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Ma J, O'Malley JJ, Kreiker M, Leng Y, Khan I, Kindel M, Penzo MA. Convergent direct and indirect cortical streams shape avoidance decisions in mice via the midline thalamus. Nat Commun 2024; 15:6598. [PMID: 39097600 PMCID: PMC11297946 DOI: 10.1038/s41467-024-50941-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 07/24/2024] [Indexed: 08/05/2024] Open
Abstract
Current concepts of corticothalamic organization in the mammalian brain are mainly based on sensory systems, with less focus on circuits for higher-order cognitive functions. In sensory systems, first-order thalamic relays are driven by subcortical inputs and modulated by cortical feedback, while higher-order relays receive strong excitatory cortical inputs. The applicability of these principles beyond sensory systems is uncertain. We investigated mouse prefronto-thalamic projections to the midline thalamus, revealing distinct top-down control. Unlike sensory systems, this pathway relies on indirect modulation via the thalamic reticular nucleus (TRN). Specifically, the prelimbic area, which influences emotional and motivated behaviors, impacts instrumental avoidance responses through direct and indirect projections to the paraventricular thalamus. Both pathways promote defensive states, but the indirect pathway via the TRN is essential for organizing avoidance decisions through disinhibition. Our findings highlight intra-thalamic circuit dynamics that integrate cortical cognitive signals and their role in shaping complex behaviors.
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Affiliation(s)
- Jun Ma
- Section on the Neural Circuits of Emotion and Motivation, National Institute of Mental Health, Bethesda, MD, USA
- Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, 221004, Xuzhou, China
| | - John J O'Malley
- Section on the Neural Circuits of Emotion and Motivation, National Institute of Mental Health, Bethesda, MD, USA
| | - Malaz Kreiker
- Section on the Neural Circuits of Emotion and Motivation, National Institute of Mental Health, Bethesda, MD, USA
| | - Yan Leng
- Section on the Neural Circuits of Emotion and Motivation, National Institute of Mental Health, Bethesda, MD, USA
| | - Isbah Khan
- Section on the Neural Circuits of Emotion and Motivation, National Institute of Mental Health, Bethesda, MD, USA
| | - Morgan Kindel
- Section on the Neural Circuits of Emotion and Motivation, National Institute of Mental Health, Bethesda, MD, USA
| | - Mario A Penzo
- Section on the Neural Circuits of Emotion and Motivation, National Institute of Mental Health, Bethesda, MD, USA.
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2
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Grubaugh CR, Dhingra A, Prakash B, Montenegro D, Sparrow JR, Daniele LL, Curcio CA, Bell BA, Hussain MM, Boesze-Battaglia K. Microsomal triglyceride transfer protein is necessary to maintain lipid homeostasis and retinal function. FASEB J 2024; 38:e23522. [PMID: 38445789 PMCID: PMC10949407 DOI: 10.1096/fj.202302491r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/07/2024]
Abstract
Lipid processing by the retinal pigment epithelium (RPE) is necessary to maintain retinal health and function. Dysregulation of retinal lipid homeostasis due to normal aging or age-related disease triggers lipid accumulation within the RPE, on Bruch's membrane (BrM), and in the subretinal space. In its role as a hub for lipid trafficking into and out of the neural retina, the RPE packages a significant amount of lipid into lipid droplets for storage and into apolipoprotein B (APOB)-containing lipoproteins (Blps) for export. Microsomal triglyceride transfer protein (MTP), encoded by the MTTP gene, is essential for Blp assembly. Herein we test the hypothesis that MTP expression in the RPE is essential to maintain lipid balance and retinal function using the newly generated RPEΔMttp mouse model. Using non-invasive ocular imaging, electroretinography, and histochemical and biochemical analyses we show that genetic depletion of Mttp from the RPE results in intracellular lipid accumulation, increased photoreceptor-associated cholesterol deposits, and photoreceptor cell death, and loss of rod but not cone function. RPE-specific reduction in Mttp had no significant effect on plasma lipids and lipoproteins. While APOB was decreased in the RPE, most ocular retinoids remained unchanged, with the exception of the storage form of retinoid, retinyl ester. Thus suggesting that RPE MTP is critical for Blp synthesis and assembly but is not directly involved in plasma lipoprotein metabolism. These studies demonstrate that RPE-specific MTP expression is necessary to establish and maintain retinal lipid homeostasis and visual function.
