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1.
Cell ; 186(21): 4662-4675.e12, 2023 Oct 12.
Article in English | MEDLINE | ID: mdl-37734372

ABSTRACT

Bats, rodents, and shrews are the most important animal sources of human infectious diseases. However, the evolution and transmission of viruses among them remain largely unexplored. Through the meta-transcriptomic sequencing of internal organ and fecal samples from 2,443 wild bats, rodents, and shrews sampled from four Chinese habitats, we identified 669 viruses, including 534 novel viruses, thereby greatly expanding the mammalian virome. Our analysis revealed high levels of phylogenetic diversity, identified cross-species virus transmission events, elucidated virus origins, and identified cases of invertebrate viruses in mammalian hosts. Host order and sample size were the most important factors impacting virome composition and patterns of virus spillover. Shrews harbored a high richness of viruses, including many invertebrate-associated viruses with multi-organ distributions, whereas rodents carried viruses with a greater capacity for host jumping. These data highlight the remarkable diversity of mammalian viruses in local habitats and their ability to emerge in new hosts.

2.
Cell ; 186(19): 4216-4234.e33, 2023 09 14.
Article in English | MEDLINE | ID: mdl-37714135

ABSTRACT

Chronic stimulation can cause T cell dysfunction and limit the efficacy of cellular immunotherapies. Improved methods are required to compare large numbers of synthetic knockin (KI) sequences to reprogram cell functions. Here, we developed modular pooled KI screening (ModPoKI), an adaptable platform for modular construction of DNA KI libraries using barcoded multicistronic adaptors. We built two ModPoKI libraries of 100 transcription factors (TFs) and 129 natural and synthetic surface receptors (SRs). Over 30 ModPoKI screens across human TCR- and CAR-T cells in diverse conditions identified a transcription factor AP4 (TFAP4) construct that enhanced fitness of chronically stimulated CAR-T cells and anti-cancer function in vitro and in vivo. ModPoKI's modularity allowed us to generate an ∼10,000-member library of TF combinations. Non-viral KI of a combined BATF-TFAP4 polycistronic construct enhanced fitness. Overexpressed BATF and TFAP4 co-occupy and regulate key gene targets to reprogram T cell function. ModPoKI facilitates the discovery of complex gene constructs to program cellular functions.


Subject(s)
Cell- and Tissue-Based Therapy , Exercise , Humans , Gene Library , Immunotherapy , Research
3.
Cell ; 182(1): 226-244.e17, 2020 07 09.
Article in English | MEDLINE | ID: mdl-32649875

ABSTRACT

Lung cancer in East Asia is characterized by a high percentage of never-smokers, early onset and predominant EGFR mutations. To illuminate the molecular phenotype of this demographically distinct disease, we performed a deep comprehensive proteogenomic study on a prospectively collected cohort in Taiwan, representing early stage, predominantly female, non-smoking lung adenocarcinoma. Integrated genomic, proteomic, and phosphoproteomic analysis delineated the demographically distinct molecular attributes and hallmarks of tumor progression. Mutational signature analysis revealed age- and gender-related mutagenesis mechanisms, characterized by high prevalence of APOBEC mutational signature in younger females and over-representation of environmental carcinogen-like mutational signatures in older females. A proteomics-informed classification distinguished the clinical characteristics of early stage patients with EGFR mutations. Furthermore, integrated protein network analysis revealed the cellular remodeling underpinning clinical trajectories and nominated candidate biomarkers for patient stratification and therapeutic intervention. This multi-omic molecular architecture may help develop strategies for management of early stage never-smoker lung adenocarcinoma.


