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

BACKGROUND AND 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 into 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 provide targets for fibrotic therapies. APPROACH AND RESULTS: We identified lncRNA 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 expression of COL1A1 and other ECM genes. To determine the role of TILAM in vivo, we annotated the mouse ortholog (Tilam), generated Tilam-deficient GFP-reporter mice, and challenged these mice in two different models of liver fibrosis. Single-cell data and analysis of GFP expression in 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 development of fibrosis in the setting of in vivo liver injury. Finally, we found that TILAM interacts with PML to regulate a feedback loop by which TGF-ß2 reinforces TILAM expression and nuclear localization of PML to promote the fibrotic activity of HSCs. CONCLUSIONS: TILAM is activated in HSCs with liver injury and interacts with PML to drive the development of fibrosis. Depletion of TILAM may serve as a therapeutic approach to combat the development of end stage liver disease.

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.

Nanchangmycin regulates FYN, PTK2, and MAPK1/3 to control the fibrotic activity of human hepatic stellate cells.

Chronic liver injury causes fibrosis, characterized by the formation of scar tissue resulting from excessive accumulation of extracellular matrix (ECM) proteins. Hepatic stellate cell (HSC) myofibroblasts are the primary cell type responsible for liver fibrosis, yet there are currently no therapies directed at inhibiting the activity of HSC myofibroblasts. To search for potential anti-fibrotic compounds, we performed a high-throughput compound screen in primary human HSC myofibroblasts and identified 19 small molecules that induce HSC inactivation, including the polyether ionophore nanchangmycin (NCMC). NCMC induces lipid re-accumulation while reducing collagen expression, deposition of collagen in the extracellular matrix, cell proliferation, and migration. We find that NCMC increases cytosolic Ca2+ and reduces the phosphorylated protein levels of FYN, PTK2 (FAK), MAPK1/3 (ERK2/1), HSPB1 (HSP27), and STAT5B. Further, depletion of each of these kinases suppress COL1A1 expression. These studies reveal a signaling network triggered by NCMC to inactivate HSC myofibroblasts and reduce expression of proteins that compose the fibrotic scar. Identification of the antifibrotic effects of NCMC and the elucidation of pathways by which NCMC inhibits fibrosis provide new tools and therapeutic targets that could potentially be utilized to combat the development and progression of liver fibrosis.

A Gapped Phase in Semimetallic Td -WTe2 Induced by Lithium Intercalation.

The Weyl semimetal WTe2 has shown several correlated electronic behaviors, such as the quantum spin Hall effect, superconductivity, ferroelectricity, and a possible exciton insulator state, all of which can be tuned by various physical and chemical approaches. Here, a new electronic phase in WTe2 induced by lithium intercalation is discovered. The new phase exhibits an increasing resistivity with decreasing temperature and its carrier density is almost two orders of magnitude lower than the carrier density of the semimetallic Td phase, probed by in situ Hall measurements as a function of lithium intercalation. The theoretical calculations predict the new lithiated phase to be a potential charge density wave (CDW) phase with a bandgap of ≈0.14 eV, in good agreement with the in situ transport data. The new phase is structurally distinct from the initial Td phase, characterized by polarization-angle-dependent Raman spectroscopy, and large lattice distortions close to 6% are predicted in the new phase. This finding of a new gapped phase in a 2D semimetal demonstrates electrochemical intercalation as a powerful tuning knob for modulating electron density and phase stability in 2D materials.

Heterointerface Effects on Lithium-Induced Phase Transitions in Intercalated MoS2.

The intercalation-induced phase transition of MoS2 from the semiconducting 2H to the semimetallic 1T' phase has been studied in detail for nearly a decade; however, the effects of a heterointerface between MoS2 and other two-dimensional (2D) crystals on the phase transition have largely been overlooked. Here, ab initio calculations show that intercalating Li at a MoS2-hexagonal boron nitride (hBN) interface stabilizes the 1T phase over the 2H phase of MoS2 by ∼100 mJ m -2, suggesting that encapsulating MoS2 with hBN may lower the electrochemical energy needed for the intercalation-induced phase transition. However, in situ Raman spectroscopy of hBN-MoS2-hBN heterostructures during the electrochemical intercalation of Li+ shows that the phase transition occurs at the same applied voltage for the heterostructure as for bare MoS2. We hypothesize that the predicted thermodynamic stabilization of the 1T'-MoS2-hBN interface is counteracted by an energy barrier to the phase transition imposed by the steric hindrance of the heterointerface. The phase transition occurs at lower applied voltages upon heating the heterostructure, which supports our hypothesis. Our study highlights that interfacial effects of 2D heterostructures can go beyond modulating electrical properties and can modify electrochemical and phase transition behaviors.

cm2-Scale Synthesis of MoTe2 Thin Films with Large Grains and Layer Control.

