Conserved long noncoding RNA TILAM promotes liver fibrosis through interaction with PML in HSCs.

BACKGROUND AND AIMS: Fibrosis is the common end point for all forms of chronic liver injury, and the progression of fibrosis leads to the development of end-stage liver disease. Activation of HSCs and their transdifferentiation into myofibroblasts results in the accumulation of extracellular matrix proteins that form the fibrotic scar. Long noncoding RNAs regulate the activity of HSCs and provide targets for fibrotic therapies. APPROACH AND RESULTS: We identified long noncoding RNA TILAM located near COL1A1 , expressed in HSCs, and induced with liver fibrosis in humans and mice. Loss-of-function studies in human HSCs and human liver organoids revealed that TILAM regulates the expression of COL1A1 and other extracellular matrix genes. To determine the role of TILAM in vivo, we annotated the mouse ortholog ( Tilam ), generated Tilam- deficient green fluorescent protein-reporter mice, and challenged these mice in 2 different models of liver fibrosis. Single-cell data and analysis of single-data and analysis of Tilam-deficient reporter mice revealed that Tilam is induced in murine HSCs with the development of fibrosis in vivo. Tilam -deficient reporter mice revealed that Tilam is induced in murine HSCs with the development of fibrosis in vivo. Furthermore, loss of Tilam expression attenuated the development of fibrosis in the setting of in vivo liver injury. Finally, we found that TILAM interacts with promyelocytic leukemia nuclear body scaffold protein to regulate a feedback loop by which TGF-ß2 reinforces TILAM expression and nuclear localization of promyelocytic leukemia nuclear body scaffold protein to promote the fibrotic activity of HSCs. CONCLUSIONS: TILAM is activated in HSCs with liver injury and interacts with promyelocytic leukemia nuclear body scaffold protein to drive the development of fibrosis. Depletion of TILAM may serve as a therapeutic approach to combat the development of end-stage liver disease.

Genetic aetiology of early infant deaths in a neonatal intensive care unit.

BACKGROUND: Congenital anomalies are the leading cause of early neonatal death in neonatal intensive care units (NICUs), but the genetic causes are unclear. This study aims to investigate the genetic causes of infant deaths in a NICU in China. METHODS: Newborns who died in the hospital or died within 1 week of discharge were enrolled from Children's Hospital of Fudan University between January 1, 2015 and December 31, 2017. Whole exome sequencing was performed in all patients after death. RESULTS: There were 223 deceased newborns with a median age at death of 13 days. In total, 44 (19.7%) infants were identified with a genetic finding, including 40 with single nucleotide variants (SNVs), two with CNVs and two with both SNVs and CNVs. Thirteen (31%, 13/42) patients with SNVs had medically actionable disorders based on genetic diagnosis, which included 10 genes. Multiple congenital malformation was identified as the leading genetic cause of death in NICUs with 13 newborns identified with variants in genes related to multiple congenital malformations. For newborns who died on the first day, the most common genetic cause of death was major heart defects, while metabolic disorders and respiratory failure were more common for newborns who died in the first 2 weeks. CONCLUSION: Our study shows genetic findings among early infant deaths in NICUs and provides critical genetic information for precise genetic counselling for the families. Effective therapies enable the improvement of more than a quarter of newborns with molecular diagnoses if diagnosed in time.

PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease.

MOTIVATION: Whole-exome sequencing (WES) is now being used in clinical practice for the diagnosis of the causal genes of Mendelian diseases. In order to make the diagnosis, however, the clinical phenotypes [e.g. Human Phenotype Ontology (HPO) terms] of a patient are needed for prioritizing the variants called from the WES data of the patient. Computational tools are therefore needed to standardize and accelerate this process. RESULTS: Here, we introduce a tool named PhenoPro for prioritizing the causal gene of Mendelian disease given both the HPO terms assigned to and the variants called from the WES data of a patient. PhenoPro has been benchmarked using both simulated patients and 287 real diagnosed patients of Chinese ancestry, and shows significant improvements over five previous tools. Moreover, the addition of an internal variant data of Chinese ancestry and the variant data from the patients' parents can further improve PhenoPro's performance. To make PhenoPro a fully automated tool, we also include a natural language processing component for automated HPO term assignment from clinical reports, and demonstrate that the natural language processing is as effective as manual HPO assignment using real clinical reports. In conclusion, PhenoPro can be used as a pre-screening tool to assist in the diagnosis of Mendelian disease genes. AVAILABILITY AND IMPLEMENTATION: The web server of PhenoPro is freely available at http://app.tianlab.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Frequent mutation of hypoxia-related genes in persistent pulmonary hypertension of the newborn.

