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1.
Cell ; 176(1-2): 239-253.e16, 2019 01 10.
Article in English | MEDLINE | ID: mdl-30503210

ABSTRACT

Csm, a type III-A CRISPR-Cas interference complex, is a CRISPR RNA (crRNA)-guided RNase that also possesses target RNA-dependent DNase and cyclic oligoadenylate (cOA) synthetase activities. However, the structural features allowing target RNA-binding-dependent activation of DNA cleavage and cOA generation remain unknown. Here, we report the structure of Csm in complex with crRNA together with structures of cognate or non-cognate target RNA bound Csm complexes. We show that depending on complementarity with the 5' tag of crRNA, the 3' anti-tag region of target RNA binds at two distinct sites of the Csm complex. Importantly, the interaction between the non-complementary anti-tag region of cognate target RNA and Csm1 induces a conformational change at the Csm1 subunit that allosterically activates DNA cleavage and cOA generation. Together, our structural studies provide crucial insights into the mechanistic processes required for crRNA-meditated sequence-specific RNA cleavage, RNA target-dependent non-specific DNA cleavage, and cOA generation.


Subject(s)
CRISPR-Associated Proteins/ultrastructure , CRISPR-Cas Systems/physiology , Clustered Regularly Interspaced Short Palindromic Repeats/physiology , Bacterial Proteins , CRISPR-Associated Proteins/chemistry , DNA/chemistry , Deoxyribonucleases/metabolism , Endoribonucleases/metabolism , Models, Molecular , RNA/chemistry , RNA, Bacterial/chemistry , RNA, Guide, Kinetoplastida/chemistry , Ribonucleases/metabolism
2.
Nat Immunol ; 21(3): 287-297, 2020 03.
Article in English | MEDLINE | ID: mdl-31932812

ABSTRACT

Cancer cells subvert immune surveillance through inhibition of T cell effector function. Elucidation of the mechanism of T cell dysfunction is therefore central to cancer immunotherapy. Here, we report that dual specificity phosphatase 2 (DUSP2; also known as phosphatase of activated cells 1, PAC1) acts as an immune checkpoint in T cell antitumor immunity. PAC1 is selectively upregulated in exhausted tumor-infiltrating lymphocytes and is associated with poor prognosis of patients with cancer. PAC1hi effector T cells lose their proliferative and effector capacities and convert into exhausted T cells. Deletion of PAC1 enhances immune responses and reduces cancer susceptibility in mice. Through activation of EGR1, excessive reactive oxygen species in the tumor microenvironment induce expression of PAC1, which recruits the Mi-2ß nucleosome-remodeling and histone-deacetylase complex, eventually leading to chromatin remodeling of effector T cells. Our study demonstrates that PAC1 is an epigenetic immune regulator and highlights the importance of targeting PAC1 in cancer immunotherapy.


Subject(s)
Dual Specificity Phosphatase 2/immunology , Neoplasms/immunology , T-Lymphocytes/immunology , Animals , Chromatin/genetics , Chromatin/metabolism , Dual Specificity Phosphatase 2/deficiency , Dual Specificity Phosphatase 2/genetics , Early Growth Response Protein 1/metabolism , Female , Humans , Lymphocyte Activation , Lymphocytes, Tumor-Infiltrating/immunology , Male , Mi-2 Nucleosome Remodeling and Deacetylase Complex/metabolism , Mice , Mice, Inbred C57BL , Mice, Inbred NOD , Mice, Knockout , Mice, SCID , Neoplasms/genetics , Neoplasms/metabolism , Reactive Oxygen Species/metabolism , Tumor Microenvironment/genetics , Tumor Microenvironment/immunology , Up-Regulation
3.
Cell ; 170(4): 714-726.e10, 2017 Aug 10.
Article in English | MEDLINE | ID: mdl-28757251

ABSTRACT

Cas13a, a type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, degrades invasive RNAs targeted by CRISPR RNA (crRNA) and has potential applications in RNA technology. To understand how Cas13a is activated to cleave RNA, we have determined the crystal structure of Leptotrichia buccalis (Lbu) Cas13a bound to crRNA and its target RNA, as well as the cryo-EM structure of the LbuCas13a-crRNA complex. The crRNA-target RNA duplex binds in a positively charged central channel of the nuclease (NUC) lobe, and Cas13a protein and crRNA undergo a significant conformational change upon target RNA binding. The guide-target RNA duplex formation triggers HEPN1 domain to move toward HEPN2 domain, activating the HEPN catalytic site of Cas13a protein, which subsequently cleaves both single-stranded target and collateral RNAs in a non-specific manner. These findings reveal how Cas13a of type VI CRISPR-Cas systems defend against RNA phages and set the stage for its development as a tool for RNA manipulation.


