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Spatial transcriptomics technology provides a valuable view for studying cellular heterogeneity due to its ability to simultaneously acquire gene expression profile and cell location information. However, benchmarking these rapidly accumulating spatial transcriptomics analysis tools is challenging owing to the limited diversity and accuracy of “gold standard” data sets annotated by pathologists. To address this issue, we proposed Spider, a flexible and unified simulator for spatial transcriptomics data guided by cell type proportion and transition matrix of adjacent cell types. Taking advantage of a heuristic batched simulated annealing algorithm (BSA) in assigning simulated cell type labels, Spider can generate spatial transcriptomics data for one million cells in just five minutes. Furthermore, Spider can generate various types of spatial transcriptomics data, including immune hot/cold tumor samples by specifying different immune cell proportions and transition matrices and layered tissue samples via an interactive interface. In addition, Spider is also a unified framework for ST data simulation in which we have implemented diverse simulators proposed by other researchers as special cases. We have systematically evaluated the performance of Spider and competing tools, and demonstrated Spider’s remarkable power to capture the spatial pattern of the reference dataset. Spider is available athttps://github.com/YANG-ERA/Artist.

Background: Hepatocellular carcinoma (HCC) is one of the most frequent cancers with a high recurrence rate and poor prognosis. eukaryotic translation initiation factor 2 subunit gamma (EIF2S3) is a heterotrimeric GTP binding protein, taking part in the recruitment of methionyl-tRNA to the 40 S ribosomal subunit. However, the role of EIF2S3 in HCC remains unclear. Materials and methods: In the present study, the expression level of EIF2S3 in pan-cancer was identified using TIMER database and its level in HCC tissues was detected by TCGA database. Univariate and multivariate Cox regression analysis was performed to evaluate the relationship between EIF2S3 and clinical characteristics in HCC. Kaplan-Meier Plotter analysis was used to assess the prognostic role of EIF2S3 in HCC patients. Function enrichment analysis was conducted by LinkedOmics database. The association between EIF2S3 level and immune infiltration, and the correlation between EIF2S3 expression and immune cell biomarkers in HCC were analyzed by TIMER and GEPIA database. Finally, the protein expression of EIF2S3 in HCC cell lines was analyzed and the proliferation, migration, invasion and apoptosis of HCC cells after silencing EIF2S3, which were detected by cell viability assay, wound healing assay, transwell assay and flow cytometry analysis, respectively. Results: EIF2S3 was overexpressed in many solid tumors. And, high EIF2S3 expression was detected in HCC and significantly related to tumor status and prognosis of HCC patients. Moreover, EIF2S3 expression was positively related to immune cell infiltration and gene marker of immune cells in HCC patients. Cell experiments showed thatEIF2S3 was overexpressed in HCC cells and EIF2S3 enhanced the proliferation, migration and invasion of HCC cells and decreased the apoptosis of HCC cells. Conclusion: EIF2S3 may be involved in the development of HCC and could be a prognostic genomic marker and a novel therapeutic target for HCC.

Long non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various biological processes, including embryonic development and cellular differentiation. Despite much progress over the past decade, the genome-wide annotation of lncRNAs remains incomplete and many known non-coding loci are still poorly characterized. Here, we report the discovery of a previously not annotated lncRNA that is transcribed upstream of the SOX17 gene and located within the same topologically associating domain. We termed it LNCSOX17 and show that it is induced following SOX17 activation but its expression is more tightly restricted to early definitive endoderm. Loss of LNCSOX17 affects crucial functions independent of SOX17 and leads to an aberrant endodermal transcriptome, signaling pathway deregulation and epithelial to mesenchymal transition defects. Consequently, cells lacking the lncRNA cannot further differentiate into more mature endodermal cell types. We identified and characterized LNCSOX17 as an essential new actor in early human endoderm, thereby further expanding the list of functionally important non-coding regulators.

Background The HSP70 family of heat shock protein plays a critical role in protein synthesis and transport to maintain protein homeostasis. Several studies have indicated that HSP70s are related to the development and occurrence of various cancers. Methods The relationship between the overall survival rate of hepatocellular carcinoma patients and the expression of 14 HSP70s from multiple databases, such as TCGA, ONCOMINE, cBioPortal was investigated. Western Blot and PCR were used to evaluate HSPA4 and HSPA14 expressions in various HCC cells to identify suitable cell lines for further experiments .Wound-healing assays, Transwell assays and EdU assays were used to verify the effects of HSPA4 and HSPA14 on the function of hepatocellular carcinoma cells, and statistical analysis was performed. Results Hepatocellular carcinoma tissues significantly expressed the 14 HSP70s compared to the normal samples. Besides, the high HSPA1A, HSPA1B, HSPA4, HSPA5, HSPA8, HSPA13, and HSPA14 expressions were inversely associated with the overall survival rate of patients, tumor grade, and cancer stage. A PPI regulatory network was constructed using the 14 HSP70s proteins with HSPA5 and HSPA8 at the network center. Univariate and multivariate analyses showed that HSPA4 and HSPA14 could be independent risk factors for the prognosis of hepatocellular carcinoma patients. Cell experiments have also confirmed that reducing HSPA4 and HSPA14 expressions can inhibit the invasion, metastasis, and proliferation of hepatocellular carcinoma cells. Conclusions Therefore, the HSP70s significantly influence the occurrence and development of hepatocellular carcinoma. For instance, HSPA4 and HSPA14 can be novel therapeutic targets and prognostic biomarkers for hepatocellular carcinoma.

