Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions

Although emerging evidence indicates that alterations in proteins within nuclear compartments elicit changes in chromosomal architecture and differentiation, the underlying mechanisms are not well understood. Here we investigate the direct role of the abundant nuclear complex protein Matrin3 (Matr3) in chromatin architecture and development in the context of myogenesis. Using an acute targeted protein degradation platform (dTAG-Matr3), we reveal the dynamics of development-related chromatin reorganization. High-throughput chromosome conformation capture (Hi-C) experiments revealed substantial chromatin loop rearrangements soon after Matr3 depletion. Notably, YY1 binding was detected, accompanied by the emergence of novel YY1-mediated enhancer-promoter loops, which occurred concurrently with changes in histone modifications and chromatin-level binding patterns. Changes in chromatin occupancy by Matr3 also correlated with these alterations. Overall, our results suggest that Matr3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and highlight a conserved and direct role for Matr3 in maintenance of chromosomal architecture.

Identifying quantitatively differential chromosomal compartmentalization changes and their biological significance from Hi-C data using DARIC

BACKGROUND

Chromosomal compartmentalization plays a critical role in maintaining proper transcriptional programs in cell differentiation and oncogenesis. However, currently the prevalent method for comparative analysis of compartmentalization landscapes between different cell types is limited to the qualitative switched compartments.

RESULTS

To identify genomic regions with quantitatively differential compartmentalization changes from genome-wide chromatin conformation data like Hi-C, we developed a computational framework named DARIC. DARIC includes three modules: compartmentalization quantification, normalization, and differential analysis. Comparing DARIC with the conventional compartment switching analysis reveals substantial regions characterized by quantitatively significant compartmentalization changes without switching. These changes are accompanied by changes in gene expression, chromatin accessibility, H3K27ac intensity, as well as the interactions with nuclear lamina proteins and nuclear positioning, highlighting the functional importance of such quantitative changes in gene regulation. We applied DARIC to dissect the quantitative compartmentalization changes during human cardiomyocyte differentiation and identified two distinct mechanisms for gene activation based on the association with compartmentalization changes. Using the quantitative compartmentalization measurement module from DARIC, we further dissected the compartment variability landscape in the human genome by analyzing a compendium of 32 Hi-C datasets from 4DN. We discovered an interesting correlation between compartmentalization variability and sub-compartments.

CONCLUSIONS

DARIC is a useful tool for analyzing quantitative compartmentalization changes and mining novel biological insights from increasing Hi-C data. Our results demonstrate the functional significance of quantitative compartmentalization changes in gene regulation, and provide new insights into the relationship between compartmentalization variability and sub-compartments in the human genome.

O-GlcNAcylation of MITF regulates its activity and CDK4/6 inhibitor resistance in breast cancer

Cyclin-dependent kinases 4 and 6 (CDK4/6) play a pivotal role in cell cycle and cancer development. Targeting CDK4/6 has demonstrated promising effects against breast cancer. However, resistance to CDK4/6 inhibitors (CDK4/6i), such as palbociclib, remains a substantial challenge in clinical settings. Using high-throughput combinatorial drug screening and genomic sequencing, we found that the microphthalmia-associated transcription factor (MITF) is activated via O-GlcNAcylation by O-GlcNAc transferase (OGT) in palbociclib-resistant breast cancer cells and tumors; O-GlcNAcylation of MITF at Serine 49 enhanced its interaction with importin α/β, thus promoting its translocation to nuclei, where it suppressed palbociclib-induced senescence; inhibition of MITF or its O-GlcNAcylation re-sensitized resistant cells to palbociclib. Remarkably, clinical studies confirmed the activation of MITF in tumors from patients who are palbociclib-resistant or undergoing palbociclib treatment. Collectively, our studies shed light on a novel mechanism regulating palbociclib-resistance, and present clinical evidence for developing therapeutic approaches to treat CDK4/6i-resistant breast cancer patients.

Identifying Quantitatively Differential Chromosomal Compartmentalization Changes and Their Biological Significance from Hi-C data using DARIC

Background

Chromosomal compartmentalization plays a critical role in maintaining proper transcriptional programs in cell differentiation and oncogenesis. However, currently the prevalent method for comparative analysis of compartmentalization landscapes between different cell types is limited to the qualitative switched compartments.

Results

To identify genomic regions with quantitatively differential compartmentalization changes from genome-wide chromatin conformation data like Hi-C, we developed a computational framework named DARIC. DARIC includes three modules: compartmentalization quantification, normalization, and differential analysis. Comparing DARIC with the conventional compartment switching analysis reveals substantial regions characterized by quantitatively significant compartmentalization changes without switching. These changes are accompanied by changes in gene expression, chromatin accessibility, H3K27ac intensity, as well as the interactions with nuclear lamina proteins and nuclear positioning, highlighting the functional importance of such quantitative changes in gene regulation. We applied DARIC to dissect the quantitative compartmentalization changes during human cardiomyocyte differentiation and identified two distinct mechanisms for gene activation based on the association with compartmentalization changes. Using the quantitative compartmentalization measurement module from DARIC, we further dissected the compartment variability landscape in the human genome by analyzing a compendium of 32 Hi-C datasets from 4DN. We discovered an interesting correlation between compartmentalization variability and sub-compartments.

Conclusions

DARIC is a useful tool for analyzing quantitative compartmentalization changes and mining novel biological insights from increasing Hi-C data. Our results demonstrate the functional significance of quantitative compartmentalization changes in gene regulation, and provide new insights into the relationship between compartmentalization variability and sub-compartments in the human genome.

Health-related quality of life and its association with socioeconomic status and diet diversity in Chinese older adults

Objectives

The study aimed at examining the combined association of socioeconomic status (SES) and diet diversity (DD) with health-related quality of life (HRQoL) and exploring whether DD played a mediating role in the relationship between varied SES and HRQoL among Chinese older persons.

Method

A multi-stage random sampling method was conducted in Shanxi Province of China, with 3,250 older adults participating in this cross-sectional survey. SES was divided into groups by quartiles and DD by means, and these variable groups were combined in pairs to generate a total of eight combinations. The PROCESS macro developed by Hayes was employed for the simple mediation analysis.

