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1.
Cell ; 186(3): 577-590.e16, 2023 02 02.
Article in English | MEDLINE | ID: mdl-36693373

ABSTRACT

Pleasurable touch is paramount during social behavior, including sexual encounters. However, the identity and precise role of sensory neurons that transduce sexual touch remain unknown. A population of sensory neurons labeled by developmental expression of the G protein-coupled receptor Mrgprb4 detects mechanical stimulation in mice. Here, we study the social relevance of Mrgprb4-lineage neurons and reveal that these neurons are required for sexual receptivity and sufficient to induce dopamine release in the brain. Even in social isolation, optogenetic stimulation of Mrgprb4-lineage neurons through the back skin is sufficient to induce a conditioned place preference and a striking dorsiflexion resembling the lordotic copulatory posture. In the absence of Mrgprb4-lineage neurons, female mice no longer find male mounts rewarding: sexual receptivity is supplanted by aggression and a coincident decline in dopamine release in the nucleus accumbens. Together, these findings establish that Mrgprb4-lineage neurons initiate a skin-to-brain circuit encoding the rewarding quality of social touch.


Subject(s)
Dopamine , Touch , Mice , Male , Female , Animals , Dopamine/metabolism , Nucleus Accumbens/metabolism , Sensory Receptor Cells/metabolism , Skin/metabolism , Reward , Dopaminergic Neurons/metabolism , Optogenetics , Receptors, G-Protein-Coupled/metabolism
2.
Cell ; 186(4): 803-820.e25, 2023 02 16.
Article in English | MEDLINE | ID: mdl-36738734

ABSTRACT

Complex diseases often involve the interplay between genetic and environmental factors. Charcot-Marie-Tooth type 2 neuropathies (CMT2) are a group of genetically heterogeneous disorders, in which similar peripheral neuropathology is inexplicably caused by various mutated genes. Their possible molecular links remain elusive. Here, we found that upon environmental stress, many CMT2-causing mutant proteins adopt similar properties by entering stress granules (SGs), where they aberrantly interact with G3BP and integrate into SG pathways. For example, glycyl-tRNA synthetase (GlyRS) is translocated from the cytoplasm into SGs upon stress, where the mutant GlyRS perturbs the G3BP-centric SG network by aberrantly binding to G3BP. This disrupts SG-mediated stress responses, leading to increased stress vulnerability in motoneurons. Disrupting this aberrant interaction rescues SG abnormalities and alleviates motor deficits in CMT2D mice. These findings reveal a stress-dependent molecular link across diverse CMT2 mutants and provide a conceptual framework for understanding genetic heterogeneity in light of environmental stress.


Subject(s)
Charcot-Marie-Tooth Disease , RNA Recognition Motif Proteins , Stress Granules , Animals , Mice , Charcot-Marie-Tooth Disease/genetics , Charcot-Marie-Tooth Disease/metabolism , Charcot-Marie-Tooth Disease/pathology , Cytoplasm , Motor Neurons , RNA Recognition Motif Proteins/metabolism
3.
Cell ; 186(18): 3882-3902.e24, 2023 08 31.
Article in English | MEDLINE | ID: mdl-37597510

ABSTRACT

Inflammation can trigger lasting phenotypes in immune and non-immune cells. Whether and how human infections and associated inflammation can form innate immune memory in hematopoietic stem and progenitor cells (HSPC) has remained unclear. We found that circulating HSPC, enriched from peripheral blood, captured the diversity of bone marrow HSPC, enabling investigation of their epigenomic reprogramming following coronavirus disease 2019 (COVID-19). Alterations in innate immune phenotypes and epigenetic programs of HSPC persisted for months to 1 year following severe COVID-19 and were associated with distinct transcription factor (TF) activities, altered regulation of inflammatory programs, and durable increases in myelopoiesis. HSPC epigenomic alterations were conveyed, through differentiation, to progeny innate immune cells. Early activity of IL-6 contributed to these persistent phenotypes in human COVID-19 and a mouse coronavirus infection model. Epigenetic reprogramming of HSPC may underlie altered immune function following infection and be broadly relevant, especially for millions of COVID-19 survivors.