Laser-driven white lighting has drawn great attention due to its high-brightness, high efficiency and compact size. However, the current laser lighting usually suffers from a low color rendering (Ra ∼ 60) due to the presence of a wide “Cyan cavity” (460–530 nm) in the luminescence spectrum. Herein, we report on the preparation and characterization of a novel cyan-green color converter, namely Ca3Sc2Si3O12:Ce3+,Na+ phosphor-in-glass (CSS-PiG) film. The addition of Na+ as a charge compensator greatly improved the internal quantum efficiency (IQE) of CSS:Ce3+ phosphors. Because of the good chemical stability and the matching refractive index between the glass matrix and embedded phosphors, the as-prepared CSS-PiG film exhibits an efficient cyan-green emission (with a peak at 508 nm and IQE ∼91%) and excellent thermal stability (maintaining 75% of the room-temperature emission intensity at 300 °C). Under the excitation of a 14.5 W mm−2 blue laser, the PiG film could produce a high-brightness white light with a forward luminous flux of 701 lm, a forward luminous efficacy of 112 lm W−1 and a Ra of 61. By coating a red-emitting CaAlSiN3:Eu2+ layer on the CSS-PiG film, the composite CSS-PiG/CaAlSiN3 film shows an ultra-broadband emission with a full-width at half maximum (FWHM) of 196 nm, which remarkably narrows the “Cyan cavity” and thus provides a Ra above 90. These results demonstrate that the CSS-PiG film is a promising candidate for laser lighting.

Er3+ and Yb3+ heavily doped monoclinic ZrO2 (m-ZrO2) stabilized by Nb5+ is prepared by solid-state reactions. The upconversion luminescence (UCL) of concentration optimized m-ZrO2:2%Er3+,9%Yb3+ shows a yellow emission which is found to be 4 times stronger than the red UCL of the optimized cubic ZrO2:2%Er3+,14%Yb3+. It is revealed that monoclinic ZrO2 has faster radiative transition rates of Er3+ and Yb3+ than cubic ZrO2 because of the lower crystal symmetry in the monoclinic phase that enables higher 4f–5d mixing of rare earth ions. The enhanced radiative transition allows 9%Yb3+ in the monoclinic phase to have a similar absorption of 980 nm excitation light to that of 14%Yb3+ in the cubic phase, thus retaining the lower energy back transfer from Er3+ in the green emitting state to Yb3+ and lower concentration quenching of Yb3+ in the monoclinic phase. The green and red dual-color optical thermometry behavior of m-ZrO2 has been explored. A large detectable temperature range, at which the absolute sensitivity is high, is realized through adopting this complementary optical thermometer. Repeated thermal experiments prove the stability of the m-ZrO2 as a temperature probe. Our results indicate that heavily doped m-ZrO2 is an excellent host for efficient luminescence of rare earth ions.

Background The effect of lncRNA FTX on non-alcoholic fatty liver disease (NAFLD) conversion to hepatocellular carcinoma (HCC) is unclear. Methods In our study, C57BL/6 mice was fed with high fat diet for obtaining NAFLD mouse model, and diethylnitrosamine induced the formation of HCC tumor. The expression of iNOS and CD206 in tissues were examined using immunohistochemistry. In addition, qRT-PCR was implemented to detect the expression of FTX and mRNAs. The percentage of M1 and M2 Kupffer cells (KCs) were determined using flow cytometry. The pathological change in liver tissues was displayed by H&E staining. Besides, immunofluorescence assay was performed to ensure the primary KCs through labeling F4/80. Results Here, we found that the expression of FTX and the ratio of M1/M2 KCs in liver tissues from NAFLD-transformed HCC (NAFLD-HCC) patients lower than in liver tissues from NAFLD patients. Subsequently, we revealed that the expression of FTX and M1/M2 KCs ratio were downregulated during NAFLD conversion to HCC. Importantly, increasing of FTX inhibited HCC tumor growth, improved liver damage and promoted M1 polarization of KCs during NAFLD conversion to HCC, while these effects of FTX were reversed by inactivating of KCs. Finally, in vitro experiments, our data indicated that FTX facilitated the M1 polarization of KCs. Conclusion In conclusion, our results demonstrated that upregulation of FTX suppressed NAFLD conversion to HCC though promoting M1 polarization of KCs. Our findings presented a new regulatory mechanism for NAFLD conversion to HCC, and provided a new biomarker for inhibiting this conversion.