Subject(s)
Bacterial Proteins/chemistry , CRISPR-Associated Proteins/chemistry , CRISPR-Cas Systems , Leptotrichia/immunology , Bacterial Proteins/ultrastructure , Base Sequence , CRISPR-Associated Proteins/ultrastructure , Leptotrichia/chemistry , Leptotrichia/metabolism , Leptotrichia/virology , Models, Molecular , RNA Processing, Post-Transcriptional , RNA, Bacterial/chemistry , RNA, Bacterial/genetics , RNA, Bacterial/ultrastructure , RNA, Guide, Kinetoplastida/chemistry , RNA, Guide, Kinetoplastida/genetics , RNA, Guide, Kinetoplastida/ultrastructure , RNA, Viral/chemistry , X-Ray Diffraction
4.
Cell ; 168(1-2): 121-134.e12, 2017 Jan 12.
Article in English | MEDLINE | ID: mdl-28086085

ABSTRACT

C2c2, the effector of type VI CRISPR-Cas systems, has two RNase activities-one for cutting its RNA target and the other for processing the CRISPR RNA (crRNA). Here, we report the structures of Leptotrichia shahii C2c2 in its crRNA-free and crRNA-bound states. While C2c2 has a bilobed structure reminiscent of all other Class 2 effectors, it also exhibits different structural characteristics. It contains the REC lobe with a Helical-1 domain and the NUC lobe with two HEPN domains. The two RNase catalytic pockets responsible for cleaving pre-crRNA and target RNA are independently located on Helical-1 and HEPN domains, respectively. crRNA binding induces significant conformational changes that are likely to stabilize crRNA binding and facilitate target RNA recognition. These structures provide important insights into the molecular mechanism of dual RNase activities of C2c2 and establish a framework for its future engineering as a RNA editing tool.


Subject(s)
CRISPR-Cas Systems , Leptotrichia/chemistry , Leptotrichia/enzymology , Ribonucleases/chemistry , Amino Acid Sequence , Catalytic Domain , Leptotrichia/classification , Leptotrichia/metabolism , Models, Molecular , Mutagenesis , RNA Processing, Post-Transcriptional , RNA, Bacterial/chemistry , RNA, Untranslated/chemistry , Sequence Alignment
5.
Nature ; 608(7921): 62-68, 2022 08.
Article in English | MEDLINE | ID: mdl-35922499

ABSTRACT

Additive manufacturing produces net-shaped components layer by layer for engineering applications1-7. The additive manufacture of metal alloys by laser powder bed fusion (L-PBF) involves large temperature gradients and rapid cooling2,6, which enables microstructural refinement at the nanoscale to achieve high strength. However, high-strength nanostructured alloys produced by laser additive manufacturing often have limited ductility3. Here we use L-PBF to print dual-phase nanolamellar high-entropy alloys (HEAs) of AlCoCrFeNi2.1 that exhibit a combination of a high yield strength of about 1.3 gigapascals and a large uniform elongation of about 14 per cent, which surpasses those of other state-of-the-art additively manufactured metal alloys. The high yield strength stems from the strong strengthening effects of the dual-phase structures that consist of alternating face-centred cubic and body-centred cubic nanolamellae; the body-centred cubic nanolamellae exhibit higher strengths and higher hardening rates than the face-centred cubic nanolamellae. The large tensile ductility arises owing to the high work-hardening capability of the as-printed hierarchical microstructures in the form of dual-phase nanolamellae embedded in microscale eutectic colonies, which have nearly random orientations to promote isotropic mechanical properties. The mechanistic insights into the deformation behaviour of additively manufactured HEAs have broad implications for the development of hierarchical, dual- and multi-phase, nanostructured alloys with exceptional mechanical properties.

6.
Nat Immunol ; 16(12): 1263-73, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26479789

ABSTRACT

Deregulation of the TH17 subset of helper T cells is closely linked with immunological disorders and inflammatory diseases. However, the mechanism by which TH17 cells are regulated remains elusive. Here we found that the phosphatase DUSP2 (PAC1) negatively regulated the development of TH17 cells. DUSP2 was directly associated with the signal transducer and transcription activator STAT3 and attenuated its activity through dephosphorylation of STAT3 at Tyr705 and Ser727. DUSP2-deficient mice exhibited severe susceptibility to experimental colitis, with enhanced differentiation of TH17 cells and secretion of proinflammatory cytokines. In clinical patients with ulcerative colitis, DUSP2 was downregulated by DNA methylation and was not induced during T cell activation. Our data demonstrate that DUSP2 is a true STAT3 phosphatase that modulates the development of TH17 cells in the autoimmune response and inflammation.