Results

Compared with the reference group (those with both high SES and high DD), older adults who were classified to have lower SES or DD had elevated odds of having worse HRQoL: low SES/ low DD (OR = 1.65, 95% CI 1.41-2.92); low SES/ high DD (OR = 1.45, 95% CI 1.17-1.80); middle low SES/ low DD (OR = 1.43, 95% CI 1.24-1.65); middle low SES/ high DD (OR = 1.23, 95% CI 1.03-1.47); upper high SES/ low DD (OR = 1.41, 95% CI 1.21-1.65); and high SES/ low DD (OR = 1.30, 95%CI 1.10-1.53). The mediation analysis revealed that DD mediated the relationship between SES and HRQoL (B=0.011, 95% CI 0.008-0.013), with its indirect effects accounting for 39.29% of the total effects.

Conclusions

These findings highlighted the role of DD as a mediator of the relationship between SES and HRQoL. As DD could be protective, modifiable, and easy for older adults to understand and implement, village clinics and community health stations should work collaboratively to design proper DD intervention measures for better HRQoL.

Lysine methyltransferase Kmt2d regulates naive CD8+ T cell activation-induced survival

Lysine specific methyltransferase 2D (Kmt2d) catalyzes the mono-methylation of histone 3 lysine 4 (H3K4me1) and plays a critical role in regulatory T cell generation via modulating Foxp3 gene expression. Here we report a role of Kmt2d in naïve CD8⁺ T cell generation and survival. In the absence of Kmt2d, the number of CD8⁺ T cells, particularly naïve CD8⁺ T cells (CD62L^hi/CD44^lo), in spleen was greatly decreased and in vitro activation-related death significantly increased from Kmt2d ^fl/flCD4cre⁺ (KO) compared to Kmt2d ^fl/flCD4cre^- (WT) mice. Furthermore, analyses by ChIPseq, RNAseq, and scRNAseq showed reduced H3K4me1 levels in enhancers and reduced expression of apoptosis-related genes in activated naïve CD8⁺ T cells in the absence of Kmt2d. Finally, we confirmed the activation-induced death of antigen-specific naïve CD8⁺ T cells in vivo in Kmt2d KO mice upon challenge with Listeria monocytogenes infection. These findings reveal that Kmt2d regulates activation-induced naïve CD8⁺ T cell survival via modulating H3K4me1 levels in enhancer regions of apoptosis and immune function-related genes.

Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells

Reactivation of fetal hemoglobin expression by the downregulation of BCL11A is a promising treatment for β-hemoglobinopathies. A detailed understanding of BCL11A-mediated repression of γ-globin gene (HBG1/2) transcription is lacking, as studies to date used perturbations by shRNA or CRISPR-Cas9 gene editing. We leveraged the dTAG PROTAC degradation platform to acutely deplete BCL11A protein in erythroid cells and examined consequences by nascent transcriptomics, proteomics, chromatin accessibility, and histone profiling. Among 31 genes repressed by BCL11A, HBG1/2 and HBZ show the most abundant and progressive changes in transcription and chromatin accessibility upon BCL11A loss. Transcriptional changes at HBG1/2 were detected in <2 h. Robust HBG1/2 reactivation upon acute BCL11A depletion occurred without the loss of promoter 5-methylcytosine (5mC). Using targeted protein degradation, we establish a hierarchy of gene reactivation at BCL11A targets, in which nascent transcription is followed by increased chromatin accessibility, and both are uncoupled from promoter DNA methylation at the HBG1/2 loci.

Same Dosages of rPRV/XJ5-gI−/gE−/TK− Prototype Vaccine or Bartha-K61 Vaccine Similarly Protects Growing Pigs Against Lethal Challenge of Emerging vPRV/XJ-5 Strain

Variant pseudorabies viruses (vPRV) have constantly emerged in China since late 2011. In the present study, a 1 × 10^6.0 TCID₅₀ per-animal dosage of a commercially available Bartha-K61 vaccine and an rPRV/XJ5-gI⁻/gE⁻/TK⁻ prototype vaccine freshly extracted from the vPRV/XJ-5 at the same dose were administered to evaluate the immune effectiveness thereof on growing pigs to prevent lethal strikes caused by vPRV/XJ-5. The results suggest that the Bartha-K61 vaccine at a dose of 1 × 10^6.0 TCID₅₀ per animal and the same dosage of the rPRV/XJ5-gI⁻/gE⁻/TK⁻ prototype vaccine protected growing pigs against the lethal challenge of vPRV/XJ-5 strain with 100% survive rate. Furthermore, the outcome of the clinical score, virus shedding, weight gain, and viral loads in different pig tissues in these two groups demonstrates that either the Bartha-K61 vaccine or the rPRV/XJ5-gI⁻/gE⁻/TK⁻ prototype vaccine at the same dose exhibited parallel efficacy in pigs against the lethal challenge with the XJ-5 strain of vPRV.

P-138 Transcriptomic signatures in trophectoderm and inner cell mass of human blastocysts with expected pregnancy rates

Study question

Is it possible to identify the molecular factors that contribute to the implantation potential of blastocysts?

Summary answer

Genes correlated with expected pregnancy rate in trophectoderm (TE) and inner cell mass (ICM) respectively were identified, and aneuploidy alone couldn’t predict the pregnancy expectation.

What is known already

The selection of suitable embryos for transfer is critical for achieving successful pregnancy outcomes in assisted reproductive technology (ART). Although pre-implantation genetic testing for aneuploidy (PGT-A) as well as morphological and chronological evaluation of embryos, have been conducted in clinical practice, they do not fully guarantee successful pregnancy. Recently, transcriptional events in early human embryonic development have been analyzed using RNA-sequencing (RNA-seq) and researchers are attempting to apply this information to ART.

Study design, size, duration

To determine the correlation between blastocyst evaluation and pregnancy rate, we retrospectively analyzed 1,890 cases underwent frozen-thawed blastocyst transfer from March 2018 to December 2020. A total of 13 blastocysts that were cryopreserved for clinical use between February 2011 and September 2018, then scheduled for disposal and with consented for research, were subjected to RNA-seq without distinguishing between conventional in vitro fertilization (c-IVF) and intracytoplasmic sperm injection (ICSI).

