Histone deacetylase HDAC2 regulates microRNA-125a expression in neuroblastoma.

BACKGROUND: Neuroblastoma (NB) is an infrequent childhood malignancy of the peripheral sympathetic nervous system and is accountable for about 10% of pediatric tumors. microRNA (miR)-125a has been implicated to serve as a tumor suppressor in various cancers. Herein, we set out to ascertain whether miR-125a exerts antitumor effects in NB. METHODS: Downregulated miRNAs were identified by miRNA microarray analysis of NB tissues and paracancerous tissues. The expression of miR-125a in NB tissues and cells was detected by reverse transcription-quantitative (RT-q) PCR, followed by prognostic analysis. Gene Ontology (GO) enrichment analysis was performed on target genes of differentially expressed miRNAs. Cell proliferation, apoptosis, and differentiation were detected by cell counting kit-8 (CCK-8), Hoechst staining, immunofluorescence, and western blot. NB cells were injected into nude mice to detect tumorigenic, apoptotic, and differentiation activities in vivo. Dual-luciferase assay and chromatin immunoprecipitation (ChIP) were carried out to verify the binding relationship between miR-125a and PHOX2B or histone deacetylases 2 (HDAC2), respectively. Finally, rescue experiments were conducted. RESULTS: miR-125a was downregulated in NB tissues and cells, which was associated with poor prognosis. miR-125a reduced NB cell proliferation and augmented apoptosis and differentiation. NB cells with miR-125a overexpression decreased cell tumorigenesis and increased apoptosis and differentiation in xenograft tumor tissues. miR-125a targeted PHOX2B, which was highly expressed in NB tissues and cells. HDAC2, highly expressed in NB tissues and cells, repressed miR-125a transcription through histone deacetylation. Overexpression of HDAC2 or PHOX2B rescued the effects of miR-125a on NB cell proliferation, apoptosis, and differentiation. CONCLUSION: HDAC2 inhibited miR-125a transcription through deacetylation, and miR-125a suppressed NB development through binding to PHOX2B.

KLF5 promotes KIF1A expression through transcriptional repression of microRNA-338 in the development of pediatric neuroblastoma.

BACKGROUND: Neuroblastoma (NB) comprises about 8-10% of pediatric cancers, and microRNA (miR)-338 downregulation has been implicated in NB. However, the underlying molecular mechanism remains largely unclear. The main goal of this study is to probe the regulatory role of miR-338 and the upstream and downstream biomolecules involved in NB. METHODS: The differentially expressed miRNAs were screened by analyzing the NB gene expression microarray GSE121513 from the GEO database, and the differences in expression of the screened miRNAs were verified in clinically collected NB tissues versus dorsal root ganglions. Subsequently, the relationship between the miR-338 expression and NB cell growth was validated in vitro and in vivo, and the upstream and downstream regulatory mechanisms of miR-338 were further analyzed by bioinformatics. Functional rescue experiments were used to verify their effects on NB cell growth. RESULTS: miR-338 expressed poorly in NB tissues, and overexpression of miR-338 significantly inhibited NB cell growth in vitro and in vivo. The prediction results showed that miR-338 could target KIF1A, and miR-338 expression was negatively correlated with the expression of KIF1A. We further found that miR-338 was transcriptionally regulated by the transcription factor KLF5. Overexpression of KLF5 or KIF1A significantly attenuated the inhibitory effect of miR-338 mimic on NB cell growth. Finally, miR-338 blocked the Hedgehog signaling pathway by inhibiting the expression of KIF1A. CONCLUSION: Overexpression of KLF5 reduced expression of miR-338, which in turn increased the expression of KIF1A and activated the Hedgehog signaling pathway, leading to the progression of NB.

Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response.

To unravel the source of SARS-CoV-2 introduction and the pattern of its spreading and evolution in the United Arab Emirates, we conducted meta-transcriptome sequencing of 1067 nasopharyngeal swab samples collected between May 9th and Jun 29th, 2020 during the first peak of the local COVID-19 epidemic. We identified global clade distribution and eleven novel genetic variants that were almost absent in the rest of the world and that defined five subclades specific to the UAE viral population. Cross-settlement human-to-human transmission was related to the local business activity. Perhaps surprisingly, at least 5% of the population were co-infected by SARS-CoV-2 of multiple clades within the same host. We also discovered an enrichment of cytosine-to-uracil mutation among the viral population collected from the nasopharynx, that is different from the adenosine-to-inosine change previously reported in the bronchoalveolar lavage fluid samples and a previously unidentified upregulation of APOBEC4 expression in nasopharynx among infected patients, indicating the innate immune host response mediated by ADAR and APOBEC gene families could be tissue-specific. The genomic epidemiological and molecular biological knowledge reported here provides new insights for the SARS-CoV-2 evolution and transmission and points out future direction on host-pathogen interaction investigation.