What is known and objective Since the December 2019 discovery of several cases of coronavirus disease 2019 (COVID‐19) in Wuhan, China, the infection has spread worldwide. Our aim is to report on the clinical characteristics, treatments and prognoses of COVID‐19. Methods This was a retrospective, single‐centre, case series of 136 patients who were diagnosed with COVID‐19 at Wuhan Third Hospital in Wuhan, China, between 28 January 2020 and 12 February 2020. The clinical characteristics, laboratory tests, treatment features and prognoses were summarized. Results and discussion The 136 patients were divided into a moderate (M) group (n = 103, 75.7%) and a severe and critical (SC) group (n = 33, 24.3%). There were significant differences in the incidences of concomitant chronic medical illnesses (eg, hypertension, diabetes and cardiovascular disease), fever, dry cough and dyspnoea among the two groups (P, Elderly patients with chronic diseases are more likely to develop severe or critical COVID‐19 with multiple organ damage or systemic injuries. The improvement of LYM and CRP may be associated with the prognoses of COVID‐19.

High-throughput methods for single cell copy number sequencing have enabled the profiling of thousands of cells in parallel, yet there remains a significant bottleneck for data analysis. Here we present CopyKit, a comprehensive set of computational methods for the pre-processing and analysis of single cell copy number data to resolve clonal substructure and reconstruct genetic lineages in tumors. We performed single cell DNA sequencing of 2977 cells from multiple spatial regions in two liver metastasis and 7365 cells from three primary tumors with matched metastatic tissues. In the liver metastases, CopyKit resolved clonal substructure in different spatial regions, which revealed both clonal intermixing and spatial segregation in the tumor mass. In the matched metastatic colorectal and breast cancers, CopyKit resolved metastatic lineages and identified subclones and genomic events that were associated with metastases. These applications show that CopyKit is comprehensive tool for resolving copy number substructure in tumors.

Intrinsic DNA properties such as bending play a crucial role in diverse biological systems. A recent advantage in the high-throughput method called loop-seq makes it possible to determine bendability of hundred thousand 50-bp DNA duplexes in one experiment. However, it’s still infeasible to assess whole sequence bendability in large genomes such as human, which needs thousands of loop-seq experiments. Here we introduce ‘BendNet’ – a neural network to accurately predict the intrinsic DNA bending at base-resolution by only given DNA sequences. BendNet can increase the resolution of experimental results, and can predict DNA bendability for any new given sequences in high accuracy. We applied BendNet to the human genome and observed high-stiffness regions located at both transcriptional start sites and transcriptional end sites. Such stiffness patterns are different for coding and non-coding genes, which matches distinct nucleosome occupancy patterns. As expected, most transcription factors (TFs) bind in DNA of low bendability. In contrast, we observed an unusually high bendability within binding elements of specific TFs such as EBF1 and regulators of genome folding such as CTCF. These factors either co-bind or compete with nucleosomes to carry out their functions. More interestingly, CTCF binding regions exhibit the highest bendability than other DNA elements, implying their potential role in trapping and holding the CTCF in the exact locations to make sure CTCF as stable anchor in loop extrusion process. Our work provides a tool to assess DNA bendability for large-scale DNA sequences and expands our understanding on DNA mechanics in chromatin regulation and genome folding.

Monoclinic ZrO2 (m-ZrO2) is an attractive material for photonic applications due to its low site symmetry and phonon energy. In this paper, we present detailed studies on the luminescence properties of Ti4+ and Eu3+ in m-ZrO2. In view of the continuing controversy over the origin of “intrinsic” white-blue luminescence in pristine m-ZrO2, more spectroscopic information obtained by characterizing m-ZrO2 intentionally doped with Ti4+, Ti3+ and other metal ions and extensive discussions on the general characteristics of different luminescence processes were provided to evidence the luminescence as the Ti3+ → O− charge transfer transition in the [Ti(IV)O7]10− complex due to the trace amount of Ti4+ impurity in ZrO2 reagent. Competitive absorption was observed between host exciton and oxygen–metal charge transfer processes (O2−–Ti4+, O2−–Eu3+), and even between the two types of charge transfer process because of the sharing of electrons at the top of the valence band, which greatly influenced the absorption and excitation processes. The spectral components comprising the broad excitation band of O2−–Ti4+ white-blue or Eu3+ red emissions in different phosphors were identified, and their evolutions with doping concentration were explained. The energy state locations of oxygen defects produced by intrinsic charge compensation in m-ZrO2:Eu3+ were proposed to be ∼2.41 eV above the top of the valence band by using Eu3+ for the luminescent probe. Efficient energy transfer from the [Ti(IV)O7]10− complex to Eu3+ was first observed in m-ZrO2:Ti4+,Eu3+ phosphors, which were demonstrated to be high performance ratiometric self-referencing optical thermometric materials based on the dual-emitting combination strategy, with the relative sensitivity amounting to ∼3.84% K−1. Optical thermometry not only covering the physiological temperature range but also with high relative sensitivity could be achieved upon appropriate doping.

