Development of an m6A-Related lncRNAs Signature Predicts Tumor Stemness and Prognosis for Low-Grade Glioma Patients

Background

Growing evidence has revealed that m6A modification of long noncoding RNAs (lncRNAs) dynamically controls tumor stemness and tumorigenesis-related processes. However, the prognostic significance of m6A-related lncRNAs and their associations with stemness in low-grade glioma (LGG) remain to be clarified.

Methods

A multicenter transcriptome analysis of lncRNA expression in 1,247 LGG samples was performed in this study. The stemness landscape of LGG tumors was presented and associations with clinical features were revealed. The m6A-related lncRNAs were identified between stemness groups and were further prioritized via least absolute shrinkage and selection operator Cox regression analysis. A risk score model based on m6A-related lncRNAs was constructed and validated in external LGG datasets.

Results

Based on the expression of LINC02984, PFKP-DT, and CRNDE, a risk model and nomogram were constructed; they successfully predicted the survival of patients and were extended to external datasets. Significant correlations were observed between the risk score and tumor stemness. Moreover, patients in different risk groups exhibited distinct tumor immune microenvironments and immune signatures. We finally provided several potential compounds suitable for specific risk groups, which may aid in LGG treatment.

Conclusions

This novel signature presents noteworthy value in the prediction of prognosis and stemness status for LGG patients and will foster future research on the development of clinical regimens.

Identification of female-enriched and disease-associated microglia (FDAMic) contributes to sexual dimorphism in late-onset Alzheimer's disease

BACKGROUND

Late-onset Alzheimer's disease (LOAD) is the most common form of dementia; it disproportionally affects women in terms of both incidence rates and severity of progression. The cellular and molecular mechanisms underlying this clinical phenomenon remain elusive and ill-defined.

METHODS

In-depth analyses were performed with multiple human LOAD single-nucleus transcriptome datasets to thoroughly characterize cell populations in the cerebral cortex. ROSMAP bulk human brain tissue transcriptome and DNA methylome datasets were also included for validation. Detailed assessments of microglial cell subpopulations and their relevance to sex-biased changes at the tissue level were performed. Clinical trait associations, cell evolutionary trajectories, and transcription regulon analyses were conducted.

RESULTS

The relative numbers of functionally defective microglia were aberrantly increased uniquely among affected females. Substratification of the microglia into different subtypes according to their transcriptomic signatures identified a group of female-enriched and disease-associated microglia (FDAMic), the numbers of which were positively associated with disease severity. Phenotypically, these cells exhibit transcriptomic signatures that support active proliferation, MHC class II autoantigen presentation and amyloid-β binding, but they are also likely defective in phagocytosis. FDAMic are likely evolved from female activated response microglia (ARMic) with an APOE4 background and compromised estrogen receptor (ER) signaling that is deemed to be active among most subtypes of microglia.

CONCLUSION

This study offered important insights at both the cellular and molecular levels into how ER signaling affects microglial heterogeneity and function. FDAMic are associated with more advanced pathologies and severe trends of cognitive decline. Their emergence could, at least in part, explain the phenomenon of greater penetrance of the APOE4 genotype found in females. The biases of FDAMic emergence toward female sex and APOE4 status may also explain why hormone replacement therapy is more effective in APOE4 carriers. The pathologic nature of FDAMic suggests that selective modulations of these cells may help to regain brain neuroimmune homeostasis, serving as a new target for future drug development.

Mapping enhancer and chromatin accessibility landscapes charts the regulatory network of Alzheimer's disease

BACKGROUND

Enhancers are regulatory elements that target and modulate gene expression and play a role in human health and disease. However, the roles of enhancer regulatory circuit abnormalities driven by epigenetic alterations in Alzheimer's disease (AD) are unclear.

METHODS

In this study, a multiomic integrative analysis was performed to map enhancer and chromatin accessibility landscapes and identify regulatory network abnormalities in AD. We identified differentially methylated enhancers and constructed regulatory networks across brain regions using AD brain tissue samples. Through the integration of snATAC-seq and snRNA-seq datasets, we mapped enhancers with DNA methylation alterations (DMA) and chromatin accessibility landscapes. Core regulatory triplets that contributed to AD neuropathology in specific cell types were further prioritized.

RESULTS

We revealed widespread DNA methylation alterations (DMA) in the enhancers of AD patients across different brain regions. In addition, the genome-wide transcription factor (TF) binding profiles showed that enhancers with DMA are pervasively regulated by TFs. The TF-enhancer-gene regulatory network analysis identified core regulatory triplets that are associated with brain and immune cell proportions and play important roles in AD pathogenesis. Enhancer regulatory circuits with DMA exhibited distinct chromatin accessibility patterns, which were further characterized at single-cell resolutions.

CONCLUSIONS

Our study comprehensively investigated DNA methylation-mediated regulatory circuit abnormalities and provided novel insights into the potential pathogenesis of AD.

Hollow CuS nanoparticles equipped with hydroxyapatite/hyaluronic acid coating for NIR/pH dual-responsive drug delivery

The near-infrared (NIR)/pH dual-responsive nanoplatform shows great potential in remote photothermal therapy for tumor on account of the near-infrared window in biological tissue and the mild acidic environment in tumor cells. CuS nanoplatform has become a rising star in the field of photothermal agents due to its excellent NIR responsiveness and photostability. In this work, hollow CuS nanoparticles with high photothermal conversion efficiency (42.42 %) were synthesized through a novel surfactant micelle-assisted method. Then, CuS@hydroxyapatite (HAP)/hyaluronic acid (HA) nanoclusters with controllable drug release property were prepared by capping HAP and HA on the surface of CuS via electrostatic self-assembly approach. The hollow structure of CuS and the large specific surface area of HAP ensure an outstanding doxorubicin hydrochloride (DOX) loading efficiency of 99.2 % in CuS@HAP/HA nanoclusters. The introduction of HA effectively retards the initial burst release of DOX and ensures the excellent biocompatibility of nanoclusters. More importantly, CuS@HAP/HA displays distinct NIR/pH dual-responsive drug release properties owing to the excellent NIR responsiveness of hollow CuS and the gradual dissolution of HAP under acidic conditions. This work provides an environmentally benign method to prepare CuS-based nanoclusters with excellent NIR/pH responsive drug delivery properties, which has great potential in remote photothermal therapy.

