells in vivo and provide markers for monitoring clinical responses. [ABSTRACT FROM AUTHOR]

Abstract: A key step in cancer development is clonal expansion. The increased number of mutant cells allows a clinical phenotype and increases the probability that one of the cells will be mutated in an additional gene. For skin cancer, observations on p53-mutant keratinocyte clones in epidermal sheets of UVB-irradiated mice reveal that mutant stem cells are normally restrained within their stem cell compartment. Chronic UVB exposure drives clonal expansion by a non-mutational mechanism, and this mechanism allows mutant stem cells to escape from their own stem cell compartment and colonize adjacent compartments. In the absence of escape, cells proliferate without occupying additional territory. The non-mutational clonal expansion mechanism appears to be UVB-induced apoptosis, which deletes DNA-damaged cells in unmutated stem cell compartments but will preferentially spare death-resistant p53-mutant cells. An additional source of apoptotic selection pressure may come from UV-irradiated melanin. [Copyright &y& Elsevier]

Melanin protects the skin against DNA damage induced by direct absorption of sunlight's UV radiation. Yet, irradiating melanin in vitro or in cultured cells also generates active oxygen species such as superoxide, which can indirectly induce oxidative base lesions and DNA strand breaks. This photosensitization is greater for phiomelanin' (yellow and red melanin) than for eumelanin (brown and black). The in vivo photosensitizing ability of melanin is unknown. We used congenic mice of black, yellow, and albino coat colon to investigate the induction of DNA lesions and apoptosis after exposure to, predominantly UVB (280-320 nm) or UVA (320 a 400 nm) `radiation. Cyclobutane pyrimidine dimers induced by direct UVB absorption were equal in all three strains, as was apoptosis measured as sunburn cells or as kerátinocytes containing active caspase-3. However, terminal deoxyn ucleotidyltransferase- mediated dUTP nick end-labeling (TUNEL)-positive cells were -3- fold more frequent in black and yellow mice, after UVB or UVA irradiation than in albino. In epidermal sheets, TUNEL-positive cells lined the upper portion of the hair follicle, consistent with UV- induced photosensitization by melanin in the hair shaft. Because the concentration of eumelanin in black mice was three times that of pheomelanin in yellow mice, pheomelanin had 3-fold greater specific activity. We conclude that UV-irradiated melanin, particue larly pheomelanin photosensitizes adjacent cells to caspase-3 independent apoptosis, and this occurs at a frequency greater than the apoptosis induced by direct DNA absorption of UV. Melanin- induced apoptosis may contribute to the increased sensitivity of individuals with blonde and red hair to sunburn and skin cancer. [ABSTRACT FROM AUTHOR]

Background: Chronic obstructive pulmonary disease (COPD) contributes to the incidence and prognosis of lung cancer. The presence of COPD significantly increases the risk of lung squamous cell carcinoma (LSCC). COPD may promote an immunosuppressive microenvironment in LSCC by regulating the expression of immune‐inhibitory factors in T cells, although the mechanisms remain unclear. In this study, we aimed to decipher the tumour microenvironment signature for LSCC with COPD at a single‐cell level. Methods: We performed single‐cell RNA sequencing on tumour tissues from LSCC with or without COPD, then investigated the features of the immune and tumour cells. We employed multiple techniques, including multispectral imaging, flow cytometry, tissue microarray analysis, survival analysis, co‐culture systems and in vitro and in vivo treatment experiments, to validate the findings obtained from single‐cell analyses. Results: LSCC with COPD showed increased proportions of tumour‐associated macrophages (TAMs) and higher levels of CD8+ T cell exhaustion molecules, which contributed to an immunosuppressive microenvironment. Further analysis revealed a critical cluster of CD74+ tumour cells that expressed both epithelial and immune cell signatures, exhibited a stronger capacity for tumorigenesis and predicted worse overall survival. Notably, migration inhibitory factor (MIF) secreted by TAMs from LSCC with COPD may promote the activation of CD74. MIF‐CD74 may interact with CD8+ T cells and impair their anti‐tumour activity by regulating the PI3K‐STAT3‐programmed cell death‐1 ligand 1 signalling pathway, facilitating tumour proliferation and immune evasion. Conclusions: Our comprehensive picture of the tumour ecosystem in LSCC with COPD provides deeper insights into relevant immune evasion mechanisms and potential targets for immunotherapy. Highlight: Our results demonstrated higher proportions of tumour‐associated macrophages (TAMs) and higher levels of exhaustion molecules in CD8+ T cells in the microenvironment of LSCC with COPD.CD74+tumour cells were associated with poor disease prognosis.Migration inhibitory factor (MIF)‐CD74 may interact with CD8+ T cells and impair their anti‐tumour activity by regulating the PI3K‐STAT3‐PD‐L1 signalling pathway, facilitating immune evasion. [ABSTRACT FROM AUTHOR]