Subject(s)
Cell Differentiation/immunology , Dual Specificity Phosphatase 2/immunology , STAT3 Transcription Factor/immunology , Th17 Cells/immunology , Animals , Cells, Cultured , Colitis/chemically induced , Colitis/genetics , Colitis/immunology , Colitis, Ulcerative/genetics , Colitis, Ulcerative/immunology , Colitis, Ulcerative/metabolism , Cytokines/immunology , Cytokines/metabolism , DNA Methylation/immunology , Dextran Sulfate , Dual Specificity Phosphatase 2/deficiency , Dual Specificity Phosphatase 2/genetics , Gene Expression Regulation/immunology , HEK293 Cells , Humans , Immunoblotting , Inflammation Mediators/immunology , Inflammation Mediators/metabolism , Mice, Inbred C57BL , Mice, Knockout , Phosphorylation/immunology , Protein Binding/immunology , Reverse Transcriptase Polymerase Chain Reaction , STAT3 Transcription Factor/metabolism , Th17 Cells/metabolism , Tyrosine/immunology , Tyrosine/metabolism
7.
Mol Cell ; 73(3): 611-620.e3, 2019 02 07.
Article in English | MEDLINE | ID: mdl-30606466

ABSTRACT

CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems provide prokaryotic cells with adaptive immunity against invading bacteriophages. Bacteriophages counteract bacterial responses by encoding anti-CRISPR inhibitor proteins (Acr). However, the structural basis for their inhibitory actions remains largely unknown. Here, we report the crystal structure of the AcrIIA2-SpyCas9-sgRNA (single-guide RNA) complex at 3.3 Å resolution. We show that AcrIIA2 binds SpyCas9 at a position similar to the target DNA binding region. More specifically, AcrIIA2 interacts with the protospacer adjacent motif (PAM) recognition residues of Cas9, preventing target double-stranded DNA (dsDNA) detection. Thus, phage-encoded AcrIIA2 appears to act as a DNA mimic that blocks subsequent dsDNA binding by virtue of its highly acidic residues, disabling bacterial Cas9 by competing with target dsDNA binding with a binding motif distinct from AcrIIA4. Our study provides a more detailed mechanistic understanding of AcrIIA2-mediated inhibition of SpyCas9, the most widely used genome-editing tool, opening new avenues for improved regulatory precision during genome editing.


Subject(s)
Bacteriophages/metabolism , CRISPR-Associated Protein 9/metabolism , CRISPR-Cas Systems , Clustered Regularly Interspaced Short Palindromic Repeats , Escherichia coli/enzymology , Gene Editing/methods , Molecular Mimicry , Viral Proteins/metabolism , Bacteriophages/genetics , Binding Sites , Binding, Competitive , CRISPR-Associated Protein 9/antagonists & inhibitors , CRISPR-Associated Protein 9/chemistry , CRISPR-Associated Protein 9/genetics , DNA/chemistry , DNA/genetics , DNA/metabolism , Escherichia coli/genetics , Escherichia coli/virology , Models, Molecular , Nucleic Acid Conformation , Protein Binding , Protein Conformation , Protein Interaction Domains and Motifs , RNA, Guide, Kinetoplastida/chemistry , RNA, Guide, Kinetoplastida/genetics , RNA, Guide, Kinetoplastida/metabolism , Structure-Activity Relationship , Viral Proteins/chemistry , Viral Proteins/genetics
8.
Mol Cell ; 76(6): 938-952.e5, 2019 12 19.
Article in English | MEDLINE | ID: mdl-31668930

ABSTRACT

High-resolution Cas9 structures have yet to reveal catalytic conformations due to HNH nuclease domain positioning away from the cleavage site. Nme1Cas9 and Nme2Cas9 are compact nucleases for in vivo genome editing. Here, we report structures of meningococcal Cas9 homologs in complex with sgRNA, dsDNA, or the AcrIIC3 anti-CRISPR protein. DNA-bound structures represent an early step of target recognition, a later HNH pre-catalytic state, the HNH catalytic state, and a cleaved-target-DNA-bound state. In the HNH catalytic state of Nme1Cas9, the active site is seen poised at the scissile phosphodiester linkage of the target strand, providing a high-resolution view of the active conformation. The HNH active conformation activates the RuvC domain. Our structures explain how Nme1Cas9 and Nme2Cas9 read distinct PAM sequences and how AcrIIC3 inhibits Nme1Cas9 activity. These structures provide insights into Cas9 domain rearrangements, guide-target engagement, cleavage mechanism, and anti-CRISPR inhibition, facilitating the optimization of these genome-editing platforms.