Participants/materials, setting, methods

Blastocysts were donated by infertile couples undergoing c-IVF or ICSI cycles at the Yamashita Shonan Yume Clinic with informed consent under ethical approval. TE and ICM cells were collected from blastocysts by using a micromanipulator and then subjected to RNA-seq. Gene expression analysis and digital karyotyping using RNA-seq were performed simultaneously for TE and ICM cells, respectively. One-way analysis of variance, chi-square test and Tukey's multiple comparison test were used for this study.

Main results and the role of chance

Blastocysts were classified into three groups to correlate with pregnancy rates based on the diameter of the blastocyst and the time to reach this size: those taking less than 130 h to reach a diameter of &gt; 170 μm (Group 1, n = 676), those taking more than 140 h to reach a diameter of &lt; 180 μm (Group 2, n = 158), and the rest (Group 3, n = 1,056). The pregnancy rates of Groups 1, 2 and 3 were 59.0%, 16.5%, and 34.2%, respectively (p &lt; 0.01). Assessing the differences in overall transcripts correlated between Group 1 (n = 5), Group 2 (n = 4), and Group 3 (n = 4), 26 and 67 differentially expressed genes (DEGs) were identified in ICM and TE cells, respectively. Importantly, downregulated genes in TE of blastocysts with lower expectation of pregnancy included tight junction-related genes, such as CXADR, CLDN10, and ATP1B1, which were implicated in peri-implantation development. Digital karyotyping revealed karyotypic abnormalities and mosaicism in all groups with no common abnormalities observed, suggesting that aneuploidy alone cannot predict the pregnancy expectation.

Limitations, reasons for caution

Although 93 genes potentially related to implantation have been identified, it is still unclear how these genes are involved in implantation. In vitro implantation models using human embryos and artificial embryos currently under development are expected to contribute to the elucidation of the functions of these genes.

Wider implications of the findings

Our results provide reliable candidates for genes that could allow for non-invasive selection of high-quality blastocysts for ART and add to the knowledge base of transcriptional events in human peri-implantation development.

Trial registration number

not applicable

MLL::AF9 degradation induces rapid changes in transcriptional elongation and subsequent loss of an active chromatin landscape

MLL rearrangements produce fusion oncoproteins that drive leukemia development, but the direct effects of MLL-fusion inactivation remain poorly defined. We designed models with degradable MLL::AF9 where treatment with small molecules induces rapid degradation. We leveraged the kinetics of this system to identify a core subset of MLL::AF9 target genes where MLL::AF9 degradation induces changes in transcriptional elongation within 15 minutes. MLL::AF9 degradation subsequently causes loss of a transcriptionally active chromatin landscape. We used this insight to assess the effectiveness of small molecules that target members of the MLL::AF9 multiprotein complex, specifically DOT1L and MENIN. Combined DOT1L/MENIN inhibition resembles MLL::AF9 degradation, whereas single-agent treatment has more modest effects on MLL::AF9 occupancy and gene expression. Our data show that MLL::AF9 degradation leads to decreases in transcriptional elongation prior to changes in chromatin landscape at select loci and that combined inhibition of chromatin complexes releases the MLL::AF9 oncoprotein from chromatin globally.

A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia

In this study, Harada et al. identified the transcription factors MEF2D and IRF8 as selective transcriptional dependencies of KMT2A-rearranged AML, where MEF2D displays partially redundant functions with its paralog, MEF2C. This study illustrates a mechanism of context-specific transcriptional addiction whereby a specific AML subclass depends on a highly specialized core regulatory module to directly enforce expression of common leukemia oncogenes.

Acute myeloid leukemia with KMT2A (MLL) rearrangements is characterized by specific patterns of gene expression and enhancer architecture, implying unique core transcriptional regulatory circuitry. Here, we identified the transcription factors MEF2D and IRF8 as selective transcriptional dependencies of KMT2A-rearranged AML, where MEF2D displays partially redundant functions with its paralog, MEF2C. Rapid transcription factor degradation followed by measurements of genome-wide transcription rates and superresolution microscopy revealed that MEF2D and IRF8 form a distinct core regulatory module with a narrow direct transcriptional program that includes activation of the key oncogenes MYC, HOXA9, and BCL2. Our study illustrates a mechanism of context-specific transcriptional addiction whereby a specific AML subclass depends on a highly specialized core regulatory module to directly enforce expression of common leukemia oncogenes.

Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture

Precise control of gene expression during differentiation relies on the interplay of chromatin and nuclear structure. Despite an established contribution of nuclear membrane proteins to developmental gene regulation, little is known regarding the role of inner nuclear proteins. Here we demonstrate that loss of the nuclear scaffolding protein Matrin-3 (Matr3) in erythroid cells leads to morphological and gene expression changes characteristic of accelerated maturation, as well as broad alterations in chromatin organization similar to those accompanying differentiation. Matr3 protein interacts with CTCF and the cohesin complex, and its loss perturbs their occupancy at a subset of sites. Destabilization of CTCF and cohesin binding correlates with altered transcription and accelerated differentiation. This association is conserved in embryonic stem cells. Our findings indicate Matr3 negatively affects cell fate transitions and demonstrate that a critical inner nuclear protein impacts occupancy of architectural factors, culminating in broad effects on chromatin organization and cell differentiation.

Clinical usefulness of a novel fluorescence technique for the intraoperative diagnosis of surgical margins in patients with breast cancer

In both 5- and 15-min data, FI was significantly higher in malignant tissues than in benign tissues. The diagnostic accuracy was similar at 5 and 15 min. Therefore, the 5-min FI was enough applying in the further analyses.

Mapping the evolving landscape of super-enhancers during cell differentiation

Background

Super-enhancers are clusters of enhancer elements that play critical roles in the maintenance of cell identity. Current investigations on super-enhancers are centered on the established ones in static cell types. How super-enhancers are established during cell differentiation remains obscure.

