Prediction of intraoperative cerebrospinal fluid leaks in endoscopic endonasal transsphenoidal pituitary surgery based on a deep neural network model trained with MRI images: a pilot study.

Objective: This study aimed to investigate the reliability of a deep neural network (DNN) model trained only on contrast-enhanced T1 (T1CE) images for predicting intraoperative cerebrospinal fluid (ioCSF) leaks in endoscopic transsphenoidal surgery (EETS). Methods: 396 pituitary adenoma (PA) cases were reviewed, only primary PAs with Hardy suprasellar Stages A, B, and C were included in this study. The T1CE images of these patients were collected, and sagittal and coronal T1CE slices were selected for training the DNN model. The model performance was evaluated and tested, and its interpretability was explored. Results: A total of 102 PA cases were enrolled in this study, 51 from the ioCSF leakage group, and 51 from the non-ioCSF leakage group. 306 sagittal and 306 coronal T1CE slices were collected as the original dataset, and data augmentation was applied before model training and testing. In the test dataset, the DNN model provided a single-slice prediction accuracy of 97.29%, a sensitivity of 98.25%, and a specificity of 96.35%. In clinical test, the accuracy of the DNN model in predicting ioCSF leaks in patients reached 84.6%. The feature maps of the model were visualized and the regions of interest for prediction were the tumor roof and suprasellar region. Conclusion: In this study, the DNN model could predict ioCSF leaks based on preoperative T1CE images, especially in PAs in Hardy Stages A, B, and C. The region of interest in the model prediction-making process is similar to that of humans. DNN models trained with preoperative MRI images may provide a novel tool for predicting ioCSF leak risk for PA patients.

Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages.

BACKGROUND: Two main subclasses of macrophages are found in almost all solid tissues: embryo-derived resident tissue macrophages and bone marrow-derived infiltrated macrophages. These macrophage subtypes show transcriptional and functional divergence, and the programs that have shaped the evolution of renal macrophages and related signaling pathways remain poorly understood. To clarify these processes, we performed data analysis based on single-cell transcriptional profiling of renal tissue-resident and infiltrated macrophages in human, mouse and rat. RESULTS: In this study, we (i) characterized the transcriptional divergence among species and (ii) illustrated variability in expression among cells of each subtype and (iii) compared the gene regulation network and (iv) ligand-receptor pairs in human and mouse. Using single-cell transcriptomics, we mapped the promoter architecture during homeostasis. CONCLUSIONS: Transcriptionally divergent genes, such as the differentially TF-encoding genes expressed in resident and infiltrated macrophages across the three species, vary among cells and include distinct promoter structures. The gene regulatory network in infiltrated macrophages shows comparatively better species-wide consistency than resident macrophages. The conserved transcriptional gene regulatory network in infiltrated macrophages among species is uniquely enriched in pathways related to kinases, and TFs associated with largely conserved regulons among species are uniquely enriched in kinase-related pathways.

Knockdown of Nrf2 radiosensitizes glioma cells by inducing redox stress and apoptosis in hypoxia.

Background: Radiotherapy remains a mainstream treatment for patients with glioma. Yet intrinsic radioresistance has largely compromised the efficacy of the treatment. Increasing concerns have been raised that overexpression of the Nrf2, along with a hypoxic tumor microenvironment, may have contributed to the deterioration of radiotherapy in tumors. So, this study investigated the role of Nrf2 in the radiation therapy of glioma cells in hypoxia. Methods: To determine the expression levels of Nrf2 and HIF-1α, surgical mastectomy specimens from patients with glioma in our institute were analyzed by immunohistochemical staining. Glioblastoma multiforme (GBM) cell lines U251 and U87 with Nrf2 knocked down were produced by transfection with lentiviral particles. Cell lines were treated with ionizing radiation in hypoxia in vitro, with expression and activity of Nrf2 examined by polymerase chain reaction and western blot. Reactive oxygen species (ROS) generation and cell apoptosis analysis were analyzed by flow cytometry. Results: Nrf2 and its downstream pathway were upregulated in surgical specimens after radiotherapy, verified by GBM cell lines treated with in vitro ionizing radiation in hypoxia. Furthermore, knockdown of Nrf2 could induce the ROS generation and cell apoptosis levels after radiation. Conclusions: Downregulation of Nrf2 could sensitize the lethal effect on GBM cells in vitro by enhancing oxidative stress and apoptosis in hypoxia.