The indispensable broad-band red phosphors for LED lighting generally show a long emission tail for wavelengths longer than 650 nm, which consumes excitation energy but contributes little luminance. Here, we report, for the first time, a broad red emission band with a steep falling edge at 652 nm, formed of widely distributed 1D2 → 3H4 emission lines of Pr3+ in Y3Si6N11 due to a large Stark splitting of the 3H4 (930 cm-1) and 1D2 (725 cm-1) levels. The red emission exhibits a 43 nm bandwidth, which is the widest in Pr3+-doped phosphors reported so far. The red Y3Si6N11:Pr3+ phosphor was applied for the fabrication of 310 nm UV chip-based white LEDs, and a high color rendering index of 96 at a low correlated color temperature of 4188 K was achieved. Furthermore, a temperature-sensing scheme was proposed based on the temperature-dependent intensity ratios of the emission lines from the thermally coupled and large Stark splitting levels of the 1D2 state. Relative sensitivities as a function of temperature were studied in the range of 93-473 K. The findings of this study indicate that Y3Si6N11:Pr3+ is an attractive broad-band red phosphor for both high color rendering white LEDs and temperature sensing applications.

In Ce3+ activated SrLn2O4 type phosphors (Ln = Y, Lu, Sc, etc.) only one Ce3+ center was previously reported to show a blue emission band. In this paper, we report the observation of a second Ce3+ center in SrLu2O4:Ce3+. The new center shows a red emission band peaking at 600 nm with an excitation band at 485 nm. We attributed the new center (Ce(II)) to the substitution of the Lu3+ site and the original blue center (Ce(I)) to the substitution of the Sr2+ site. Spectroscopy studies indicate that Ce(I) centers are preferentially formed at a low doping concentration and the number ratio of Ce(I)/Ce(II) decreases with increasing Ce3+ concentration until beyond 0.002. The fluorescence lifetimes of the two centers were measured for various doping concentrations. Energy transfer from Ce(I) to Ce(II) was observed. It was found that the emission intensity of Ce(II) centers reduces much faster than that of Ce(I) with increasing temperature from 83 K up to 350 K, implying their potential application in temperature sensing based on their temperature dependent intensity ratios. A relative sensing sensitivity as high as 2.28% K−1 at 283 K was achieved.

To investigate the clinical characteristic of coagulation, possible causes and countermeasures of patients with severe corona virus disease 2019 (COVID-19).The clinical data of the 142 patients diagnosed as COVID-19 at Wuhan Third Hospital in Wuhan, China, from February 10 to February 16, 2020 were collected and analyzed retrospective. Among the patients, 17 cases of dead patients were divided into observe group, and 125 cases of cured patients were divided into control group. The clinical characteristics, laboratory tests, influencing factors, anticoagulant therapy, embolization and bleeding events of the two groups were observed.The average hospital stay time in 142 patients was 22 d. For the 17 dead patients in the observe group, the average hospital stay time was 9.9 d, and the D-dimer, prothrombin time, WBC count and Padua score of the patients in the observe group were significantly higher as compared with the patients in the control group. PT(OR=1.064, 95%CI 1.012-1.119) and D-D(OR=1.045, 95%CI 1.027-1.064) were the independent risk factors that causing the death of COVID-19 patients. Among the patients, 36(25.4%) patients received low-molecular-weight heparin for anticoagulant therapy, with the average course of 9.6 d. The cumulative incidence of the embolism of the patients in the observe group was 7（41.2%）, while 2(11.8%) patients developed to deep vein thrombosis (DVT) and pulmonary embolism (PE), 3 (17.6%) patients occurred acute cerebral infarction and 2 (11.8%) patients occurred acute myocardial infarction. 3 (17.6%) dead patients revealed dominant disseminated intravascular coagulation (DIC).Most patients with severe COVID-19 shows a variety of risk factors for thrombus, and those with coagulation dysfunction shows a high dead rate and rapid disease progression. Therefore, coagulation indicators should be dynamically monitored, and mechanical and drug prevention should be actively carried out.新型冠状病毒肺炎重症患者凝血功能的特征和影响因素分析.分析新型冠状病毒肺炎（COVID-19）重症患者凝血功能的临床特点，并探讨凝血功能异常的可能原因与应对措施.收集并回顾性分析2020年2月10日至2020年2月16日武汉市第三医院收治的COVID-19重症患者142例的临床资料，17例死亡患者设为观察组，125例治愈出院患者为对照组。观察2组患者的临床特点，实验室指标和影响因素，抗凝治疗现状，栓塞和出血事件.142例患者平均住院时间为22 d。观察组患者平均住院时间为9.9 d，均较对照组患者有更高的D-二聚体(D-D)、凝血酶原时间(PT)、活化部分凝血酶原时间（APTT）、白细胞计数（WBC）、中性粒细胞百分比（NEU%）和Padua评分。PT(OR=1.064, 95%CI 1.012-1.119)、D-D(OR=1.045, 95%CI 1.027-1.064)是导致COVID-19患者死亡的独立危险因素(P均0.05)。36（25.4%）例患者进行了低分子肝素抗凝治疗，平均疗程9.6 d。观察组栓塞事件复合发生率为7例（41.2%），其中2例（11.8%）患者伴发深静脉血栓形成（DVT）和肺栓塞（PE），3例（17.6%）伴发脑梗死，2例（11.8%）心肌梗死，较对照组的2例（1.6%）有显著性差异。3例（17.6%）死亡患者合并有显性弥散性血管内凝血（DIC）.COVID-19重症患者通常存在多种血栓事件的危险因素，存在出凝血功能障碍的患者死亡率较高，疾病进展速度快，应动态监测凝血指标，积极进行机械及药物预防.