Subject(s)
Bacteriophages/metabolism , CRISPR-Associated Protein 9/metabolism , CRISPR-Cas Systems , Clustered Regularly Interspaced Short Palindromic Repeats , DNA/metabolism , Neisseria meningitidis/enzymology , Viral Proteins/metabolism , Bacteriophages/genetics , Binding Sites , CRISPR-Associated Protein 9/genetics , CRISPR-Associated Protein 9/ultrastructure , Catalysis , DNA/genetics , DNA/ultrastructure , Escherichia coli/enzymology , Escherichia coli/genetics , Neisseria meningitidis/genetics , Protein Binding , Protein Domains , RNA, Guide, Kinetoplastida/genetics , RNA, Guide, Kinetoplastida/metabolism , Structure-Activity Relationship , Viral Proteins/genetics , Viral Proteins/ultrastructure
9.
Proc Natl Acad Sci U S A ; 121(8): e2319696121, 2024 Feb 20.
Article in English | MEDLINE | ID: mdl-38346181

ABSTRACT

The phylogeny and divergence timing of the Neoavian radiation remain controversial despite recent progress. We analyzed the genomes of 124 species across all Neoavian orders, using data from 25,460 loci spanning four DNA classes, including 5,756 coding sequences, 12,449 conserved nonexonic elements, 4,871 introns, and 2,384 intergenic segments. We conducted a comprehensive sensitivity analysis to account for the heterogeneity across different DNA classes, leading to an optimal tree of Neoaves with high resolution. This phylogeny features a novel Neoavian dichotomy comprising two monophyletic clades: a previously recognized Telluraves (land birds) and a newly circumscribed Aquaterraves (waterbirds and relatives). Molecular dating analyses with 20 fossil calibrations indicate that the diversification of modern birds began in the Late Cretaceous and underwent a constant and steady radiation across the KPg boundary, concurrent with the rise of angiosperms as well as other major Cenozoic animal groups including placental and multituberculate mammals. The KPg catastrophe had a limited impact on avian evolution compared to the Paleocene-Eocene Thermal Maximum, which triggered a rapid diversification of seabirds. Our findings suggest that the evolution of modern birds followed a slow process of gradualism rather than a rapid process of punctuated equilibrium, with limited interruption by the KPg catastrophe. This study places bird evolution into a new context within vertebrates, with ramifications for the evolution of the Earth's biota.


Subject(s)
Fossils , Magnoliopsida , Pregnancy , Female , Animals , Magnoliopsida/genetics , Placenta , Phylogeny , Birds/genetics , Mammals/genetics , DNA, Mitochondrial/genetics , Biological Evolution
10.
Proc Natl Acad Sci U S A ; 121(12): e2315707121, 2024 Mar 19.
Article in English | MEDLINE | ID: mdl-38489388

ABSTRACT

KCTD10 belongs to the KCTD (potassiumchannel tetramerization domain) family, many members of which are associated with neuropsychiatric disorders. However, the biological function underlying the association with brain disorders remains to be explored. Here, we reveal that Kctd10 is highly expressed in neuronal progenitors and layer V neurons throughout brain development. Kctd10 deficiency triggers abnormal proliferation and differentiation of neuronal progenitors, reduced deep-layer (especially layer V) neurons, increased upper-layer neurons, and lowered brain size. Mechanistically, we screened and identified a unique KCTD10-interacting protein, KCTD13, associated with neurodevelopmental disorders. KCTD10 mediated the ubiquitination-dependent degradation of KCTD13 and KCTD10 ablation resulted in a considerable increase of KCTD13 expression in the developing cortex. KCTD13 overexpression in neuronal progenitors led to reduced proliferation and abnormal cell distribution, mirroring KCTD10 deficiency. Notably, mice with brain-specific Kctd10 knockout exhibited obvious motor deficits. This study uncovers the physiological function of KCTD10 and provides unique insights into the pathogenesis of neurodevelopmental disorders.