Characterization of functional transposable element enhancers in acute myeloid leukemia.

Transposable elements (TEs) have been shown to have important gene regulatory functions and their alteration could lead to disease phenotypes. Acute myeloid leukemia (AML) develops as a consequence of a series of genetic changes in hematopoietic precursor cells, including mutations in epigenetic factors. Here, we set out to study the gene regulatory role of TEs in AML. We first explored the epigenetic landscape of TEs in AML patients using ATAC-seq data. We show that a large number of TEs in general, and more specifically mammalian-wide interspersed repeats (MIRs), are more enriched in AML cells than in normal blood cells. We obtained a similar finding when analyzing histone modification data in AML patients. Gene Ontology enrichment analysis showed that genes near MIRs in open chromatin regions are involved in leukemogenesis. To functionally validate their regulatory role, we selected 19 MIR regions in AML cells, and tested them for enhancer activity in an AML cell line (Kasumi-1) and a chronic myeloid leukemia (CML) cell line (K562); the results revealed several MIRs to be functional enhancers. Taken together, our results suggest that TEs are potentially involved in myeloid leukemogenesis and highlight these sequences as potential candidates harboring AML-associated variation.

A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-dimensional RNA-Seq Analysis.

In vertebrates, hematopoiesis occurring in different niches is orchestrated by intrinsic and extrinsic regulators. Previous studies have revealed numerous linear and planar regulatory mechanisms. However, a multi-dimensional transcriptomic atlas of any given hematopoietic organ has not yet been established. Here, we use multiple RNA sequencing (RNA-seq) approaches, including cell type-specific, temporal bulk RNA-seq, in vivo GEO-seq, and single-cell RNA-seq (scRNA-seq), to characterize the detailed spatiotemporal transcriptome during hematopoietic stem and progenitor cell (HSPC) expansion in the caudal hematopoietic tissue (CHT) of zebrafish. Combinatorial expression profiling reveals that, in the CHT niche, HSPCs and their neighboring supporting cells are co-regulated by shared signaling pathways and intrinsic factors, such as integrin signaling and Smchd1. Moreover, scRNA-seq analysis unveils the strong association between cell cycle status and HSPC differentiation. Taken together, we report a global transcriptome landscape that provides valuable insights and a rich resource to understand HSPC expansion in an intact vertebrate hematopoietic organ.

Retraction Note: Pre-treatment DWI as a predictor of overall survival in locally advanced pancreatic cancer treated with Cyberknife radiotherapy and sequential S-1 therapy.

The authors have retracted this article because Figs. 2, 3 and 4, as well as parts of the text have been previously published [1]. This article is therefore redundant. Yu Zhang, Denghui Liu, Jiaqi Song, Huojun Zhang and Jianping Lu agree to this retraction. Xiaofei Zhu has not responded to any correspondence from the publisher about this retraction.

Pre-treatment DWI as a predictor of overall survival in locally advanced pancreatic cancer treated with Cyberknife radiotherapy and sequential S-1 therapy.

BACKGROUND: To identify the value of the pre-treatment apparent diffusion coefficient (ADC) derived from diffusion weighted imaging (DWI) in predicting the overall survival (OS) for locally advanced pancreatic cancer (LAPC) treated with Cyberknife followed by sequential S-1 chemotherapy. METHODS: Patients with UICC-T4 LAPC who underwent DWI scan (3.0 Tesla) using two b-values (0, 600 s/mm2) in our center between 2015 and 2017 were enrolled. Mean ADCs of the region of interest (ROI) drawn manually on DWI imaging were measured by two independent radiologists at an interval of 1 month. The association between prognostic factors and patient survival was determined using univariate and multivariate analyses. Cox proportional hazard model was used for identification of independent prognostic factors of OS. RESULTS: A total of 41 patients (28 males and 13 females) were included, with a median age of 64 years, with 5 patients (3 males and 2 females) lost. The median OS was 11.7 months (range 2.8-23.3) among all 41 patients. The 1-year OS was 46% (95% CI 30%-62%). Univariate and multivariate analyses indicated that pre-treatment ADC value (HR 10.652, P = 0.0093), age (HR 0.952, P = 0.015), CA19-9 (HR 1.001, P = 0.0022) and administration of S-1 (HR 0.128, P = 0.0002) were independent predicting factors of OS. CONCLUSION: The mean ADC value of the primary tumor on pre-treatment DWI imaging was an independent predictor of OS in patients with LAPC receiving Cyberknife followed by sequential S-1.