Intra-tumor heterogeneity (ITH) of human tumors is important for tumor progression, treatment response, and drug resistance. However, the spatial distribution of ITH remains incompletely understood. Here, we present spatial analysis of ITH in lung adenocarcinomas from 147 patients using multi-region mass spectrometry of5,000 regions, single-cell copy number sequencing of ~2,000 single cells, and cyclic immunofluorescence of10 million cells. We identified two distinct spatial patterns among tumors, termed clustered and random geographic diversification (GD). These patterns were observed in the same samples using both proteomic and genomic data. The random proteomic GD pattern, which is characterized by decreased cell adhesion and lower levels of tumor-interacting endothelial cells, was significantly associated with increased risk of recurrence or death in two independent patient cohorts. Our study presents comprehensive spatial mapping of ITH in lung adenocarcinoma and provides insights into the mechanisms and clinical consequences of GD.

Advances in single cell copy number sequencing technologies have enabled the generation of data on hundreds to thousands of cells in parallel. Despite the rapid development in these technologies, there is a significant bottleneck for the analysis of the resulting large-scale datasets. Here we present CopyKit, a comprehensive and user-friendly toolkit for the analysis of single cell copy number data. CopyKit provides a suite of tools for pre-processing, QC, copy number inference, and subclone clustering to delineate the clonal diversity of tumors. We performed single cell copy number sequencing of 2977 cells from two breast tumor liver metastasis. CopyKit identified 4 and 12 subclonal populations, including amplification of PDGFRA, KRAS, and MYC as well as losses of PTEN, FOXO1, RB1, and BRCA1, many of which were spatially segregated in the tumor mass of the two tumors. Additionally, we applied CopyKit to study metastatic dissemination from a primary ER+ breast tumor with two matched metastatic sites and two colorectal carcinomas with matched liver metastatic tissues. This analysis demonstrated that the breast metastatic tumors selected for subclones that were lacking ERBB2 amplification in the primary site. Furthermore, the liver metastasis had deletions of chromosomes 18, 19, and 20p and a focal gain of FGFR1, while the pleural effusion acquired two additional focal gains on chromosome 8, including MYC. The colorectal metastatic tumors diverged from the primary tumor with copy number events affecting important cancer genes such as gain of SOX4, MYC, CDK8 and deletions of FHIT, CHEK1, and CHEK2. Collectively, this study shows that CopyKit provides a comprehensive set of tools for resolving clonal substructure from single cell copy number data for diverse applications in cancer biology. Citation Format: Darlan Conterno Minussi, Junke Wang, Aislyn Schalck, Yun Yan, Hua-Jun Wu, Cheng Peng, Min Hu, Emi Sei, Mary Edgerton, Hui Chen, Alejandro Contreras, David Hui, Senthil Damodaran, Scott Kopetz, Bora Lim, Nicholas Navin. Resolving clonal substructure from single cell genomic data in primary and metastatic tumors using CopyKit [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1210.

