Secretory GFP reconstitution labeling of neighboring cells interrogates cell-cell interactions in metastatic niches

Cancer cells inevitably interact with neighboring host tissue-resident cells during the process of metastatic colonization, establishing a metastatic niche to fuel their survival, growth, and invasion. However, the underlying mechanisms in the metastatic niche are yet to be fully elucidated owing to the lack of methodologies for comprehensively studying the mechanisms of cell-cell interactions in the niche. Here, we improve a split green fluorescent protein (GFP)-based genetically encoded system to develop secretory glycosylphosphatidylinositol-anchored reconstitution-activated proteins to highlight intercellular connections (sGRAPHIC) for efficient fluorescent labeling of tissue-resident cells that neighbor on and putatively interact with cancer cells in deep tissues. The sGRAPHIC system enables the isolation of metastatic niche-associated tissue-resident cells for their characterization using a single-cell RNA sequencing platform. We use this sGRAPHIC-leveraged transcriptomic platform to uncover gene expression patterns in metastatic niche-associated hepatocytes in a murine model of liver metastasis. Among the marker genes of metastatic niche-associated hepatocytes, we identify Lgals3, encoding galectin-3, as a potential pro-metastatic factor that accelerates metastatic growth and invasion.

PDIVAS: Pathogenicity predictor for Deep-Intronic Variants causing Aberrant Splicing

BACKGROUND

Deep-intronic variants that alter RNA splicing were ineffectively evaluated in the search for the cause of genetic diseases. Determination of such pathogenic variants from a vast number of deep-intronic variants (approximately 1,500,000 variants per individual) represents a technical challenge to researchers. Thus, we developed a Pathogenicity predictor for Deep-Intronic Variants causing Aberrant Splicing (PDIVAS) to easily detect pathogenic deep-intronic variants.

RESULTS

PDIVAS was trained on an ensemble machine-learning algorithm to classify pathogenic and benign variants in a curated dataset. The dataset consists of manually curated pathogenic splice-altering variants (SAVs) and commonly observed benign variants within deep introns. Splicing features and a splicing constraint metric were used to maximize the predictive sensitivity and specificity, respectively. PDIVAS showed an average precision of 0.92 and a maximum MCC of 0.88 in classifying these variants, which were the best of the previous predictors. When PDIVAS was applied to genome sequencing analysis on a threshold with 95% sensitivity for reported pathogenic SAVs, an average of 27 pathogenic candidates were extracted per individual. Furthermore, the causative variants in simulated patient genomes were more efficiently prioritized than the previous predictors.

CONCLUSION

Incorporating PDIVAS into variant interpretation pipelines will enable efficient detection of disease-causing deep-intronic SAVs and contribute to improving the diagnostic yield. PDIVAS is publicly available at https://github.com/shiro-kur/PDIVAS .

CCL21-Ser expression in melanoma cells recruits CCR7+ naïve T cells to tumor tissues and promotes tumor growth

CCL21-Ser, a chemokine encoded by the Ccl21a gene, is constitutively expressed in the thymic epithelial cells and stromal cells of secondary lymphoid organs. It regulates immune cell migration and survival through its receptor CCR7. Herein, using CCL21-Ser-expressing melanoma cells and the Ccl21a-deficient mice, we demonstrated the functional role of cancer cell-derived CCL21-Ser in melanoma growth in vivo. The B16-F10 tumor growth was significantly decreased in Ccl21a-deficient mice compared with that in wild-type mice, indicating that host-derived CCL21-Ser contributes to melanoma proliferation in vivo. In Ccl21a-deficient mice, tumor growth of melanoma cells expressing CCL21-Ser was significantly enhanced, suggesting that CCL21-Ser from melanoma cells promotes tumor growth in the absence of host-derived CCL21-Ser. The increase in tumor growth was associated with an increase in the CCR7+ CD62L+ T cell frequency in the tumor tissue but was inversely correlated with Treg frequency, suggesting that naïve T cells primarily promote tumor growth. Adoptive transfer experiments demonstrated that naïve T cells are preferentially recruited from the blood into tumors with melanoma cell-derived CCL21-Ser expression. These results suggest that CCL21-Ser from melanoma cells promotes the infiltration of CCR7+ naïve T cells into the tumor tissues and creates a tumor microenvironment favorable for melanoma growth.

Abstract 5093: Chemically inducible splice-neoantigens for cancer immunotherapy

Although immune checkpoint blockade therapies have dramatically improved the survival rate of patients with cancer compared with other treatment approaches, a substantial number of patients show poor response or resistance to these therapies. Meta-analyses for programmed cell death 1 (PD-1) blockade responses highlight the importance of neoantigens, derived from non-synonymous mutations in cancer cells, for antitumor immune responses. Intriguingly, recent transcriptome and genomics studies predict the presence of putative neoantigens as a result of an irregular pre-mRNA splicing regulation in cancer cells, indicating that alterations in RNA splicing in cancer cells might induce antitumor immune responses. Here, we report that induction of serine/arginine-rich splicing factor (SRSF)-dependent splicing boosts the production of splicing-associated neoantigens (splice-neoantigens) and potentiates the response to PD-1 blockade. Administration of a synthetic SRSF activator RECTAS suppressed tumor growth in a host CD8+ T cell- and tumor major histocompatibility complex class I-dependent manner and promoted the antitumor effect of anti-PD-L1 antibody without detectable autoimmunity. Subsequent transcriptome analysis and validation for immunogenicity identified six splice-neoantigen candidates whose expression was induced by RECTAS treatment. Importantly, vaccination of the identified neoepitopes elicited T cell responses capable of killing cancer cells in vitro, in addition to suppression of tumor growth in vivo upon sensitization with RECTAS. Collectively, these results provide support for the further development of splice variant-inducing treatments for cancer immunotherapy.