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Affiliation(s)
- Catharina R. Grubaugh
- Department of Basic and Translational Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anuradha Dhingra
- Department of Basic and Translational Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Binu Prakash
- Department of Foundations of Medicine, New York University Grossman Long Island School of Medicine, Mineola, NY, 11501 USA
| | - Diego Montenegro
- Department of Ophthalmology and Department of Pathology and Cell Biology, Columbia University, New York, NY, 10027 USA
| | - Janet R. Sparrow
- Department of Ophthalmology and Department of Pathology and Cell Biology, Columbia University, New York, NY, 10027 USA
| | - Lauren L. Daniele
- Department of Basic and Translational Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christine A. Curcio
- Department of Ophthalmology and Visual Sciences, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brent A. Bell
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - M. Mahmood Hussain
- Department of Foundations of Medicine, New York University Grossman Long Island School of Medicine, Mineola, NY, 11501 USA
| | - Kathleen Boesze-Battaglia
- Department of Basic and Translational Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
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3
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Grubaugh CR, Dhingra A, Prakash B, Montenegro D, Sparrow JR, Daniele LL, Curcio CA, Bell BA, Hussain MM, Boesze-Battaglia K. Microsomal triglyceride transfer protein is necessary to maintain lipid homeostasis and retinal function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570418. [PMID: 38105975 PMCID: PMC10723417 DOI: 10.1101/2023.12.06.570418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Lipid processing by the retinal pigment epithelium (RPE) is necessary to maintain retinal health and function. Dysregulation of retinal lipid homeostasis due to normal aging or to age-related disease triggers lipid accumulation within the RPE, on Bruch's membrane (BrM), and in the subretinal space. In its role as a hub for lipid trafficking into and out of the neural retina, the RPE packages a significant amount of lipid into lipid droplets for storage and into apolipoprotein B (apoB)-containing lipoproteins (Blps) for export. Microsomal triglyceride transfer protein (MTP), encoded by the MTTP gene, is essential for Blp assembly. Herein we test the hypothesis that MTP expression in the RPE is essential to maintain lipid balance and retinal function using the newly generated RPEΔMttp mouse model. Using non-invasive ocular imaging, electroretinography, and histochemical and biochemical analyses we show that genetic deletion of Mttp from the RPE results in intracellular lipid accumulation, increased photoreceptor -associated cholesterol deposits and photoreceptor cell death, and loss of rod but not cone function. RPE-specific ablation of Mttp had no significant effect on plasma lipids and lipoproteins. While, apoB was decreased in the RPE, ocular retinoid concentrations remained unchanged. Thus suggesting that RPE MTP is critical for Blp synthesis and assembly but not directly involved in ocular retinoid and plasma lipoprotein metabolism. These studies demonstrate that RPE-specific MTP expression is necessary to establish and maintain retinal lipid homeostasis and visual function.
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Affiliation(s)
- Catharina R. Grubaugh
- Department of Basic and Translational Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anuradha Dhingra
- Department of Basic and Translational Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Binu Prakash
- Department of Foundations of Medicine, New York University Grossman Long Island School of Medicine, Mineola, NY, 11501 USA
| | - Diego Montenegro
- Department of Ophthalmology and Department of Pathology and Cell Biology, Columbia University, New York, NY,10027 USA
| | - Janet R. Sparrow
- Department of Ophthalmology and Department of Pathology and Cell Biology, Columbia University, New York, NY,10027 USA
| | - Lauren L. Daniele
- Department of Basic and Translational Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christine A. Curcio
- Department of Ophthalmology and Visual Sciences, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brent A. Bell
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - M. Mahmood Hussain
- Department of Foundations of Medicine, New York University Grossman Long Island School of Medicine, Mineola, NY, 11501 USA
| | - Kathleen Boesze-Battaglia
- Department of Basic and Translational Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
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4
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Hammer PM, Wang A, Beard C, Zdravkovic S, Tenney T, Liang B, Das I, Bremer R, Wang LC, McCluggage WG, Stewart CJR, Howitt BE. Detection of FOXL2 C134W Mutation Status by a Novel BaseScope In Situ Hybridization Assay is Highly Sensitive and Specific for Adult Granulosa Cell Tumors. Mod Pathol 2023; 36:100318. [PMID: 37634867 DOI: 10.1016/j.modpat.2023.100318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 07/13/2023] [Accepted: 08/21/2023] [Indexed: 08/29/2023]