Precise control of mammalian gene expression is facilitated through epigenetic mechanisms and nuclear organization. In particular, insulated chromosome structures are important for regulatory control, but the phenotypic consequences of their boundary disruption on developmental processes are complex and remain insufficiently understood. Here, we generated deeply sequenced Hi-C data for human pluripotent stem cells (hPSCs) that allowed us to identify CTCF loop domains that have highly conserved boundary CTCF sites and show a notable enrichment of individual developmental regulators. Importantly, perturbation of such a boundary in hPSCs interfered with proper differentiation through deregulated distal enhancer-promoter activity. Finally, we found that germline variations affecting such boundaries are subject to purifying selection and are underrepresented in the human population. Taken together, our findings highlight the importance of developmental gene isolation through chromosomal folding structures as a mechanism to ensure their proper expression., The phenotypic consequence of 3D genome boundary disruption on developmental processes remains insufficiently understood. Here, the authors show that perturbation of a SOX17 boundary in human pluripotent stem cells interferes with proper differentiation and that germline variations affecting such boundaries are subject to selection, resulting in underrepresentation in the human population.

Background CRISPR‐Cas9‐based technologies have revolutionized experimental manipulation of mammalian genomes. None‐the‐less, limitations of the delivery and efficacy of these technologies restrict their application in primary cells. Aims To create an optimized protocol for penetrant, reproducible, and fast targeted genome editing in cell cultures derived from primary cells, using patient‐derived glioblastoma stem‐like cells (GSCs) and human neural stem/progenitor cells (NSCs) for proof‐of‐concept experiments. Methods and results We employed transient nucleofection of Cas9:sgRNA ribonucleoprotein complexes composed of chemically synthesized 2′‐O‐methyl 3′phosphorothioate‐modified sgRNAs and purified Cas9 protein. Insertion‐deletion mutation (indel) frequency and size distribution were measured via computational deconvolution of Sanger sequencing trace data. We found that this optimized technique routinely allows for >90% indel formation in only 3 days, without the need to create clonal lines for simple loss‐of‐function experiments. Using Western blotting, we observed near‐total protein loss of target genes in cell pools. Additionally, we found that this approach allows for the creation of targeted genomic deletions. Furthermore, by using RNA‐seq in edited NSCs to assess gene expression changes resulting from knockout of tumor suppressors commonly altered in glioblastoma, we also demonstrated the utility of this method for quickly creating a series of gene knockouts that allow for the study of oncogenic activities. Conclusion Our data suggest that this relatively simple method can be used for highly efficient and fast gene knockout, as well as for targeted genomic deletions, even in hyperdiploid cells (such as GSCs). This represents an extremely useful tool for the cancer research community when wishing to inactivate not only coding genes, but also non‐coding RNAs, UTRs, enhancers, and promoters. This method can be readily applied to diverse cell types by varying the nucleofection conditions.

BackgroundCRISPR-Cas9-based technologies have revolutionized experimental manipulation of mammalian genomes. None-the-less, limitations of the delivery and efficacy of these technologies restrict their application in primary cells.AimsTo create an optimized protocol for penetrant, reproducible, and fast targeted insertiondeletion mutation (indel) formation in cell cultures derived from primary cells, using patient-derived glioblastoma (GBM) stem-like cells (GSCs) and human neural stem/progenitor cells (NSCs) for proof-of-concept experiments.MethodsWe employed transient nucleofection of Cas9:sgRNA ribonucleoprotein complexes using chemically synthesized 2’-O-methyl 3’phosphorothioate-modified sgRNAs and purified Cas9 protein. Indel frequency and size distribution were measured via computational deconvolution of Sanger sequencing trace data. Western blotting was used to evaluate protein loss. RNA-seq in edited NSCs was used to assess gene expression changes resulting from knockout of tumor suppressors commonly altered in GBM.ResultsWe found that with this optimized technique, we can routinely achieve >90% indel formation in only 3 days, without the need to create clonal lines for simple loss-of-function experiments. We observed near-total protein loss of target genes in cell pools. Additionally, we found that this approach allows for the creation of targeted genomic deletions. We also demonstrated the utility of this method for quickly creating a series of gene knockouts that allow for the study of oncogenic activities.ConclusionOur data suggest that this relatively simple method can be used for highly efficient and fast gene knockout, as well as for targeted genomic deletions, even in hyperdiploid cells (such as GSCs). This represents an extremely useful tool for the cancer research community when wishing to inactivate not only coding genes, but also non-coding RNAs, UTRs, enhancers, and promoters. This method can be readily applied to diverse cell types by varying the nucleofection conditions.