Molecular screening of Entamoeba spp. (E. histolytica, E. dispar, E. coli, and E. hartmanni) and Giardia intestinalis using PCR and sequencing

A wide range of intestinal protozoan parasites inhabit the human gut. To establish a more comprehensive molecular screening, we designed PCR-sequencing screening methods for Entamoeba spp., including commensal species, and Giardia intestinalis, and performed such methods using 174 stool samples collected from Kenyan children. The prevalences of the target species were as follows: E. histolytica (2/174, 1.1%), E. dispar (20/174, 11.5%), E. coli (107/174, 61.5%), E. hartmanni (77/174, 44.3%), and G. intestinalis (54/174, 31.0%). PCR amplicons specific to G. intestinalis was differentiated to assemblages A (8/174, 4.6%) and B (46/174, 26.4%). PCR specificity for Entamoeba spp. was quite high, except for some cross-reactions between E. hartmanni detection primers and G. intestinalis, although the false-positive amplicons were discernible by the band size. The 18S rRNA PCR primers that was designed by Monis et al. in 1999 for G. intestinalis, have specificity issue, therefore amplicon sequencing was essential not only to determine assemblage classifications but also to confirm the positive results by eliminating potential non-specific reactions. The detection sensitivity of both the Entamoeba universal PCR and the G. intestinalis PCR was more than 100 copies of the target loci, which is sufficient for detecting a single trophozoite or cyst of both species.

Pan-cancer analyses reveal multi-omic signatures and clinical implementations of the forkhead-box gene family

BACKGROUND

Forkhead box (FOX) proteins belong to one of the largest transcription factor families and play crucial roles in the initiation and progression of cancer. Prior research has linked several FOX genes, such as FOXA1 and FOXM1, to the crucial process of carcinogenesis. However, the overall picture of FOX gene family across human cancers is far from clear.

METHODS

To investigate the broad molecular signatures of the FOX gene family, we conducted study on multi-omics data (including genomics, epigenomics and transcriptomics) from over 11,000 patients with 33 different types of human cancers.

RESULTS

Pan-cancer analysis reveals that FOX gene mutations were found in 17.4% of tumor patients with a substantial cancer type-dependent pattern. Additionally, high expression heterogeneity of FOX genes across cancer types was discovered, which can be partially attributed to the genomic or epigenomic alteration. Co-expression network analysis reveals that FOX genes may exert functions by regulating the expression of both their own and target genes. For a clinical standpoint, we provided 103 FOX gene-drug target-drug predictions and found FOX gene expression have potential survival predictive value. All of the results have been included in the FOX2Cancer database, which is freely accessible at http://hainmu-biobigdata.com/FOX2Cancer.

CONCLUSION

Our findings may provide a better understanding of roles FOX genes played in the development of tumors, and help to offer new avenues for uncovering tumorigenesis and unprecedented therapeutic targets.

[Bioinformatics analysis and prokaryotic expression of Strongyloides stercoralis serine protease inhibitor 1]

OBJECTIVE

To predict the structure and antigenic epitope of the Strongyloides stercoralis serine protease inhibitor 1 (Ss-SRPN-1) protein using bioinformatics tools, and to construct prokaryotic expression plasmids for expression of recombinant Ss-SRPN-1 protein, so as to provide the basis for unraveling the function of the Ss-SRPN-1 protein.

METHODS

The amino acid sequence of the Ss-SRPN-1 protein was downloaded from the NCBI database, and the physicochemical properties, structure and antigenic epitopes of the Ss-SRPN-1 protein were predicted using bioinformatics tools, including ExPASy, SWISS-MODEL and Protean. Primers were designed according to the nucleotide sequences of Ss-SRPN-1, and the Ss-SRPN-1 gene was amplified, cloned and sequenced with genomic DNA extracted from the infective third-stage larvae of S. stercoralis as a template. The Ss-SRPN-1 protein sequence was cloned into the pET28a (+) expression vector and transformed into Escherichia coli BL21 (DE) cells for induction of the recombinant Ss-SRPN-1 protein expression. The recombinant Ss-SRPN-1 protein was then purified and identified using Western blotting and mass spectrometry.

RESULTS

Bioinformatics analysis showed that the Ss-SRPN-1 protein, which was composed of 372 amino acids and had a molecular formula of C₁₉₄₈H₃₀₄₆N₄₈₈O₅₇₅S₁₆, was a stable hydrophilic protein, and the subcellular localization of the protein was predicted to be extracellular. The Ss-SRPN-1 protein was predicted to contain 11 dominant B-cell antigenic epitopes and 20 T-cell antigenic epitopes. The Ss-SRPN-1 gene with a length of 1 119 bp was successfully amplified, and the recombinant plasmid pET28a (+)/Ss-SRPN-1 was constructed and transformed into E. coli BL21(DE) cells. The expressed recombinant Ss-SRPN-1 protein had a molecular weight of approximately 43 kDa, and was characterized as a Ss-SRPN-1 protein.

CONCLUSIONS

The recombinant Ss-SRPN-1 protein has been expressed successfully, and this recombinant protein may be a potential vaccine candidate against strongyloidiasis.

[Expression of CD47 and its ligands in pregnant mice infected with Toxoplasma gondii during pregnancy]

OBJECTIVE

To investigate the dynamic expression of cluster of differentiation 47 (CD47) and its ligands signaling regulatory protein α (SIRPα) and thrombospondin-1 (TSP-1) in mice infected with Toxoplasma gondii in the second and third trimesters.