Subject(s)
Brain Diseases , Neurodevelopmental Disorders , Potassium Channels, Voltage-Gated , Animals , Mice , Proteins/metabolism , Brain/metabolism , Neurons/metabolism , Neurodevelopmental Disorders/genetics , Brain Diseases/genetics , Neurogenesis/genetics , Potassium Channels, Voltage-Gated/metabolism
11.
Brief Bioinform ; 25(4)2024 May 23.
Article in English | MEDLINE | ID: mdl-38920346

ABSTRACT

Estimating transmission rates is a challenging yet essential aspect of comprehending and controlling the spread of infectious diseases. Various methods exist for estimating transmission rates, each with distinct assumptions, data needs, and constraints. This study introduces a novel phylogenetic approach called transRate, which integrates genetic information with traditional epidemiological approaches to estimate inter-population transmission rates. The phylogenetic method is statistically consistent as the sample size (i.e. the number of pathogen genomes) approaches infinity under the multi-population susceptible-infected-recovered model. Simulation analyses indicate that transRate can accurately estimate the transmission rate with a sample size of 200 ~ 400 pathogen genomes. Using transRate, we analyzed 40,028 high-quality sequences of SARS-CoV-2 in human hosts during the early pandemic. Our analysis uncovered significant transmission between populations even before widespread travel restrictions were implemented. The development of transRate provides valuable insights for scientists and public health officials to enhance their understanding of the pandemic's progression and aiding in preparedness for future viral outbreaks. As public databases for genomic sequences continue to expand, transRate is increasingly vital for tracking and mitigating the spread of infectious diseases.


Subject(s)
COVID-19 , Phylogeny , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/transmission , COVID-19/epidemiology , COVID-19/virology , Pandemics , Communicable Diseases/transmission , Communicable Diseases/epidemiology , Genome, Viral
12.
J Virol ; : e0052224, 2024 Jun 20.
Article in English | MEDLINE | ID: mdl-38899899

ABSTRACT

The 3' untranslated region (3'UTR) of the hepatitis C virus (HCV) RNA genome, which contains a highly conserved 3' region named the 3'X-tail, plays an essential role in RNA replication and promotes viral IRES-dependent translation. Although our previous work has found a cis-acting element for genome encapsidation within 3'X, there is limited information on the involvement of the 3'UTR in particle formation. In this study, proteomic analyses identified host cell proteins that bind to the 3'UTR containing the 3'X region but not to the sequence lacking the 3'X. Further characterization showed that RNA-binding proteins, ribosomal protein L17 (RPL17), and Y-box binding protein 1 (YBX1) facilitate the efficient production of infectious HCV particles in the virus infection cells. Using small interfering RNA (siRNA)-mediated gene silencing in four assays that distinguish between the various stages of the HCV life cycle, RPL17 and YBX1 were found to be most important for particle assembly in the trans-packaging assay with replication-defective subgenomic RNA. In vitro assays showed that RPL17 and YBX1 bind to the 3'UTR RNA and deletion of the 3'X region attenuates their interaction. Knockdown of RPL17 or YBX1 resulted in reducing the amount of HCV RNA co-precipitating with the viral Core protein by RNA immunoprecipitation and increasing the relative distance in space between Core and double-stranded RNA by confocal imaging, suggesting that RPL17 and YBX1 potentially affect HCV RNA-Core interaction, leading to efficient nucleocapsid assembly. These host factors provide new clues to understanding the molecular mechanisms that regulate HCV particle formation. IMPORTANCE: Although basic research on the HCV life cycle has progressed significantly over the past two decades, our understanding of the molecular mechanisms that regulate the process of particle formation, in particular encapsidation of the genome or nucleocapsid assembly, has been limited. We present here, for the first time, that two RNA-binding proteins, RPL17 and YBX1, bind to the 3'X in the 3'UTR of the HCV genome, which potentially acts as a packaging signal, and facilitates the viral particle assembly. Our study revealed that RPL17 and YBX1 exert a positive effect on the interaction between HCV RNA and Core protein, suggesting that the presence of both host factors modulate an RNA structure or conformation suitable for packaging the viral genome. These findings help us to elucidate not only the regulatory mechanism of the particle assembly of HCV but also the function of host RNA-binding proteins during viral infection.