AIMS: Persistent pulmonary hypertension of the newborn (PPHN) is characterized by sustained high levels of pulmonary vascular resistance after birth with etiology unclear; Arterial blood oxygen saturation of Tibetan newborns at high latitudes is higher than that of Han newborns at low latitudes, suggesting that genetic adaptation may allow sufficient oxygen to confer Tibetan populations with resistance to pulmonary hypertension; We have previously identified genetic factors related to PPHN through candidate gene sequencing; In this study, we first performed whole exome sequencing in PPHN patients to screen for genetic-related factors. METHODS AND RESULTS: In this two-phase genetic study, we first sequenced the whole exome of 20 Tibetan PPHN patients and compared it with the published genome sequences of 50 healthy high-altitude Tibetanshypoxia-related genes, a total of 166 PPHN-related variants were found, of which 49% were from 43 hypoxia-related genes; considering many studies have shown that the differences in the genetic background between Tibet and Han are characterized by hypoxia-related genetic polymorphisms, so it is necessary to further verify whether the association between hypoxia-related variants and PPHN is independent of high-altitude life. During the validation phase, 237 hypoxia-related genes were sequenced in another 80 Han PPHN patients living in low altitude areas, including genes at the discovery stage and known hypoxia tolerance, of which 413 variants from 127 of these genes were shown to be significantly associated with PPHN.hypoxia-related genes. CONCLUSIONS: Our results indicates that the association of hypoxia-related genes with PPHN does not depend on high-altitude life, at the same time, 21 rare mutations associated with PPHN were also found, including three rare variants of the tubulin tyrosine ligase-like family member 3 gene (TTLL3:p.E317K, TTLL3:p.P777S) and the integrin subunit alpha M gene (ITGAM:p.E1071D). These novel findings provide important information on the genetic basis of PPHN.

A simple microsphere-based mold to rapidly fabricate microwell arrays for multisize 3D tumor culture.

Three-dimensional (3D) tumor has been considered as the best in vitro model for cancer research. In recent years, various methods have been developed to controllable prepare multisize 3D tumors. Nonetheless, reported technologies are still problematic and difficult to produce 3D tumors with highly uniform size and cell content. Here, a novel and simple microsphere-based mold approach is proposed to rapidly fabricate spherical microwell arrays for multisize 3D tumors formation, culture, and recovery. Larger amounts of HepG2 3D tumors with excellent quality and uniformity can be efficiently generated using this method. In addition, the tumor size can also be simply controlled by adjusting the diameter of the microwell arrays. All experimental results indicated that the proposed method offers a promising platform to generate and recover highly controlled multisize 3D tumors for various cell-based biomedical research.

Whole genome sequencing identifies a novel ALMS1 gene mutation in two Chinese siblings with Alström syndrome.

BACKGROUND: Alström syndrome is a rare multi-systemic disorder with a broad spectrum of symptoms. This syndrome is characterized by childhood retinal degeneration; sensorineural hearing loss; obesity; type 2 diabetes mellitus; cardiomyopathy; systemic fibrosis; and pulmonary, hepatic, and renal failure. CASE PRESENTATION: A Chinese quartet family with two siblings predominantly affected by cone-rod dystrophy and short stature were recruited. The craniofacial dysmorphism and on-set age-of-cone-rod dystrophy in the proband showed a minor intrafamilial variability. Whole genome sequencing was performed to provide the full spectrum of the two siblings' genetic variations. In this study, we present the patients' clinical features and our interpretation of the whole genome sequencing data. After examining the data, we focus on two compound heterozygous mutations, (c.3902C > A, p.S1301X; c.6436C > T, p.R2146X) in ALMS1, which are shared by two siblings. CONCLUSION: We reported a novel ALMS1 mutation. Whole genome sequencing is a powerful tool to provide the full spectrum of genetic variations for heterogeneous disorders such as Alström syndrome.

IFNγ-IL12 axis regulates intercellular crosstalk in metabolic dysfunction-associated steatotic liver disease.