Abstract
Adult granulosa cell tumors (AGCTs) are a molecularly distinct group of malignant ovarian sex cord-stromal tumors (SCSTs) characterized by a nearly ubiquitous c.402C>G/p.C134W mutation in FOXL2 (hereafter referred to as "C134W"). In some cases, AGCT exhibits marked morphologic overlap with other SCSTs and has an identical immunophenotype, and molecular testing may be necessary to help confirm the diagnosis. However, molecular testing is time consuming, relatively expensive, and unavailable in many pathology laboratories. We describe the development and validation of an in situ hybridization (ISH) custom BaseScope assay for the detection of the FOXL2 C134W mutation. We evaluated 106 ovarian SCSTs, including 78 AGCTs, 9 juvenile granulosa cell tumors, 18 fibromas (cellular and conventional), and 1 SCST, not otherwise specified, as well as 53 epithelial ovarian tumors (42 endometrioid carcinomas and 11 carcinosarcomas) and 1 STK11 adnexal tumor for the presence or absence of FOXL2 wild-type and FOXL2 C134W RNA expression via BaseScope-ISH. Fifty-one tumors had previously undergone DNA sequencing of the FOXL2 gene. Across the entire cohort, the FOXL2 C134W probe staining was positive in 77 of 78 (98.7%) AGCTs. Two of 81 (2.5%) non-AGCTs also showed positive staining, both of which were epithelial ovarian tumors. The assay worked in tissue from blocks >20 years old. There was 100% concordance between the FOXL2 sequencing and BaseScope-ISH results. Overall, assessment of FOXL2 mutation status by custom BaseScope-ISH demonstrated 98.7% sensitivity and 97.5% specificity for the diagnosis of AGCT. BaseScope-ISH for FOXL2 C134W represents a reasonable alternative to sequencing, is quicker and less expensive, and is more easily incorporated than molecular testing into many pathology laboratories. It also has the advantage of requiring less tissue, and the neoplastic cells can be directly visualized on stained sections.
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Affiliation(s)
- Phoebe M Hammer
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Aihui Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Crystal Beard
- Department of Pathology, Stanford University School of Medicine, Stanford, California; Meharry Medical College, School of Medicine, Nashville, Tennessee
| | - Sabrina Zdravkovic
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Troy Tenney
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Brooke Liang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Ishani Das
- Advanced Cell Diagnostics-a Bio-Techne brand, Newark, California
| | - Ryan Bremer
- Advanced Cell Diagnostics-a Bio-Techne brand, Newark, California
| | - Li-Chong Wang
- Advanced Cell Diagnostics-a Bio-Techne brand, Newark, California
| | - W Glenn McCluggage
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Colin J R Stewart
- Department of Histopathology, King Edward Memorial Hospital and School for Women's and Infants' Health, University of Western Australia, Perth, Western Australia, Australia
| | - Brooke E Howitt
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
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5
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Goodman RL, Moore AM, Onslow K, Hileman SM, Hardy SL, Bowdridge EC, Walters BA, Agus S, Griesgraber MJ, Aerts EG, Lehman MN, Coolen LM. Lesions of KNDy and Kiss1R Neurons in the Arcuate Nucleus Produce Different Effects on LH Pulse Patterns in Female Sheep. Endocrinology 2023; 164:bqad148. [PMID: 37776515 PMCID: PMC10587900 DOI: 10.1210/endocr/bqad148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/02/2023]
Abstract
The current model for the synchronization of GnRH neural activity driving GnRH and LH pulses proposes that a set of arcuate (ARC) neurons that contain kisspeptin, neurokinin B, and dynorphin (KNDy neurons) is the GnRH pulse generator. This study tested the functional role of ovine KNDy neurons in pulse generation and explored the roles of nearby Kiss1 receptor (Kiss1R)-containing cells using lesions produced with saporin (SAP) conjugates. Injection of NK3-SAP ablated over 90% of the KNDy cells, while Kiss-SAP (saporin conjugated to kisspeptin-54) lesioned about two-thirds of the Kiss1R population without affecting KNDy or GnRH cell number. Both lesions produced a dramatic decrease in LH pulse amplitude but had different effects on LH pulse patterns. NK3-SAP increased interpulse interval, but Kiss-SAP did not. In contrast, Kiss-SAP disrupted the regular hourly occurrence of LH pulses, but NK3-SAP did not. Because Kiss1R is not expressed in KNDy cells, HiPlex RNAScope was used to assess the colocalization of 8 neurotransmitters and 3 receptors in ARC Kiss1R-containing cells. Kiss1R cells primarily contained transcript markers for GABA (68%), glutamate (28%), ESR1 (estrogen receptor-α) mRNA, and OPRK1 (kappa opioid receptor) mRNA. These data support the conclusion that KNDy neurons are essential for GnRH pulses in ewes, whereas ARC Kiss1R cells are not but do maintain the amplitude and regularity of GnRH pulses. We thus propose that in sheep, ARC Kiss1R neurons form part of a positive feedback circuit that reinforces the activity of the KNDy neural network, with GABA or glutamate likely being involved.