Citation Format: Shingo Matsushima, Masahiko Ajiro, Kei Iida, Kenji Chamoto, Tasuku Honjo, Masatoshi Hagiwara. Chemically inducible splice-neoantigens for cancer immunotherapy. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5093.

Integrated-gut-liver-on-a-chip platform as an in vitro human model of non-alcoholic fatty liver disease

Non-alcoholic fatty liver disease (NAFLD) afflicts a significant percentage of the population; however, no effective treatments have yet been established because of the unsuitability of in vitro assays and animal experimental models. Here, we present an integrated-gut-liver-on-a-chip (iGLC) platform as an in vitro human model of the gut-liver axis (GLA) by co-culturing human gut and liver cell lines interconnected via microfluidics in a closed circulation loop, for the initiation and progression of NAFLD by treatment with free fatty acids (FFAs) for 1 and 7 days, respectively. Co-cultured Caco-2 gut-mimicking cells and HepG2 hepatocyte-like cells demonstrate the protective effects from apoptosis against FFAs treatment, whereas mono-cultured cells exhibit induced apoptosis. Phenotype and gene expression analyses reveal that the FFAs-treated gut and liver cells accumulated intracellular lipid droplets and show an increase in gene expression associated with a cellular response to copper ions and endoplasmic reticulum stress. As an in vitro human GLA model, the iGLC platform may serve as an alternative to animal experiments for investigating the mechanisms of NAFLD.

Identification of the α2 chain of interleukin-13 receptor as a potential biomarker for predicting castration resistance of prostate cancer using patient-derived xenograft models

BACKGROUND

Several treatment strategies use upfront chemotherapy or androgen receptor axis-targeting therapies for metastatic prostate cancer. However, there are no useful biomarkers for selecting appropriate patients who urgently require these treatments.

METHODS

Novel patient-derived xenograft (PDX) castration-sensitive and -resistant models were established and gene expression patterns were comprehensively compared. The function of a gene highly expressed in the castration-resistant models was evaluated by its overexpression in LNCaP prostate cancer cells. Protein expression in the tumors and serum of patients was examined by immunohistochemistry and ELISA, and correlations with castration resistance were analyzed.

RESULTS

Expression of the α2 chain of interleukin-13 receptor (IL13Rα2) was higher in castration-resistant PDX tumors. LNCaP cells overexpressing IL13Rα2 acquired castration resistance in vitro and in vivo. In tissue samples, IL13Rα2 expression levels were significantly associated with castration-resistant progression (p < 0.05). In serum samples, IL13Rα2 levels could be measured in 5 of 28 (18%) castration-resistant prostate cancer patients.

CONCLUSION

IL13Rα2 was highly expressed in castration-resistant prostate cancer PDX models and was associated with the castration resistance of prostate cancer cells. It might be a potential tissue and serum biomarker for predicting castration resistance in prostate cancer patients.

Chemical induction of splice-neoantigens attenuates tumor growth in a preclinical model of colorectal cancer

Neoantigen production is a determinant of cancer immunotherapy. However, the expansion of neoantigen abundance for cancer therapeutics is technically challenging. Here, we report that the synthetic compound RECTAS can induce the production of splice-neoantigens that could be used to boost antitumor immune responses. RECTAS suppressed tumor growth in a CD8⁺ T cell- and tumor major histocompatibility complex class I-dependent manner and enhanced immune checkpoint blockade efficacy. Subsequent transcriptome analysis and validation for immunogenicity identified six splice-neoantigen candidates whose expression was induced by RECTAS treatment. Vaccination of the identified neoepitopes elicited T cell responses capable of killing cancer cells in vitro, in addition to suppression of tumor growth in vivo upon sensitization with RECTAS. Collectively, these results provide support for the further development of splice variant-inducing treatments for cancer immunotherapy.

Method for Identifying Sequence Motifs in Pre-miRNAs for Small-Molecule Binding

Non-coding RNAs are emerging targets for drug development because they are involved in various cellular processes. However, there are a few reliable design strategies for small molecules that can target RNAs. This paper reports a simple and efficient method to comprehensively analyze RNA motifs that can be bound by a specific small molecule. The method involves Dicer-mediated pre-miRNA cleavage and subsequent analysis of the reaction products by high-throughput sequencing. A pre-miRNA mutant library containing a randomized region at the Dicer cleavage site was used as the substrate for the reaction. Sequencing analysis of the products of the reaction carried out in the presence or absence of a synthetic small molecule identified the pre-miRNA mutants whose Dicer-mediated cleavage was significantly altered by the addition of the small molecule. The binding of the small molecule to the identified pre-miRNA mutants was confirmed by surface plasmon resonance, demonstrating the feasibility of our method.