METHODS

C57BL/6J mice (6 to 8 weeks old) were used for modeling T. gondii infection in the first trimester, and the pregnant mice were randomly divided into the normal control and infection groups, of 10 mice in each group. Pregnant mice in the infection group were intraperitoneally injected with 150 T. gondii tachyzoites on gestational day (Gd) 6.5, while pregnant mice in the normal control group were intraperitoneally injected with the same volume of physiological saline at the same time. The uterine and placental specimens were collected from all pregnant mice on Gd12.5 and Gd18.5, and the pregnant outcomes were recorded. The pathological damages of mouse uterine and placental specimens were observed using hematoxylin-eosin (HE) staining on Gd12.5 and Gd18.5. The relative expression of CD47, SIRPα, TSP-1, surface antigen 1 (SAG1), interferon-γ (IFN-γ), interleukin-2 (IL-2), IL-4 and IL-13 mRNA was quantified in mouse uterine and placental specimens using real-time fluorescence quantitative PCR (qPCR) assay, and the CD47, SIRPα, TSP-1 expression was determined in mouse uterine and placental specimens using immunohistochemical staining.

RESULTS

As compared with those in the normal control group, the pregnant mice in the infection group showed back arching, bristling, trembling and listlessness during pregnancy, and several mice presented virginal bleeding and abortion. Pathological examinations showed inflammatory cell infiltration, congestion and necrosis in uterine and placental specimens of pregnant mice in the infection group, a higher abortion rate of pregnant mice was seen in the infection group than in the normal control group on Gd12.5 (χ² = 20.405, P < 0.001) and Gd18.5 (χ² = 28.644, P < 0.001). qPCR assay showed significant differences in the expression of CD47, SIRPα, TSP-1, SAG1, INF-γ, IL-2, IL-4 and IL-13 genes in mouse placental specimens between the normal control and infection groups on Gd12.5 and Gd18.5 [F' (F) = 37.511, 29.337, 97.343, 53.755, 67.188, 21.145, 8.658 and 13.930, all P values < 0.001]. Higher CD47, SIRPα and TSP-1 gene expression was quantified in mouse placental specimens in the infection group than in the normal control group on Gd12.5 (all P values < 0.01), and lower CD47, SIRPα and TSP-1 gene expression was quantified in the infection group than in the normal control group on Gd18.5 (all P values < 0.001), while higher SAG1 gene expression was detected in placental specimens of pregnant mice in the infection group than in the normal control group on Gd12.5 and Gd18.5 (both P values < 0.01). In addition, higher INF-γ and IL-2 expression and lower IL-4 and IL-13 expression was detected in mouse placental specimens in the infection group than in the normal control group on Gd12.5 and Gd18.5 (all P values < 0.001), and there were significant differences in the CD47, SIRPα, TSP-1, SAG1, INF-γ, IL-2, IL-4 and IL-13 gene expression in uterine specimens of pregnant mice between the normal control and infection groups on Gd12.5 and Gd18.5 [H(F' and F) = 14.951, 25.977, 18.711, 48.595, 39.318, 14.248 and 15.468, all P values < 0.01], and higher CD47 and TSP-1 expression was detected in mouse uterine specimens in the infection group than in the control group on Gd12.5 and Gd18.5 (all P values < 0.01); however, no significant difference was found in the SIRPα expression (P > 0.05). Higher SAG1 expression was detected in uterine specimens of pregnant mice in the infection group than in the normal control group on Gd12.5 and Gd18.5 (both P values < 0.01), and higher INF-γ and IL-2 gene expression and lower IL-4 and IL-13 gene expression was found in the placental specimens of pregnant mice in the infection group than in the normal control group on Gd12.5 and Gd18.5 (all P values < 0.001). Spearman correlation analysis showed that the CD47 gene expression correlated positively with IFN-γ (r_s = 0.735, P < 0.05) and IL-2 (r_s = 0.655, P < 0.05) and negatively with IL-4 (r_s = -0.689, P < 0.05) and IL-13 expression (r_s = -0.795, P < 0.05) in the placental specimens of pregnant mice in the infection group on Gd12.5, and the CD47 gene expression correlated negatively with IFN-γ (r_s = -0.745, P < 0.05) and IL-2 expression (r_s = -0.816, P < 0.05) and positively with IL-4 (r_s = 0.704, P < 0.05) and IL-13 (r_s = 0.802, P < 0.05) in the placental specimens of pregnant mice in the infection group on Gd18.5. Immunohistochemical staining showed mild CD47, SIRPα and TSP-1 expression in uterine and placental specimens of pregnant mice in the normal control group on Gd12.5 and Gd18.5, strong CD47, SIRPα and TSP-1 expression in the placental specimens of pregnant mice in the infection group on Gd12.5 and strong CD47 and TSP-1 expression in the uterine specimens of pregnant mice in the infection group on Gd12.5.

CONCLUSIONS

T. gondii infection in the first trimester may cause abnormal expression of CD47 and its ligands SIRPα and TSP-1 in the maternal-fetal interface of pregnant mice in the second and third trimesters, which may be associated with the immune escape of T. gondii at the maternal-fetal interface.

Enhanced insulin-regulated phagocytic activities support extreme health span and longevity in multiple populations

The immune system plays a central role in many processes of age-related disorders and it remains unclear if the innate immune system may play roles in shaping extreme longevity. By an integrated analysis with multiple bulk and single cell transcriptomic, so as DNA methylomic datasets of white blood cells, a previously unappreciated yet commonly activated status of the innate monocyte phagocytic activities is identified. Detailed analyses revealed that the life cycle of these monocytes is enhanced and primed to a M2-like macrophage phenotype. Functional characterization unexpectedly revealed an insulin-driven immunometabolic network which supports multiple aspects of phagocytosis. Such reprogramming is associated to a skewed trend of DNA demethylation at the promoter regions of multiple phagocytic genes, so as a direct transcriptional effect induced by nuclear-localized insulin receptor. Together, these highlighted that preservation of insulin sensitivity is a key to healthy lifespan and extended longevity, via boosting the function of innate immune system in advanced ages.