Subject(s)
COVID-19 , Epigenetic Memory , Post-Acute COVID-19 Syndrome , Animals , Humans , Mice , Cell Differentiation , COVID-19/immunology , Disease Models, Animal , Hematopoietic Stem Cells , Inflammation/genetics , Trained Immunity , Monocytes/immunology , Post-Acute COVID-19 Syndrome/genetics , Post-Acute COVID-19 Syndrome/immunology , Post-Acute COVID-19 Syndrome/pathology
4.
Cell ; 184(22): 5608-5621.e18, 2021 10 28.
Article in English | MEDLINE | ID: mdl-34637701

ABSTRACT

Mammals use glabrous (hairless) skin of their hands and feet to navigate and manipulate their environment. Cortical maps of the body surface across species contain disproportionately large numbers of neurons dedicated to glabrous skin sensation, in part reflecting a higher density of mechanoreceptors that innervate these skin regions. Here, we find that disproportionate representation of glabrous skin emerges over postnatal development at the first synapse between peripheral mechanoreceptors and their central targets in the brainstem. Mechanoreceptor synapses undergo developmental refinement that depends on proximity of their terminals to glabrous skin, such that those innervating glabrous skin make synaptic connections that expand their central representation. In mice incapable of sensing gentle touch, mechanoreceptors innervating glabrous skin still make more powerful synapses in the brainstem. We propose that the skin region a mechanoreceptor innervates controls the developmental refinement of its central synapses to shape the representation of touch in the brain.


Subject(s)
Brain Stem/metabolism , Mechanoreceptors/metabolism , Synapses/metabolism , Touch Perception/physiology , Action Potentials/physiology , Animals , Animals, Newborn , Axons/metabolism , Ion Channels/metabolism , Mice, Knockout , Neurons/metabolism , Optical Imaging , Optogenetics , Skin/innervation
5.
Annu Rev Cell Dev Biol ; 38: 419-446, 2022 10 06.
Article in English | MEDLINE | ID: mdl-36201298

ABSTRACT

The peripheral nervous system (PNS) endows animals with the remarkable ability to sense and respond to a dynamic world. Emerging evidence shows the PNS also participates in tissue homeostasis and repair by integrating local changes with organismal and environmental changes. Here, we provide an in-depth summary of findings delineating the diverse roles of peripheral nerves in modulating stem cell behaviors and immune responses under steady-state conditions and in response to injury and duress, with a specific focus on the skin and the hematopoietic system. These examples showcase how elucidating neuro-stem cell and neuro-immune cell interactions provides a conceptual framework that connects tissue biology and local immunity with systemic bodily changes to meet varying demands. They also demonstrate how changes in these interactions can manifest in stress, aging, cancer, and inflammation, as well as how these findings can be harnessed to guide the development of new therapeutics.


Subject(s)
Neurobiology , Neuroimmunomodulation , Animals , Homeostasis , Inflammation , Stem Cells
6.
Cell ; 181(5): 1080-1096.e19, 2020 05 28.
Article in English | MEDLINE | ID: mdl-32380006

ABSTRACT

Environmental signals shape host physiology and fitness. Microbiota-derived cues are required to program conventional dendritic cells (cDCs) during the steady state so that they can promptly respond and initiate adaptive immune responses when encountering pathogens. However, the molecular underpinnings of microbiota-guided instructive programs are not well understood. Here, we report that the indigenous microbiota controls constitutive production of type I interferons (IFN-I) by plasmacytoid DCs. Using genome-wide analysis of transcriptional and epigenetic regulomes of cDCs from germ-free and IFN-I receptor (IFNAR)-deficient mice, we found that tonic IFNAR signaling instructs a specific epigenomic and metabolic basal state that poises cDCs for future pathogen combat. However, such beneficial biological function comes with a trade-off. Instructed cDCs can prime T cell responses against harmless peripheral antigens when removing roadblocks of peripheral tolerance. Our data provide fresh insights into the evolutionary trade-offs that come with successful adaptation of vertebrates to their microbial environment.