Results

Here, by developing an unbiased approach to systematically analyze the evolving landscape of super-enhancers during cell differentiation in multiple lineages, we discover a general trend where super-enhancers emerge through three distinct temporal patterns: conserved, temporally hierarchical, and de novo. The three types of super-enhancers differ further in association patterns in target gene expression, functional enrichment, and 3D chromatin organization, suggesting they may represent distinct structural and functional subtypes. Furthermore, we dissect the enhancer repertoire within temporally hierarchical super-enhancers, and find enhancers that emerge at early and late stages are enriched with distinct transcription factors, suggesting that the temporal order of establishment of elements within super-enhancers may be directed by underlying DNA sequence. CRISPR-mediated deletion of individual enhancers in differentiated cells shows that both the early- and late-emerged enhancers are indispensable for target gene expression, while in undifferentiated cells early enhancers are involved in the regulation of target genes.

Conclusions

In summary, our analysis highlights the heterogeneity of the super-enhancer population and provides new insights to enhancer functions within super-enhancers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-021-02485-x.

O-154 First mitotic spindle formation led by sperm centrosome-dependent microtubule organising centres may cause high incidence of zygotic division errors in humans

Study question

Why do multinucleated blastomeres appear at high frequency in two-cell-stage embryos in humans?

Summary answer

Failure in microtubule assembly during the first mitotic spindle body formation by sperm centrosome-dependent microtubule organising centres (MTOCs) may lead to chromosomal instability.

What is known already

Unlike that in mice, multinucleated blastomeres appear at high frequency in two-cell-stage embryos in humans. However, the underlying mechanism remains elusive. In mice, multiple acentriolar MTOCs appear around the male and female pronuclei after pronuclear disappearance and contribute to dual-spindle formation, engulfing each parental chromosome. This spindle formation may ensure an error-free division, keeping the chromosomes stable during the first cleavage, as observed in mice, but it is unclear whether a similar mechanism exists in humans.

Study design, size, duration

To examine how sperm centrosomes contribute to MTOC formation in humans, two types of 3PN zygotes derived fromeither conventional in vitro fertilization (c-IVF, n = 30) or intracytoplasmic sperm injection (ICSI, n = 10) were used. The zygotes were collected from October 2018 to January 2020. MTOC and mitotic spindle formation at consecutive stages of development during the first cleavage were analysed under static and dynamic conditions using immunofluorescence assay and fluorescent live-cell imaging.

Participants/materials, setting, methods

Under ethics approval, 3PN zygotes were donated by infertile couples undergoing c-IVF or ICSI cycles at the Yamashita Shonan Yume Clinic in Japan. All participants provided informed consent. Immunofluorescence assay was performed using antibodies against α-tubulin, pericentrin, and H3K9me3 after fixation with MTSB-XF solution. Fluorescent live-cell imaging was performed using TagGFP2-H2B mRNA (chromosome marker) and FusionRed-MAP4 mRNA (microtubule marker).

Main results and the role of chance

Immunofluorescence revealed that while 3PN zygotes derived from c-IVF showed four pericentrin dots, those derived from ICSI exhibited two pericentrin dots. In pro-metaphase, an independent group of chromosomes derived from each pronucleus and MTOCs were formed by the sperm centrosome at the core. Microtubules from each MTOC extended toward the chromosomes in the early metaphase; a quadrupolar spindle was formed in the c-IVF-derived zygotes, and a bipolar spindle was formed in the ICSI-derived zygotes by the MTOCs at the zygote apex after chromosome alignment. In pro-metaphase, the microtubules extended from the MTOCs to the nearest chromosome. Since microtubule assembly was found on oocyte-derived chromosomes, we hypothesised that whether a chromosome is surrounded by microtubules depends on the location of the MTOCs, irrespective of its origin. Live-cell imaging of histone H2B and MAP4 revealed that four MTOCs appeared around the three pronuclei just before the disappearance of the pronuclear membrane; microtubules then extended from the MTOCs toward the chromosomes, beginning to form a mitotic spindle as the chromosomes moved to the centre of the oocyte. Interestingly, one of the three assembled chromosome groups showed no microtubule assembly in the pro-metaphase. Similar results were obtained in all six 3PN zygotes subjected.

Limitations, reasons for caution

We demonstrated the high risk of developing bare chromosomes not surrounded by microtubules during the formation of the first mitotic spindle, using human tripronuclear zygotes. However, owing to unavailability of normal fertilized oocytes for this study because of the clinical use, we were unable to confirm this in normal zygotes.

Wider implications of the findings

Although two sperm centrosome-dependent MTOCs are expected to be formed in normal fertilized oocytes, these MTOCs are not sufficient to completely enclose physically separated female and male chromosomes with the microtubules. This explains the high frequency of zygotic division errors that lead to unstable human chromosomes.

Trial registration number

not applicable

P–248 Statistical estimation for incidence of blastocyst trophectoderm vesicles (TVs) and efficacy of assisted hatching (AH)

Study question

The aim of this study is to analyse the association between blastocyst diameter and TVs development, and to examine the efficacy of AH.

Summary answer

Blastocysts with a diameter of more than 170 μm leads to high incidence of TVs and AH applied from the incidence should be effective.

What is known already

TVs are protrusion of trophectoderm cells often observed in expanding blastocyst stages. TVs can be observed in expanding blastocysts regardless of Intracytoplasmic sperm injection (ICSI) and Conventional-IVF (C-IVF), when the internal pressure of blastocysts increase. The rate of TVs incidence in blastocysts inseminated by ICSI is higher than that by C-IVF, due to penetration of the needle into the zona pellucida. Moreover, it has been reported that TVs may inhibit blastocyst hatching. However, the developmental timing of TVs is still unclear, and there is no study that has analysed the association between blastocyst diameter and the incidence of TVs.

Study design, size, duration

1) Diameters and TVs incidence of blastocysts by ICSI and C-IVF were measured, and the cut-off value and the area under the curve (AUC) of the receiver operating characteristic (ROC) curve were calculated to estimate the timing of TV incidence. 2) We analysed the clinical pregnancy rates of blastocysts with TVs treated by AH compared to those of blastocysts by C-IVF not subjected to AH.

Participants/materials, setting, methods

This study included 821 transferred frozen blastocysts ranging from March 2018 to November 2019. The embryos were cultured in a dry incubator after insemination by ICSI or C-IVF. Blastocyst freezing conditions were set at day5 to day7 with a diameter of more than 150 μm in inner diameter of zona pellucida, and this was measured before freezing. The ROC curve was performed using EZR statistical analysis software.