Involvement of endothelins in neuroprotection of valosin-containing protein modulators against retinal ganglion cell damage

We have previously shown that Kyoto University Substances (KUSs), valosin-containing protein (VCP) modulators, suppress cell death in retinal ganglion cells of glaucoma mouse models through alterations of various genes expressions. In this study, among the genes whose expression in retinal ganglion cells was altered by KUS treatment in the N-methyl-d-aspartic acid (NMDA) injury model, we focused on two genes, endothelin-1 (Edn1) and endothelin receptor type B (Ednrb), whose expression was up-regulated by NMDA and down-regulated by KUS treatment. First, we confirmed that the expression of Edn1 and Ednrb was upregulated by NMDA and suppressed by KUS administration in mice retinae. Next, to clarify the influence of KUSs on cell viability in relation to the endothelin signaling, cell viability was examined with or without antagonists or agonists of endothelin and with or without KUS in 661W retinal cells under stress conditions. KUS showed a significant protective effect under glucose-free conditions and tunicamycin-induced stress. This protective effect was partially attenuated in the presence of an endothelin antagonist or agonist under glucose-free conditions. These results suggest that KUSs protect cells partially by suppressing the upregulated endothelin signaling under stress conditions.

Structure of two-and three-alpha systems in cold neutron matter

We present stability and structure of two-and three-alpha systems embedded in dilute cold neutron matter. By solving a few-alpha Schrödinger equation with quasiparticle properties, i.e.,effective mass and induced two-and three-alpha interactions, which are evaluated in terms of Fermi polarons,itis shown that 8Be and the Hoyle state become bound at densities of about10−4 and 10−3 of the saturation density, respectively. It is also seen that, under cold neutron matter environment, both systems become smaller than the corresponding systems in vacuum. Our results would affect astrophysical models for stellar collapse and neutron star mergers, as well as relevant reaction rates for nucleosynthesis.

Therapeutic manipulation of IKBKAP mis-splicing with a small molecule to cure familial dysautonomia

Approximately half of genetic disease-associated mutations cause aberrant splicing. However, a widely applicable therapeutic strategy to splicing diseases is yet to be developed. Here, we analyze the mechanism whereby IKBKAP-familial dysautonomia (FD) exon 20 inclusion is specifically promoted by a small molecule splice modulator, RECTAS, even though IKBKAP-FD exon 20 has a suboptimal 5' splice site due to the IVS20 + 6 T > C mutation. Knockdown experiments reveal that exon 20 inclusion is suppressed in the absence of serine/arginine-rich splicing factor 6 (SRSF6) binding to an intronic splicing enhancer in intron 20. We show that RECTAS directly interacts with CDC-like kinases (CLKs) and enhances SRSF6 phosphorylation. Consistently, exon 20 splicing is bidirectionally manipulated by targeting cellular CLK activity with RECTAS versus CLK inhibitors. The therapeutic potential of RECTAS is validated in multiple FD disease models. Our study indicates that small synthetic molecules affecting phosphorylation state of SRSFs is available as a new therapeutic modality for mechanism-oriented precision medicine of splicing diseases.

CDC2-like (CLK) protein kinase inhibition as a novel targeted therapeutic strategy in prostate cancer

Dysregulation of alternative splicing is a feature of cancer, both in aetiology and progression. It occurs because of mutations in splice sites or sites that regulate splicing, or because of the altered expression and activity of splice factors and of splice factor kinases that regulate splice factor activity. Recently the CDC2-like kinases (CLKs) have attracted attention due to their increasing involvement in cancer. We measured the effect of the CLK inhibitor, the benzothiazole TG003, on two prostate cancer cell lines. TG003 reduced cell proliferation and increased apoptosis in PC3 and DU145 cells. Conversely, the overexpression of CLK1 in PC3 cells prevented TG003 from reducing cell proliferation. TG003 slowed scratch closure and reduced cell migration and invasion in a transwell assay. TG003 decisively inhibited the growth of a PC3 cell line xenograft in nude mice. We performed a transcriptomic analysis of cells treated with TG003. We report widespread and consistent changes in alternative splicing of cancer-associated genes including CENPE, ESCO2, CKAP2, MELK, ASPH and CD164 in both HeLa and PC3 cells. Together these findings suggest that targeting CLKs will provide novel therapeutic opportunities in prostate cancer.

Improvement of Moloney murine leukemia virus reverse transcriptase thermostability by introducing a disulfide bridge in the ribonuclease H region

Moloney murine leukemia virus (MMLV) reverse transcriptase (RT) is widely used in research and clinical diagnosis. Improvement of MMLV RT thermostability has been an important topic of research for increasing the efficiency of cDNA synthesis. In this study, we attempted to increase MMLV RT thermostability by introducing a disulfide bridge in its RNase H region using site-directed mutagenesis. Five variants were designed, focusing on the distance between the two residues to be mutated into cysteine. The variants were expressed in Escherichia coli and purified. A551C/T662C was determined to be the most thermostable variant.

S1PR3-G12-biased agonist ALESIA targets cancer metabolism and promotes glucose starvation

Metabolic activities are altered in cancer cells compared with those in normal cells, and the cancer-specific pathway becomes a potential therapeutic target. Higher cellular glucose consumption, which leads to lower glucose levels, is a hallmark of cancer cells. In an objective screening for chemicals that induce cell death under low-glucose conditions, we discovered a compound, denoted as ALESIA (Anticancer Ligand Enhancing Starvation-induced Apoptosis). By our shedding assay of transforming growth factor α in HEK293A cells, ALESIA was determined to act as a sphingosine-1-phosphate receptor 3-G₁₂-biased agonist that promotes nitric oxide production and oxidative stress. The oxidative stress triggered by ALESIA resulted in the exhaustion of glucose, cellular NADPH deficiency, and then cancer cell death. Intraperitoneal administration of ALESIA improved the survival of mice with peritoneally disseminated rhabdomyosarcoma, indicating its potential as a new type of anticancer drug for glucose starvation therapy.