Subject(s)
Dendritic Cells/immunology , Interferon Type I/immunology , Microbiota/immunology , Adaptive Immunity/immunology , Adaptive Immunity/physiology , Animals , CD8-Positive T-Lymphocytes/immunology , Dendritic Cells/microbiology , Female , Male , Mice , Mice, Inbred C57BL , Microbiota/physiology , Receptor, Interferon alpha-beta/metabolism , Signal Transduction/immunology
7.
Cell ; 181(3): 574-589.e14, 2020 04 30.
Article in English | MEDLINE | ID: mdl-32259485

ABSTRACT

Sensory neurons initiate defensive reflexes that ensure airway integrity. Dysfunction of laryngeal neurons is life-threatening, causing pulmonary aspiration, dysphagia, and choking, yet relevant sensory pathways remain poorly understood. Here, we discover rare throat-innervating neurons (∼100 neurons/mouse) that guard the airways against assault. We used genetic tools that broadly cover a vagal/glossopharyngeal sensory neuron atlas to map, ablate, and control specific afferent populations. Optogenetic activation of vagal P2RY1 neurons evokes a coordinated airway defense program-apnea, vocal fold adduction, swallowing, and expiratory reflexes. Ablation of vagal P2RY1 neurons eliminates protective responses to laryngeal water and acid challenge. Anatomical mapping revealed numerous laryngeal terminal types, with P2RY1 neurons forming corpuscular endings that appose laryngeal taste buds. Epithelial cells are primary airway sentinels that communicate with second-order P2RY1 neurons through ATP. These findings provide mechanistic insights into airway defense and a general molecular/genetic roadmap for internal organ sensation by the vagus nerve.


Subject(s)
Glossopharyngeal Nerve/physiology , Pharynx/innervation , Vagus Nerve/physiology , Afferent Pathways , Animals , Female , Gene Expression Regulation/genetics , Glossopharyngeal Nerve/metabolism , Larynx/pathology , Male , Mice , Mice, Inbred C57BL , Receptors, Purinergic P2Y1/genetics , Receptors, Purinergic P2Y1/metabolism , Sensory Receptor Cells/metabolism , Vagus Nerve/metabolism
8.
Cell ; 176(4): 716-728.e18, 2019 02 07.
Article in English | MEDLINE | ID: mdl-30712871

ABSTRACT

Sensory axons degenerate following separation from their cell body, but partial injury to peripheral nerves may leave the integrity of damaged axons preserved. We show that an endogenous ligand for the natural killer (NK) cell receptor NKG2D, Retinoic Acid Early 1 (RAE1), is re-expressed in adult dorsal root ganglion neurons following peripheral nerve injury, triggering selective degeneration of injured axons. Infiltration of cytotoxic NK cells into the sciatic nerve by extravasation occurs within 3 days following crush injury. Using a combination of genetic cell ablation and cytokine-antibody complex stimulation, we show that NK cell function correlates with loss of sensation due to degeneration of injured afferents and reduced incidence of post-injury hypersensitivity. This neuro-immune mechanism of selective NK cell-mediated degeneration of damaged but intact sensory axons complements Wallerian degeneration and suggests the therapeutic potential of modulating NK cell function to resolve painful neuropathy through the clearance of partially damaged nerves.


Subject(s)
Killer Cells, Natural/physiology , Nuclear Matrix-Associated Proteins/metabolism , Nucleocytoplasmic Transport Proteins/metabolism , Peripheral Nerve Injuries/metabolism , Animals , Axons , Ganglia, Spinal/cytology , Ganglia, Spinal/metabolism , Killer Cells, Natural/metabolism , Male , Mice , Mice, Inbred C57BL , NK Cell Lectin-Like Receptor Subfamily K/metabolism , Nerve Regeneration , Neurons/cytology , Neurons, Afferent/immunology , Neurons, Afferent/metabolism , Nuclear Matrix-Associated Proteins/physiology , Nucleocytoplasmic Transport Proteins/physiology , Pain , Peripheral Nerve Injuries/immunology , Peripheral Nervous System Diseases , Sciatic Nerve , Sensory Receptor Cells/metabolism
9.
Immunity ; 57(3): 541-558.e7, 2024 Mar 12.
Article in English | MEDLINE | ID: mdl-38442708