Background : This study aimed to explore the role of miR-29a in hepatocellular carcinoma (HCC) cells. Further, to confirm whether miR-29a targetes vascular endothelial growth factor (VEGF) in HCC cells. Methods: Cell counting Kit-8 (CCK8) and clone formation assay were used to analyze the proliferation of HCC cells. Flow cytometry was performed to analyze the apoptosis and cell cycle of HCC cells. Western blot was used to analyze the expression of Bax, B-cell lymphoma-2 (Bcl-2), cyclin dependent kinase 4 (CDK4), CyclinD1, Retinoblastoma (Rb), p53 and myeloid cell leukemia-1 (MCL1). The targeting relations between miR-29a and VEGF was measuered by dual luciferase assay. Results : Overexpression of miR-29a could distinctly inhibit the proliferation and promote apoptosis of HCC cells. Overexpression of miR-29a obviously up-regulated the expressions of Bax and Rb, and reduced the expressions of CDK4, Bcl-2, Cyclin D1, p53, MCL1 and VEGF in HCC cells. Dual luciferase assay proved that VEGF was the target of miR-29a. Rescue experiments showed that miR-29a targeted VEGF to regulate the proliferation and apoptosis in HCC cells. Conclusions : These results indicated overexpression of miR-29a inhibited the HCC cells proliferation through targeting VEGF.

Glioblastoma multiforme (GBM) is an aggressive primary brain cancer that includes focal amplification of PDGFRα and for which there are no effective therapies. Herein, we report the development of a genetically engineered mouse model of GBM based on autocrine, chronic stimulation of overexpressed PDGFRα, and the analysis of GBM signaling pathways using proteomics. We discover the tubulin-binding protein Stathmin1 (STMN1) as a PDGFRα phospho-regulated target, and that this mis-regulation confers sensitivity to vinblastine (VB) cytotoxicity. Treatment of PDGFRα-positive mouse and a patient-derived xenograft (PDX) GBMs with VB in mice prolongs survival and is dependent on STMN1. Our work reveals a previously unconsidered link between PDGFRα activity and STMN1, and highlight an STMN1-dependent cytotoxic effect of VB in GBM., Amplification of PDGFRα is a common alteration in glioblastoma. In this study, the authors develop a genetically engineered mouse model of GBM based on autocrine, chronic stimulation of overexpressed PDGFR and discover Stathmin1 as an important PDGFRα regulated-protein involved in the response to vinstabline.

Blue-emitting phosphors for near ultraviolet (NUV) based tri-color RGB phosphor blend converted white light emitting diodes (LEDs) have been extensively investigated in the past few years. LED chip peaked near 400 nm is the most efficient among the NUV chips currently. However, most of blue phosphors show inefficient excitation around 400 nm. Herein, a novel blue phosphor SrLu2O4:Ce3+ matching well with near 400 nm chip and showing high thermal stability has been developed. The photoluminescence spectrum presents a broad emission band peaking at 460 nm with a bandwidth of nearly 90 nm. By optimizing the Ce3+ concentration, an internal quantum efficiency (IQE) as high as 76% was achieved. Furthermore, 86% of the room-temperature emission intensity is still maintained at 150 °C, indicating a good thermal stability and practicality. A series of white LEDs were fabricated based on 405 nm chips coated with a blend of the new blue phosphor with the commercial yellow and red phosphors. High color rendering indexes (≥90) were achieved while the correlated color temperature was tuneable in the range of 3094 to 8990 K. These results suggest that SrLu2O4:Ce3+ can be utilized as a blue-emitting phosphor in NUV based white LEDs.

The red emission through upconversion (UC) upon 980 nm excitation based on Er3+/Yb3+ combination is very attractive for bioimaging applications. The intensity of the red emission is observed to be strongly dependent on the host materials. However, the origin of the behavior and the quantitative dependence remain unclear. Here, the effectiveness of the second step UC excitation from the Er3+ intermediate state 4I13/2 to the 4F9/2 level by energy transfer from Yb3+ is studied for three popular hosts (β-NaYF4, Ba5Gd8Zn4O21, and Y2O3) that have different phonon energies. Their emission efficiencies of the red emitting state are calculated, and the radiative lifetime of the 4F9/2 level in Ba5Gd8Zn4O21 is reported for the first time. We present a spectroscopic method to evaluate the relative energy transfer coefficients for the three hosts and find the coefficient increases markedly with the increase of phonon energy, reflecting the nature of phonon-assisted energy transfer. The coefficient for β-NaYF4 is 89 an...

Glioblastoma is the most frequently occurring and invariably fatal primary brain tumor in adults. The vast majority of glioblastomas is characterized by chromosomal copy number alterations, including gain of whole chromosome 7 and loss of whole chromosome 10. Gain of whole chromosome 7 is an early event in gliomagenesis that occurs in proneural-like precursor cells, which give rise to all isocitrate dehydrogenase (IDH) wild-type glioblastoma transcriptional subtypes. Platelet-derived growth factor A (PDGFA) is one gene on chromosome 7 known to drive gliomagenesis, but, given its location near the end of 7p, there are likely several other genes located along chromosome 7 that select for its increased whole-chromosome copy number within glioblastoma cells. To identify other potential genes that could select for gain of whole chromosome 7, we developed an unbiased bioinformatics approach that identified homeobox A5 (HOXA5) as a gene whose expression correlated with gain of chromosome 7 and a more aggressive phenotype of the resulting glioma. High expression of HOXA5 in glioblastoma was associated with a proneural gene expression pattern and decreased overall survival in both human proneural and PDGF-driven mouse glioblastoma. Furthermore, HOXA5 overexpression promoted cellular proliferation and potentiated radioresistance. We also found enrichment of HOXA5 expression in recurrent human and mouse glioblastoma at first recurrence after radiotherapy. Overall, this study implicates HOXA5 as a chromosome 7-associated gene-level locus that promotes selection for gain of whole chromosome 7 and an aggressive phenotype in glioblastoma.