Subject(s)
Disease Progression , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Proteogenomics , Smoking/genetics , Adenocarcinoma of Lung/genetics , Adenocarcinoma of Lung/pathology , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Carcinogens/toxicity , Cohort Studies , Cytosine Deaminase/metabolism , Asia, Eastern , Gene Expression Regulation, Neoplastic , Gene Regulatory Networks , Genome, Human , Humans , Matrix Metalloproteinases/metabolism , Mutation/genetics , Principal Component Analysis
4.
Nature ; 625(7996): 805-812, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38093011

ABSTRACT

CRISPR-enabled screening is a powerful tool for the discovery of genes that control T cell function and has nominated candidate targets for immunotherapies1-6. However, new approaches are required to probe specific nucleotide sequences within key genes. Systematic mutagenesis in primary human T cells could reveal alleles that tune specific phenotypes. DNA base editors are powerful tools for introducing targeted mutations with high efficiency7,8. Here we develop a large-scale base-editing mutagenesis platform with the goal of pinpointing nucleotides that encode amino acid residues that tune primary human T cell activation responses. We generated a library of around 117,000 single guide RNA molecules targeting base editors to protein-coding sites across 385 genes implicated in T cell function and systematically identified protein domains and specific amino acid residues that regulate T cell activation and cytokine production. We found a broad spectrum of alleles with variants encoding critical residues in proteins including PIK3CD, VAV1, LCP2, PLCG1 and DGKZ, including both gain-of-function and loss-of-function mutations. We validated the functional effects of many alleles and further demonstrated that base-editing hits could positively and negatively tune T cell cytotoxic function. Finally, higher-resolution screening using a base editor with relaxed protospacer-adjacent motif requirements9 (NG versus NGG) revealed specific structural domains and protein-protein interaction sites that can be targeted to tune T cell functions. Base-editing screens in primary immune cells thus provide biochemical insights with the potential to accelerate immunotherapy design.


Subject(s)
Alleles , Gene Editing , Mutagenesis , T-Lymphocytes , Humans , Amino Acids/genetics , CRISPR-Cas Systems/genetics , Mutagenesis/genetics , RNA, Guide, CRISPR-Cas Systems/genetics , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , Lymphocyte Activation , Cytokines/biosynthesis , Cytokines/metabolism , Gain of Function Mutation , Loss of Function Mutation
5.
Nature ; 629(8013): 937-944, 2024 May.
Article in English | MEDLINE | ID: mdl-38720067

ABSTRACT

QS-21 is a potent vaccine adjuvant and remains the only saponin-based adjuvant that has been clinically approved for use in humans1,2. However, owing to the complex structure of QS-21, its availability is limited. Today, the supply depends on laborious extraction from the Chilean soapbark tree or on low-yielding total chemical synthesis3,4. Here we demonstrate the complete biosynthesis of QS-21 and its precursors, as well as structural derivatives, in engineered yeast strains. The successful biosynthesis in yeast requires fine-tuning of the host's native pathway fluxes, as well as the functional and balanced expression of 38 heterologous enzymes. The required biosynthetic pathway spans seven enzyme families-a terpene synthase, P450s, nucleotide sugar synthases, glycosyltransferases, a coenzyme A ligase, acyl transferases and polyketide synthases-from six organisms, and mimics in yeast the subcellular compartmentalization of plants from the endoplasmic reticulum membrane to the cytosol. Finally, by taking advantage of the promiscuity of certain pathway enzymes, we produced structural analogues of QS-21 using this biosynthetic platform. This microbial production scheme will allow for the future establishment of a structure-activity relationship, and will thus enable the rational design of potent vaccine adjuvants.


Subject(s)
Adjuvants, Immunologic , Metabolic Engineering , Saccharomyces cerevisiae , Saponins , Adjuvants, Immunologic/biosynthesis , Adjuvants, Immunologic/chemistry , Adjuvants, Immunologic/genetics , Adjuvants, Immunologic/metabolism , Biosynthetic Pathways/genetics , Drug Design , Enzymes/genetics , Enzymes/metabolism , Metabolic Engineering/methods , Plants/enzymology , Plants/genetics , Plants/metabolism , Saccharomyces cerevisiae/cytology , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saponins/biosynthesis , Saponins/chemistry , Saponins/genetics , Saponins/metabolism , Structure-Activity Relationship
6.
Mol Cell ; 82(7): 1278-1287.e5, 2022 04 07.
Article in English | MEDLINE | ID: mdl-35271814