Esophageal variceal ligation plus sclerotherapy vs. ligation alone for the treatment of esophageal varices.

Background: This study aimed to evaluate the efficacy and adverse events of esophageal variceal ligation (EVL) vs. EVL combined with endoscopic injection sclerosis (EIS) in the therapy of esophageal varices. Methods: Patients from January 2017 to August 2021 who received EVL alone (control group) or EVL plus EIS (intervention group) were enrolled in this retrospective study. Efficacy, including rebleeding (clinically hematemesis or melena, confirmed by endoscopy as esophagogastric varices bleeding), variceal recurrence rate (the presence of esophagogastric varices which is needed to be treated again) the number of sessions performed to complete eradication of varices, and safety (adverse events) were compared. The variceal recurrence-associated factors were derived by univariate and multivariate logistic regression analyses. Results: The variceal recurrence and rebleeding rate in the intervention group showed significantly lower than the control group (2.6% vs 10.3%, P = 0.006 and 20.7% vs 37.5%, P = 0.029, P = 0.006, respectively, in the 12-month follow-up). The adverse events (fever, chest pain, swallowing, and esophageal stricture) showed no significant difference between the two groups (P > 0.05). Further research showed that the efficacy of the intervention group was better than the control group only achieved in prophylactically endoscopic treatment patients. The diameter of esophageal varices and gastric varices co-exist showed significant effects on variceal recurrence in intervention group [odds ratio (OR) = 15.856; 95% confidence interval (CI), 1.709-160.143; P = 0.016 and OR = 4.5; 95% CI, 1.42-20.028; P = 0.021; respectively]. Conclusions: The intervention group may obtain lower recurrence, rebleeding rate, and fewer sessions performed to complete eradication of varices (number of sessions) and similar incidence of adverse events, especially for prophylactically treatment. Among the intervention group, the diameter of esophageal varices and gastric varices were closely associated with variceal recurrence.

Towards population-specific pharmacogenomics in the era of next-generation sequencing.

Pharmacogenomics (PGx) has essential roles in identifying optimal drug responders, optimizing dosage regimens and avoiding adverse events. Population-specific therapeutic interventions that tackle the genetic root causes of clinical outcomes are an important precision medicine strategy. In this perspective, we discuss next-generation sequencing genotyping and its significance for population-specific PGx applications. We emphasize the potential of NGS for preemptive pharmacogenotyping, which is crucial to population-specific clinical studies and patient care. We also provide examples that use publicly available population-based genomics data for population-specific PGx studies. Last, we discuss the remaining challenges and regulatory efforts towards improvements in this field.

A comprehensive rat transcriptome built from large scale RNA-seq-based annotation.

The rat is an important model organism in biomedical research for studying human disease mechanisms and treatments, but its annotated transcriptome is far from complete. We constructed a Rat Transcriptome Re-annotation named RTR using RNA-seq data from 320 samples in 11 different organs generated by the SEQC consortium. Totally, there are 52 807 genes and 114 152 transcripts in RTR. Transcribed regions and exons in RTR account for ∼42% and ∼6.5% of the genome, respectively. Of all 73 074 newly annotated transcripts in RTR, 34 213 were annotated as high confident coding transcripts and 24 728 as high confident long noncoding transcripts. Different tissues rather than different stages have a significant influence on the expression patterns of transcripts. We also found that 11 715 genes and 15 852 transcripts were expressed in all 11 tissues and that 849 house-keeping genes expressed different isoforms among tissues. This comprehensive transcriptome is freely available at http://www.unimd.org/rtr/. Our new rat transcriptome provides essential reference for genetics and gene expression studies in rat disease and toxicity models.

microRNA-32-5p targets KLF2 to promote gastric cancer by activating PI3K/AKT signaling pathway.