ABSTRACT

Cancer patients often receive a combination of antibodies targeting programmed death-ligand 1 (PD-L1) and cytotoxic T lymphocyte antigen-4 (CTLA4). We conducted a window-of-opportunity study in head and neck squamous cell carcinoma (HNSCC) to examine the contribution of anti-CTLA4 to anti-PD-L1 therapy. Single-cell profiling of on- versus pre-treatment biopsies identified T cell expansion as an early response marker. In tumors, anti-PD-L1 triggered the expansion of mostly CD8+ T cells, whereas combination therapy expanded both CD4+ and CD8+ T cells. Such CD4+ T cells exhibited an activated T helper 1 (Th1) phenotype. CD4+ and CD8+ T cells co-localized with and were surrounded by dendritic cells expressing T cell homing factors or antibody-producing plasma cells. T cell receptor tracing suggests that anti-CTLA4, but not anti-PD-L1, triggers the trafficking of CD4+ naive/central-memory T cells from tumor-draining lymph nodes (tdLNs), via blood, to the tumor wherein T cells acquire a Th1 phenotype. Thus, CD4+ T cell activation and recruitment from tdLNs are hallmarks of early response to anti-PD-L1 plus anti-CTLA4 in HNSCC.


Subject(s)
CD8-Positive T-Lymphocytes , Head and Neck Neoplasms , Humans , Squamous Cell Carcinoma of Head and Neck , B7-H1 Antigen/genetics , CTLA-4 Antigen , Head and Neck Neoplasms/drug therapy , CD4-Positive T-Lymphocytes , Tumor Microenvironment
10.
Immunity ; 56(4): 864-878.e4, 2023 04 11.
Article in English | MEDLINE | ID: mdl-36996809

ABSTRACT

T cells are a critical component of the response to SARS-CoV-2, but their kinetics after infection and vaccination are insufficiently understood. Using "spheromer" peptide-MHC multimer reagents, we analyzed healthy subjects receiving two doses of the Pfizer/BioNTech BNT162b2 vaccine. Vaccination resulted in robust spike-specific T cell responses for the dominant CD4+ (HLA-DRB1∗15:01/S191) and CD8+ (HLA-A∗02/S691) T cell epitopes. Antigen-specific CD4+ and CD8+ T cell responses were asynchronous, with the peak CD4+ T cell responses occurring 1 week post the second vaccination (boost), whereas CD8+ T cells peaked 2 weeks later. These peripheral T cell responses were elevated compared with COVID-19 patients. We also found that previous SARS-CoV-2 infection resulted in decreased CD8+ T cell activation and expansion, suggesting that previous infection can influence the T cell response to vaccination.


Subject(s)
COVID-19 , Vaccines , Humans , CD8-Positive T-Lymphocytes , BNT162 Vaccine , SARS-CoV-2 , Vaccination , Antibodies, Viral
11.
Genes Dev ; 36(3-4): 133-148, 2022 02 01.
Article in English | MEDLINE | ID: mdl-35086862

ABSTRACT

The regeneration of peripheral nerves is guided by regeneration tracks formed through an interplay of many cell types, but the underlying signaling pathways remain unclear. Here, we demonstrate that macrophages are mobilized ahead of Schwann cells in the nerve bridge after transection injury to participate in building regeneration tracks. This requires the function of guidance receptor Plexin-B2, which is robustly up-regulated in infiltrating macrophages in injured nerves. Conditional deletion of Plexin-B2 in myeloid lineage resulted in not only macrophage misalignment but also matrix disarray and Schwann cell disorganization, leading to misguided axons and delayed functional recovery. Plexin-B2 is not required for macrophage recruitment or activation but enables macrophages to steer clear of colliding axons, in particular the growth cones at the tip of regenerating axons, leading to parallel alignment postcollision. Together, our studies unveil a novel reparative function of macrophages and the importance of Plexin-B2-mediated collision-dependent contact avoidance between macrophages and regenerating axons in forming regeneration tracks during peripheral nerve regeneration.


Subject(s)
Nerve Regeneration , Peripheral Nerves , Axons/physiology , Cell Adhesion Molecules , Macrophages/metabolism , Nerve Regeneration/genetics , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/metabolism , Peripheral Nerves/metabolism , Schwann Cells/metabolism
12.
Annu Rev Neurosci ; 42: 87-106, 2019 07 08.
Article in English | MEDLINE | ID: mdl-30702961

ABSTRACT

Acute pain is adaptive, but chronic pain is a global challenge. Many chronic pain syndromes are peripheral in origin and reflect hyperactivity of peripheral pain-signaling neurons. Current treatments are ineffective or only partially effective and in some cases can be addictive, underscoring the need for better therapies. Molecular genetic studies have now linked multiple human pain disorders to voltage-gated sodium channels, including disorders characterized by insensitivity or reduced sensitivity to pain and others characterized by exaggerated pain in response to normally innocuous stimuli. Here, we review recent developments that have enhanced our understanding of pathophysiological mechanisms in human pain and advances in targeting sodium channels in peripheral neurons for the treatment of pain using novel and existing sodium channel blockers.