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Affiliation(s)
- Robert L Goodman
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV 26506, USA
| | - Aleisha M Moore
- Brain Health Research Institute, Kent State University, Kent, OH 44242, USA
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Kayla Onslow
- Brain Health Research Institute, Kent State University, Kent, OH 44242, USA
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Stanley M Hileman
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV 26506, USA
| | - Steve L Hardy
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV 26506, USA
| | - Elizabeth C Bowdridge
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV 26506, USA
| | - Burgundy A Walters
- Brain Health Research Institute, Kent State University, Kent, OH 44242, USA
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Sami Agus
- Brain Health Research Institute, Kent State University, Kent, OH 44242, USA
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Max J Griesgraber
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV 26506, USA
| | - Eliana G Aerts
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV 26506, USA
| | - Michael N Lehman
- Brain Health Research Institute, Kent State University, Kent, OH 44242, USA
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Lique M Coolen
- Brain Health Research Institute, Kent State University, Kent, OH 44242, USA
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
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6
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Tang Q, Godschall E, Brennan CD, Zhang Q, Abraham-Fan RJ, Williams SP, Güngül TB, Onoharigho R, Buyukaksakal A, Salinas R, Sajonia IR, Olivieri JJ, Calhan OY, Deppmann CD, Campbell JN, Podyma B, Güler AD. Leptin receptor neurons in the dorsomedial hypothalamus input to the circadian feeding network. SCIENCE ADVANCES 2023; 9:eadh9570. [PMID: 37624889 PMCID: PMC10456850 DOI: 10.1126/sciadv.adh9570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
Salient cues, such as the rising sun or availability of food, entrain biological clocks for behavioral adaptation. The mechanisms underlying entrainment to food availability remain elusive. Using single-nucleus RNA sequencing during scheduled feeding, we identified a dorsomedial hypothalamus leptin receptor-expressing (DMHLepR) neuron population that up-regulates circadian entrainment genes and exhibits calcium activity before an anticipated meal. Exogenous leptin, silencing, or chemogenetic stimulation of DMHLepR neurons disrupts the development of molecular and behavioral food entrainment. Repetitive DMHLepR neuron activation leads to the partitioning of a secondary bout of circadian locomotor activity that is in phase with the stimulation and dependent on an intact suprachiasmatic nucleus (SCN). Last, we found a DMHLepR neuron subpopulation that projects to the SCN with the capacity to influence the phase of the circadian clock. This direct DMHLepR-SCN connection is well situated to integrate the metabolic and circadian systems, facilitating mealtime anticipation.
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Affiliation(s)
- Qijun Tang
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Elizabeth Godschall
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Charles D. Brennan
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Qi Zhang
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | | | - Sydney P. Williams
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Taha Buğra Güngül
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Roberta Onoharigho
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Aleyna Buyukaksakal
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Ricardo Salinas
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Isabelle R. Sajonia
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Joey J. Olivieri
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - O. Yipkin Calhan
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Christopher D. Deppmann
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
- Program in Fundamental Neuroscience, Charlottesville, VA 22904, USA
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22904, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904, USA
- Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - John N. Campbell
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
- Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Brandon Podyma
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
- Medical Scientist Training Program, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Ali D. Güler
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
- Program in Fundamental Neuroscience, Charlottesville, VA 22904, USA
- Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
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7
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Puram SV, Mints M, Pal A, Qi Z, Reeb A, Gelev K, Barrett TF, Gerndt S, Liu P, Parikh AS, Ramadan S, Law T, Mroz EA, Rocco JW, Adkins D, Thorstad WL, Gay HA, Ding L, Paniello RC, Pipkorn P, Jackson RS, Wang X, Mazul A, Chernock R, Zevallos JP, Silva-Fisher J, Tirosh I. Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma. Nat Genet 2023; 55:640-650. [PMID: 37012457 PMCID: PMC10191634 DOI: 10.1038/s41588-023-01357-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/27/2023] [Indexed: 04/05/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) includes a subset of cancers driven by human papillomavirus (HPV). Here we use single-cell RNA-seq to profile both HPV-positive and HPV-negative oropharyngeal tumors, uncovering a high level of cellular diversity within and between tumors. First, we detect diverse chromosomal aberrations within individual tumors, suggesting genomic instability and enabling the identification of malignant cells even at pathologically negative margins. Second, we uncover diversity with respect to HNSCC subtypes and other cellular states such as the cell cycle, senescence and epithelial-mesenchymal transitions. Third, we find heterogeneity in viral gene expression within HPV-positive tumors. HPV expression is lost or repressed in a subset of cells, which are associated with a decrease in HPV-associated cell cycle phenotypes, decreased response to treatment, increased invasion and poor prognosis. These findings suggest that HPV expression diversity must be considered during diagnosis and treatment of HPV-positive tumors, with important prognostic ramifications.