Background: Detection of lung cancer at earlier stage can greatly improve patient survival. We aim to develop, validate, and implement a cost-effective ctDNA-methylation-based plasma test to aid lung cancer early detection. Methods: Case-control studies were designed to select the most relevant markers to lung cancer. Patients with lung cancer or benign lung disease and healthy individuals were recruited from different clinical centers. A multi-locus qPCR assay, LunaCAM, was developed for lung cancer alertness by ctDNA methylation. Two LunaCAM models were built for screening (-S) or diagnostic aid (-D) to favor sensitivity or specificity, respectively. The performance of the models was validated for different intended uses in clinics. Results: Profiling DNA methylation on 429 plasma samples including 209 lung cancer, 123 benign diseases and 97 healthy participants identified the top markers that detected lung cancer from benign diseases and healthy with an AUC of 0.85 and 0.95, respectively. The most effective methylation markers were verified individually in 40 tissues and 169 plasma samples to develop LunaCAM assay. Two models corresponding to different intended uses were trained with 513 plasma samples, and validated with an independent collection of 172 plasma samples. In validation, LunaCAM-S model achieved an AUC of 0.90 (95% CI: 0.88–0.94) between lung cancer and healthy individuals, whereas LunaCAM-D model stratified lung cancer from benign pulmonary diseases with an AUC of 0.81 (95% CI: 0.78–0.86). When implemented sequentially in the validation set, LunaCAM-S enables to identify 58 patients of lung cancer (90.6% sensitivity), followed by LunaCAM-D to remove 20 patients with no evidence of cancer (83.3% specificity). LunaCAM-D significantly outperformed the blood test of carcinoembryonic antigen (CEA), and the combined model can further improve the predictive power for lung cancer to an overall AUC of 0.86. Conclusions: We developed two different models by ctDNA methylation assay to sensitively detect early-stage lung cancer or specifically classify lung benign diseases. Implemented at different clinical settings, LunaCAM models has a potential to provide a facile and inexpensive avenue for early screening and diagnostic aids for lung cancer. [ABSTRACT FROM AUTHOR]

This study was conducted to investigate oropharyngeal microbiota alterations during the progression of coronavirus disease 2019 (COVID-19) by analyzing these alterations during the infection and clearance processes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The diagnosis of COVID-19 was confirmed by using positive SARS-CoV-2 quantitative reverse transcription polymerase chain reaction (RT-qPCR). The alterations in abundance, diversity, and potential function of the oropharyngeal microbiome were identified using metatranscriptomic sequencing analyses of oropharyngeal swab specimens from 47 patients with COVID-19 (within a week after diagnosis and within two months after recovery from COVID-19) and 40 healthy individuals. As a result, in the infection process of SARS-CoV-2, compared to the healthy individuals, the relative abundances of Prevotella, Aspergillus, and Epstein–Barr virus were elevated; the alpha diversity was decreased; the beta diversity was disordered; the relative abundance of Gram-negative bacteria was increased; and the relative abundance of Gram-positive bacteria was decreased. After the clearance of SARS-CoV-2, compared to the healthy individuals and patients with COVID-19, the above disordered alterations persisted in the patients who had recovered from COVID-19 and did not return to the normal level observed in the healthy individuals. Additionally, the expressions of several antibiotic resistance genes (especially multi-drug resistance, glycopeptide, and tetracycline) in the patients with COVID-19 were higher than those in the healthy individuals. After SARS-CoV-2 was cleared, the expressions of these genes in the patients who had recovered from COVID-19 were lower than those in the patients with COVID-19, and they were different from those in the healthy individuals. In conclusion, our findings provide evidence that potential secondary infections with oropharyngeal bacteria, fungi, and viruses in patients who have recovered from COVID-19 should not be ignored; this evidence also highlights the clinical significance of the oropharyngeal microbiome in the early prevention of potential secondary infections of COVID-19 and suggests that it is imperative to choose appropriate antibiotics for subsequent bacterial secondary infection in patients with COVID-19. [ABSTRACT FROM AUTHOR]