Main results and the role of chance

1) The incidence of TVs in blastocysts by ICSI and C-IVF was 27.5% (117/424) and 14.6% (58/397) respectively. The rate of the incidence of TVs in blastocysts inseminated by ICSI and C-IVF; 8.6% (12/140) and 0.95% (1/105) in 150–159 μm, 12.7% (14/110) and 8.2% (6/73) in 160–169 μm, 40.6% (28/69) and 10.5% (6/57) in 170–179 μm, 55.6% (30/54) and 25.5% (13/51) in 180–189 μm, 66.7% (20/30) and 35.7% (10/28) in 190–199 μm, and 68.4% (13/19) and 26.8% (22/82) in the diameter of more than 200 μm. The cut-off value of the ROC curve was respectively 170 μm (sensitivity 78.6% and specificity 73.0%) and 176 μm (sensitivity 84.5% and specificity 59.6%) in the diameter; the AUC was 0.8 [95%CI:0.752–0.848] and 0.74 [95%CI:0.687–0.793] respectively. 2) The clinical pregnancy rate of TVs blastocyst vs C-IVF blastocyst was 52.7% (88/167) vs 57.8% (37/64) respectively. There is no significant difference between the two clinical pregnancy rates (P = 0.556).

Limitations, reasons for caution

The findings of this study have to be seen in light of some limitations. Since this study aimed to analyse the incidence of TVs based on blastocyst size, we did not take into account the grade according to the Gardner classification and the number of trophectoderm cells.

Wider implications of the findings: Blastocysts inseminated by ICSI and C-IVF were highly likely to have TVs above 170 μm and 176 μm respectively. The clinical pregnancy rates of the blastocyst with TV treated by AH was similar to those of the C-IVF blastocyst.

Trial registration number

Not applicable

Insights into the stabilization of landfill by assessing the diversity and dynamic succession of bacterial community and its associated bio-metabolic process

The distribution of bacterial community in an actual landfill was analyzed and the bioprocess involved in refuse degradation was clarified. The results showed that the degradation degree of refuse showed great differences with the landfill age, in which the contents of organic matter (OM) and total Kjeldahl nitrogen (TKN) in refuse as well as the chemical oxygen demand (COD) in leachate presented decreasing trends with increasing landfill age. The diversity of bacterial community increased first and then decreased with increasing landfill age. The main bacterial phyla involved in refuse degradation were Proteobacteria, Firmicutes and Bacteroidetes, among which, Proteobacteria had an absolute advantage with a relative abundance ranging of 66-78%. With increasing landfill age, the abundance of Firmicutes decreased gradually, while that of Bacteroidetes increased. Pseudomonas, Thiopseudomonas, Psychrobacter and Desemzia were the main genera. The distribution of bacterial community in samples with landfill ages of 0-1 and 1-3 years were greatly influenced by TKN and pH, respectively. Amino acid and carbohydrate metabolism were the main biological pathways according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and the biodegradation of xenobiotics as well as terpenoids and polyketides also accounted relatively high frequencies in the landfill. These results provide a better understanding of landfill microbiology and bioprocesses for landfill stabilization.

Transcription factor competition at the γ-globin promoters controls hemoglobin switching

BCL11A, the major regulator of fetal hemoglobin (HbF, α₂γ₂) level, represses γ-globin expression through direct promoter binding in adult erythroid cells in a switch to adult hemoglobin (HbA, α₂β₂). To uncover how BCL11A initiates repression, we used CRISPR-Cas9, dCas9, dCas9-KRAB and dCas9-VP64 screens to dissect the γ-globin promoters and identified an activator element near the BCL11A-binding site. Using CUT&RUN and base editing, we demonstrate that a proximal CCAAT box is occupied by the activator NF-Y. BCL11A competes with NF-Y binding through steric hindrance to initiate repression. Occupancy of NF-Y is rapidly established following BCL11A depletion, and precedes γ-globin derepression and locus control region (LCR)-globin loop formation. Our findings reveal that the switch from fetal to adult globin gene expression within the >50-kb β-globin gene cluster is initiated by competition between a stage-selective repressor and a ubiquitous activating factor within a remarkably discrete region of the γ-globin promoters.

Evaluating the physicochemical properties of refuse with a short-term landfill age and odorous pollutants emission during landfill mining: A case study

A field excavation of refusewitha short-termlandfillage from the Qingdao Xiaojianxi municipal solid waste (MSW) landfill was conducted. The physical composition and chemical properties of refuse with landfill ages of 1-4 years were studied, and the emission characteristics of odorous pollutants during the excavation period were monitored. The refuse aged 1-2 years has a higher proportion of combustible material than that the refuse aged 3-4 years, and the volatile content and calorific value in refuse aged 1-2 years were also higher than those in refuse aged 3-4 years, indicating that the refuse with a short-term landfill age was more suitable for incineration than refuse with a long-term landfill age. The pH and availablephosphorus (AP) gradually increased with increasing landfill age, while the total Kjeldahlnitrogen (TKN) and organic matter (OM) decreased. The contents of the heavy metals Cu, Zn, Ni, Pb and As generally decreased with landfill age, especially in refuse aged 2-4 years, whereas the Cr content showed no significant differences in refuse aged 1-4 years. The main odorous pollutants emitted during the excavation and screening periods were ammonia (NH₃) and carbon disulfide (CS₂), and the odor intensity of excavated refuse aged 1-3 years was higher than that of refuse aged 4 years. Under the condition of a small excavation area and continuous deodorization, the pollution intensity can meet the discharge standards of the factory boundary.

Key internal factors leading to the variability in CO2 fixation efficiency of different sulfur-oxidizing bacteria during autotrophic cultivation

Variability in the apparent CO₂ fixation yield of four aerobic sulfur-oxidizing bacteria (Halothiobacillus neapolitanus DSM 15147, Thiobacillus thioparus DSM 505, Thiomonas intermedia DSM 18155, and Starkeya novella DSM 506) in autotrophic culturing was studied, and mutual effects of key intrinsic factors on CO₂ fixation were explored. DSM 15147 and DSM 505 exhibited much higher CO₂ fixation yields than DSM 18155 and DSM 506. The differences in CO₂ fixation yield were determined not only by cbb gene transcription, but also by cell synthesis rate, which was determined by rRNA gene copy number; the rRNA gene copy number had a more significant effect than cbb gene transcription on the apparent CO₂ fixation yield. Moreover, accumulation of EDOC was observed in all four strains during chemoautotrophic cultivation, and the proportion of EDOC accounting for total fixed organic carbon (TOC; EDOC/TOC ratio) was much higher in DSM 18155 and DSM 506 than in DSM 15147 and DSM 505. The accumulation of EDOC led to a significant decrease in the cbb gene transcription efficiency during cultivation, and a further feedback inhibitory effect on CO₂ fixation.