ABSTRACT

Cholesterol molecules specifically bind to the resting αßTCR to inhibit cytoplasmic CD3ζ ITAM phosphorylation through sequestering the TCR-CD3 complex in an inactive conformation. The mechanisms of cholesterol-mediated inhibition of TCR-CD3 and its activation remain unclear. Here, we present cryoelectron microscopy structures of cholesterol- and cholesterol sulfate (CS)-inhibited TCR-CD3 complexes and an auto-active TCR-CD3 variant. The structures reveal that cholesterol molecules act like a latch to lock CD3ζ into an inactive conformation in the membrane. Mutations impairing binding of cholesterol molecules to the tunnel result in the movement of the proximal C terminus of the CD3ζ transmembrane helix, thereby activating the TCR-CD3 complex in human cells. Together, our data reveal the structural basis of TCR inhibition by cholesterol, illustrate how the cholesterol-binding tunnel is allosterically coupled to TCR triggering, and lay a foundation for the development of immunotherapies through directly targeting the TCR-CD3 complex.


Subject(s)
Receptor-CD3 Complex, Antigen, T-Cell , T-Lymphocytes , CD3 Complex/genetics , CD3 Complex/metabolism , Cholesterol/metabolism , Cryoelectron Microscopy , Humans , Receptor-CD3 Complex, Antigen, T-Cell/genetics , Receptor-CD3 Complex, Antigen, T-Cell/metabolism , Receptors, Antigen, T-Cell/genetics , Receptors, Antigen, T-Cell/metabolism , T-Lymphocytes/metabolism
7.
Nature ; 617(7960): 403-408, 2023 05.
Article in English | MEDLINE | ID: mdl-37138074

ABSTRACT

Biosynthesis is an environmentally benign and renewable approach that can be used to produce a broad range of natural and, in some cases, new-to-nature products. However, biology lacks many of the reactions that are available to synthetic chemists, resulting in a narrower scope of accessible products when using biosynthesis rather than synthetic chemistry. A prime example of such chemistry is carbene-transfer reactions1. Although it was recently shown that carbene-transfer reactions can be performed in a cell and used for biosynthesis2,3, carbene donors and unnatural cofactors needed to be added exogenously and transported into cells to effect the desired reactions, precluding cost-effective scale-up of the biosynthesis process with these reactions. Here we report the access to a diazo ester carbene precursor by cellular metabolism and a microbial platform for introducing unnatural carbene-transfer reactions into biosynthesis. The α-diazoester azaserine was produced by expressing a biosynthetic gene cluster in Streptomyces albus. The intracellularly produced azaserine was used as a carbene donor to cyclopropanate another intracellularly produced molecule-styrene. The reaction was catalysed by engineered P450 mutants containing a native cofactor with excellent diastereoselectivity and a moderate yield. Our study establishes a scalable, microbial platform for conducting intracellular abiological carbene-transfer reactions to functionalize a range of natural and new-to-nature products and expands the scope of organic products that can be produced by cellular metabolism.


Subject(s)
Azaserine , Azaserine/biosynthesis , Azaserine/chemistry , Biological Products/chemistry , Biological Products/metabolism , Multigene Family/genetics , Styrene/chemistry , Cyclopropanes/chemistry , Coenzymes/chemistry , Coenzymes/metabolism , Biocatalysis , Cytochrome P-450 Enzyme System/genetics , Cytochrome P-450 Enzyme System/metabolism
8.
Nature ; 604(7905): 273-279, 2022 04.
Article in English | MEDLINE | ID: mdl-35418634