Er3+ and Yb3+ codoped Gd2Mo4O15 upconversion (UC) phosphors are synthesized by high temperature solid state reaction. The crystalline phase and morphology are studied in detail by X-ray diffraction (XRD), Raman spectroscopy and scanning electron microscopy (SEM). Under 980 nm laser excitation, the phosphors show a significant green UC luminescence contributed from 2H11/2/4S3/2 → 4I15/2 transitions of Er3+, while the popular red 4F9/2 → 4I15/2 emission is quite weak. The temporal evolutions of Er3+ and Yb3+ emissions after 980 nm pulse excitation are studied as a function of Er3+ and Yb3+ concentrations. It is revealed that the weak red UC emission is due to its low emission efficiency in Gd2Mo4O15 that has a high cutoff phonon energy of 960 cm−1. The temperature sensing behaviors based on the thermally coupled 2H11/2 and 4S3/2 levels have been explored. A high absolute sensitivity of 0.00853 K−1 at 554 K is achieved and an excellent thermal durability is observed. The relative absorptance of 4I15/2 → 2H11/2 transition to the 4I15/2 → 4S3/2 transition is proposed as a good measure for evaluating the absolute sensitivity based on the comparative study of some familiar materials. Our results imply that Gd2Mo4O15 is a promising green UC phosphor for optical thermometry.

Er3+-induced intensity enhancement of ∼2 μm emission is observed in 2 atom % Tm3+ doped Lu2O3 under 782 nm excitation. The maximum enhancement reaches 41.9% with only 0.05 atom % Er3+. Er3+ introduces a new quantum cutting process which is proved to be a Tm3+ → Er3+ → Tm3+ forward-backward energy transfer (FBET) system. The FBET system is observed to work efficiently even at very low Er3+ concentration. Thus, energy loss due to energy migration among Tm3+ ions is suggested to be suppressed by the FBET process. The Tm3+ → Er3+ → Tm3+ FBET system may be a new route to improve the performance of Tm3+ lasers.

// Yi Zhang 1, * , Rong-Bo Liao 2, * , Li-Lin Hu 3 , Bi-Xia Tong 4 , Teng-Fei Hao 2 and Hua-Jun Wu 2 1 Department of General Surgery, The First People’s Hospital of Neijiang, Neijiang 641000, Sichuan Province, P.R. China 2 Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330000, Jiangxi Province, P.R. China 3 Department of Medicine, Nanchang University, Nanchang 330000, Jiangxi Province, P.R. China 4 Department of Nursing, Shangrao People’s Hospital, Shangrao 334000, Jiangxi Province, P.R. China * These two authors contributed equally to this work Correspondence to: Hua-Jun Wu, email: 445079124@qq.com Keywords: miR-10b, carcinoma, metastasis, meta-analysis Received: April 21, 2017 Accepted: August 17, 2017 Published: September 30, 2017 ABSTRACT Background: Reported studies on carcinoma have evaluated the significance of the microRNA miR-10b in the development and progression of many cancers. Increased expression of miR-10b is associated with the susceptibility to lymph node metastasis and distant metastasis in various tumors. Results: The results of the meta-analysis revealed that lymph node metastasis occurred more frequently in the patients group with high expression level of miR-10b than in the patients group with low expression level of miR-10b (OR=4.65, 95% CI: 3.40–6.37, P

In this paper, we synthesized series of Eu 2+ activated CaO ceramic powders by conventional solid state reaction. Using NH 4 Cl as a reducing additives, the Eu 3+ has been successfully reduced to Eu 2+ . An intense blue emission peaked at 460 nm from Eu 2+ was observed. The luminescent intensity of the doping-optimized CaO:Eu 2+ sample can be as high as 106% of commercial BAM blue phosphor under 400 nm near-ultraviolet (NUV) excitation. The effect of Eu 2+ and NH 4 Cl contents on photoluminescence properties and crystal phase formation have been investigated, respectively. The thermal stable property which is an important performance for LED application has also been measured. The emission intensity at 120 °C can maintain 94% of that at room temperature. Our results suggest that CaO: Eu 2+ ceramic powder could be used as a promising blue emitting phosphor for NUV chip based white LEDs.