13.
Mol Cell ; 65(2): 310-322, 2017 Jan 19.
Article in English | MEDLINE | ID: mdl-27989439

ABSTRACT

C2c1 is a type V-B CRISPR-Cas system dual-RNA-guided DNA endonuclease. Here, we report the crystal structure of Alicyclobacillus acidoterrestris C2c1 in complex with a chimeric single-molecule guide RNA (sgRNA). AacC2c1 exhibits a bi-lobed architecture consisting of a REC and NUC lobe. The sgRNA scaffold forms a tetra-helical structure, distinct from previous predictions. The crRNA is located in the central channel of C2c1, and the tracrRNA resides in an external surface groove. Although AacC2c1 lacks a PAM-interacting domain, our analysis revealed that the PAM duplex has a similar binding position found in Cpf1. Importantly, C2c1-sgRNA system is highly sensitive to single-nucleotide mismatches between guide RNA and target DNA. The resulting reduction in off-target cleavage renders C2c1 a valuable addition to the current arsenal of genome-editing tools. Together, our findings indicate that sgRNA assembly is achieved through a mechanism distinct from that reported previously for Cas9 or Cpf1 endonucleases.


Subject(s)
Alicyclobacillus/enzymology , Bacterial Proteins/metabolism , CRISPR-Associated Proteins/metabolism , CRISPR-Cas Systems , DNA Breaks, Double-Stranded , DNA, Bacterial/metabolism , Endodeoxyribonucleases/metabolism , Nucleic Acid Heteroduplexes/metabolism , RNA, Bacterial/metabolism , RNA, Guide, Kinetoplastida/metabolism , Alicyclobacillus/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , CRISPR-Associated Proteins/chemistry , CRISPR-Associated Proteins/genetics , Clustered Regularly Interspaced Short Palindromic Repeats , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , Endodeoxyribonucleases/chemistry , Endodeoxyribonucleases/genetics , Models, Molecular , Nucleic Acid Conformation , Nucleic Acid Heteroduplexes/chemistry , Nucleic Acid Heteroduplexes/genetics , Protein Binding , Protein Interaction Domains and Motifs , RNA, Bacterial/chemistry , RNA, Bacterial/genetics , RNA, Guide, Kinetoplastida/chemistry , RNA, Guide, Kinetoplastida/genetics , Structure-Activity Relationship
14.
Proc Natl Acad Sci U S A ; 119(48): e2206829119, 2022 11 29.
Article in English | MEDLINE | ID: mdl-36409915

ABSTRACT

Retinal ganglion cells (RGCs) are heterogeneous projection neurons that convey distinct visual features from the retina to brain. Here, we present a high-throughput in vivo RGC activity assay in response to light stimulation using noninvasive Ca2+ imaging of thousands of RGCs simultaneously in living mice. Population and single-cell analyses of longitudinal RGC Ca2+ imaging reveal distinct functional responses of RGCs and unprecedented individual RGC activity conversions during traumatic and glaucomatous degeneration. This study establishes a foundation for future in vivo RGC function classifications and longitudinal activity evaluations using more advanced imaging techniques and visual stimuli under normal, disease, and neural repair conditions. These analyses can be performed at both the population and single-cell levels using temporal and spatial information, which will be invaluable for understanding RGC pathophysiology and identifying functional biomarkers for diverse optic neuropathies.


Subject(s)
Glaucoma , Retinal Ganglion Cells , Animals , Mice , Diagnostic Imaging , Retina , Glaucoma/diagnostic imaging , Brain
15.
PLoS Genet ; 18(4): e1010137, 2022 04.
Article in English | MEDLINE | ID: mdl-35421082

ABSTRACT

Viral infections can alter host transcriptomes by manipulating host splicing machinery. Despite intensive transcriptomic studies on SARS-CoV-2, a systematic analysis of alternative splicing (AS) in severe COVID-19 patients remains largely elusive. Here we integrated proteomic and transcriptomic sequencing data to study AS changes in COVID-19 patients. We discovered that RNA splicing is among the major down-regulated proteomic signatures in COVID-19 patients. The transcriptome analysis showed that SARS-CoV-2 infection induces widespread dysregulation of transcript usage and expression, affecting blood coagulation, neutrophil activation, and cytokine production. Notably, CD74 and LRRFIP1 had increased skipping of an exon in COVID-19 patients that disrupts a functional domain, which correlated with reduced antiviral immunity. Furthermore, the dysregulation of transcripts was strongly correlated with clinical severity of COVID-19, and splice-variants may contribute to unexpected therapeutic activity. In summary, our data highlight that a better understanding of the AS landscape may aid in COVID-19 diagnosis and therapy.