Colonisation of mice and pigs by a chimeric porcine circovirus 1-2 prototype vaccine strain and a PCV2 isolate originating in China and their induction of cytokines

A chimeric porcine circovirus (PCV) 1-2b vaccine strain and its parental wild-type PCV2b strain from China (PCV2-J) were used separately to vaccinate BALB/c mice and tissue and serum samples were collected from the mice to investigate whether the replication properties of the viruses differed. The spleen lymphocytes from the infected mice were cultured in vitro; the amounts of interferon-γ-secreting cells (IFN-γ-SCs) and levels of interleukin (IL) 2, IL-4 and IL-10 in the culture fluids were monitored. The results showed that PCV1-2b induced higher levels of antibody production in the infected mice than the PCV2b-J isolate. Viremia declined gradually in both infection groups and the DNA copy numbers were nearly equal in both groups of mouse tissues tested. The IFN-γ-SC levels were clearly up-regulated in both the PCV1-2b- and PCV2b-J-infected mice. In both mouse groups, IL-2 was up-regulated, and IL-10 was detected at low levels, while IL-4 was always below the limit of detection. Similar experiments were performed in pigs and the results showed that when infected with either PCV1-2b or PCV2b-J the pigs experienced high-level antibody responses, with no significant differences between the infection groups. In the pig model, the development of IFN-γ-SCs in response to PCV1-2b and PCV2b-J infections was detected. However, the PCV1-2b strain tended to elicit more IFN-γ-SCs in the peripheral blood mononuclear cell population of the infected pigs from 21 to 28 days post infection than the PCV2b-J isolate did. The concentrations of IL-2 were transiently different between the PCV1-2b and PCV2b-J infected pigs, while those of IL-10 and IL-2 were similar in both groups, but were lower than those elicited in mice. These results indicated that BALB/c mouse could be used as an alternate model for evaluating the efficacy of attenuated PCV1-2b vaccines.

Secretome profiling identifies neuron-derived neurotrophic factor as a tumor-suppressive factor in lung cancer

Clinical and preclinical studies show tissue-specific differences in tumorigenesis. Tissue specificity is controlled by differential gene expression. We prioritized genes that encode secreted proteins according to their preferential expression in normal lungs to identify candidates associated with lung cancer. Indeed, most of the lung-enriched genes identified in our analysis have known or suspected roles in lung cancer. We focused on the gene encoding neuron-derived neurotrophic factor (NDNF), which had not yet been associated with lung cancer. We determined that NDNF was preferentially expressed in the normal adult lung and that its expression was decreased in human lung adenocarcinoma and a mouse model of this cancer. Higher expression of NDNF was associated with better clinical outcome of patients with lung adenocarcinoma. Purified NDNF inhibited proliferation of lung cancer cells, whereas silencing NDNF promoted tumor cell growth in culture and in xenograft models. We determined that NDNF is downregulated through DNA hypermethylation near CpG island shores in human lung adenocarcinoma. Furthermore, the lung cancer-related DNA hypermethylation sites corresponded to the methylation sites that occurred in tissues with low NDNF expression. Thus, by analyzing the tissue-specific secretome, we identified a tumor-suppressive factor, NDNF, which is associated with patient outcomes in lung adenocarcinoma.

Efficacy of the Bartha-K61 vaccine and a gE-/gI-/TK- prototype vaccine against variant porcine pseudorabies virus (vPRV) in piglets with sublethal challenge of vPRV

Pseudorabies has caused huge economic losses in China's pig industry and recurred on many large pig farms since late 2011. The disease is caused by highly pathogenic, antigenic variant pseudorabies virus (vPRV) strains. Therefore, the prevention and control of this recurrence of pseudorabies in China has been given priority. In a previous study, we showed that a suitable dose [1 × 10^6.3 50% tissue culture infectious dose (TCID₅₀) per animal] of commercial Bartha-K61 vaccine protects growing pigs against lethal challenge by the emerging vPRV strain XJ5. In this study, different doses of the Bartha-K61 vaccine and our newly developed rPRV-gI^-/gE^-/TK^- prototype vaccine derived from the vPRV strain XJ5 were used to evaluate immune protection against sublethal challenge by the vPRV strain XJ5. Pigs vaccinated with high doses of the Bartha-K61 vaccine or rPRV-gI^-/gE^-/TK^- prototype vaccine showed no differences in their humoral immune responses, clinical symptoms, body weight gains, viral shedding, or gross and histological lesions after sublethal challenge by the vPRV strain XJ5. Therefore, we concluded that the Bartha-K61 vaccine at a dose of 1 × 10⁵ TCID₅₀ per animal protects pigs against sublethal challenge by the vPRV strain XJ5 and performs equally well as the same dose of the rPRV-gI^-/gE^-/TK^- vaccine, whereas lower doses of the Bartha-K61 vaccine alone do not protect pigs from this challenge. These findings provide useful information for vaccination interventions and the ultimate eradication of pseudorabies caused by vPRV strains emerging in China.

Predicting CTCF-mediated chromatin interactions by integrating genomic and epigenomic features

The CCCTC-binding zinc-finger protein (CTCF)-mediated network of long-range chromatin interactions is important for genome organization and function. Although this network has been considered largely invariant, we find that it exhibits extensive cell-type-specific interactions that contribute to cell identity. Here, we present Lollipop, a machine-learning framework, which predicts CTCF-mediated long-range interactions using genomic and epigenomic features. Using ChIA-PET data as benchmark, we demonstrate that Lollipop accurately predicts CTCF-mediated chromatin interactions both within and across cell types, and outperforms other methods based only on CTCF motif orientation. Predictions are confirmed computationally and experimentally by Chromatin Conformation Capture (3C). Moreover, our approach identifies other determinants of CTCF-mediated chromatin wiring, such as gene expression within the loops. Our study contributes to a better understanding about the underlying principles of CTCF-mediated chromatin interactions and their impact on gene expression.