Epigenetically regulated lncRNAs dissect the intratumoural heterogeneity and facilitate immune evasion of glioblastomas

Background: Glioblastomas are the most common and malignant central nervous system (CNS) tumors that occupied a highly heterogeneous tumor microenvironment (TIME). Long noncoding RNAs (lncRNAs), whose expression can be modified by DNA methylation, are emerging as critical regulators in the immune system. However, knowledge about the epigenetic changes in lncRNAs and their contribution to the immune heterogeneity of glioma is still lacking. Methods: In this study, we integrated paired methylome and transcriptome datasets of glioblastomas and identified 2 robust immune subtypes based on lncRNA methylation features. The immune characteristics of glioma subtypes were compared. Furthermore, immune-related lncRNAs were identified and their relationships with immune evasion were evaluated. Results: Glioma immunophenotypes exhibited distinct immune-related characteristics as well as clinical and epigenetic features. 149 epigenetically regulated (ER) lncRNAs were recognized that possessed inverse variation in epigenetic and transcriptional levels between glioma subtypes. Immune-related lncRNAs were further identified through the investigation of their correlation with immune cell infiltrations and immune-related pathways. In particular, the 'Hot' glioma subtype with higher immunoactivity while a worse survival outcome was found to character immune evasion features. We finally prioritized candidate ER lncRNAs associated with immune evasion markers and response to glioma immunotherapy. Among them, CD109-AS1 and LINC02447 were validated as novel immunoevasive biomarkers for glioma through in vitro experiments. Conclusion: In summary, our study systematically reveals the crosstalk among DNA methylation, lncRNA, and immune regulation in glioblastomas, and will facilitate the development of epigenetic immunotherapy approaches.

HCDT: an integrated highly confident drug-target resource

Drug-target association plays an important role in drug discovery, drug repositioning, drug synergy prediction, etc. Currently, a lot of drug-related databases, such as DrugBank and BindingDB, have emerged. However, these databases are separate, incomplete and non-uniform with different criteria. Here, we integrated eight drug-related databases; collected, filtered and supplemented drugs, target genes and experimentally validated (highly confident) associations and built a highly confident drug-target (HCDT: http://hainmu-biobigdata.com/hcdt) database. HCDT database includes 500 681 HCDT associations between 299 458 drugs and 5618 target genes. Compared to individual databases, HCDT database contains 1.1 to 254.2 times drugs, 1.8-5.5 times target genes and 1.4-27.7 times drug-target associations. It is normative, publicly available and easy for searching, browsing and downloading. Together with multi-omics data, it will be a good resource in analyzing the drug functional mechanism, mining drug-related biological pathways, predicting drug synergy, etc. Database URL: http://hainmu-biobigdata.com/hcdt.

Clinical and genetic characterization of Epstein-Barr virus-associated T/NK-cell lymphoproliferative diseases

BACKGROUND

Epstein-Barr virus (EBV)-associated T-/natural killer (T/NK)-cell lymphoproliferative diseases clinically take on various forms, ranging from an indolent course to an aggressive condition.

OBJECTIVE

Clinically, failure to establish precise diagnosis and provide proper treatment makes it difficult to help patients. We sought to better understand the underlying pathogenesis and to identify genetic prognostic factors to achieve better treatment efficacy.

METHODS

In this study, 119 cases of EBV-associated lymphoproliferative diseases, including EBV-associated hemophagocytic lymphohistiocytosis (n = 46) and chronic active EBV disease of T/NK cell type (n = 73), were retrospectively examined.

RESULTS

Adults aged >20 years at onset accounted for 71.4% of our cohort. About 54.6% patients with unfavorable overall survival developed hemophagocytic lymphohistiocytosis and had higher plasma EBV load. Allogenic hematopoietic stem-cell transplantation was the sole independent favorable factor. We systematically screened germline and somatic aberrations by whole-exome and targeted sequencing. Among 372 antiviral immunity genes, germline variants of 8 genes were significantly enriched. From a panel of 24 driver genes, somatic mutations were frequently identified in dominant EBV-infected T/NK cells. Patients carrying any germline/somatic aberrations in epigenetic modifiers and RIG-I-like receptor (RLR) pathway had worse overall survival than those without 2 type aberrations. Importantly, patients with IFIH1 and/or DDX3X aberrations in the RLR pathway had higher plasma and NK-cell EBV load. Knockdown of DDX3X in NKYS cells downregulated RLR signaling activities and elevated the expression of EBV-encoded oncogenes such as LMP1 and EBNA1.

CONCLUSION

Genetic defects were prevalent in adult EBV-associated hemophagocytic lymphohistiocytosis patients and patients with chronic active EBV disease of T/NK cell type; these defects were associated with unfavorable prognosis. These findings can help clinicians work out more precise staging of the condition and provide new insights into these EBV-associated diseases.

NBAS, a gene involved in cytotoxic degranulation, is recurrently mutated in pediatric hemophagocytic lymphohistiocytosis

Hemophagocytic lymphohistiocytosis (HLH), particularly primary HLH (pHLH), is a rare, life-threatening disease. Germline genetic deficiency of 12 known HLH genes impairs cytotoxic degranulation in natural killer (NK) cells or cytotoxic T lymphocytes (CTLs) and contributes to pHLH development. However, no pathogenic mutations in these HLH genes are found in nearly 10% of HLH patients, despite a strong suspicion of pHLH, suggesting that the underlying genetic basis of HLH is still unclear. To discover novel susceptibility genes, we first selected 13 children with ppHLH (presumed primary HLH patients in the absence of detectable known HLH gene variants) and their parents for initial screening. Whole-genome sequencing (WGS) in one trio and whole-exome sequencing (WES) in twelve trios revealed that two ppHLH patients carried biallelic NBAS variants, a gene that is involved in Golgi-to-endoplasmic reticulum (ER) retrograde transport upstream of the degranulation pathway. Additionally, two candidate genes, RAB9B and KLC3, showed a direct relationship with known HLH genes in protein-protein interaction (PPI) network analysis. We analyzed NBAS, RAB9B, KLC3 and known HLH genes in an independent validation cohort of 224 pediatric HLH patients. Only biallelic NBAS variants were identified in three patients who harbored no pathogenic variants in any of the known HLH genes. Functionally, impaired NK-cell cytotoxicity and degranulation were revealed in both NBAS biallelic variant patients and in an NBAS-deficient NK-cell line. Knockdown of NBAS in an NK-cell line (IMC-1) using short hairpin RNA (shRNA) resulted in loss of lytic granule polarization and a decreased number of cytotoxic vesicles near the Golgi apparatus. According to our findings, NBAS is the second most frequently mutated gene (2.11%) in our HLH cohort after PRF1. NBAS deficiency may contribute to the development of HLH via a dysregulated lytic vesicle transport pathway.