Owing to the small energy differences between its polymorphs, MoTe2 can access a full spectrum of electronic states from the 2H semiconducting state to the 1T' semimetallic state and from the Td Weyl semimetallic state to the superconducting state in the 1T' and Td phase at low temperature. Thus, it is a model system for phase transformation studies as well as quantum phenomena such as the quantum spin Hall effect and topological superconductivity. Careful studies of MoTe2 and its potential applications require large-area MoTe2 thin films with high crystallinity and thickness control. Here, we present cm2-scale synthesis of 2H-MoTe2 thin films with layer control and large grains that span several microns. Layer control is achieved by controlling the initial thickness of the precursor MoOx thin films, which are deposited on sapphire substrates by atomic layer deposition and subsequently tellurized. Despite the van der Waals epitaxy, the precursor-substrate interface is found to critically determine the uniformity in thickness and grain size of the resulting MoTe2 films: MoTe2 grown on sapphire show uniform films while MoTe2 grown on amorphous SiO2 substrates form islands. This synthesis strategy decouples the layer control from the variabilities of growth conditions for robust growth results and is applicable to growing other transition-metal dichalcogenides with layer control.

lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation.

Cooperation between DNA, RNA and protein regulates gene expression and controls differentiation through interactions that connect regions of nucleic acids and protein domains and through the assembly of biomolecular condensates. Here, we report that endoderm differentiation is regulated by the interaction between the long non-coding RNA (lncRNA) DIGIT and the bromodomain and extraterminal domain protein BRD3. BRD3 forms phase-separated condensates of which the formation is promoted by DIGIT, occupies enhancers of endoderm transcription factors and is required for endoderm differentiation. BRD3 binds to histone H3 acetylated at lysine 18 (H3K18ac) in vitro and co-occupies the genome with H3K18ac. DIGIT is also enriched in regions of H3K18ac, and the depletion of DIGIT results in decreased recruitment of BRD3 to these regions. Our findings show that cooperation between DIGIT and BRD3 at regions of H3K18ac regulates the transcription factors that drive endoderm differentiation and suggest that protein-lncRNA phase-separated condensates have a broader role as regulators of transcription.

Unveiling the Interfacial Effects for Enhanced Hydrogen Evolution Reaction on MoS2 /WTe2 Hybrid Structures.

Using the MoS2 -WTe2 heterostructure as a model system combined with electrochemical microreactors and density function theory calculations, it is shown that heterostructured contacts enhance the hydrogen evolution reaction (HER) activity of monolayer MoS2 . Two possible mechanisms are suggested to explain this enhancement: efficient charge injection through large-area heterojunctions between MoS2 and WTe2 and effective screening of mirror charges due to the semimetallic nature of WTe2 . The dielectric screening effect is proven minor, probed by measuring the HER activity of monolayer MoS2 on various support substrates with dielectric constants ranging from 4 to 300. Thus, the enhanced HER is attributed to the increased charge injection into MoS2 through large-area heterojunctions. Based on this understanding, a MoS2 /WTe2 hybrid catalyst is fabricated with an HER overpotential of -140 mV at 10 mA cm-2 , a Tafel slope of 40 mV dec-1 , and long stability. These results demonstrate the importance of interfacial design in transition metal dichalcogenide HER catalysts. The microreactor platform presents an unambiguous approach to probe interfacial effects in various electrocatalytic reactions.

Revealing the Contribution of Individual Factors to Hydrogen Evolution Reaction Catalytic Activity.

For the electrochemical hydrogen evolution reaction (HER), the electrical properties of catalysts can play an important role in influencing the overall catalytic activity. This is particularly important for semiconducting HER catalysts such as MoS2 , which has been extensively studied over the last decade. Herein, on-chip microreactors on two model catalysts, semiconducting MoS2 and semimetallic WTe2 , are employed to extract the effects of individual factors and study their relations with the HER catalytic activity. It is shown that electron injection at the catalyst/current collector interface and intralayer and interlayer charge transport within the catalyst can be more important than thermodynamic energy considerations. For WTe2 , the site-dependent activities and the relations of the pure thermodynamics to the overall activity are measured and established, as the microreactors allow precise measurements of the type and area of the catalytic sites. The approach presents opportunities to study electrochemical reactions systematically to help establish rational design principles for future electrocatalysts.

Genome-Wide Maps of m6A circRNAs Identify Widespread and Cell-Type-Specific Methylation Patterns that Are Distinct from mRNAs.

N6-methyladenosine (m6A) is the most abundant internal modification of mRNAs and is implicated in all aspects of post-transcriptional RNA metabolism. However, little is known about m6A modifications to circular (circ) RNAs. We developed a computational pipeline (AutoCirc) that, together with depletion of ribosomal RNA and m6A immunoprecipitation, defined thousands of m6A circRNAs with cell-type-specific expression. The presence of m6A circRNAs is corroborated by interaction between circRNAs and YTHDF1/YTHDF2, proteins that read m6A sites in mRNAs, and by reduced m6A levels upon depletion of METTL3, the m6A writer. Despite sharing m6A readers and writers, m6A circRNAs are frequently derived from exons that are not methylated in mRNAs, whereas mRNAs that are methylated on the same exons that compose m6A circRNAs exhibit less stability in a process regulated by YTHDF2. These results expand our understanding of the breadth of m6A modifications and uncover regulation of circRNAs through m6A modification.