CTCF mediates long-range chromatin interactions which are important for genome organization and function. Here, the authors demonstrate that CTCF-mediated interactome exhibits extensive plasticity and present Lollipop, a machine-learning framework which predicts CTCF-mediated long-range interactions using genomic and epigenomic features.

Juvenile migration of the exclusively pelagic cyprinid, Gnathopogon caerulescens (Honmoroko) in Lake Biwa, Central Japan

Migration of wild and cultivated juvenile honmoroko Gnathopogon caerulescens of from the spawning and nursery areas in Lake Biwa were investigated, both in the Ibanaiko Lagoon and its outlet to Daido River, using beam-trawl surveys in 2013 and 2014. The study demonstrated migration of G. caerulescens from a nursery lagoon toward Lake Biwa after the juvenile stage. These findings appear to be the first direct evidence for migration of an exclusively pelagic cyprinid species from a littoral nursery to a pelagic adult habitat in a large deep lake.

DUOXA1-mediated ROS production promotes cisplatin resistance by activating ATR-Chk1 pathway in ovarian cancer

The acquisition of resistance is a major obstacle to the clinical use of platinum drugs for ovarian cancer treatment. Increase of DNA damage response is one of major mechanisms contributing to platinum-resistance. However, how DNA damage response is regulated in platinum-resistant ovarian cancer cells remains unclear. Using quantitative high throughput combinational screen (qHTCS) and RNA-sequencing (RNA-seq), we show that dual oxidase maturation factor 1 (DUOXA1) is overexpressed in platinum-resistant ovarian cancer cells, resulting in over production of reactive oxygen species (ROS). Elevated ROS level sustains the activation of ATR-Chk1 pathway, leading to resistance to cisplatin in ovarian cancer cells. Moreover, using qHTCS we identified two Chk1 inhibitors (PF-477736 and AZD7762) that re-sensitize resistant cells to cisplatin. Blocking this novel pathway by inhibiting ROS, DUOXA1, ATR or Chk1 effectively overcomes cisplatin resistance in vitro and in vivo. Significantly, the clinical studies also confirm the activation of ATR and DOUXA1 in ovarian cancer patients, and elevated DOUXA1 or ATR-Chk1 pathway correlates with poor prognosis. Taken together, our findings not only reveal a novel mechanism regulating cisplatin resistance, but also provide multiple combinational strategies to overcome platinum-resistance in ovarian cancer.

Autocrine activation of JAK2 by IL-11 promotes platinum drug resistance

Antineoplastic platinum agents are used in first-line treatment of ovarian cancer, but treatment failure frequently results from platinum drug resistance. Emerging observations suggest a role of reactive oxygen species (ROS) in the resistance of cancer drugs including platinum drugs. However, the molecular link between ROS and cellular survival pathway is poorly understood. Using quantitative high-throughput combinational screen (qHTCS) and genomic sequencing, we show that in platinum-resistant ovarian cancer elevated ROS levels sustain high level of IL-11 by stimulating FRA1-mediated IL-11 expression and increased IL-11 causes resistance to platinum drugs by constitutively activating JAK2-STAT5 via an autocrine mechanism. Inhibition of JAK2 by LY2784544 or IL-11 by anti-IL-11 antibody overcomes the platinum resistance in vitro or in vivo. Significantly, clinic studies also confirm the activated IL-11-JAK2 pathway in platinum-resistant ovarian cancer patients, which highly correlates with poor prognosis. These findings not only identify a novel ROS-IL-11-JAK2-mediated platinum resistance mechanism but also provide a new strategy for using LY2784544- or IL-11-mediated immunotherapy to treat platinum-resistant ovarian cancer.

Loss of KDM6A Activates Super-Enhancers to Induce Gender-Specific Squamous-like Pancreatic Cancer and Confers Sensitivity to BET Inhibitors

KDM6A, an X chromosome-encoded histone demethylase and member of the COMPASS-like complex, is frequently mutated in a broad spectrum of malignancies and contributes to oncogenesis with poorly characterized mechanisms. We found that KDM6A loss induced squamous-like, metastatic pancreatic cancer selectively in females through deregulation of the COMPASS-like complex and aberrant activation of super-enhancers regulating ΔNp63, MYC, and RUNX3 oncogenes. This subtype of tumor developed in males had concomitant loss of UTY and KDM6A, suggesting overlapping roles, and points to largely demethylase independent tumor suppressor functions. We also demonstrate that KDM6A-deficient pancreatic cancer is selectively sensitive to BET inhibitors, which reversed squamous differentiation and restrained tumor growth in vivo, highlighting a therapeutic niche for patient tailored therapies.

Genetic diversity and population structure of Hyporhamphus sajori (Beloniformes: Hemiramphidae) inferred from mtDNA control region and msDNA markers

This paper presents preliminary data on the genetic diversity and population structure of Hyporhamphus sajori by analysing a 510 bp sequence in the mitochondrial DNA (mtDNA) control region and eight polymorphic microsatellite DNA loci. The H. sajori individuals from different locations were indistinguishable from one another based on mtDNA variation, as demonstrated with a neighbour-joining tree and minimum spanning network analysis. Low level of genetic diversity and the absence of population structure in H. sajori from the north-west Pacific Ocean, combined with negative indices for neutral evolution in these populations, suggest that H. sajori underwent a population expansion after a recent bottleneck. The Structure analysis, discriminant analysis of principal components (DAPC) and the pair-wise Φ_ST values after Bonferroni correction using eight microsatellite loci provided no clear inference on the genetic differentiation and thus no evidence of population structure of H. sajori. The genetic connectivity among locations might be due to fairly high gene flow via transport of eggs and larvae by the Kuroshio and Tsushima warm current. This study revealed low levels of genetic diversity and suggested high level of contemporary gene flow among populations of H. sajori in the East (Japan) Sea and the Pacific Ocean.

Foramen Magnum Dural Arteriovenous Fistulae with Repeated Subarachnoid Haemorrhage

We report a patient who had dural arteriovenous fistulae in the region of the foramen magnum with repeated subarachnoid haemorrhage. Magnetic resonance imaging revealed abnormal vascular structures on the right side of the medulla oblongata in an extra-axial portion.