Subject(s)
Sodium Channel Blockers/therapeutic use , Sodium Channels/physiology , Somatoform Disorders/physiopathology , Animals , Carbamazepine/pharmacology , Carbamazepine/therapeutic use , Drug Evaluation, Preclinical , Forecasting , Ganglia, Spinal/physiopathology , Genetic Association Studies , Humans , Nerve Tissue Proteins/chemistry , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/physiology , Peripheral Nerves/physiopathology , Pharmacogenomic Testing , Protein Domains , Sensory Receptor Cells/physiology , Sodium Channel Blockers/pharmacology , Sodium Channels/chemistry , Sodium Channels/genetics , Somatoform Disorders/drug therapy , Somatoform Disorders/genetics , Structure-Activity Relationship
13.
CA Cancer J Clin ; 70(1): 47-70, 2020 01.
Article in English | MEDLINE | ID: mdl-31815293

ABSTRACT

Historical advances in the care of patients with non-Hodgkin lymphoma (NHL) have been restricted largely to patients with B-cell lymphoma. The peripheral T-cell lymphomas (PTCLs), which are rare and heterogeneous in nature, have yet to experience the same degree of improvement in outcome over the past 20 to 30 years. It is estimated that there are approximately 80,000 and 14,000 cases, respectively, of NHL and Hodgkin lymphoma per year in the United States. As a subgroup of NHL, the PTCLs account for 6% to 10% of all cases of NHL, making them exceedingly rare. In addition, the World Health Organization 2017 classification describes 29 distinct subtypes of PTCL. This intrinsic diversity, coupled with its rarity, has stymied progress in the disease. In addition, most subtypes carry an inferior prognosis compared with their B-cell counterparts, an outcome largely attributed to the fact that most treatment paradigms for patients with PTCL have been derived from B-cell neoplasms, a radically different disease. In fact, the first drug ever approved for patients with PTCL was approved only a decade ago. The plethora of recent drug approvals in PTCL, coupled with a deeper understanding of the molecular pathogenesis of the disease, has stimulated the field to pursue new avenues of research that are now largely predicated on the development of novel, targeted small molecules, which include a host of epigenetic modifiers and biologics. There is an expectation these advances may begin to favorably challenge the chemotherapy paradigms that have been used in the T-cell malignancies.


Subject(s)
Antineoplastic Agents/therapeutic use , Lymphoma, T-Cell, Peripheral/drug therapy , Neoplasm Staging , Humans , Lymphoma, T-Cell, Peripheral/pathology , Prognosis
14.
Mol Cell ; 73(4): 763-774.e10, 2019 02 21.
Article in English | MEDLINE | ID: mdl-30661980

ABSTRACT

The biosynthesis of coenzyme Q presents a paradigm for how cells surmount hydrophobic barriers in lipid biology. In eukaryotes, CoQ precursors-among nature's most hydrophobic molecules-must somehow be presented to a series of enzymes peripherally associated with the mitochondrial inner membrane. Here, we reveal that this process relies on custom lipid-binding properties of COQ9. We show that COQ9 repurposes the bacterial TetR fold to bind aromatic isoprenes with high specificity, including CoQ intermediates that likely reside entirely within the bilayer. We reveal a process by which COQ9 associates with cardiolipin-rich membranes and warps the membrane surface to access this cargo. Finally, we identify a molecular interface between COQ9 and the hydroxylase COQ7, motivating a model whereby COQ9 presents intermediates directly to CoQ enzymes. Overall, our results provide a mechanism for how a lipid-binding protein might access, select, and deliver specific cargo from a membrane to promote biosynthesis.