Obesity is a major cause of metabolic dysfunction-associated steatohepatitis (MASH) and is characterized by inflammation and insulin resistance. Interferon-γ (IFNγ) is a pro-inflammatory cytokine elevated in obesity and modulating macrophage functions. Here, we show that male mice with loss of IFNγ signaling in myeloid cells (Lyz-IFNγR2-/-) are protected from diet-induced insulin resistance despite fatty liver. Obesity-mediated liver inflammation is also attenuated with reduced interleukin (IL)-12, a cytokine primarily released by macrophages, and IL-12 treatment in vivo causes insulin resistance by impairing hepatic insulin signaling. Following MASH diets, Lyz-IFNγR2-/- mice are rescued from developing liver fibrosis, which is associated with reduced fibroblast growth factor (FGF) 21 levels. These results indicate critical roles for IFNγ signaling in macrophages and their release of IL-12 in modulating obesity-mediated insulin resistance and fatty liver progression to MASH. In this work, we identify the IFNγ-IL12 axis in regulating intercellular crosstalk in the liver and as potential therapeutic targets to treat MASH.

Conserved long noncoding RNA TILAM promotes liver fibrosis through interaction with PML in hepatic stellate cells.

Background & Aims: Fibrosis is the common endpoint for all forms of chronic liver injury, and progression of fibrosis leads to the development of end-stage liver disease. Activation of hepatic stellate cells (HSCs) and their transdifferentiation to myofibroblasts results in the accumulation of extracellular matrix (ECM) proteins that form the fibrotic scar. Long noncoding (lnc) RNAs regulate the activity of HSCs and may provide targets for fibrotic therapies. Methods: We identified lncRNA TILAM as expressed near COL1A1 in human HSCs and performed loss-of-function studies in human HSCs and liver organoids. Transcriptomic analyses of HSCs isolated from mice defined the murine ortholog of TILAM . We then generated Tilam -deficient GFP reporter mice and quantified fibrotic responses to carbon tetrachloride (CCl 4 ) and choline-deficient L-amino acid defined high fat diet (CDA-HFD). Co-precipitation studies, mass spectrometry, and gene expression analyses identified protein partners of TILAM . Results: TILAM is conserved between human and mouse HSCs and regulates expression of ECM proteins, including collagen. Tilam is selectively induced in HSCs during the development of fibrosis in vivo . In both male and female mice, loss of Tilam results in reduced fibrosis in the setting of CCl 4 and CDA-HFD injury models. TILAM interacts with promyelocytic leukemia protein (PML) to stabilize PML protein levels and promote the fibrotic activity of HSCs. Conclusion: TILAM is activated in HSCs and interacts with PML to drive the development of liver fibrosis. Depletion of TILAM may serve as a therapeutic approach to combat the development of end stage liver disease.

Flnc: Machine Learning Improves the Identification of Novel Long Noncoding RNAs from Stand-Alone RNA-Seq Data.

Long noncoding RNAs (lncRNAs) play critical regulatory roles in human development and disease. Although there are over 100,000 samples with available RNA sequencing (RNA-seq) data, many lncRNAs have yet to be annotated. The conventional approach to identifying novel lncRNAs from RNA-seq data is to find transcripts without coding potential but this approach has a false discovery rate of 30-75%. Other existing methods either identify only multi-exon lncRNAs, missing single-exon lncRNAs, or require transcriptional initiation profiling data (such as H3K4me3 ChIP-seq data), which is unavailable for many samples with RNA-seq data. Because of these limitations, current methods cannot accurately identify novel lncRNAs from existing RNA-seq data. To address this problem, we have developed software, Flnc, to accurately identify both novel and annotated full-length lncRNAs, including single-exon lncRNAs, directly from RNA-seq data without requiring transcriptional initiation profiles. Flnc integrates machine learning models built by incorporating four types of features: transcript length, promoter signature, multiple exons, and genomic location. Flnc achieves state-of-the-art prediction power with an AUROC score over 0.92. Flnc significantly improves the prediction accuracy from less than 50% using the conventional approach to over 85%. Flnc is available via GitHub platform.

Green and sustainable cellulose-derived humidity sensors: A review.

Cellulose, as the most abundant natural polysaccharide, is an excellent material for developing green humidity sensors, especially due to its humidity responsiveness as a result of its rich hydrophilic groups. In combination with other components including carbon materials and polymers, cellulose and its derivatives can be used to design high-performance humidity sensors that meet various application requirements. This review summarizes the recent advances in the field of various cellulose-derived humidity sensors, with particular attention paid to different sensing mechanisms including resistance, capacitance, colorimetry and gravity, and so on. Furthermore, the roles of cellulose and its derivatives are highlighted. This work may promote the development of cellulose-derived humidity sensors, as well as other cellulose-based intelligent materials.

Asymmetrically Patterned Cellulose Nanofibers/Graphene Oxide Composite Film for Humidity Sensing and Moist-Induced Electricity Generation.