Krüppel-like factor 2 (KLF2) is a member of the zinc finger family, which is considered a potential tumor suppressor gene due to its reduced expression in gastric cancer. MicroRNAs (miRNAs) are a class of short non-coding single-stranded RNAs that are closely related to the development of gastric cancer. The purpose of this study was to investigate the miRNAs that regulate KLF2 and explore its specific mechanism in gastric cancer. Bioinformatics software Targetscan identified that microRNA-32-5p (miRNA-32-5p) may bind to KLF2 mRNA to regulate its expression. In order to verify the regulatory effect of miRNA-32-5p on KLF2, the proliferation and migration assays were performed in both KLF2 overexpression and KLF2 knockdown gastric cancer cells. Dual-Luciferase reporter assay proved that KLF2 could bind to the PTEN promoter to induce its expression. Moreover, research on molecular mechanisms indicated that both miRNA-32-5p and shKLF2 downregulated the expression of PTEN and activated the PI3K/AKT signaling to promote the development of gastric cancer. Targeting miRNA-32-5p and KLF2 is expected to provide new sign and target for gastric cancer treatment.

Five-Feature Model for Developing the Classifier for Synergistic vs. Antagonistic Drug Combinations Built by XGBoost.

Combinatorial drug therapy can improve the therapeutic effect and reduce the corresponding adverse events. In silico strategies to classify synergistic vs. antagonistic drug pairs is more efficient than experimental strategies. However, most of the developed methods have been applied only to cancer therapies. In this study, we introduce a novel method, XGBoost, based on five features of drugs and biomolecular networks of their targets, to classify synergistic vs. antagonistic drug combinations from different drug categories. We found that XGBoost outperformed other classifiers in both stratified fivefold cross-validation (CV) and independent validation. For example, XGBoost achieved higher predictive accuracy than other models (0.86, 0.78, 0.78, and 0.83 for XGBoost, logistic regression, naïve Bayesian, and random forest, respectively) for an independent validation set. We also found that the five-feature XGBoost model is much more effective at predicting combinatorial therapies that have synergistic effects than those with antagonistic effects. The five-feature XGBoost model was also validated on TCGA data with accuracy of 0.79 among the 61 tested drug pairs, which is comparable to that of DeepSynergy. Among the 14 main anatomical/pharmacological groups classified according to WHO Anatomic Therapeutic Class, for drugs belonging to five groups, their prediction accuracy was significantly increased (odds ratio < 1) or reduced (odds ratio > 1) (Fisher's exact test, p < 0.05). This study concludes that our five-feature XGBoost model has significant benefits for classifying synergistic vs. antagonistic drug combinations.

QuaPra: Efficient transcript assembly and quantification using quadratic programming with Apriori algorithm.

RNA sequencing (RNA-seq) has greatly facilitated the exploring of transcriptome landscape for diverse organisms. However, transcriptome reconstruction is still challenging due to various limitations of current tools and sequencing technologies. Here, we introduce an efficient tool, QuaPra (Quadratic Programming combined with Apriori), for accurate transcriptome assembly and quantification. QuaPra could detect at least 26.5% more low abundance (0.1-1 FPKM) transcripts with over 2.1% increase of sensitivity and precision on simulated data compared to other currently popular tools. Moreover, around one-quarter more known transcripts were correctly assembled by QuaPra than other assemblers on real sequencing data. QuaPra is freely available at https://doi.org/www.megabionet.org/QuaPra/ .

Targeting Long Noncoding RNA in Glioma: A Pathway Perspective.

Long noncoding RNAs (lncRNAs) participate extensively in biological processes of various cancers. The majority of these transcripts are uniquely expressed in differentiated tissues or specific cancer types. lncRNAs are aberrantly expressed in gliomas and exert diverse functions. In this article, we provided an overview of how lncRNAs regulate cellular processes in glioma, enumerated the lncRNAs that may act as glioma biomarkers, and showed their potential clinical implications.

Chrysin suppresses proliferation, migration, and invasion in glioblastoma cell lines via mediating the ERK/Nrf2 signaling pathway.