Subject(s)
COVID-19 , Alternative Splicing/genetics , COVID-19/genetics , COVID-19 Testing , Humans , Proteomics , SARS-CoV-2/genetics , Transcriptome
16.
Nano Lett ; 24(5): 1784-1791, 2024 Feb 07.
Article in English | MEDLINE | ID: mdl-38265953

ABSTRACT

Selective control of light is essential for optical science and technology, with numerous applications. However, optical selectivity in the angular momentum of light has been quite limited, remaining constant by increasing the incident light power on previous passive optical devices. Here, we demonstrate a nonlinear boost of optical selectivity in both the spin and orbital angular momentum of light through near-field selective excitation of single-mode nanolasers. Our designed hybrid nanolaser circuits consist of plasmonic metasurfaces and individually placed perovskite nanowires, enabling subwavelength focusing of angular-momentum-distinctive plasmonic fields and further selective excitation of nanolasers in nanowires. The optically selected nanolaser with a nonlinear increase of light emission greatly enhances the baseline optical selectivity offered by the metasurface from about 0.4 up to near unity. Our demonstrated hybrid nanophotonic platform may find important applications in all-optical logic gates and nanowire networks, ultrafast optical switches, nanophotonic detectors, and on-chip optical and quantum information processing.

17.
Nano Lett ; 24(2): 733-740, 2024 Jan 17.
Article in English | MEDLINE | ID: mdl-38166427

ABSTRACT

The Hall effect has played a vital role in unraveling the intricate properties of electron transport in solid materials. Here, we report on a crystal symmetry-dependent in-plane Hall effect (CIHE) observed in a CuPt/CoPt ferromagnetic heterostructure. Unlike the planar Hall effect (PHE), the CIHE in CuPt/CoPt strongly depends on the current flowing direction (ϕI) with respect to the crystal structure. It reaches its maximum when the current is applied along the low crystal-symmetry axes and vanishes when applied along the high crystal-symmetry axes, exhibiting an unconventional angular dependence of cos(3ϕI). Utilizing a symmetry analysis based on the Invariant Theory, we demonstrate that the CIHE can exist in magnetic crystals possessing C3v symmetry. Using a tight-binding model and realistic first-principles calculations on the metallic heterostructure, we find that the CIHE originates from the trigonal warping of the Fermi surface. Our observations highlight the critical role of crystal symmetry in generating new types of Hall effects.

18.
Gut ; 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38955401

ABSTRACT

OBJECTIVE: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy because it is often diagnosed at a late-stage. Signal transducer and activator of transcription 5 (STAT5) is a transcription factor implicated in the progression of various cancer types. However, its role in KRAS-driven pancreatic tumourigenesis remains unclear. DESIGN: We performed studies with LSL-Kras G12D; Ptf1a-Cre ERT (KCERT) mice or LSL-KrasG12D; LSL-Trp53R172H ; Pdx1-Cre (KPC) mice crossed with conditional disruption of STAT5 or completed deficiency interleukin (IL)-22. Pancreatitis was induced in mice by administration of cerulein. Pharmacological inhibition of STAT5 on PDAC prevention was studied in the orthotopic transplantation and patient-derived xenografts PDAC model, and KPC mice. RESULTS: The expression and phosphorylation of STAT5 were higher in human PDAC samples than control samples and high levels of STAT5 in tumour cells were associated with a poorer prognosis. The loss of STAT5 in pancreatic cells substantially reduces the KRAS mutation and pancreatitis-derived acinar-to-ductal metaplasia (ADM) and PDAC lesions. Mechanistically, we discovered that STAT5 binds directly to the promoters of ADM mediators, hepatocyte nuclear factor (HNF) 1ß and HNF4α. Furthermore, STAT5 plays a crucial role in maintaining energy metabolism in tumour cells during PDAC progression. IL-22 signalling induced by chronic inflammation enhances KRAS-mutant-mediated STAT5 phosphorylation. Deficiency of IL-22 signalling slowed the progression of PDAC and ablated STAT5 activation. CONCLUSION: Collectively, our findings identified pancreatic STAT5 activation as a key downstream effector of oncogenic KRAS signalling that is critical for ADM initiation and PDAC progression, highlighting its potential therapeutic vulnerability.