Identification and functional analysis of N6-methyladenine (m6 A)-related lncRNA across 33 cancer types

BACKGROUND

N6-methyladenosine (m⁶ A) plays an essential role in tumorigenesis and cancer progression. Long noncoding RNAs (lncRNAs) are discovered to be important targets of m⁶ A modification, and they play fundamental roles in diverse biological processes. However, there is still a lack of knowledge with regards to the association between m⁶ A and lncRNAs in human tumors.

METHODS

The relationship between lncRNAs and 21 m⁶ A regulators was comprehensively explored, through the integration of multi-omics data from M6A2Target, m6A-Atlas, and TCGA (The Cancer Genome Atlas). In order to explore the potential roles of m6A-related lncRNAs in human tumors, three applicable methods were introduced, which include the construction of ceRNA networks, drug sensitivity estimation, and survival analysis.

RESULTS

A substantial number of positive correlation events across 33 cancer types were found. Moreover, cancer-specific lncRNAs were associated with tissue specificity, and cancer-common lncRNAs were conserved in cancer-related biological function. In particular, the m⁶ A-related lncRNA FGD5-AS1 was found to be associated with cancer treatment, through its influence on cisplatin resistance in breast cancer patients. Finally, a user-friendly interface Lnc2m6A, which is enriched with various browsing sections resource for the exhibition of relationships and putative biogenesis between lncRNAs and m⁶ A modifications, is offered in http://hainmu-biobigdata.com/Lnc2m6A.

CONCLUSIONS

In summary, the results from this paper will provide a valuable resource that guides both mechanistic and therapeutic roles of m⁶ A-related lncRNAs in human tumors.

How placenta promotes the successful reproduction in high-altitude populations: a transcriptome comparison between adaptation and acclimatization

As the best adapted high altitude population, Tibetans feature a relatively high offspring survival rate. Genome-wide studies have identified hundreds of candidate SNPs related to high altitude adaptation of Tibetans, although most of them have unknown functional relevance. To explore the mechanisms behind successful reproduction at high altitudes, we compared the placental transcriptomes of Tibetans, sea level Hans (SLHan), and Han immigrants (ImHan). Among the three populations, placentas from ImHan showed a hyperactive gene expression pattern. Their increased activation demonstrates a hypoxic stress response similar to sea level individuals experiencing hypoxic conditions. Unlike ImHan, Tibetan placentas were characterized by the significant up-regulation of placenta-specific genes, and the activation of autophagy and the tricarboxylic acid (TCA) cycle. Certain conserved hypoxia response functions, including the antioxidant system and angiogenesis, were activated in both ImHan and Tibetans, but mediated by different genes. The coherence of specific transcriptome features linked to possible genetic contribution was observed in Tibetans. Furthermore, we identified a novel Tibetan-specific EPAS1 isoform with a partial deletion at exon six, which may be involved in the adaption to hypoxia through the EPAS1-centred gene network in the placenta. Overall, our results show that the placenta grants successful pregnancies in Tibetans by strengthening the natural functions of the placenta itself. On the other hand, the placenta of ImHan was in an inhabiting time-dependent acclimatization process representing a common hypoxic stress response pattern.

Comprehensive Analysis of the Carcinogenic Process, Tumor Microenvironment, and Drug Response in HPV-Positive Cancers

Human papillomavirus (HPV) is a common virus, and about 5% of all cancers worldwide is caused by persistent high-risk HPV infections. Here, we reported a comprehensive analysis of the molecular features for HPV-related cancer types using TCGA (The Cancer Genome Atlas) data with HPV status. We found that the HPV-positive cancer patients had a unique oncogenic process, tumor microenvironment, and drug response compared with HPV-negative patients. In addition, HPV improved overall survival for the four cancer types, namely, cervical squamous cell carcinoma (CESC), head and neck squamous cell carcinoma (HNSC), stomach adenocarcinoma (STAD), and uterine corpus endometrial carcinoma (UCEC). The stronger activity of cell-cycle pathways and lower driver gene mutation rates were observed in HPV-positive patients, which implied the different carcinogenic processes between HPV-positive and HPV-negative groups. The increased activities of immune cells and differences in metabolic pathways helped explain the heterogeneity of prognosis between the two groups. Furthermore, we constructed HPV prediction models for different cancers by the virus infection score (VIS) which was linearly correlated with HPV load and found that VIS was associated with drug response. Altogether, our study reveals that HPV-positive cancer patients have unique molecular characteristics which help the development of precision medicine in HPV-positive cancers.

Prognostic Implications and Immune Infiltration Characteristics of Chromosomal Instability-Related Dysregulated CeRNA in Lung Adenocarcinoma

An accumulating body of research indicates that long-noncoding RNAs (lncRNAs) regulate the target genes and act as competitive endogenous RNAs (ceRNAs) playing an indispensable role in lung adenocarcinoma (LUAD). LUAD is frequently accompanied by the feature of chromosomal instability (CIN); however, CIN-related ceRNAs have not been investigated yet. We systematically analyzed and integrated CIN-related dysregulated ceRNAs characteristics in LUAD samples for the first time. In TCGA LUAD cohort, CIN in tumor samples was significantly higher than that in those of adjacent, and patients with high CIN risk tended to have worse clinical outcomes. We constructed a double-weighted CIN-related dysregulated ceRNA network, in which edge weight and node weight represented the disorder extent of ceRNA and the correlation of RNA expression level and prognosis, respectively. After module mining and analysis, a potential prognostic biomarker composed of 12 RNAs (8 mRNAs and 4 lncRNAs) named CIN-related dysregulated ceRNAs (CRDC) was obtained. The CRDC risk score had a positive relation with clinical stage and CIN, and patients with high CRDC risk scores exhibited poor prognosis. Moreover, CRDC tended to be an independent risk factor with high robustness to overcome the effect of multicollinearity among other explanatory variables for disease-specific survival (DSS) in TCGA and two GEO cohorts. The result of functional analysis indicated that CRDC was involved in multiple cancer progresses, especially immune-related pathways. The patients with lower CRDC risk had higher B cell, T cell CD4+, T cell CD8+, neutrophil, macrophage, and myeloid dendritic cell infiltration than the patients with higher CRDC risk. Meanwhile, patients with lower CRDC risk could get more benefits from immunological therapy. The results suggested that the CRDC could be a potential prognostic biomarker and an immunotherapy predictor for lung adenocarcinoma.