BACKGROUND: Chrysin, an active natural bioflavonoid, has been proven to protect against carcinogenesis. However, the role of chrysin in glioblastoma and the potential molecular mechanisms remain to be elucidated. In our previous study, we found that nuclear factor erythroid 2 (NF-E2)-related factor 2 (Nrf2) is highly expressed in a variety of glioblastoma cell lines associated with the mitogen-activated protein kinase (MAPK) pathway. The aim of this study was to evaluate the antitumor effects of chrysin in glioblastoma cells and how chrysin is related to the MAPK/Nrf2 signaling pathway. METHODS: A Cell Counting Kit-8 assay and a plate colony formation assay were performed to evaluate cell proliferation. Cell migration ability was tested by a wound-healing assay. Transwell migration and Matrigel invasion assay were used to test the migration and invasion potential of cells. Nrf2 was knocked down by shRNA transfection. Protein expression was determined by Western blotting and immunofluorescence staining. The in vivo anticancer effect was measured using tumor xenografts in nude mice. RESULTS: Chrysin inhibited the proliferation, migration, and invasion capacity of glioblastoma cells in dose- and time-dependent manners. Mechanistically, chrysin deactivated the Nrf2 signaling pathway by decreasing the translocation of Nrf2 into the nucleus and suppressing the expression of hemeoxygenase-1 (HO-1) and NAD(P)H quinine oxidoreductase-1, meanwhile, Nrf2 shRNA attenuated the anticancer activity of chrysin. Furthermore, chrysin downregulated the protein expression of p-extracellular signal-regulated kinase 1 and 2 (ERK1/2), but did not significantly affect p-JNK and p-P38 expression levels. However, the downregulated level of Nrf2 and the antitumor effect of chrysin in glioblastoma cell lines were partially abrogated by the ERK1/2 signaling inhibitor (U0126). Finally, chrysin inhibited tumor growth in U87 xenografts. CONCLUSION: Our results show that chrysin exerts anticancer activity in glioblastoma cell lines possibly via the ERK/Nrf2 signaling pathway and indicate the potential application of chrysin as a natural sensitizer in chemotherapy.

Targeting Long Noncoding RNA HMMR-AS1 Suppresses and Radiosensitizes Glioblastoma.

Emergent evidences revealed that long noncoding RNAs (lncRNAs) participate in neoplastic progression. HMMR is an oncogene that is highly expressed in glioblastoma (GBM) and supports GBM growth. Whether lncRNAs regulate HMMR in GBM remains unknown. Herein, we identify that an HMMR antisense lncRNA, HMMR-AS1, is hyperexpressed in GBM cell lines and stabilizes HMMR mRNA. Knockdown of HMMR-AS1 reduces HMMR expression; inhibits cell migration, invasion, and mesenchymal phenotypes; and suppresses GBM cell growth both in vitro and in vivo. Moreover, knockdown of HMMR-AS1 radiosensitizes GBM by reducing DNA repair proteins ATM, RAD51, and BMI1. Our data demonstrate a mechanism of sense-antisense interference between HMMR and HMMR-AS1 in GBM and suggest that targeting HMMR-AS1 is a potential strategy for GBM treatment.

COX-2/sEH dual inhibitor PTUPB suppresses glioblastoma growth by targeting epidermal growth factor receptor and hyaluronan mediated motility receptor.

AIMS: Cyclooxygenase-2 (COX-2)/soluble epoxide hydrolase (sEH) dual inhibitor, PTUPB, has been demonstrated to inhibit angiogenesis, primary tumor growth and metastasis. The aim of this study is to investigate the effects of PTUPB on glioblastoma cells and xenograft model. RESULTS: We show here that PTUPB inhibits glioblastoma cell proliferation and G1 phase cell cycle arrest in vitro, and suppresses the tumor growth and angiogenesis in vivo. The expression and activation of epidermal growth factor receptor (EGFR) and its downstream kinases, ERK1/2 and AKT, are reduced by PTUPB, indicating that the EGF/EGFR signaling pathway is a potential target. Moreover, PTUPB dramatically suppresses expression of hyaluronan mediated motility receptor (HMMR) in the glioblastoma cell lines and xenograft mouse model, suggesting that the HMMR is the other potential target. MATERIALS AND METHODS: Cellular immunofluorescence assays were used for cell staining of actin fibers and HMMR. CCK-8 kit was used for cell proliferation assay. Cell-cycle analysis was performed by flow cytometry. Quantitative real-time PCR assay was performed to test mRNA level. Western blot analysis was used to test protein expression. Immunohistochemical staining assay was used for xenograft tumor tissue staining of Ki-67, CD31 and HMMR. The SPSS version 17.0 software was applied for statistical analysis. CONCLUSIONS: Our data demonstrate that PTUPB is a potential therapeutic agent to treat glioblastomas.