Inference of differentiation time for single cell transcriptomes using cell population reference data.

Single-cell RNA sequencing (scRNA-seq) is a powerful method for dissecting intercellular heterogeneity during development. Conventional trajectory analysis provides only a pseudotime of development, and often discards cell-cycle events as confounding factors. Here using matched cell population RNA-seq (cpRNA-seq) as a reference, we developed an "iCpSc" package for integrative analysis of cpRNA-seq and scRNA-seq data. By generating a computational model for reference "biological differentiation time" using cell population data and applying it to single-cell data, we unbiasedly associated cell-cycle checkpoints to the internal molecular timer of single cells. Through inferring a network flow from cpRNA-seq to scRNA-seq data, we predicted a role of M phase in controlling the speed of neural differentiation of mouse embryonic stem cells, and validated it through gene knockout (KO) experiments. By linking temporally matched cpRNA-seq and scRNA-seq data, our approach provides an effective and unbiased approach for identifying developmental trajectory and timing-related regulatory events.

Astaxanthin mitigates cobalt cytotoxicity in the MG-63 cells by modulating the oxidative stress.

BACKGROUND: With the re-popularity of metal-on-metal (MoM) bearing in recent years, the cobalt toxicity has been a cause for concern in the total hip replacement surgery by both physicians and patients. METHODS: MG-63 cell line was cultured in vitro and incubated with cobalt (II) chloride (CoCl2) and/or with astaxanthin (ASX) for 24 h. MTT assay was conducted to evaluate the cell viability after cobalt exposure and ASX treatment. Fluorescence-activated cell sorting (FACS) analysis was performed to examine the reactive oxygen species (ROS) level. Quantitative real-time polymerase chain reaction (PCR) was adopted to determine the mRNA levels of related targets. And western blot analysis was used to examine the protein expressions. One-way ANOVA with posttest Newman-Keuls multiple comparisons was adopted to analysis all the obtained data. RESULTS: In the current study, ASX exhibited significant protective effect against the Co(II)-induced cytotoxicity in MG-63 cell line. We also found that ASX protected the cells against Co-induced apoptosis by regulating the expression of Bcl-2 family proteins. Besides, heme oxygenase 1 (HO-1) could be activated by Co exposure; ASX treatment significantly inhibited HO-1 activation, suppressing the oxidative stress induced by Co exposure. Moreover, c-Jun N-terminal Kinase (JNK) phosphorylation was shown to participate in the signaling pathway of the protective effect of ASX. However, knockdown of JNK expression by siRNA transfection or JNK inhibitor SP600125 treatment did not affect the protective effect of ASX against cobalt cytotoxicity in MG-63 cells. CONCLUSIONS: ASX mitigated cobalt cytotoxicity in the MG-63 cells by modulating the oxidative stress. And ASX could be a promising therapy against cobalt toxicity in the hip articulation surgery.

Early failure of the Durom prosthesis in metal-on-metal hip resurfacing in Chinese patients.

Hip resurfacing (HR) is being used increasingly as an alterative to total hip arthroplasty in osteonecrosis (ON) and ankylosing spondylitis (AS) of the hip. We performed 141 consecutive HR arthroplasties in 111 patients comprising 3 etiology groups: ON, AS, and osteoarthritis (OA). After retrospective study of retrieved components, we hypothesized that the main reason for revision was femoral loosening in the ON group (4 of 46 hips; 8.7%) and femoral-neck fracture in the AS group (3 of 58 hips; 5.2%). Necrotic areas were seen on femoral heads retrieved from patients with femoral loosening, whereas femoral heads were fixed tightly to components in patients with femoral-neck fractures. Etiology may be an important risk factor for postoperative complications.