Examining the Beneficial Aspects of Nutritional Guidance Using Estimated Daily Salt Intake in Cancer Patients with Ischemic Heart Disease

BACKGROUND The outcomes associated with nutritional guidance for patients with ischemic heart disease undergoing cancer treatment have not been explored. We examined the effects of nutritional guidance using estimated daily salt intake in cancer patients with ischemic heart disease. MATERIAL AND METHODS We examined the data from physical examinations and laboratory assessments of 27 patients with suspected excessive salt intake who underwent coronary angiography for the first time and received nutritional guidance on their next visit to the Department of Cardiology of Shizuoka Cancer Center between May 2018 and March 2020. Salinity measurement was not used in the nutritional guidance method, but the patients were instructed to reduce consumption of salt-containing foods. We compared the frequency of the estimated daily salt intake with the frequency of categories requiring salt control (food, cooking, and table salts). RESULTS The median age of the participants was 74 (range, 63-86) years. The estimated daily salt intake and the rate of change in the triglyceride level were negatively correlated (r=-0.61, P<0.01). The estimated daily salt intake was reduced in 16 cases; there was a relative decrease in the frequency of food intake among categories requiring salt control compared with that in the nonimproved cases (P<0.01). No difference was found between the cancer stage and the affected site of the digestive system in either group (P=0.64, P=0.39). CONCLUSIONS Nutritional guidance on dietary habits without using salinity measurement was beneficial in preventing ischemic heart disease and food intake reduction in cancer patients.

Comparison of Measured Data between Pre- and Post-Radiotherapy in a Patient with Cardiac Resynchronization Therapy Defibrillator

Although some researches proved the influence of radiation therapy (RT) on pacemakers and implantable cardioverter defibrillators, little has been reported on cardiac resynchronization therapy defibrillators (CRTDs). We experienced a case of RT on CRTD and had a new finding.A patient with CRTD implanted for dilated cardiomyopathy was diagnosed with lung squamous cell carcinoma and started receiving RT. All the implanted devices, including the main body of CRTD, left ventricular lead (LV), right ventricular lead with high-voltage conductor, and right atrial lead, were from the same manufacturer. The radiation targeted the tumor of 67 mm in diameter in the right superior lobe for 5 min per session. The CRTD was outside the radiation field, which is 65 mm, but the leads were inside. Plan 1 used 2 Gy/fr with 8 megavolt photons, and Plan 1 was irradiated at 0° and 180° for 16 RT sessions. The dosage was increased to 3 Gy for Plan 2 for 4 sessions. Plan 3 used 2 Gy with 6 and 8 megavolt photons, and Plan 3 was irradiated at 27.7° and 200.7° for 11 RT sessions. Changes in measured parameters were assessed before and after RT.Changes in impedance of LV and high-voltage lead exceeded prespecified threshold. However, no significant errors were detected in the CRTD on the dosages and energy we used.We hypothesize that the lead insulator could have been affected by radiation.

Identification of Qk as a Glial Precursor Cell Marker that Governs the Fate Specification of Neural Stem Cells to a Glial Cell Lineage

During brain development, neural stem cells (NSCs) initially produce neurons and change their fate to generate glias. While the regulation of neurogenesis is well characterized, specific markers for glial precursor cells (GPCs) and the master regulators for gliogenesis remain unidentified. Accumulating evidence suggests that RNA-binding proteins (RBPs) have significant roles in neuronal development and function, as they comprehensively regulate the expression of target genes in a cell-type-specific manner. We systematically investigated the expression profiles of 1,436 murine RBPs in the developing mouse brain and identified quaking (Qk) as a marker of the putative GPC population. Functional analysis of the NSC-specific Qk-null mutant mouse revealed the key role of Qk in astrocyte and oligodendrocyte generation and differentiation from NSCs. Mechanistically, Qk upregulates gliogenic genes via quaking response elements in their 3′ untranslated regions. These results provide crucial directions for identifying GPCs and deciphering the regulatory mechanisms of gliogenesis from NSCs.

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Differential expression analysis identified Qk as a glial precursor cell marker

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Loss of Qk ablated both astrocyte and OL production from neural stem cells

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Qk^−/− NSCs failed to become glia and aberrantly expressed neural genes

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Qk comprehensively upregulates essential genes for gliogenesis as regulons via QREs

Multilateral Bioinformatics Analyses Reveal the Function-Oriented Target Specificities and Recognition of the RNA-Binding Protein SFPQ

RNA-binding proteins (RBPs) recognize consensus sequences and regulate specific target mRNAs. However, large-scale CLIP-seq revealed loose and broad binding of RBPs to larger proportion of expressed mRNAs: e.g. SFPQ binds to >10,000 pre-mRNAs but distinctly regulates <200 target genes during neuronal development. Identification of crucial binding for regulation and rules of target recognition is highly anticipated for systemic understanding of RBP regulations. For a breakthrough solution, we developed a bioinformatical method for CLIP-seq and transcriptome data by adopting iterative hypothesis testing. Essential binding was successfully identified in C-rich sequences close to the 5' splice sites of long introns, which further proposed target recognition mechanism via association between SFPQ and splicing factors during spliceosome assembly. The identified features of functional binding enabled us to predict regulons and also target genes in different species. This multilateral bioinformatics approach facilitates the elucidation of functionality, regulatory mechanism, and regulatory networks of RBPs.