ABSTRACT

Metals with nanocrystalline grains have ultrahigh strengths approaching two gigapascals. However, such extreme grain-boundary strengthening results in the loss of almost all tensile ductility, even when the metal has a face-centred-cubic structure-the most ductile of all crystal structures1-3. Here we demonstrate that nanocrystalline nickel-cobalt solid solutions, although still a face-centred-cubic single phase, show tensile strengths of about 2.3 gigapascals with a respectable ductility of about 16 per cent elongation to failure. This unusual combination of tensile strength and ductility is achieved by compositional undulation in a highly concentrated solid solution. The undulation renders the stacking fault energy and the lattice strains spatially varying over length scales in the range of one to ten nanometres, such that the motion of dislocations is thus significantly affected. The motion of dislocations becomes sluggish, promoting their interaction, interlocking and accumulation, despite the severely limited space inside the nanocrystalline grains. As a result, the flow stress is increased, and the dislocation storage is promoted at the same time, which increases the strain hardening and hence the ductility. Meanwhile, the segment detrapping along the dislocation line entails a small activation volume and hence an increased strain-rate sensitivity, which also stabilizes the tensile flow. As such, an undulating landscape resisting dislocation propagation provides a strengthening mechanism that preserves tensile ductility at high flow stresses.


Subject(s)
Cobalt , Metals , Cobalt/chemistry , Materials Testing , Metals/chemistry , Tensile Strength
9.
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.

10.
Nature ; 610(7933): 661-666, 2022 10.
Article in English | MEDLINE | ID: mdl-36198794

ABSTRACT

Networks of optical clocks find applications in precise navigation1,2, in efforts to redefine the fundamental unit of the 'second'3-6 and in gravitational tests7. As the frequency instability for state-of-the-art optical clocks has reached the 10-19 level8,9, the vision of a global-scale optical network that achieves comparable performances requires the dissemination of time and frequency over a long-distance free-space link with a similar instability of 10-19. However, previous attempts at free-space dissemination of time and frequency at high precision did not extend beyond dozens of kilometres10,11. Here we report time-frequency dissemination with an offset of 6.3 × 10-20 ± 3.4 × 10-19 and an instability of less than 4 × 10-19 at 10,000 s through a free-space link of 113 km. Key technologies essential to this achievement include the deployment of high-power frequency combs, high-stability and high-efficiency optical transceiver systems and efficient linear optical sampling. We observe that the stability we have reached is retained for channel losses up to 89 dB. The technique we report can not only be directly used in ground-based applications, but could also lay the groundwork for future satellite time-frequency dissemination.

11.
Nature ; 609(7925): 174-182, 2022 09.
Article in English | MEDLINE | ID: mdl-36002574

ABSTRACT

The efficacy of adoptive T cell therapies for cancer treatment can be limited by suppressive signals from both extrinsic factors and intrinsic inhibitory checkpoints1,2. Targeted gene editing has the potential to overcome these limitations and enhance T cell therapeutic function3-10. Here we performed multiple genome-wide CRISPR knock-out screens under different immunosuppressive conditions to identify genes that can be targeted to prevent T cell dysfunction. These screens converged on RASA2, a RAS GTPase-activating protein (RasGAP) that we identify as a signalling checkpoint in human T cells, which is downregulated upon acute T cell receptor stimulation and can increase gradually with chronic antigen exposure. RASA2 ablation enhanced MAPK signalling and chimeric antigen receptor (CAR) T cell cytolytic activity in response to target antigen. Repeated tumour antigen stimulations in vitro revealed that RASA2-deficient T cells show increased activation, cytokine production and metabolic activity compared with control cells, and show a marked advantage in persistent cancer cell killing. RASA2-knockout CAR T cells had a competitive fitness advantage over control cells in the bone marrow in a mouse model of leukaemia. Ablation of RASA2 in multiple preclinical models of T cell receptor and CAR T cell therapies prolonged survival in mice xenografted with either liquid or solid tumours. Together, our findings highlight RASA2 as a promising target to enhance both persistence and effector function in T cell therapies for cancer treatment.


Subject(s)
Antigens, Neoplasm , Neoplasms , T-Lymphocytes , ras GTPase-Activating Proteins , Animals , Antigens, Neoplasm/immunology , Bone Marrow , CRISPR-Cas Systems , Disease Models, Animal , Gene Knockdown Techniques , Humans , Immunotherapy, Adoptive , Leukemia/immunology , Leukemia/pathology , Leukemia/therapy , Mice , Neoplasms/immunology , Neoplasms/pathology , Neoplasms/therapy , Receptors, Antigen, T-Cell/immunology , Receptors, Chimeric Antigen/immunology , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , Time Factors , Xenograft Model Antitumor Assays , ras GTPase-Activating Proteins/deficiency , ras GTPase-Activating Proteins/genetics
12.
Nat Methods ; 21(2): 247-258, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38200227