Angiographic findings showed that the lesion was supplied from the meningeal arteries and drained directly into the subarachnoid vein. There was venous dilatation. Embolisation was performed via the transarterial approach using a micro coil and liquid material.

Three years after treatment, the patients' condition is good and follow-up angiograms confirmed the stability of the treatment outcome. While dural arteriovenous fistulae of the foramen magnum are rare, this malformation results in a high rate of bleeding and requires treatment.

Lysine-specific histone demethylases in normal and malignant hematopoiesis

The epigenetic control of gene expression is central to the development of the hematopoietic system and the execution of lineage-specific transcriptional programs. During the last 10 years, mounting evidence has implicated the family of lysine-specific histone demethylases as critical regulators of normal hematopoiesis, whereas their deregulation is found in a broad spectrum of hematopoietic malignancies. Here, we review recent findings on the role of these enzymes in normal and malignant hematopoiesis and highlight how aberrant epigenetic regulation facilitates hematopoietic cell transformation through subversion of cell fate and lineage commitment programs.

dbVar structural variant cluster set for data analysis and variant comparison

dbVar houses over 3 million submitted structural variants (SSV) from 120 human studies including copy number variations (CNV), insertions, deletions, inversions, translocations, and complex chromosomal rearrangements. Users can submit multiple SSVs to dbVAR  that are presumably identical, but were ascertained by different platforms and samples,  to calculate whether the variant is rare or common in the population and allow for cross validation. However, because SSV genomic location reporting can vary – including fuzzy locations where the start and/or end points are not precisely known – analysis, comparison, annotation, and reporting of SSVs across studies can be difficult. This project was initiated by the Structural Variant Comparison Group for the purpose of generating a non-redundant set of genomic regions defined by counts of concordance for all human SSVs placed on RefSeq assembly GRCh38 (RefSeq accession GCF_000001405.26). We intend that the availability of these regions, called structural variant clusters (SVCs), will facilitate the analysis, annotation, and exchange of SV data and allow for simplified display in genomic sequence viewers for improved variant interpretation. Sets of SVCs were generated by variant type for each of the 120 studies as well as for a combined set across all studies. Starting from 3.64 million SSVs, 2.5 million and 3.4 million non-redundant SVCs with count >=1 were generated by variant type for each study and across all studies, respectively. In addition, we have developed utilities for annotating, searching, and filtering SVC data in GVF format for computing summary statistics, exporting data for genomic viewers, and annotating the SVC using external data sources.

Histone demethylase KDM2B regulates lineage commitment in normal and malignant hematopoiesis

The development of the hematopoietic system is a dynamic process that is controlled by the interplay between transcriptional and epigenetic networks to determine cellular identity. These networks are critical for lineage specification and are frequently dysregulated in leukemias. Here, we identified histone demethylase KDM2B as a critical regulator of definitive hematopoiesis and lineage commitment of murine hematopoietic stem and progenitor cells (HSPCs). RNA sequencing of Kdm2b-null HSPCs and genome-wide ChIP studies in human leukemias revealed that KDM2B cooperates with polycomb and trithorax complexes to regulate differentiation, lineage choice, cytokine signaling, and cell cycle. Furthermore, we demonstrated that KDM2B exhibits a dichotomous role in hematopoietic malignancies. Specifically, we determined that KDM2B maintains lymphoid leukemias, but restrains RAS-driven myeloid transformation. Our study reveals that KDM2B is an important mediator of hematopoietic cell development and has opposing roles in tumor progression that are dependent on cellular context.

Synthesis of Ag nanoparticles decorated MnO2/sulfonated graphene composites with 3D macroporous structure for high performance capacitors electrode materials

3D porous Ag–MnO₂/SG composites with high rate performance and low charge transfer resistance was synthesized.

The M, F and HN genes of genotype VIId Newcastle disease virus are associated with the severe pathological changes in the spleen of chickens

BACKGROUND

The strains of the genotype VIId Newcastle disease virus (NDV) induce more severe tissue damage in lymphoid organs than other virulent strains. The underlying molecular mechanisms are poorly understood.

METHODS

Genotype IV NDV Herts/33 and genotype VIId NDV JS5/05 have a distinctive pathological profile in the spleen. These two strains of viruses were selected as parental viruses to generate a panel of chimeric viruses by replacing the M, F and HN genes of Herts/33 individually or in combination with the corresponding genes of JS5/05 using reverse genetic. Virulence and in vitro characteristics of the recombinant viruses were assessed. In addition, pathological changes, virus load, and transcriptional cytokine response in the spleen of chickens infected with these recombinant viruses were also analyzed.

RESULTS

Pathogenicity test showed that all chimeric viruses are virulent. In vitro characterization revealed that gene replacement did not change growth kinetics and HN expression on cell surface of the recombinant viruses. However, replacement of the M, F and HN genes resulted in apparent changes in the fusion activity. Moreover, pathological studies revealed that only inclusion of the homologous M, F and HN genes of JS5/05 in Herts/33 backbone resulted in severe pathological changes characterized by extensive necrosis in the spleen, similar to that induced by JS5/05. In addition, this gene replacement significantly increased virus replication and the levels of transcriptional cytokine response, compared to Herts/33. Conversely, inclusion of the M, F and HN genes of Herts/33 into JS5/05 backbone resulted in Herts/33-specific pathological changes and significantly decreased virus load and the expression levels of cytokine genes, compared to JS5/05.

CONCLUSIONS

The M, F and HN genes are related to the severe pathological changes in the spleen of chickens infected with genotype VIId NDV.

Diel patterns of larval drift of honmoroko Gnathopogon caerulescens in an inlet of Ibanaiko Lagoon, Lake Biwa, Japan

Diel drift patterns of larvae of the endangered cyprinid Gnathopogon caerelescens in an inlet of the Ibanaiko Lagoon, connected to Lake Biwa in Japan, were assessed in April 2012. Peak occurrence of yolk-sac larvae was within a few hours after dark. Drift of newly hatched larvae is considered to be an important biological mechanism that ensures larval dispersal and recruitment from the inlets (spawning grounds) to the lagoon which functions as a nursery ground.