Interplay of transcription factors and microRNAs during embryonic hematopoiesis.

Hematopoietic stem cells (HSCs), which are localized in the bone marrow of adult mammals, come from hematopoietic endothelium during embryonic stages. Although the basic processes of HSC generation and differentiation have been described in the past, the epigenetic regulation of embryonic hematopoiesis remains to be fully described. Here, by utilizing an in vitro differentiation system of mouse embryonic stem cells (ESCs), we identified more than 20 microRNAs that were highly enriched in embryonic hematopoietic cells, including some (e.g. miR-10b, miR-15b, and miR-27a) with previously unknown functions in blood formation. Luciferase and gene expression assays further revealed combinational binding and regulation of these microRNAs by key transcription factors in blood cells. Finally, bioinformatics and functional analyses supported an interactive regulatory control between transcription factors and microRNAs in hematopoiesis.

Mild Hypothermia Combined with Hydrogen Sulfide Treatment During Resuscitation Reduces Hippocampal Neuron Apoptosis Via NR2A, NR2B, and PI3K-Akt Signaling in a Rat Model of Cerebral Ischemia-Reperfusion Injury.

We investigated whether mild hypothermia combined with sodium hydrosulfide treatment during resuscitation improves neuron survival following cerebral ischemia-reperfusion injury beyond that observed for the individual treatments. Male Sprague-Dawley rats were divided into seven groups (n = 20 for each group). All rats underwent Pulsinelli 4-vessel occlusion. Ischemia was induced for 15 min using ligatures around the common carotid arteries, except for the sham group. Immediately after initiating reperfusion, the mild hypothermia (MH), sodium hydrosulfide (NaHS), hydroxylamine (HA), MH + NaHS, MH + HA, and ischemia-reperfusion (I/R) control groups received an intraperitoneal injection of saline, sodium hydrosulfide, hydroxylamine, sodium hydrosulfide, hydroxylamine, and saline, respectively, and mild hypothermia (32 to 33 °C) was induced in the MH, MH + NaHS, and MH + HA groups for 6 h. The levels of NR2A, NR2B, p-Akt, and p-Gsk-3ß in the hippocampus of the MH, NaHS, and MH + NaHS groups were higher than those in the I/R control group, with the highest levels observed in the MH + NaHS group (P < 0.05). Treatment with hydroxylamine reduced the levels of these proteins in the HA and MH + HA groups, compared with the I/R control and MH groups, respectively. The apoptotic index of the CA1 region of the hippocampus was 45.2, 66.5, 63.5, and 84.8 % in the MH + NaHS, MH, NaHS, and I/R control groups, respectively (P < 0.05), indicating that the combination treatment shifted the NR2A/NR2B balance in favor of synaptic neuron stimulation and phosphatidylinositol 3'-kinase (PI3K)/Akt signaling. The combination of mild hypothermia and sodium hydrosulfide treatment for resuscitation following ischemia-reperfusion injury was more beneficial for reducing hippocampal apoptosis and pathology than that of mild hypothermia or hydrogen sulfide treatment alone.

Hydrogen sulphide and mild hypothermia activate the CREB signaling pathway and prevent ischemia-reperfusion injury.