Background. Various studies have produced contradictory results on the prognostic role of the CpG island methylator phenotype (CIMP) among colorectal cancer (CRC) patients. Although a meta-analysis published in 2014 reported a worse prognosis of CIMP among CIMP-high (CIMP-H) CRC patients, the sample sizes of the major included studies were small. In this study, we included the most recent studies with large sample sizes and performed an updated meta-analysis on the relationship between CIMP and CRC prognosis. Methods. A search of MEDLINE, Web of Science, and Cochrane for studies related to CIMP and CRC published until July 2021 was conducted based on the PICO (participant, intervention, control, outcome) framework. Data extraction and literature analyses were performed according to PRISMA standards. Results. In the present update, 36 eligible studies (20 recently published) reported survival data in 15315 CRC patients, 18.3% of whom were characterized as CIMP-H. Pooled analysis suggested that CIMP-H was associated with poorer overall survival (OS) (hazard ratio HR = 1.37 , 95% CI: 1.26–1.48) and disease-free survival/progression-free survival/recurrence-free survival (DFS/PFS/RFS) (HR = 1.51 , 95% CI: 1.19–1.91) among CRC patients. Subgroup analysis based on tumor stage and DNA mismatch repair (MMR) status showed that only patients with stages III-IV and proficient MMR (pMMR) tumors showed a significant association between CIMP-H and shorter OS, with HRs of 1.52 and 1.37, respectively. Three studies were pooled to explore the predictive value of CIMP on CRC patient DFS after receiving postoperative chemotherapy, and no significant correlation was found. Conclusion. CIMP-H is associated with a significantly poor prognosis in CRC patients, especially those with stage III-IV and pMMR tumors. However, the predictive value of CIMP needs to be confirmed by more prospective randomized studies. [ABSTRACT FROM AUTHOR]

Chronic irradiation of human or murine epidermis with ultraviolet B (UVB) induces clones of p53-mutant keratinocytes. Clones precede and parallel the induction of carcinomas, suggesting that they are an early stage of UVB carcinogenesis. In the absence of UVB, these clones rapidly regress. For UVB-induced murine skin tumors and papillomas, regression is known to involve antigen-specific immunity. To determine whether antigen-specific immunity influences the creation, expansion, or regression of p53-mutant clones, we studied Rag1 knockout mice deficient in the recombination activating gene 1 required for development of B, aßT, ?dT, and natural killer T cells. Since tissue homeostasis could affect proliferation or persistence of clones, we also examined the effect of Rag1 on UVB-induced hyperplasia and apoptosis. Mice were irradiated with UVB daily for 7-11 weeks to create p53-mutant clones, and then retained in the absence of UV. After UV ended, epidermal thickness decreased and p53-mutant clones observed in the epidermal sheets regressed, with no significant differences between Rag1-/- and wild type. During the initial chronic UVB irradiation, increasing irradiation time increased both the number and size of p53-mutant clones, with no significant difference between genotypes. We conclude that antigen-specific immunity is not involved in the initiation, expansion, or acute regression of p53-mutant clones.Oncogene (2003) 22, 6369-6376. doi:10.1038/sj.onc.1206657 [ABSTRACT FROM AUTHOR]