Subject(s)
Membrane Lipids/metabolism , Mitochondrial Membranes/enzymology , Mitochondrial Proteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/enzymology , Ubiquinone/biosynthesis , Binding Sites , Cardiolipins/metabolism , Crystallography , Mitochondrial Proteins/chemistry , Mitochondrial Proteins/genetics , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Binding , Protein Conformation, alpha-Helical , Protein Transport , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Structure-Activity Relationship , Tryptophan , Ubiquinone/chemistry , Ubiquinone/genetics
15.
Proc Natl Acad Sci U S A ; 121(16): e2320416121, 2024 Apr 16.
Article in English | MEDLINE | ID: mdl-38588428

ABSTRACT

Pores through ion channels rapidly transport small inorganic ions along their electrochemical gradients. Here, applying single-channel electrophysiology and mutagenesis to the archetypal muscle nicotinic acetylcholine receptor (AChR) channel, we show that a conserved pore-peripheral salt bridge partners with those in the other subunits to regulate ion transport. Disrupting the salt bridges in all five receptor subunits greatly decreases the amplitude of the unitary current and increases its fluctuations. However, disrupting individual salt bridges has unequal effects that depend on the structural status of the other salt bridges. The AChR ε- and δ-subunits are structurally unique in harboring a putative palmitoylation site near each salt bridge and bordering the lipid membrane. The effects of disrupting the palmitoylation sites mirror those of disrupting the salt bridges, but the effect of disrupting either of these structures depends on the structural status of the other. Thus, rapid ion transport through the AChR channel is maintained by functionally interdependent salt bridges linking the pore to the lipid membrane.


Subject(s)
Receptors, Cholinergic , Receptors, Nicotinic , Receptors, Nicotinic/genetics , Receptors, Nicotinic/chemistry , Muscles , Ion Transport , Lipids
16.
EMBO J ; 41(22): e111038, 2022 11 17.
Article in English | MEDLINE | ID: mdl-36215698

ABSTRACT

Impaired clearance of beta-amyloid (Aß) is a primary cause of sporadic Alzheimer's disease (AD). Aß clearance in the periphery contributes to reducing brain Aß levels and preventing Alzheimer's disease pathogenesis. We show here that erythropoietin (EPO) increases phagocytic activity, levels of Aß-degrading enzymes, and Aß clearance in peripheral macrophages via PPARγ. Erythropoietin is also shown to suppress Aß-induced inflammatory responses. Deletion of EPO receptor in peripheral macrophages leads to increased peripheral and brain Aß levels and exacerbates Alzheimer's-associated brain pathologies and behavioral deficits in AD-model mice. Moreover, erythropoietin signaling is impaired in peripheral macrophages of old AD-model mice. Exogenous erythropoietin normalizes impaired EPO signaling and dysregulated functions of peripheral macrophages in old AD-model mice, promotes systemic Aß clearance, and alleviates disease progression. Erythropoietin treatment may represent a potential therapeutic approach for Alzheimer's disease.


Subject(s)
Alzheimer Disease , Erythropoietin , Animals , Mice , Alzheimer Disease/pathology , Amyloid beta-Peptides/metabolism , Erythropoietin/pharmacology , Erythropoietin/therapeutic use , Brain/metabolism , Macrophages/metabolism , Mice, Transgenic , Disease Models, Animal
17.
Annu Rev Med ; 75: 293-306, 2024 Jan 29.
Article in English | MEDLINE | ID: mdl-38285516

ABSTRACT

Diabetic neuropathy is a highly prevalent complication of diabetes. It consists of a broad range of neuropathic conditions, such as distal symmetric polyneuropathy and various forms of autonomic neuropathies involving the cardiovascular, gastrointestinal, and urogenital systems. Prevention or diagnosis in early stages of disease is crucial to prevent symptomatic onset and progression, particularly in the absence of current disease-modifying therapies. In this review, we describe the four main types of diabetic neuropathy. We review current understanding with respect to diagnosis and treatment while highlighting knowledge gaps and future directions.