19.
Glia ; 72(5): 857-871, 2024 May.
Article in English | MEDLINE | ID: mdl-38234042

ABSTRACT

Tumor-associated astrocytes (TAAs) in the glioblastoma microenvironment play an important role in tumor development and malignant progression initiated by glioma stem cells (GSCs). In the current study, normal human astrocytes (NHAs) were cultured and continuously treated with GSC-derived exosomes (GSC-EXOs) induction to explore the mechanism by which GSCs affect astrocyte remodeling. This study revealed that GSC-EXOs can induce the transformation of NHAs into TAAs, with relatively swollen cell bodies and multiple extended processes. In addition, high proliferation, elevated resistance to temozolomide (TMZ), and increased expression of TAA-related markers (TGF-ß, CD44, and tenascin-C) were observed in the TAAs. Furthermore, GSC-derived exosomal miR-3065-5p could be delivered to NHAs, and miR-3065-5p levels increased significantly in TAAs, as verified by miRNA expression profile sequencing and Reverse transcription polymerase chain reaction. Overexpression of miR-3065-5p also enhanced NHA proliferation, elevated resistance to TMZ, and increased the expression levels of TAA-related markers. In addition, both GSC-EXO-induced and miR-3065-5p-overexpressing NHAs promoted tumorigenesis of GSCs in vivo. Discs Large Homolog 2 (DLG2, downregulated in glioblastoma) is a direct downstream target of miR-3065-5p in TAAs, and DLG2 overexpression could partially reverse the transformation of NHAs into TAAs. Collectively, these data demonstrate that GSC-EXOs induce the transformation of NHAs into TAAs via the miR-3065-5p/DLG2 signaling axis and that TAAs can further promote the tumorigenesis of GSCs. Thus, precisely blocking the interactions between astrocytes and GSCs via exosomes may be a novel strategy to inhibit glioblastoma development, but more in-depth mechanistic studies are still needed.


Subject(s)
Exosomes , Glioblastoma , Glioma , MicroRNAs , Humans , Glioblastoma/pathology , Astrocytes/metabolism , MicroRNAs/genetics , MicroRNAs/metabolism , Exosomes/metabolism , Glioma/pathology , Temozolomide/pharmacology , Temozolomide/metabolism , Neoplastic Stem Cells/metabolism , Carcinogenesis/genetics , Cell Proliferation , Tumor Microenvironment , Tumor Suppressor Proteins/metabolism , Guanylate Kinases/metabolism
20.
Ann Surg ; 279(1): 138-146, 2024 01 01.
Article in English | MEDLINE | ID: mdl-37226826

ABSTRACT

OBJECTIVE: To compare the clinical and patient-reported outcomes of minimal access and conventional nipple-sparing mastectomy (C-NSM). The secondary outcomes investigated included medical costs and oncological safety. BACKGROUND: Minimal-access NSM has been increasingly applied in the treatment of patients with breast cancer. However, prospective multicenter trials comparing robotic-assisted NSM (R-NSM) versus C-NSM or endoscopic-assisted NSM (E-NSM) are lacking. METHODS: A prospectively designed 3-arm multicenter, nonrandomized trial (NCT04037852) was conducted from October 1, 2019 to December 31, 2021, to compare R-NSM with C-NSM or E-NSM. RESULTS: A total of 73 R-NSM, 74 C-NSM, and 84 E-NSM procedures were enrolled. The median wound length and operation time of C-NSM was (9 cm, 175 minutes), (4 cm, and 195 minutes) in R-NSM, and (4 cm and 222 minutes) in E-NSM. Complications were comparable among the groups. Better wound healing was observed in the minimal-access NSM group. The R-NSM procedure was 4000 and 2600 United States Dollars more expensive than C-NSM and E-NSM, respectively. Wound/scar and postoperative acute pain evaluation favored the use of minimal access NSM over C-NSM. Quality of life in terms of chronic breast/chest pain, mobility, and range of motion of the upper extremity showed no significant differences. The preliminary oncologic results showed no differences among the 3 groups. CONCLUSIONS: R-NSM or E-NSM is a safe alternative if compared with C-NSM in terms of perioperative morbidities, especially with better wound healing. The advantage of minimal access groups was higher wound-related satisfaction. Higher costs remain one of the major limiting factors in the widespread adoption of R-NSM.


Subject(s)
Breast Implants , Breast Neoplasms , Mammaplasty , Robotic Surgical Procedures , Humans , Female , Breast Neoplasms/surgery , Breast Neoplasms/etiology , Mastectomy/methods , Nipples/surgery , Prospective Studies , Quality of Life , Mammaplasty/methods , Patient Reported Outcome Measures , Retrospective Studies
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