Thin film growth of CaAgAs by molecular beam epitaxy

We have grown thin films of CaAgAs by molecular beam epitaxy, which was theoretically proposed to be a topological insulator. The temperature dependence of resistivity and the carrier concentration at 4 K were similar to the reported results of bulk samples. However, the magnetoresistance exhibited a steep increase at low magnetic fields, a behavior not observed for bulk samples. This steep increase of resistivity is ascribable to the weak antilocalization effect and provides clues to the nature of the topological surface state of CaAgAs.

Effect of VCP modulators on gene expression profiles of retinal ganglion cells in an acute injury mouse model

In glaucoma, retinal ganglion cells are damaged, leading to the progressive constriction of the visual field. We have previously shown that the valosin-containing protein (VCP) modulators, Kyoto University Substance (KUS)121 and KUS187, prevent the death of retinal ganglion cells in animal models of glaucoma, including the one generated by N-methyl-D-aspartate (NMDA)-induced neurotoxicity. KUSs appeared to avert endoplasmic reticulum (ER) stress by maintaining ATP levels, resulting in the protection of ganglion cells from cell death. To further elucidate the protective mechanisms of KUSs, we examined gene expression profiles in affected ganglion cells. We first injected KUS-treated mice with NMDA and then isolated the affected retinal ganglion cells using fluorescence-activated cell sorting. Gene expression in the cells was quantified using a next-generation sequencer. Resultantly, we found that KUS121 upregulated several genes involved in energy metabolism. In addition, we observed the upregulation of Zfp667, which has been reported to suppress apoptosis-related genes and prevent cell death. These results further support the suitability of KUS121 as a therapeutic drug in protecting retinal ganglion cells in ophthalmic disorders, such as glaucoma.

Loss of Sfpq Causes Long-Gene Transcriptopathy in the Brain

Genes specifically expressed in neurons contain members with extended long introns. Longer genes present a problem with respect to fulfilment of gene length transcription, and evidence suggests that dysregulation of long genes is a mechanism underlying neurodegenerative and psychiatric disorders. Here, we report the discovery that RNA-binding protein Sfpq is a critical factor for maintaining transcriptional elongation of long genes. We demonstrate that Sfpq co-transcriptionally binds to long introns and is required for sustaining long-gene transcription by RNA polymerase II through mediating the interaction of cyclin-dependent kinase 9 with the elongation complex. Phenotypically, Sfpq disruption caused neuronal apoptosis in developing mouse brains. Expression analysis of Sfpq-regulated genes revealed specific downregulation of developmentally essential neuronal genes longer than 100 kb in Sfpq-disrupted brains; those genes are enriched in associations with neurodegenerative and psychiatric diseases. The identified molecular machinery yields directions for targeted investigations of the association between long-gene transcriptopathy and neuronal diseases.

P2622Use of intravenous vasodilators in patients hospitalized with acute heart failure: insights from Tokyo cardiovascular care unit network database

Background

Despite recommendations from clinical practice guidelines, there is scant evidence confirming the effects of vasodilators on clinical outcomes in patients with acute heart failure (AHF).

Purpose

We sought to investigate the effects of intravenous vasodilators on clinical outcomes and to identify the potential patient populations that would benefit from its use.

Methods

Data of 26 212 consecutive patients urgently hospitalized for AHF between 2009 and 2015 were extracted from a multicenter data registration system (Tokyo Cardiovascular Care Unit Network Database, including 72 institutions within the Tokyo metropolitan area in Japan). Patients who did not present with typical AHF episodes, including those without pulmonary congestion on physical and/or chest X-ray and serum B-type natriuretic peptide level <500 pg/ml, as well as those who had hypotension and/or hypoperfusion (systolic blood pressure [SBP] <100 mmHg) as dominant presentation, were excluded. Propensity scores were calculated with multiple imputation and 1:1 matching performed between patients with and without vasodilators. The primary endpoint was in-hospital mortality and the secondary endpoints were length of intensive/cardiovascular care unit (ICU/CCU) stay and hospital stay.

Results

Overall, 8 863 patients were included in the present analysis; they were predominantly male (57%) with a median age of 79 (interquartile range: 70–86) years. Compared with the group without vasodilator use, the vasodilator group had higher SBPs and heart rates and higher frequency of assisted ventilation use, but lower frequency of intravenous diuretics use. After propensity score matching, there were no significant differences in in-hospital mortality rates (7.8% vs. 8.9% in patients without vasodilators, p=0.16) or in length of ICU/CCU stay (5.8 days vs. 5.4 days, p=0.44) and hospital stay (22.7 days vs. 23.8 days, p=0.22) between the groups. However, in subgroup analyses, favorable impacts of vasodilator use on in-hospital mortality were observed among patients who had higher SBPs and among those who had no atrial fibrillation upon admission (Figure). In addition, vasodilators were likely to be more effective in AHF patients with SBP increasing; while levels below 140 mmHg of SBP appeared to be associated with an increased risk for mortality among patients treated with vasodilators compared with those without vasodilators.

Figure 1

Conclusions

In patients with AHF, vasodilator use was not universally associated with improved in-hospital outcomes; however, its effect was dependent of individual clinical presentation. Detailed phenotyping might aid tailoring of treatment strategies for patients with AHF.