BACKGROUND: Both hydrogen sulphide (H2S) and mild hypothermia have been reported to prevent brain damage caused by reperfusion assault through regulating the N-methyl-D-aspartate receptor (NMDAR). However, the relationship between the two treatments and how they exert neuro-protective effects through NMDARs remain to be elucidated. METHODS: Transient cerebral ischemia was induced using the Pulsinelli four-vessel occlusion method. We used sodium hydrosulphide (NaHS) as the H2S donor. We randomly divided 100 Sprague-Dawley rats into five groups of 20: Sham operation group (Sh), normothermic (36-37 °C) ischemia group (NT), mild hypothermic (32-33 °C) ischemia group (mHT), normothermic ischemia combined with NaHS treatment group (NT + NaHS), and mild hypothermic ischemia combined with NaHS treatment group (mHT + NaHS). After 6 hrs of reperfusion, rats were decapitated and hippocampus samples were immediately collected. We measured NR2A (GluN1), NR2B (GluN2) and p-CREB protein levels using western blotting. We further analyzed BDNF mRNA expression by real-time PCR. Hematoxylin and eosin (HE) staining was used to examine pyramidal cell histology at the CA1 region. All statistical analyses were carried out by ANOVA and LSD t-test as implemented by the SPSS 13.0 software. RESULTS: In the four test groups with ischemia-reperfusion, hippocampal H2S concentration increased following treatment, and administration of NaHS further increased H2S levels. Moreover, administration of both NaHS and mild hypothermia resulted in up-regulation of NR2A and NR2B protein expressions, as well as p-CREB protein and BDNF mRNA levels. At the cellular level, NaHS and mild hypothermia groups exhibited lower damage caused by ischemia-reperfusion in the CA1 region of the hippocampus. The strongest protective effect was observed in rats treated with combined NaHS and mild hypothermia, suggesting their effects were additive. CONCLUSION: Our results support previous findings that hydrogen sulphide and mild hypothermia can prevent ischemia-reperfusion injury. Both treatments caused an up-regulation of NMDA receptors, as well as an elevation in p-CREB protein and BDNF mRNA levels. Thus, hydrogen sulphide and mild hypothermia may provide neuro-protective effect through activating the pro-survival CREB signaling pathway.

Re-annotation of presumed noncoding disease/trait-associated genetic variants by integrative analyses.

Using RefSeq annotations, most disease/trait-associated genetic variants identified by genome-wide association studies (GWAS) appear to be located within intronic or intergenic regions, which makes it difficult to interpret their functions. We reassessed GWAS-Associated single-nucleotide polymorphisms (herein termed as GASs) for their potential functionalities using integrative approaches. 8834 of 9184 RefSeq "noncoding" GASs were reassessed to have potential regulatory functionalities. As examples, 3 variants (rs3130320, rs3806932 and rs6890853) were shown to have regulatory properties in HepG2, A549 and 293T cells. Except rs3130320 as a known expression quantitative trait loci (eQTL), rs3806932 and rs6890853 were not reported as eQTLs in previous reports. 1999 of 9184 "noncoding" GASs were re-annotated to the promoters or intragenic regions using Ensembl, UCSC and AceView gene annotations but they were not annotated into corresponding regions in RefSeq database. Moreover, these GAS-harboring genes were broadly expressed across different tissues and a portion of them was expressed in a tissue-specific manner, suggesting that they could be functional. Collectively, our study demonstrates the benefits of using integrative analyses to interpret genetic variants and may help to predict or explain disease susceptibility more accurately and comprehensively.

Quantitative anatomic comparison of the extended pterional transtemporal transtentorial approach and the subtemporal transtentorial approach to the petroclival region.

AIM: The anatomic characters and applicability of the extended pterional transtemporal transtentorial (EPTT) approach versus the subtemporal transtentorial (ST) approach for surgical treatment of petroclival tumors were evaluated. MATERIAL AND METHODS: Ten sides from five adult Chinese injected cadavers were manipulated using both two approaches. Four deep bony anatomic landmarks were specified in the skull base to create two adjoining triangles that were respectively located in the anterior and posterior petroclival region. The real, projected area and the percentage of the projected area were determined and calculated to compare the deep exposure from the two approaches. RESULTS: There was no difference regarding the percentage of the projected area was calculated in the anterior triangles (EPTT, 21.5±12.5%; ST, 28.8±14.9%; p=0.1948), but a significant difference was present in the posterior triangles (EPTT, 74.0±4.5%; ST, 51.5±4.3%; p < 0.01). Compared with the ST approach, the EPTT approach provides an equivalent percentage of projected area in the middle cranial fossa and a wider exposed area in the posterior cranial fossa. CONCLUSION: Through anatomic comparative analysis the EPTT approach provides better exposure and is more appropriate than the ST approach for large and giant petroclival tumors predominantly in the posterior cranial fossa with extensive invasion to parasellar structures and the cavernous sinus.