ABSTRACT

RNA-binding proteins (RBPs) regulate diverse cellular processes by dynamically interacting with RNA targets. However, effective methods to capture both stable and transient interactions between RBPs and their RNA targets are still lacking, especially when the interaction is dynamic or samples are limited. Here we present an assay of reverse transcription-based RBP binding site sequencing (ARTR-seq), which relies on in situ reverse transcription of RBP-bound RNAs guided by antibodies to identify RBP binding sites. ARTR-seq avoids ultraviolet crosslinking and immunoprecipitation, allowing for efficient and specific identification of RBP binding sites from as few as 20 cells or a tissue section. Taking advantage of rapid formaldehyde fixation, ARTR-seq enables capturing the dynamic RNA binding by RBPs over a short period of time, as demonstrated by the profiling of dynamic RNA binding of G3BP1 during stress granule assembly on a timescale as short as 10 minutes.


Subject(s)
RNA , Reverse Transcription , RNA/genetics , RNA/metabolism , DNA Helicases/metabolism , Poly-ADP-Ribose Binding Proteins/genetics , Poly-ADP-Ribose Binding Proteins/metabolism , RNA Helicases/genetics , RNA Helicases/metabolism , RNA Recognition Motif Proteins/genetics , RNA Recognition Motif Proteins/metabolism , RNA-Binding Proteins/metabolism , Binding Sites/genetics , Protein Binding
13.
Trends Immunol ; 45(7): 523-534, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38944621

ABSTRACT

Basophils, rare granulocytes, have long been acknowledged for their roles in type 2 immune responses. However, the mechanisms by which basophils adapt their functions to diverse mammalian microenvironments remain unclear. Recent advancements in specific research tools and single-cell-based technologies have greatly enhanced our understanding of basophils. Several studies have shown that basophils play a role in maintaining homeostasis but can also contribute to pathology in various tissues and organs, including skin, lung, and others. Here, we provide an overview of recent basophil research, including cell development, characteristics, and functions. Based on an increasing understanding of basophil biology, we suggest that the precise targeting of basophil features might be beneficial in alleviating certain pathologies such as asthma, atopic dermatitis (AD), and others.


Subject(s)
Basophils , Cell Differentiation , Basophils/immunology , Humans , Animals , Cell Differentiation/immunology , Dermatitis, Atopic/immunology , Asthma/immunology , Homeostasis/immunology
14.
Cell ; 148(5): 873-85, 2012 Mar 02.
Article in English | MEDLINE | ID: mdl-22385957

ABSTRACT

Tumor heterogeneity presents a challenge for inferring clonal evolution and driver gene identification. Here, we describe a method for analyzing the cancer genome at a single-cell nucleotide level. To perform our analyses, we first devised and validated a high-throughput whole-genome single-cell sequencing method using two lymphoblastoid cell line single cells. We then carried out whole-exome single-cell sequencing of 90 cells from a JAK2-negative myeloproliferative neoplasm patient. The sequencing data from 58 cells passed our quality control criteria, and these data indicated that this neoplasm represented a monoclonal evolution. We further identified essential thrombocythemia (ET)-related candidate mutations such as SESN2 and NTRK1, which may be involved in neoplasm progression. This pilot study allowed the initial characterization of the disease-related genetic architecture at the single-cell nucleotide level. Further, we established a single-cell sequencing method that opens the way for detailed analyses of a variety of tumor types, including those with high genetic complex between patients.