Acknowledgement/Funding

the Tokyo Metropolitan Government

Cancer-associated cerebral infarction during direct oral anticoagulant treatment in cancer patients: a case series

The effect of direct oral anticoagulants (DOACs) on cancer-associated cerebral infarction (CI) is unclear. We present the clinical course of 20 consecutive patients with cancer-associated CI that developed during treatment with DOACs. The incidence rate of cancer-associated CI during the treatment with DOACs was 3.4%. The median modified Rankin scale (mRS) and Karnofsky performance status (KPS) after CI were 5 and 30, respectively. The median survival time after CI was 1 month. In the group in which the thrombus due to venous thromboembolism (VTE) was reduced before CI, the median mRS, KPS, and prognosis after CI were significantly better than in those of the group with unchanged thrombus. Cancer-associated CI also developed in patients taking DOACs and those who did not show VTE recurrence. When the VTE thrombus decreased or disappeared with DOAC treatment, the clinical course after cancer-associated CI was improved.

Integrative network analysis reveals biological pathways associated with Williams syndrome

BACKGROUND

Williams syndrome (WS) is a neurodevelopmental disorder that has been attributed to heterozygous deletions in chromosome 7q11.23 and exhibits a variety of physical, cognitive, and behavioral features. However, the genetic basis of this phenotypic variability is unclear. In this study, we identified genetic clues underlying these complex phenotypes.

METHODS

Neurobehavioral function was assessed in WS patients and healthy controls. Total RNA was extracted from peripheral blood and subjected to microarray analysis, RNA-sequencing, and qRT-PCR. Weighted gene co-expression network analysis was performed to identify specific alterations related to intermediate disease phenotypes. To functionally interpret each WS-related module, gene ontology and disease-related gene enrichment were examined. We also investigated the micro (mi)RNA expression profiles and miRNA co-expression networks to better explain the regulation of the transcriptome in WS.

RESULTS

Our analysis identified four significant co-expression modules related to intermediate WS phenotypes. Notably, the three upregulated WS-related modules were composed exclusively of genes located outside the 7q11.23 region. They were significantly enriched in genes related to B-cell activation, RNA processing, and RNA transport. BCL11A, which is known for its association with speech disorders and intellectual disabilities, was identified as one of the hub genes in the top WS-related module. Finally, these key upregulated mRNA co-expression modules appear to be inversely correlated with a specific downregulated WS-related miRNA co-expression module.

CONCLUSIONS

Dysregulation of the mRNA/miRNA network involving genes outside of the 7q11.23 region is likely related to the complex phenotypes observed in WS patients.

Loss of RNA-Binding Protein Sfpq Causes Long-Gene Transcriptopathy in Skeletal Muscle and Severe Muscle Mass Reduction with Metabolic Myopathy

Growing evidences are suggesting that extra-long genes in mammals are vulnerable for full-gene length transcription and dysregulation of long genes is a mechanism underlying human genetic disorders. How long-distance transcription is achieved is a fundamental question to be elucidated. In previous study, we had discovered that RNA-binding protein SFPQ preferentially binds to long pre-mRNAs and specifically regulates the cluster of neuronal genes >100 kbp. Here we investigated the roles of SFPQ for long gene expression, target specificities, and also physiological functions in skeletal muscle. Loss of Sfpq selectively downregulated genes >100 kbp including Dystrophin, which is 2.26 Mbp in length. Sfpq knockout (KO) mice showed progressive muscle mass reduction and metabolic myopathy characterized by glycogen accumulation and decreased abundance of mitochondrial oxidative phosphorylation complexes. Functional clustering analysis identified energy metabolism pathway genes as SFPQ's targets. These findings indicate target gene specificities and tissue-specific physiological functions of SFPQ in skeletal muscle.

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SFPQ is essential for long gene expression, including Dystrophin, in skeletal muscle

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Disruption of Sfpq caused severe muscle mass reduction and premature death

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SFPQ is required for metabolic pathway gene expression in skeletal muscle

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Loss of Sfpq decreased OXPHOS complexes and caused glycogen accumulation

Use of direct oral anti-coagulants for the treatment of venous thromboembolism in patients with advanced cancer: a prospective observational study

BACKGROUND

The efficacy of direct oral anti-coagulants (DOACs) for the treatment of venous thromboembolism (VTE) in Japanese patients with advanced cancer is largely unknown.

METHODS

This prospective single-center observational study enrolled Japanese patients with unresectable advanced cancer who started DOAC treatment for new-onset VTE between December 2015 and May 2018. Patients were followed for 3 months to evaluate bleeding and VTE recurrences. The primary study endpoint was major and non-major bleeding.

RESULTS

One hundred and forty-five of 147 enrolled patients were analyzed. Of these, 8 [5.5%, 95% confidence interval (CI) 2.8-10.5] and 29 patients (20%, 95% CI 14.3-27.2) experienced major and non-major bleeding, respectively. Patients with bleeding were more likely to have a poor performance status (PS) [hazard rate (HR) 2.04, 95% CI 1.15-3.63] and more frequent use of non-steroidal anti-inflammatory drugs (NSAIDs) (HR 2.75, 95% CI 1.62-4.67) relative to those without bleeding. In a multivariate analysis, combined DOAC and NSAID use correlated significantly with bleeding (odds ratio 4.63, 95% CI 1.70-12.9, p = 0.003). Among 105 of 145 patients included in the VTE recurrence assessment, 9 experienced a VTE recurrence (8.6%, 95% CI 4.6-15.5).

CONCLUSIONS

Our findings confirm the risk of bleeding during DOAC treatment for VTE in Japanese patients with advanced cancer, particularly those with poor PS and those using NSAIDs. The risk of bleeding in these patients may be reduced by avoiding the combined use of DOACs and NSAIDs.