A Pan-Cancer Analysis of Cystatin E/M Reveals Its Dual Functional Effects and Positive Regulation of Epithelial Cell in Human Tumors

Cystatin E/M (CST6), a representative cysteine protease inhibitor, plays both tumor-promoting and tumor-suppressing functions and is pursued as an epigenetically therapeutic target in special cancer types. However, a comprehensive and systematic analysis for CST6 in pan-cancer level is still lacking. In the present study, we explored the expression pattern of CST6 in multiple cancer types across ∼10,000 samples from TCGA (The Cancer Genome Atlas) and ∼8,000 samples from MMDs (Merged Microarray-acquired Datasets). We found that the dynamic expression alteration of CST6 was consistent with dual function in different types of cancer. In addition, we observed that the expression of CST6 was globally regulated by the DNA methylation in its promoter region. CST6 expression was positively correlated with the epithelial cell infiltration involved in epithelial-to-mesenchymal transition (EMT) and proliferation. The relationship between CST6 and tumor microenvironment was also explored. In particular, we found that CST6 serves a protective function in the process of melanoma metastasis. Finally, the clinical association analysis further revealed the dual function of CST6 in cancer, and a combination of the epithelial cell infiltration and CST6 expression could predict the prognosis for SKCM patients. In summary, this first CST6 pan-cancer study improves the understanding of the dual functional effects on CST6 in different types of human cancer.

Reduced Nonradiative Recombination Energy Loss Enabled Efficient Polymer Solar Cells via Tuning Alkyl Chain Positions on Pendent Benzene Units of Polymers

Nonradiative recombination energy loss (ΔE₃) plays a key role in enhancing device efficiencies for polymer solar cells (PSCs). Until now, there is no clear resolution for reducing ΔE₃ via molecular design. Herein, we report two conjugated polymers, PBDB-P-p and PBDB-P-m, which are integrated from benzo[1,2-b:4,5-b']dithiophene with alkylthio chain substituted at para- or meta-position on pendent benzene and benzo[1,2-c:4,5-c']dithiophene-4,8-dione. Both the polymers have different temperature-dependent aggregation properties but similar molecular energy levels. When BO-4Cl was used as an acceptor to fabricate PSCs, the device of PBDB-P-p:BO-4Cl displayed a maximal power conversion efficiency (PCE) of 13.83%, while the best device of PBDB-P-m:BO-4Cl exhibited a higher PCE of 14.12%. The close J_SCs and fill factors in both PSCs are attributed to their formation of effective nanoscale phase separation as confirmed by atomic force microscopy measurements. We find that the PBDB-P-m-based device has 1 order of magnitude higher electroluminescence quantum efficiency (EQE_EL) than in the PBDB-P-p-based one, which could arise from the relatively weak aggregation in the PBDB-P-m-based film. Thus, the PBDB-P-m-based device has a remarkably enhanced V_OC of 0.86 V in contrast to 0.80 V in the PBDB-P-p-based device. This study offers a feasible structural optimization way on the alkylthio side chain substitute position on the conjugated polymer to enhance V_OC by reducing nonradiative recombination energy loss in the resulting PSCs.

Cerebral Venous Thrombosis: MR Black-Blood Thrombus Imaging with Enhanced Blood Signal Suppression

BACKGROUND AND PURPOSE

The residual blood flow artifact is a critical confounder for MR black-blood thrombus imaging of cerebral venous sinus thrombosis. This study aimed to conduct a validation of a new MR black-blood thrombus imaging technique with enhanced blood signal suppression.

MATERIALS AND METHODS

Twenty-six participants (13 volunteers and 13 patients) underwent conventional imaging methods followed by 2 randomized black-blood thrombus imaging scans, with a preoptimized delay alternating with nutation for tailored excitation (DANTE) preparation switched on and off, respectively. The signal intensity of residual blood, thrombus, brain parenchyma, normal lumen, and noise on black-blood thrombus images were measured. The thrombus volume, SNR of residual blood, and contrast-to-noise ratio for residual blood versus normal lumen, thrombus versus residual blood, and brain parenchyma versus normal lumen were compared between the 2 black-blood thrombus imaging techniques. Segmental diagnosis of venous sinus thrombosis was evaluated for each black-blood thrombus imaging technique using a combination of conventional imaging techniques as a reference.

RESULTS

In the volunteer group, the SNR of residual blood (11.3 ± 2.9 versus 54.0 ± 23.4, P < .001) and residual blood-to-normal lumen contrast-to-noise ratio (7.5 ± 3.4 versus 49.2 ± 23.3, P < .001) were significantly reduced using the DANTE preparation. In the patient group, the SNR of residual blood (16.4 ± 8.0 versus 75.0 ± 35.1, P = .002) and residual blood-to-normal lumen contrast-to-noise ratio (12.4 ± 7.8 versus 68.8 ± 35.4, P = .002) were also significantly lower on DANTE-prepared black-blood thrombus imaging. The new black-blood thrombus imaging technique provided higher thrombus-to-residual blood contrast-to-noise ratio, significantly lower thrombus volume, and substantially improved diagnostic specificity and agreement with conventional imaging methods.

CONCLUSIONS

DANTE-prepared black-blood thrombus imaging is a reliable MR imaging technique for diagnosing cerebral venous sinus thrombosis.