Subject(s)
Clonal Evolution , Gene Expression Profiling , High-Throughput Nucleotide Sequencing/methods , Janus Kinase 2/genetics , Myeloproliferative Disorders/genetics , Myeloproliferative Disorders/pathology , Single-Cell Analysis/methods , Thrombocythemia, Essential/genetics , Exome , Genome, Human , Humans , Male , Middle Aged , Mutation
15.
Nature ; 594(7864): 583-588, 2021 06.
Article in English | MEDLINE | ID: mdl-34135510

ABSTRACT

The metabotropic glutamate receptors (mGlus) have key roles in modulating cell excitability and synaptic transmission in response to glutamate (the main excitatory neurotransmitter in the central nervous system)1. It has previously been suggested that only one receptor subunit within an mGlu homodimer is responsible for coupling to G protein during receptor activation2. However, the molecular mechanism that underlies the asymmetric signalling of mGlus remains unknown. Here we report two cryo-electron microscopy structures of human mGlu2 and mGlu4 bound to heterotrimeric Gi protein. The structures reveal a G-protein-binding site formed by three intracellular loops and helices III and IV that is distinct from the corresponding binding site in all of the other G-protein-coupled receptor (GPCR) structures. Furthermore, we observed an asymmetric dimer interface of the transmembrane domain of the receptor in the two mGlu-Gi structures. We confirmed that the asymmetric dimerization is crucial for receptor activation, which was supported by functional data; this dimerization may provide a molecular basis for the asymmetric signal transduction of mGlus. These findings offer insights into receptor signalling of class C GPCRs.


Subject(s)
GTP-Binding Proteins/chemistry , Receptors, Metabotropic Glutamate/chemistry , Binding Sites , Cryoelectron Microscopy , Humans , Protein Multimerization , Protein Structure, Tertiary , Signal Transduction
16.
Proc Natl Acad Sci U S A ; 121(16): e2318935121, 2024 Apr 16.
Article in English | MEDLINE | ID: mdl-38588421

ABSTRACT

Glucose is required for generating heat during cold-induced nonshivering thermogenesis in adipose tissue, but the regulatory mechanism is largely unknown. CREBZF has emerged as a critical mechanism for metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as nonalcoholic fatty liver disease (NAFLD). We investigated the roles of CREBZF in the control of thermogenesis and energy metabolism. Glucose induces CREBZF in human white adipose tissue (WAT) and inguinal WAT (iWAT) in mice. Lys208 acetylation modulated by transacetylase CREB-binding protein/p300 and deacetylase HDAC3 is required for glucose-induced reduction of proteasomal degradation and augmentation of protein stability of CREBZF. Glucose induces rectal temperature and thermogenesis in white adipose of control mice, which is further potentiated in adipose-specific CREBZF knockout (CREBZF FKO) mice. During cold exposure, CREBZF FKO mice display enhanced thermogenic gene expression, browning of iWAT, and adaptive thermogenesis. CREBZF associates with PGC-1α to repress thermogenic gene expression. Expression levels of CREBZF are negatively correlated with UCP1 in human adipose tissues and increased in WAT of obese ob/ob mice, which may underscore the potential role of CREBZF in the development of compromised thermogenic capability under hyperglycemic conditions. Our results reveal an important mechanism of glucose sensing and thermogenic inactivation through reversible acetylation.


Subject(s)
Adipose Tissue, Brown , Glucose , Mice , Humans , Animals , Glucose/metabolism , Adipose Tissue, Brown/metabolism , Acetylation , Adipose Tissue, White/metabolism , Energy Metabolism , Obesity/genetics , Obesity/metabolism , Thermogenesis/genetics , Mice, Inbred C57BL , Basic-Leucine Zipper Transcription Factors/metabolism
17.
Proc Natl Acad Sci U S A ; 121(17): e2322332121, 2024 Apr 23.
Article in English | MEDLINE | ID: mdl-38625948