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Affiliation(s)
- Sidharth V Puram
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA.
| | - Michael Mints
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Ananya Pal
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Zongtai Qi
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Ashley Reeb
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Kyla Gelev
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Thomas F Barrett
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Sophie Gerndt
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Ping Liu
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Anuraag S Parikh
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Salma Ramadan
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Travis Law
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Edmund A Mroz
- Department of Otolaryngology-Head and Neck Surgery, Ohio State University, Columbus, OH, USA
| | - James W Rocco
- Department of Otolaryngology-Head and Neck Surgery, Ohio State University, Columbus, OH, USA
| | - Doug Adkins
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Wade L Thorstad
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Hiram A Gay
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Li Ding
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Randal C Paniello
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Patrik Pipkorn
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryan S Jackson
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Xiaowei Wang
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Angela Mazul
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Rebecca Chernock
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jose P Zevallos
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Jessica Silva-Fisher
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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8
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Gao C, Gohel CA, Leng Y, Ma J, Goldman D, Levine AJ, Penzo MA. Molecular and spatial profiling of the paraventricular nucleus of the thalamus. eLife 2023; 12:81818. [PMID: 36867023 PMCID: PMC10014079 DOI: 10.7554/elife.81818] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/02/2023] [Indexed: 03/04/2023] Open
Abstract
The paraventricular nucleus of the thalamus (PVT) is known to regulate various cognitive and behavioral processes. However, while functional diversity among PVT circuits has often been linked to cellular differences, the molecular identity and spatial distribution of PVT cell types remain unclear. To address this gap, here we used single nucleus RNA sequencing (snRNA-seq) and identified five molecularly distinct PVT neuronal subtypes in the mouse brain. Additionally, multiplex fluorescent in situ hybridization of top marker genes revealed that PVT subtypes are organized by a combination of previously unidentified molecular gradients. Lastly, comparing our dataset with a recently published single-cell sequencing atlas of the thalamus yielded novel insight into the PVT's connectivity with the cortex, including unexpected innervation of auditory and visual areas. This comparison also revealed that our data contains a largely non-overlapping transcriptomic map of multiple midline thalamic nuclei. Collectively, our findings uncover previously unknown features of the molecular diversity and anatomical organization of the PVT and provide a valuable resource for future investigations.
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Affiliation(s)
- Claire Gao
- National Institute of Mental HealthBethesdaUnited States
- Department of Neuroscience, Brown UniversityProvidenceUnited States
| | - Chiraag A Gohel
- National Institute on Alcohol Abuse and AlcoholismRockvilleUnited States
| | - Yan Leng
- National Institute of Mental HealthBethesdaUnited States
| | - Jun Ma
- National Institute of Mental HealthBethesdaUnited States
| | - David Goldman
- National Institute on Alcohol Abuse and AlcoholismRockvilleUnited States
| | - Ariel J Levine
- National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Mario A Penzo
- National Institute of Mental HealthBethesdaUnited States
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9
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Tang Q, Godschall E, Brennan CD, Zhang Q, Abraham-Fan RJ, Williams SP, Güngül TB, Onoharigho R, Buyukaksakal A, Salinas R, Olivieri JJ, Deppmann CD, Campbell JN, Podyma B, Güler AD. A leptin-responsive hypothalamic circuit inputs to the circadian feeding network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529901. [PMID: 36865258 PMCID: PMC9980144 DOI: 10.1101/2023.02.24.529901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Salient cues, such as the rising sun or the availability of food, play a crucial role in entraining biological clocks, allowing for effective behavioral adaptation and ultimately, survival. While the light-dependent entrainment of the central circadian pacemaker (suprachiasmatic nucleus, SCN) is relatively well defined, the molecular and neural mechanisms underlying entrainment associated with food availability remains elusive. Using single nucleus RNA sequencing during scheduled feeding (SF), we identified a leptin receptor (LepR) expressing neuron population in the dorsomedial hypothalamus (DMH) that upregulates circadian entrainment genes and exhibits rhythmic calcium activity prior to an anticipated meal. We found that disrupting DMHLepR neuron activity had a profound impact on both molecular and behavioral food entrainment. Specifically, silencing DMHLepR neurons, mis-timed exogenous leptin administration, or mis-timed chemogenetic stimulation of these neurons all interfered with the development of food entrainment. In a state of energy abundance, repetitive activation of DMHLepR neurons led to the partitioning of a secondary bout of circadian locomotor activity that was in phase with the stimulation and dependent on an intact SCN. Lastly, we discovered that a subpopulation of DMHLepR neurons project to the SCN with the capacity to influence the phase of the circadian clock. This leptin regulated circuit serves as a point of integration between the metabolic and circadian systems, facilitating the anticipation of meal times.