The exploration of advanced functional materials from natural resources is significantly important to green and sustainable development. Herein, we design an ultrafast humidity-driven bending response system using asymmetrically patterned cellulose nanofiber (CNF)/graphene oxide (GO) composite films. The CNF/GO composite films are fabricated by vacuum-assisted filtration, followed by a surface imprinting technique. The results reveal that the composite films possess excellent linear response to humidity change and cycle stability in the relative humidity (RH) range from 25 to 85%. The curvature of the film varies from 0.012 to 0.260 cm-1 as the RH changes from 25 to 85%, and the response time is only 3-5 s. The outstanding humidity response is attributed to the addition of GO that actively interacts with water, enhancing the flexibility and humidity sensitivity of the composite films. In addition, asymmetrical patterning improves the water transfer rate by confinement and renders an easy deformation of composite films under the same stress. Molecular dynamics simulation and finite element analysis are used to further elucidate the mechanism therein. Furthermore, this CNF/GO composite film is also an effective hygroelectric generator, with an output voltage as high as 286 mV. This smart CNF/GO film with responsive humidity-driven deformation shows potential applications as a biomimetic leaf, a proximity sensor, and a moisture-driven electricity generator. This work inspires a new approach of smart material design with nanocellulose and GO and promotes their further applications.

A multifunctional self-crosslinked chitosan/cationic guar gum composite hydrogel and its versatile uses in phosphate-containing water treatment and energy storage.

A new self-crosslinked composite hydrogel is prepared with chitosan (CS) and cationic guar gum (CGG), based on the imine and acetal chemistry for gelation. The CS/CGG hydrogel exhibits thermal/pH responsiveness, injectability, adhesiveness and good compressive strength. The hydrogel is effective in removing phosphate from wastewater through an adsorption process, during which KH2PO4 is used as a phosphate model. The adsorption complies with the Freundlich model, indicating that it is a multilayered process with complex adsorption mechanisms. Considering their porous structure and nitrogen/phosphorus heteroatoms doping, the phosphate-adsorbed hydrogels are made into porous N,P doped carbon aerogels that can be potentially used as electrodes for a supercapacitor. The results indicate that these carbon aerogels possess excellent capacitive performance (best specific capacitance of 302.2 ± 4.9 F/g), as well as good cycling stability after 5000 times of charging/discharging.

Colorimetric hydrazine detection and fluorescent hydrogen peroxide imaging by using a multifunctional chemical probe.

Among organic small molecules, hydrogen peroxide (H2O2) and hydrazine (NH2NH2) often cause concern because they are widely used in biological and chemical industries. Here, we present a novel probe RH-1 for colorimetric detection of NH2NH2 and fluorescent imaging of H2O2. In this probe, rhodamine was used as the main skeleton due to its favorable spectroscopic performance and stable absorption. Importantly, a benzoic acid group is present in the rhodamine skeleton, which can react with NH2NH2 by amidation. The rhodamine skeleton can also be modified with chromogens to detect H2O2. Results showed that RH-1 can be used for colorimetric detection of NH2NH2 and fluorescent monitoring of H2O2 with high selectivity and sensitivity. The detection limits for NH2NH2 and H2O2 were 0.27 and 0.16 µM, respectively. Moreover, RH-1 can fluorescently image H2O2 in living cells with low cytotoxicity.

Tri-(2-picolyl)amine-modificated triarylborane: Synthesis, photophysical properties and distinguish for cyanide and fluoride anions in aqueous solution.

We designed and synthesized a tri-(2-picolyl) amine (TPA) functionalized triarylborane, 1-(6-(4-(dimesitylboryl)phenyl)pyridin-2-yl)-N,N-bis(pyridin-2-ylmethyl)methanamine (PB2). The photophysical properties of PB2 were thoroughly explored. Moreover, PB2 can capture CN- and F- in aqueous solution through strong chelation induced by the synergy of a boron atom and metal ion gripped by TPA to display entirely different fluorogenic responses such as fluorescence enhancement for CN- and fluorescence quenching for F-. The results of TOF-MS-EI analysis and theoretical calculations indicate that the complexing of PB2 with CN- formed a 2-to-2 adduct with a stabilized configuration, resulting in strong emission. The complexing of PB2 with F- formed a 1-to-1 adduct with a loose configuration, resulting in weak emission. In pure water, the detection limit of PB2 for CN- is 0.79 µM, and in H2O/THF (1:9 v/v) system, the detection limits of PB2 for CN- and F- can reach 0.39 and 2.12 µM, respectively, indicating its potential application for effective detection and discrimination of CN- and F-.