ABSTRACT

Apolipoprotein AV (APOA5) lowers plasma triglyceride (TG) levels by binding to the angiopoietin-like protein 3/8 complex (ANGPTL3/8) and suppressing its capacity to inhibit lipoprotein lipase (LPL) catalytic activity and its ability to detach LPL from binding sites within capillaries. However, the sequences in APOA5 that are required for suppressing ANGPTL3/8 activity have never been defined. A clue to the identity of those sequences was the presence of severe hypertriglyceridemia in two patients harboring an APOA5 mutation that truncates APOA5 by 35 residues ("APOA5Δ35"). We found that wild-type (WT) human APOA5, but not APOA5Δ35, suppressed ANGPTL3/8's ability to inhibit LPL catalytic activity. To pursue that finding, we prepared a mutant mouse APOA5 protein lacking 40 C-terminal amino acids ("APOA5Δ40"). Mouse WT-APOA5, but not APOA5Δ40, suppressed ANGPTL3/8's capacity to inhibit LPL catalytic activity and sharply reduced plasma TG levels in mice. WT-APOA5, but not APOA5Δ40, increased intracapillary LPL levels and reduced plasma TG levels in Apoa5-/- mice (where TG levels are high and intravascular LPL levels are low). Also, WT-APOA5, but not APOA5Δ40, blocked the ability of ANGPTL3/8 to detach LPL from cultured cells. Finally, an antibody against a synthetic peptide corresponding to the last 26 amino acids of mouse APOA5 reduced intracapillary LPL levels and increased plasma TG levels in WT mice. We conclude that C-terminal sequences in APOA5 are crucial for suppressing ANGPTL3/8 activity in vitro and for regulating intracapillary LPL levels and plasma TG levels in vivo.


Subject(s)
Apolipoproteins , Lipoprotein Lipase , Mice , Humans , Animals , Angiopoietin-like Proteins/genetics , Angiopoietin-like Proteins/metabolism , Lipoprotein Lipase/metabolism , Angiopoietin-Like Protein 3 , Amino Acids , Triglycerides/metabolism , Apolipoprotein A-V/genetics
18.
N Engl J Med ; 389(1): 45-57, 2023 Jul 06.
Article in English | MEDLINE | ID: mdl-37318140

ABSTRACT

BACKGROUND: Guidelines recommend normocapnia for adults with coma who are resuscitated after out-of-hospital cardiac arrest. However, mild hypercapnia increases cerebral blood flow and may improve neurologic outcomes. METHODS: We randomly assigned adults with coma who had been resuscitated after out-of-hospital cardiac arrest of presumed cardiac or unknown cause and admitted to the intensive care unit (ICU) in a 1:1 ratio to either 24 hours of mild hypercapnia (target partial pressure of arterial carbon dioxide [Paco2], 50 to 55 mm Hg) or normocapnia (target Paco2, 35 to 45 mm Hg). The primary outcome was a favorable neurologic outcome, defined as a score of 5 (indicating lower moderate disability) or higher, as assessed with the use of the Glasgow Outcome Scale-Extended (range, 1 [death] to 8, with higher scores indicating better neurologic outcome) at 6 months. Secondary outcomes included death within 6 months. RESULTS: A total of 1700 patients from 63 ICUs in 17 countries were recruited, with 847 patients assigned to targeted mild hypercapnia and 853 to targeted normocapnia. A favorable neurologic outcome at 6 months occurred in 332 of 764 patients (43.5%) in the mild hypercapnia group and in 350 of 784 (44.6%) in the normocapnia group (relative risk, 0.98; 95% confidence interval [CI], 0.87 to 1.11; P = 0.76). Death within 6 months after randomization occurred in 393 of 816 patients (48.2%) in the mild hypercapnia group and in 382 of 832 (45.9%) in the normocapnia group (relative risk, 1.05; 95% CI, 0.94 to 1.16). The incidence of adverse events did not differ significantly between groups. CONCLUSIONS: In patients with coma who were resuscitated after out-of-hospital cardiac arrest, targeted mild hypercapnia did not lead to better neurologic outcomes at 6 months than targeted normocapnia. (Funded by the National Health and Medical Research Council of Australia and others; TAME ClinicalTrials.gov number, NCT03114033.).