[The protective effect of pigment epithelial-derived factor modified human umbilical cord mesenchymal stem cells on rats with diabetic retinopathy]

Objective: To investigate the effect of pigment epithelial-derived factor (PEDF) gene-modified human umbilical cord mesenchymal stem cells (MSC) on rats with diabetic retinopathy (DR). Methods: Experimental study. Human umbilical cord MSC were transfected by lentivirus packaging PEDF-MSC-green fluorescent protein (GFP) and GFP-MSC plasmid vectors, and the expression of PEDF and vascular endothelial growth factor (VEGF) was measured in the cell culture medium. Fifty adult male Sprague-Dawley rats were randomly divided into five groups: normal control group (group A), DR control group (group B), phosphate-buffered saline (PBS) treated group (group C), GFP-MSC treated group (group D) and PEDF-MSC-GFP treated group (group E), with 10 rats in each group. Streptozotocin was intraperitoneally injected to make early DR models. After four-month intervention, groups D and E were given intravitreal injection of GFP-MSC and PEDF-MSC-GFP; group C was given intravitreal injection of phosphate-buffered saline; groups A and B did not receive special treatment. The changes of retina in different groups were detected by hematoxylin and eosin staining, and the thickness of inner plexiform layer, inner nuclear layer and outer nuclear layer was measured by computer-based image analytical system. Immunohistochemistry was applied to observe PEDF and VEGF. Real-time quantitative polymerase chain reaction was used to detect the expression of PEDF and VEGF mRNA. Results: The expression of CD105, CD73 and CD90 was positive, while the expression of CD34, CD45, CD11b, CD19 and HLA-DR was negative. ELISA results showed that after transfection PEDF protein expression in the supernatant of PEDF-MSC (84.09±7.07) μg/L was higher than the control group (9.03±0.14) μg/L (P<0.05). At 2 weeks after intravitreal injection, green fluorescence was observed in the rat vitreous of groups D and E under a fluorescence microscope; no obvious green fluorescence was found in the retina. After 2 months of intravitreal injection, the thickness of inner plexiform layer in group E was significantly decreased; the thickness of inner nuclear layer and outer nuclear layer was higher (P<0.05). Immunohistochemical staining showed that 2 months after intravitreal treatment, the average optical density values of PEDF were improved, but the average optical density values of VEGF were decreased in group E (P<0.05). Real-time polymerase chain reaction showed that 2 months after treatment, the expression level of PEDF mRNA in group E was improved, but the expression level of VEGF mRNA was decreased (P<0.05). Conclusions: Intravitreal injection of PEDF-MSC could up-regulate the expression of PEDF and down-regulate the expression of VEGF in diabetic rats and may represent a novel candidate resource for cell therapy of DR nerve damage. (Chin J Ophthalmol, 2017, 53, 540-547).

Clinical, neuroimaging and prognostic study of 127 cases with infarction of the corpus callosum

Background and purpose

The aim of this study was to retrospectively investigate clinical and neuroimaging characteristics in the largest sample size of patients with corpus callosum infarction to date and then to follow up these patients for 1 year to clarify the prognosis of this rare stroke entity.

Methods

A total of 127 patients with acute callosal infarction out of 5584 acute ischaemic stroke patients were included in this study. The recruited patients were divided into a pure callosal infarction group and a complex callosal infarction group (coupled with other infarct locations simultaneously), and clinical and neuroimaging features were analyzed. Some of the patients were followed up for 1 year to evaluate recurrence rate and mortality.

Results

The incidence of acute callosal infarction was 2.3%. Most patients presented with advanced neurological dysfunction with or without mild to moderate motor or sensory disorders on admission. The negative rate of computed tomography scan was still 76.4% even at >24 h after onset. Large‐artery atherosclerosis was the most common etiological type. Compared with complex callosal infarction, the pure callosal infarction group had more mental disorders (P = 0.030). Compared with common basal ganglia infarction, the pure callosal infarction group had better short‐term recovery (P = 0.016) but higher 1‐year mortality (P = 0.037). Age and mental disorders were independent risk factors for death in callosal infarction.

Conclusions

Callosal infarction is a white matter stroke that occurs with low incidence. Elderly patients with vascular risk factors showed sudden mental or cognitive disorders and callosal infarction could not be excluded. More attention should be paid to the early diagnosis and secondary prevention of callosal infarction because of its poor long‐term outcome.

[Reliability and validity of the Chinese version on Comprehensive Scores for Financial Toxicity based on the patient-reported outcome measures]

Objective: To evaluate the reliability and validity of the Chinese version on comprehensive scores for financial toxicity (COST), based on the patient-reported outcome measures. Methods: A total of 118 cancer patients were face-to-face interviewed by well-trained investigators. Cronbach's α and Pearson correlation coefficient were used to evaluate reliability. Content validity index (CVI) and exploratory factor analysis (EFA) were used to evaluate the content validity and construct validity, respectively. Results: The Cronbach's α coefficient appeared as 0.889 for the whole questionnaire, with the results of test-retest were between 0.77 and 0.98. Scale-content validity index (S-CVI) appeared as 0.82, with item-content validity index (I-CVI) between 0.83 and 1.00. Two components were extracted from the Exploratory factor analysis, with cumulative rate as 68.04% and loading>0.60 on every item. Conclusion: The Chinese version of COST scale showed high reliability and good validity, thus can be applied to assess the financial situation in cancer patients.

An NIR-emitting lysosome-targeting probe with large Stokes shift via coupling cyanine and excited-state intramolecular proton transfer

An NIR-emitting probe (λ_em ∼ 700 nm) with a large Stokes shift (Δλ ≈ 234 nm) is synthesized by using excited-state intramolecular proton transfer (ESIPT). The phenolic proton, which controls ESIPT, acts as a switch to give strong fluorescence at pH ≈ 5. The probe can selectively show lysosome organelles, therefore leading to a lysosome probe without exhibiting "an alkalinizing effect".