Effect of Switching from the Initial Direct Oral Anticoagulant to Another One on Exacerbation of Venous Thromboembolism in Patients with Cancer: A Retrospective Study

Objective: To determine the effect of switching from the initial direct oral anticoagulant (DOAC) to another DOAC on exacerbation of deep vein thrombosis (DVT).

Materials and Methods: We retrospectively reviewed the data of patients with advanced cancer who experienced exacerbated DVT during initial treatment with DOAC due to new venous thromboembolism (VTE). After switching to another DOAC for VTE recurrence, changes in the thrombus and bleeding were evaluated for 3 months. Eighteen patients met these criteria. We compared the effect of anticoagulant switching on the switched-drug group in those 18 patients with the effect of no anticoagulant switching on the single-drug group of patients (n=78) with a similar background.

Results: The recurrence rate of VTE in the switched-drug group was 6%. Non-major bleeding occurred in 11% of patients. Recurrent VTE occurred in 6% of patients in both the switched-drug and single-drug groups, respectively [risk ratio (RR): 0.9, 95% confidence interval (CI): 0.11–7.6]. Non-major bleeding occurred in 11% and 14% of patients in the switched-drug and single-drug groups, respectively (RR: 0.79, 95%CI: 0.19–3.2).

Conclusion: Switching DOAC may be a treatment option for exacerbation of DVT in patients with advanced cancer.

Disseminated toxoplasmosis with atypical symptoms which developed with exacerbation of systemic lupus erythematosus

Toxoplasma is a common parasite worldwide that mainly affects the brain, lungs and eyes. Although toxoplasmic encephalitis is a lethal disease without treatment, past case reports show most patients with systemic lupus erythematosus who developed toxoplasmic encephalitis were misdiagnosed and treated as neuropsychiatric systemic lupus erythematosus, which led to unfavorable outcomes. We herein describe a case of disseminated toxoplasmosis affecting all the above organs with atypical symptoms, which developed with exacerbation of systemic lupus erythematosus. She had initially manifested with retinochoroiditis without vitritis, mild cognitive impairment and an isolated lung mass. These are completely different from the classic symptoms of toxoplasmosis that have been reported in patients with HIV infection and/or those after hematopoietic transplantation. Our case, together with previously reported cases, suggests the manifestation of toxoplasmosis that develops in systemic lupus erythematosus patients can be different from that seen in conventional cases and varies between individual patients. Our case highlights both the difficulty in and the importance of diagnosing toxoplasmosis in patients with systemic lupus erythematosus and provides helpful information to identify this rare, devastating, yet treatable disease.

SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology

We report a microfluidic system that physically separates nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) from a single cell and enables single-cell integrated nucRNA and cytRNA-sequencing (SINC-seq). SINC-seq constructs two individual RNA-seq libraries, nucRNA and cytRNA, per cell, quantifies gene expression in the subcellular compartments, and combines them to create novel single-cell RNA-seq data. Leveraging SINC-seq, we discover distinct natures of correlation among cytRNA and nucRNA that reflect the transient physiological state of single cells. These data provide unique insights into the regulatory network of messenger RNA from the nucleus toward the cytoplasm at the single-cell level.

A Patient with a Massive Single Cardiac Metastasis of Lung Adenocarcinoma, Diagnosed via a Biopsy

A patient with a history of lung adenocarcinoma was admitted because of palpitation. Transthoracic echocardiogram revealed a mass (74×42 mm) in the right ventricle. Computed tomography showed a tumor lesion in the right ventricular cavity but no other distant metastasis. Coronary angiography revealed well-developed small branches to the tumor. After right heart catheterization, a pathological analysis of a tumor biopsy demonstrated adenocarcinoma. We diagnosed the patient with right ventricular metastasis of lung cancer. With large cardiac metastasis, a tumor biopsy with a right heart catheter may help obtain a pathological diagnosis and also serve as a re-biopsy to confirm the gene mutation status.

Characteristics of cellular composition in malignant pericardial effusion and its association with the clinical course of carcinomatous pericarditis

To date, the cellular composition of malignant pericardial effusion (MPE) and its association with the clinical course of carcinomatous pericarditis remain unclear. We aimed to determine the MPE cellular composition and its association with carcinomatous pericarditis. Forty-four cases indicated for pericardial drainage due to symptomatic carcinomatous pericarditis were retrospectively reviewed; the blood cell count and composition of MPE were examined. The most dominant cells in MPE were neutrophils. The appearance ratio of an atypical cell in cytologically positive MPE was 95.5%. Low neutrophil and high lymphocyte counts were significantly associated with good effusion failure-free survival at 1 month. The survival after pericardial drainage was significantly shorter when the neutrophil/lymphocyte ratio was 3.5 or more (P = 0.041). Patients whose performance status improved due to drainage had significantly high leukocyte counts in MPE (P = 0.02). Prediction of the course of drainage through basic examination of MPE cellular composition might be beneficial in clinical practice.

Decision Support for Psychiatric Diagnosis Based on a Simple Questionnaire

This paper compares two classifiers: Pseudo Bayesian and Neural Network for assisting in making diagnoses of psychiatric patients based on a simple yes/no questionnaire which is provided at the outpatient’s first visit to the hospital. The classifiers categorize patients into three most commonly seen ICD classes, i.e. schizophrenic, emotional and neurotic disorders. One hundred completed questionnaires were utilized for constructing and evaluating the classifiers. Average correct decision rates were 73.3% for the Pseudo Bayesian Classifier and 77.3% for the Neural Network classifier. These rates were higher than the rate which an experienced psychiatrist achieved based on the same restricted data as the classifiers utilized. These classifiers may be effectively utilized for assisting psychiatrists in making their final diagnoses.