Subject(s)
Cardiopulmonary Resuscitation , Coma , Hypercapnia , Out-of-Hospital Cardiac Arrest , Adult , Humans , Carbon Dioxide/blood , Coma/blood , Coma/etiology , Hospitalization , Hypercapnia/blood , Hypercapnia/etiology , Out-of-Hospital Cardiac Arrest/blood , Out-of-Hospital Cardiac Arrest/complications , Out-of-Hospital Cardiac Arrest/therapy , Critical Care
19.
Brief Bioinform ; 25(3)2024 Mar 27.
Article in English | MEDLINE | ID: mdl-38711368

ABSTRACT

Common genetic variants and susceptibility loci associated with Alzheimer's disease (AD) have been discovered through large-scale genome-wide association studies (GWAS), GWAS by proxy (GWAX) and meta-analysis of GWAS and GWAX (GWAS+GWAX). However, due to the very low repeatability of AD susceptibility loci and the low heritability of AD, these AD genetic findings have been questioned. We summarize AD genetic findings from the past 10 years and provide a new interpretation of these findings in the context of statistical heterogeneity. We discovered that only 17% of AD risk loci demonstrated reproducibility with a genome-wide significance of P < 5.00E-08 across all AD GWAS and GWAS+GWAX datasets. We highlighted that the AD GWAS+GWAX with the largest sample size failed to identify the most significant signals, the maximum number of genome-wide significant genetic variants or maximum heritability. Additionally, we identified widespread statistical heterogeneity in AD GWAS+GWAX datasets, but not in AD GWAS datasets. We consider that statistical heterogeneity may have attenuated the statistical power in AD GWAS+GWAX and may contribute to explaining the low repeatability (17%) of genome-wide significant AD susceptibility loci and the decreased AD heritability (40-2%) as the sample size increased. Importantly, evidence supports the idea that a decrease in statistical heterogeneity facilitates the identification of genome-wide significant genetic loci and contributes to an increase in AD heritability. Collectively, current AD GWAX and GWAS+GWAX findings should be meticulously assessed and warrant additional investigation, and AD GWAS+GWAX should employ multiple meta-analysis methods, such as random-effects inverse variance-weighted meta-analysis, which is designed specifically for statistical heterogeneity.


Subject(s)
Alzheimer Disease , Genetic Predisposition to Disease , Genome-Wide Association Study , Alzheimer Disease/genetics , Humans , Genome-Wide Association Study/methods , Polymorphism, Single Nucleotide , Genetic Heterogeneity
20.
PLoS Pathog ; 20(6): e1011970, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38885264

ABSTRACT

Reactivation from latency plays a significant role in maintaining persistent lifelong Epstein-Barr virus (EBV) infection. Mechanisms governing successful activation and progression of the EBV lytic phase are not fully understood. EBV expresses multiple viral microRNAs (miRNAs) and manipulates several cellular miRNAs to support viral infection. To gain insight into the host miRNAs regulating transitions from EBV latency into the lytic stage, we conducted a CRISPR/Cas9-based screen in EBV+ Burkitt lymphoma (BL) cells using anti-Ig antibodies to crosslink the B cell receptor (BCR) and induce reactivation. Using a gRNA library against >1500 annotated human miRNAs, we identified miR-142 as a key regulator of EBV reactivation. Genetic ablation of miR-142 enhanced levels of immediate early and early lytic gene products in infected BL cells. Ago2-PAR-CLIP experiments with reactivated cells revealed miR-142 targets related to Erk/MAPK signaling, including components directly downstream of the B cell receptor (BCR). Consistent with these findings, disruption of miR-142 enhanced SOS1 levels and Mek phosphorylation in response to surface Ig cross-linking. Effects could be rescued by inhibitors of Mek (cobimetinib) or Raf (dabrafenib). Taken together, these results show that miR-142 functionally regulates SOS1/Ras/Raf/Mek/Erk signaling initiated through the BCR and consequently, restricts EBV entry into the lytic cycle.


Subject(s)
CRISPR-Cas Systems , Epstein-Barr Virus Infections , Herpesvirus 4, Human , MicroRNAs , Virus Activation , Virus Latency , Humans , Herpesvirus 4, Human/genetics , MicroRNAs/genetics , MicroRNAs/metabolism , Epstein-Barr Virus Infections/virology , Epstein-Barr Virus Infections/genetics , Epstein-Barr Virus Infections/metabolism , Burkitt Lymphoma/virology , Burkitt Lymphoma/genetics , Burkitt Lymphoma/metabolism , Cell Line, Tumor
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