Effect of Cation-π Interaction on Macroionic Self-Assembly

A series of rod-shaped polyoxometalates (POMs) [Bu₄ N]₇ [Mo₆ O₁₈ NC(CH₂ O)₃ MnMo₆ O₁₈ (OCH₂ )₃ CNMo₆ O₁₈ ] and [Bu₄ N]₇ [ArNMo₆ O₁₇ NC(CH₂ O)₃ MnMo₆ O₁₈ (OCH₂ )₃ CNMo₆ O₁₇ NAr] (Ar=2,6-dimethylphenyl, naphthyl and 1-methylnaphthyl) were chosen to study the effects of cation-π interaction on macroionic self-assembly. Diffusion ordered spectroscopy (DOSY) and isothermal titration calorimetry (ITC) techniques show that the binding affinity between the POMs and Zn²⁺ ions is enhanced significantly after grafting aromatic groups onto the clusters, leading to the effective replacement of tetrabutylammonium counterions (TBAs) upon the addition of ZnCl₂ . The incorporation of aromatic groups results in the significant contribution of cation-π interaction to the self-assembly, as confirmed by the opposite trend of assembly size vs. ionic strength when compared with those without aromatic groups. The small difference between two aromatic groups toward the Zn²⁺ ions is amplified after combining with the clusters, which consequently triggers the self-recognition behavior between two highly similar macroanions.

CCAAT enhancer binding protein β promotes tumor growth and inhibits apoptosis in prostate cancer by methylating estrogen receptor β

The CCAAT enhancer binding protein β (C/EBPβ) is overexpressed at late stages in carcinogenesis of prostate cancer (PCa), suggesting that it could potentially contribute to progression of PCa. Estrogen receptor beta (ERβ) is a tumor suppressor gene in PCa. However, whether C/EBPβ could regulate ERβ by promoter methylation is still poorly understood.In this study, expression levels of C/EBPβ and ERβ in two PC lines (LNCap and PC-3), prostatic epithelial cell line (RWPE-1), forty-eight paired non-cancerous and cancerous peripheral blood samples were examined via qRT-PCR, western blotting and methylation-specific PCR. In addition, PCa cell line was infected with pCDH-C/EBPβ and pLKO.1-C/EBPβ and expression levels of C/EBPβ, ERβ and DNA methyltransferases were detected. Finally, the role of C/EBPβ in proliferation and apoptosis of PCa cell lines was examined by MTT and flow cytometer assay. Our results show a higher frequency of promoter methylation of ERβ levels in blood samples from PCa patients (16 of 48 cases) compared with that from healthy controls (3 of 48). Besides, elevated expression levels of C/EBPβ were found in PCa patients and two PCa lines (LNCap and PC-3) compared to non-cancerous cases or prostatic epithelial cell line (RWPE-1), while opposite expression levels of ERβ were found. Overexpression of C/EBPβ could regulate ERβ expression, DNA methyltransferases expression, cell proliferation and apoptosis. Our results support the conclusion that C/EBPβ down-regulated ERβ expression through increasing its promoter methylation, and then regulated proliferation and apoptosis in PCa.

[The protective effect of human umbilical cord mesenchymal stem cells-induced neural stem cells in the vitreous on the blood-retinal barrier in diabetic rats]

Objective: To investigate the effect of intravitreal injection of neural stem cells (NSC) induced from human umbilical cord mesenchymal stem cells, and to provide a theoretical basis for the clinical treatment of blood-retinal barrier damage due to diabetic retinopathy (DR). Methods: Experimental study. Sixty male Sprague-Dawley rats were randomly divided into control group, DR group and NSC group. Diabetic rats were induced by injection of streptozotocin, and the control rats were injected with an equal volume of solvent. Three months after the establishment of diabetic models, the NSC group was injected with 2 μl of NSC in the right vitreous, and the DR group was injected with 2 μl of phosphate-buffered saline. One month later, all the rats were sacrificed. The retinal vessels and leakage were examined with flat-mounted retinas. Vascular permeability was quantified by analyzing albumin leakage using the Evans blue (EB) method. Retina was examined by hematoxylin and eosin staining. Results: Retinal blood vessels of the control rats were normal, with no EB leakage outside the vessels. The background fluorescence was enhanced and focal leakage and focal dilated vessels were detected in the DR group. In the NSC group, background fluorescence was enhanced slightly and EB leakage area decreased significantly compared with the DR group. The average EB in control group, DR group and NSC group were (9.91±1.53), (24.67±2.26) and (12.85±2.58)μg/g, The EB leakage in the NSC group decreased significantly compared with the DR group (q=9.748, P<0.05). Pathological hematoxylin and eosin staining showed that the retinal layer structure was normal and clear in the control group, the retina was thin, the cell arrangement was in disorder and the nucleus was swelling in the DR group, the status of the NSC group was between the other two groups. Conclusions: Transferring human umbilical cord mesenchymal stem cells-induced NSC in vitro to diabetic rat models by intravitreal injection could reduce leakage of blood vessels and attenuate blood-retinal barrier breakdown induced by diabetes. (Chin J Ophthalmol, 2017, 53: 53-58).

Solvatochromic fluorescent probes for recognition of human serum albumin in aqueous solution: Insights into structure-property relationship

Human serum albumin (HSA) as the most abundant protein in human blood plasma, serves many physiological functions. The dysregulation of HSA in serum or in urine is associated with various diseases, such as cirrhosis of liver, multiple myeloma, and cardiovascular disease. Therefore, to quantify HSA in body fluids with high selectivity and sensitivity is of great significance for disease diagnosis and preventive medicine. We herein developed a series of amide-functionalized flavonoids probes, 1-3, for recognition of human serum albumin. All flavonoids could be easily prepared by a Claisen-Schmidt condensation and Algar-Flynn-Oyamada reaction, and showed positive solvatochromism on their dual emissions. The chemical structure of flavonoids played an important role on their HSA-sensing abilities. Among three probes, the compound 1 showed the highest sensitivity, the remarkable selectivity, and the quantitive response for HSA in aqueous solution. Together with its high tolerance of environmental pH, anti-interference properties, and time-insensitivity, thus it provides a promising sensing method for HSA.