Prevalence of deep venous thrombosis detected by ultrasonography before surgery in patients with gastric cancer: a retrospective study of 1140 consecutive patients

BACKGROUND

The prevalence of deep venous thrombosis (DVT) in patients with gastric cancer before surgery is unknown. This study aimed to clarify the risk factors for DVT of the lower extremities in patients with gastric cancer before surgery and to evaluate the usefulness of ultrasonographic screening for prevention of postoperative pulmonary thromboembolism (PTE).

METHODS

Patients who had undergone lower-extremity venous ultrasonography before surgery for gastric cancer were retrospectively analyzed. Univariate and multivariate logistic regression analyses were performed to identify the predictors of DVT before surgery. Perioperative management of patients with DVTs and the incidence of postoperative PTE were investigated.

RESULTS

Of the total 1140 patients, 86 had DVT preoperatively. On univariate analysis, the incidence of DVT was significantly higher with: female sex; age ≥80 years; PS ≥ 1 (vs. PS = 0); stage IV (vs. stages I-III); history of preoperative chemotherapy; and the presence of a central venous catheter (CVC). Multivariate logistic regression analysis demonstrated that sex, age ≥80 years, PS ≥ 1, history of preoperative chemotherapy, and the presence of CVC were significantly correlated with DVT before surgery. Postoperative PTE occurred in 2 patients with proximal DVT. No patients in whom DVT was not detected developed PTE.

CONCLUSIONS

Female sex, older age, worse PS, the presence of CVC, and a history of preoperative chemotherapy were the independent risk factors for DVT. Routine lower-extremity venous ultrasonographic screening is useful for prevention of PTE because it can identify patients at high or low risk for PTE.

Novel Stress-Inducible Antisense RNAs of Protein-Coding Loci Are Synthesized by RNA-Dependent RNA Polymerase

Our previous study identified approximately 6,000 abiotic stress-responsive noncoding transcripts existing on the antisense strand of protein-coding genes and implied that a type of antisense RNA was synthesized from a sense RNA template by RNA-dependent RNA polymerase (RDR). Expression analyses revealed that the expression of novel abiotic stress-induced antisense RNA on 1,136 gene loci was reduced in the rdr1/2/6 mutants. RNase protection indicated that the RD29A antisense RNA and other RDR1/2/6-dependent antisense RNAs are involved in the formation of dsRNA. The accumulation of stress-inducible antisense RNA was decreased and increased in dcp5 and xrn4, respectively, but not changed in dcl2/3/4, nrpd1a and nrpd1b RNA-seq analyses revealed that the majority of the RDR1/2/6-dependent antisense RNA loci did not overlap with RDR1/2/6-dependent 20-30 nt RNA loci. Additionally, rdr1/2/6 mutants decreased the degradation rate of the sense RNA and exhibited arrested root growth during the recovery stage following a drought stress, whereas dcl2/3/4 mutants did not. Collectively, these results indicate that RDRs have stress-inducible antisense RNA synthesis activity and a novel biological function that is different from the known endogenous small RNA pathways from protein-coding genes. These data reveal a novel mechanism of RNA regulation during abiotic stress response that involves complex RNA degradation pathways.

Next-generation sequencing-based analysis of reverse transcriptase fidelity

In this study, we devised a simple and rapid method to analyze fidelity of reverse transcriptase (RT) using next-generation sequencing (NGS). The method comprises a cDNA synthesis reaction from standard RNA with a primer containing a tag of 14 randomized bases and the RT to be tested, PCR using high-fidelity DNA polymerase, and NGS. By comparing the sequence of each read with the reference sequence, mutations were identified. The mutation can be identified to be due to an error introduced by either cDNA synthesis, PCR, or NGS based on whether the sequence reads with the same tag contain the same mutation or not. The error rates in cDNA synthesis with Moloney murine leukemia virus (MMLV) RT thermostable variant MM4 or the recently developed 16-tuple variant of family B DNA polymerase with RT activity, RTX, from Thermococcus kodakarensis, were 0.75-1.0 × 10^-4 errors/base, while that in the reaction with the wild-type human immunodeficiency virus type 1 (HIV-1) RT was 2.6 × 10^-4 errors/base. Overall, our method could precisely evaluate the fidelity of various RTs with different reaction conditions in a high-throughput manner without the use of expensive optics and troublesome adaptor ligation.

Selective mass enhancement close to the quantum critical point in BaFe2(As1-x P x )2

A quantum critical point (QCP) is currently being conjectured for the BaFe₂(As_1-x P _x )₂ system at the critical value x _c  ≈ 0.3. In the proximity of a QCP, all thermodynamic and transport properties are expected to scale with a single characteristic energy, given by the quantum fluctuations. Such a universal behavior has not, however, been found in the superconducting upper critical field H _c2. Here we report H _c2 data for epitaxial thin films extracted from the electrical resistance measured in very high magnetic fields up to 67 Tesla. Using a multi-band analysis we find that H _c2 is sensitive to the QCP, implying a significant charge carrier effective mass enhancement at the doping-induced QCP that is essentially band-dependent. Our results point to two qualitatively different groups of electrons in BaFe₂(As_1-x P _x )₂. The first one (possibly associated to hot spots or whole Fermi sheets) has a strong mass enhancement at the QCP, and the second one is insensitive to the QCP. The observed duality could also be present in many other quantum critical systems.