Tricyclic Antidepressants Promote Ceramide Accumulation to Regulate Collagen Production in Human Hepatic Stellate Cells.

Activation of hepatic stellate cells (HSCs) in response to injury is a key step in hepatic fibrosis, and is characterized by trans-differentiation of quiescent HSCs to HSC myofibroblasts, which secrete extracellular matrix proteins responsible for the fibrotic scar. There are currently no therapies to directly inhibit hepatic fibrosis. We developed a small molecule screen to identify compounds that inactivate human HSC myofibroblasts through the quantification of lipid droplets. We screened 1600 compounds and identified 21 small molecules that induce HSC inactivation. Four hits were tricyclic antidepressants (TCAs), and they repressed expression of pro-fibrotic factors Alpha-Actin-2 (ACTA2) and Alpha-1 Type I Collagen (COL1A1) in HSCs. RNA sequencing implicated the sphingolipid pathway as a target of the TCAs. Indeed, TCA treatment of HSCs promoted accumulation of ceramide through inhibition of acid ceramidase (aCDase). Depletion of aCDase also promoted accumulation of ceramide and was associated with reduced COL1A1 expression. Treatment with B13, an inhibitor of aCDase, reproduced the antifibrotic phenotype as did the addition of exogenous ceramide. Our results show that detection of lipid droplets provides a robust readout to screen for regulators of hepatic fibrosis and have identified a novel antifibrotic role for ceramide.

DIGIT Is a Conserved Long Noncoding RNA that Regulates GSC Expression to Control Definitive Endoderm Differentiation of Embryonic Stem Cells.

Long noncoding RNAs (lncRNAs) exhibit diverse functions, including regulation of development. Here, we combine genome-wide mapping of SMAD3 occupancy with expression analysis to identify lncRNAs induced by activin signaling during endoderm differentiation of human embryonic stem cells (hESCs). We find that DIGIT is divergent to Goosecoid (GSC) and expressed during endoderm differentiation. Deletion of the SMAD3-occupied enhancer proximal to DIGIT inhibits DIGIT and GSC expression and definitive endoderm differentiation. Disruption of the gene encoding DIGIT and depletion of the DIGIT transcript reveal that DIGIT is required for definitive endoderm differentiation. In addition, we identify the mouse ortholog of DIGIT and show that it is expressed during development and promotes definitive endoderm differentiation of mouse ESCs. DIGIT regulates GSC in trans, and activation of endogenous GSC expression is sufficient to rescue definitive endoderm differentiation in DIGIT-deficient hESCs. Our study defines DIGIT as a conserved noncoding developmental regulator of definitive endoderm.

Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins.

BACKGROUND: Hepatic fibrosis is the underlying cause of cirrhosis and liver failure in nearly every form of chronic liver disease, and hepatic stellate cells (HSCs) are the primary cell type responsible for fibrosis. Long noncoding RNAs (lncRNAs) are increasingly recognized as regulators of development and disease; however, little is known about their expression in human HSCs and their function in hepatic fibrosis. METHODS: We performed RNA sequencing and ab initio assembly of RNA transcripts to define the lncRNAs expressed in human HSC myofibroblasts. We analyzed chromatin immunoprecipitation data and expression data to identify lncRNAs that were regulated by transforming growth factor beta (TGF-ß) signaling, associated with super-enhancers and restricted in expression to HSCs compared with 43 human tissues and cell types. Co-expression network analyses were performed to discover functional modules of lncRNAs, and principle component analysis and K-mean clustering were used to compare lncRNA expression in HSCs with other myofibroblast cell types. RESULTS: We identified over 3600 lncRNAs that are expressed in human HSC myofibroblasts. Many are regulated by TGF-ß, a major fibrotic signal, and form networks with genes encoding key components of the extracellular matrix (ECM), which is the substrate of the fibrotic scar. The lncRNAs directly regulated by TGF-ß signaling are also enriched at super-enhancers. More than 400 of the lncRNAs identified in HSCs are uniquely expressed in HSCs compared with 43 other human tissues and cell types and HSC myofibroblasts demonstrate different patterns of lncRNA expression compared with myofibroblasts originating from other tissues. Co-expression analyses identified a subset of lncRNAs that are tightly linked to collagen genes and numerous proteins that regulate the ECM during formation of the fibrotic scar. Finally, we identified lncRNAs that are induced during progression of human liver disease. CONCLUSIONS: lncRNAs are likely key contributors to the formation and progression of fibrosis in human liver disease.