Subject(s)
Diabetes Mellitus , Diabetic Neuropathies , Humans , Diabetic Neuropathies/diagnosis , Diabetic Neuropathies/therapy
18.
Am J Hum Genet ; 110(11): 1903-1918, 2023 11 02.
Article in English | MEDLINE | ID: mdl-37816352

ABSTRACT

Despite whole-genome sequencing (WGS), many cases of single-gene disorders remain unsolved, impeding diagnosis and preventative care for people whose disease-causing variants escape detection. Since early WGS data analytic steps prioritize protein-coding sequences, to simultaneously prioritize variants in non-coding regions rich in transcribed and critical regulatory sequences, we developed GROFFFY, an analytic tool that integrates coordinates for regions with experimental evidence of functionality. Applied to WGS data from solved and unsolved hereditary hemorrhagic telangiectasia (HHT) recruits to the 100,000 Genomes Project, GROFFFY-based filtration reduced the mean number of variants/DNA from 4,867,167 to 21,486, without deleting disease-causal variants. In three unsolved cases (two related), GROFFFY identified ultra-rare deletions within the 3' untranslated region (UTR) of the tumor suppressor SMAD4, where germline loss-of-function alleles cause combined HHT and colonic polyposis (MIM: 175050). Sited >5.4 kb distal to coding DNA, the deletions did not modify or generate microRNA binding sites, but instead disrupted the sequence context of the final cleavage and polyadenylation site necessary for protein production: By iFoldRNA, an AAUAAA-adjacent 16-nucleotide deletion brought the cleavage site into inaccessible neighboring secondary structures, while a 4-nucleotide deletion unfolded the downstream RNA polymerase II roadblock. SMAD4 RNA expression differed to control-derived RNA from resting and cycloheximide-stressed peripheral blood mononuclear cells. Patterns predicted the mutational site for an unrelated HHT/polyposis-affected individual, where a complex insertion was subsequently identified. In conclusion, we describe a functional rare variant type that impacts regulatory systems based on RNA polyadenylation. Extension of coding sequence-focused gene panels is required to capture these variants.


Subject(s)
Smad4 Protein , Telangiectasia, Hereditary Hemorrhagic , Humans , Base Sequence , DNA , Leukocytes, Mononuclear/pathology , Nucleotides , Polyadenylation/genetics , RNA , Smad4 Protein/genetics , Telangiectasia, Hereditary Hemorrhagic/genetics , Whole Genome Sequencing
19.
Development ; 150(9)2023 05 01.
Article in English | MEDLINE | ID: mdl-37170957

ABSTRACT

The peripheral nervous system (PNS) represents a highly heterogeneous entity with a broad range of functions, ranging from providing communication between the brain and the body to controlling development, stem cell niches and regenerative processes. According to the structure and function, the PNS can be subdivided into sensory, motor (i.e. the nerve fibers of motor neurons), autonomic and enteric domains. Different types of neurons correspond to these domains and recent progress in single-cell transcriptomics has enabled the discovery of new neuronal subtypes and improved the previous cell-type classifications. The developmental mechanisms generating the domains of the PNS reveal a range of embryonic strategies, including a variety of cell sources, such as migratory neural crest cells, placodal neurogenic cells and even recruited nerve-associated Schwann cell precursors. In this article, we discuss the diversity of roles played by the PNS in our body, as well as the origin, wiring and heterogeneity of every domain. We place a special focus on the most recent discoveries and concepts in PNS research, and provide an outlook of future perspectives and controversies in the field.


Subject(s)
Neurogenesis , Peripheral Nervous System , Neural Crest , Schwann Cells , Motor Neurons
20.
Development ; 150(10)2023 05 15.
Article in English | MEDLINE | ID: mdl-37213081

ABSTRACT

The most anterior structure of the ascidian larva is made of three palps with sensory and adhesive functions essential for metamorphosis. They derive from the anterior neural border and their formation is regulated by FGF and Wnt. Given that they also share gene expression profiles with vertebrate anterior neural tissue and cranial placodes, their study should shed light on the emergence of the unique vertebrate telencephalon. We show that BMP signaling regulates two phases of palp formation in Ciona intestinalis. During gastrulation, the anterior neural border is specified in a domain of inactive BMP signaling, and activating BMP prevented its formation. During neurulation, BMP defines ventral palp identity and indirectly specifies the inter-papilla territory separating the ventral and dorsal palps. Finally, we show that BMP has similar functions in the ascidian Phallusia mammillata, for which we identified novel palp markers. Collectively, we provide a better molecular description of palp formation in ascidians that will be instrumental for comparative studies.


Subject(s)
Urochordata , Animals , Urochordata/genetics , Nervous System/metabolism , Signal Transduction , Gastrulation/genetics , Neural Plate/metabolism , Gene Expression Regulation, Developmental
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