A previously unknown beta coronavirus, SARS‐CoV‐2, was discovered from a cluster of patients with pneumonia of unknown cause in Wuhan since the end of 2019. Ever since the start of COVID‐19, government administrations, academic institutions, and technology enterprises are under unprecedented cooperation in controlling this outbreak from pathogen identification, epidemic situation assessment, to outbreak containment. Timely identification, isolation, and whole‐genome sequencing of SARS‐CoV‐2 have laid the foundation for effective control of this novel infection. With the increasing case numbers worldwide, more real‐time information is emerging, changing our understandings to SARS‐CoV‐2 outbreak, and nonetheless refining the outbreak control responses. The efficient management of COVID‐19 requires global collaboration and an efficient share of information. [ABSTRACT FROM AUTHOR]

DNA mismatch repair (MMR) status was considered to be a potential prognostic factor for colorectal cancer (CRC) but with conflicting reports, and varied in terms of TNM stages. Its relationship with prognosis in stage II‐III CRC had not yet been systematically established. Therefore, we retrieved eligible studies published through May 2019, and screened out 51 studies that reported survival data (overall survival [OS] and/or disease‐free survival [DFS]) in 28 331 CRC patients at stage II‐III, totally 16.4% of whom were characterized as deficient MMR (dMMR). Significant associations of dMMR status were observed with longer OS (Hazard Ratio [HR] = 0.74, 95% CI: 0.68‐0.82; P <.001), as well as DFS (HR = 0.67, 95% CI: 0.59‐0.75, P <.001). However, dMMR patients received no statistically significant benefit from fluoropyrimidine‐based treatment for either OS (HR = 0.84, 95%CI: 0.60‐1.17; P =.31) or DFS (HR = 0.83, 95%CI: 0.60‐1.15; P =.27), compared with that in proficient MMR (pMMR) patients for both OS (HR = 0.55, 95% CI: 0.43‐0.71; P <.001) and DFS (HR = 0.60, 95% CI: 0.50‐0.73; P <.001). Our analysis indicate that dMMR CRC patients at stage II‐III had higher OS and DFS than pMMR ones, and fluoropyrimidine‐based chemotherapy could improve survival in pMMR patients rather than dMMR ones. [ABSTRACT FROM AUTHOR]

• Developed a fully discrete ECC model accounting for strain softening of the cementitious matrix, with a damage variable modifying the pairwise force function. • Introduced "cycle broken bonds number" to enhance calculation speed of the PD fatigue crack propagation model. • Analyzed the influence of stress level, fiber volume fraction, and fiber length on fatigue performance of ECC beams in four-point bending fatigue loading. Fatigue crack propagation is crucial in studying fatigue in engineered cementitious composites (ECC). This paper established a peridynamics (PD)-based fatigue crack propagation model for ECC, incorporating the "cycle broken bonds number" to enhance calculation efficiency. First, the PD fatigue crack propagation model was constructed, and the validity of the model was verified by simulating the fatigue crack propagation path of an inclined edge crack in the plate. Secondly, an improved PMB model considering the strain softening stage was used to model the ECC cement matrix, and the fibers were modeled as one-dimensional cyclic dynamic rods to establish a PD fully discrete model of ECC. At the same time, an interface exponential friction attenuation model was introduced. Then, the effectiveness and validness of the fully discrete model were verified by simulating single fiber pull-out tests and uniaxial tensile tests of ECC specimens. Finally, the fatigue crack propagation forms of ECC beams with mid span Type I cracks under three-point bending fatigue loads were studied, and the effects of fiber volume fraction, stress level, and fiber length on the crack propagation forms and structural deflection of ECC beams under four-point bending fatigue loads were investigated. [ABSTRACT FROM AUTHOR]

Single-cell sequencing (SCS) is a fast-growing, exciting field in genomic medicine. It enables the high-resolution study of cellular heterogeneity, and reveals the molecular basis of complicated systems, which facilitates the identification of new biomarkers for diagnosis and for targeting therapies. It also directly promotes the next generation of genomic medicine because of its ultra-high resolution and sensitivity that allows for the non-invasive and early detection of abnormalities, such as aneuploidy, chromosomal translocation, and single-gene disorders. This review provides an overview of the current progress and prospects for the diagnostic applications of SCS, specifically in pre-implantation genetic diagnosis/screening, non-invasive prenatal diagnosis, and analysis of circulating tumor cells. These analyses will accelerate the early and precise control of germline- or somatic-mutation-based diseases, particularly single-gene disorders, chromosome abnormalities, and cancers. [ABSTRACT FROM AUTHOR]

Cooperating with other signaling pathways, Wnt signaling controls cell proliferation, morphology, motility, and embryonic development destination and maintains the homeostasis of tissues including skin, blood, intestine, and brain by regulating somatic stem cells and their niches throughout adult life. Abnormal regulation of Wnt pathways leads to neoplastic proliferation in these tissues. Recent research shows that Wnt signaling is also associated with the regulation of cancer stem cells (CSCs) through a similar mechanism to that observed in normal adult stem cells. Thus, the Wnt/β-catenin signaling pathway has been intensively studied and characterized. For this review, we will focus on the regulation of the Wnt/β-catenin signaling pathway in skin cancer. With the important role in stemness and skin CSC proliferation, the Wnt/β-catenin signaling pathway and its elements have the potential to be targets for skin cancer therapy. [ABSTRACT FROM AUTHOR]

The E2f1 transcription factor, which regulates genes required for S-phase entry[SUP1-4], also induces apoptosis by transcriptional and post-translational mechanisms[SUP5-8]. As E2f1 is inducible by DNA damage[SUP9,10] we investigated its importancein vivo in ultraviolet (UV)-induced apoptosis, a protective mechanism that prevents the epidermis from accumulating UV-induced mutations[SUP11,12]. Contrary to expectation,E2f1[SUP-/-] mice demonstrated enhanced keratinocyte apoptosis after UVB exposure, whereas apoptosis was suppressed by epidermis-specific overexpression of human E2F1. Apoptosis induced by γ-radiation was also repressed by E2f1.E2f1[SUP-/-];Trp53[SUP-/-]double knockout mice exhibited the elevated UVB-induced apoptosis ofE2f1[SUP-/-] alone, rather than the profound apoptosis defect seen inTrp53[SUP-/-] mice, indicating that Trp53 (p53) lies functionally upstream of E2f1. Transfecting E2F1 intoE2f1[SUP-/-];Trp53[SUP-/-] primary fibroblasts suppressed UVB-induced apoptosis and this suppression was relieved byTrp53. The double knockout also reverted the abnormal sex ratio and early-onset tumours ofTrp53[SUP-/-] mice. These results imply that E2f1 functions as a suppressor of an apoptosis pathway that is initiated by DNA photoproducts and perhaps genetic abnormalities; p53 relieves this suppression. [ABSTRACT FROM AUTHOR]

BRAF mutations occur in approximately 50% of melanoma patients. The mutated BRAF kinase continuously activates the mitogen-activated protein kinase (MAPK) pathway to promote cell growth and proliferation. Vemurafenib as a specific BRAF inhibitor can significantly prolong progression-free survival in melanoma patients. However, most patients developed resistance to Vemurafenib after 6 months. The mechanism of drug resistance is not yet fully understood. In this study, we found that proteins secreted by drug-resistant cells protect sensitive cells from Vemurafenib. By RNA-seq, we compared differentially expressed genes between resistant and sensitive cells. We demonstrated that drug-resistant cells secrete more IL-6 protein than sensitive cells. For the first time, we found that IL-6 expressed by drug-resistant cells consists of the following transcripts: IL6-201, IL6-202 and IL6-205. We confirmed that it is the IL6-202 and IL6-205 transcripts that confer drug resistance to Vemurafenib by reactivating the MAPK pathway while IL6-201 is not responsible for the resistance in A375 melanoma cells. Neutralizing IL-6 significantly increased the sensitivity of drug-resistant cells to Vemurafenib. Overall, these results reveal a new mechanism of drug resistance in melanoma. • Vemurafenib-resistant A375 cells secrete more IL-6 proteins than the parental A375 cells. • IL-6 expressed by Vemurafenib-resistant A375 cells consists of IL6-201, IL6-202 and IL6-205 transcripts. • IL6-202 and IL6-205 confer Vemurafenib resistance by reactivating the MAPK pathway in A375 cells. [ABSTRACT FROM AUTHOR]