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Affiliation(s)
- Qijun Tang
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Elizabeth Godschall
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Charles D. Brennan
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Qi Zhang
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | | | - Sydney P. Williams
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Taha Buğra Güngül
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Roberta Onoharigho
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Aleyna Buyukaksakal
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Ricardo Salinas
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Joey J. Olivieri
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Christopher D. Deppmann
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
- Program in Fundamental Neuroscience, Charlottesville, VA 22904, USA
- Department of Cell Biology, University of Virginia, Charlottesville, VA, 22904, USA
- Department Biomedical Engineering, University of Virginia, Charlottesville, VA, 22904, USA
- Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - John N. Campbell
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
- Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Brandon Podyma
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
- Medical Scientist Training Program, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Ali D. Güler
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
- Program in Fundamental Neuroscience, Charlottesville, VA 22904, USA
- Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
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10
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Mann JT, Riley BA, Baker SF. All differential on the splicing front: Host alternative splicing alters the landscape of virus-host conflict. Semin Cell Dev Biol 2023; 146:40-56. [PMID: 36737258 DOI: 10.1016/j.semcdb.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
Alternative RNA splicing is a co-transcriptional process that richly increases proteome diversity, and is dynamically regulated based on cell species, lineage, and activation state. Virus infection in vertebrate hosts results in rapid host transcriptome-wide changes, and regulation of alternative splicing can direct a combinatorial effect on the host transcriptome. There has been a recent increase in genome-wide studies evaluating host alternative splicing during viral infection, which integrates well with prior knowledge on viral interactions with host splicing proteins. A critical challenge remains in linking how these individual events direct global changes, and whether alternative splicing is an overall favorable pathway for fending off or supporting viral infection. Here, we introduce the process of alternative splicing, discuss how to analyze splice regulation, and detail studies on genome-wide and splice factor changes during viral infection. We seek to highlight where the field can focus on moving forward, and how incorporation of a virus-host co-evolutionary perspective can benefit this burgeoning subject.
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Affiliation(s)
- Joshua T Mann
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Brent A Riley
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Steven F Baker
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA.
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11
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Shilo A, Pegoraro G, Misteli T. HiFENS: high-throughput FISH detection of endogenous pre-mRNA splicing isoforms. Nucleic Acids Res 2022; 50:e130. [PMID: 36243969 PMCID: PMC9825148 DOI: 10.1093/nar/gkac869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/01/2022] [Accepted: 09/27/2022] [Indexed: 01/29/2023] Open
Abstract
Splicing factors play an essential role in regulation of alternative pre-mRNA splicing. While much progress has been made in delineating the mechanisms of the splicing machinery, the identity of signal transduction pathways and upstream factors that regulate splicing factor activity is largely unknown. A major challenge in the discovery of upstream regulatory factors of pre-mRNA splicing is the scarcity of functional genomics screening methods to monitor splicing outcomes of endogenous genes. Here, we have developed HiFENS (high throughput FISH detection of endogenous splicing isoforms), a high-throughput imaging assay based on hybridization chain reaction (HCR) and used HiFENS to screen for cellular factors that regulate alternative splicing of endogenous genes. We demonstrate optimized detection with high specificity of endogenous splicing isoforms and multiplexing of probes for accurate detection of splicing outcomes with single cell resolution. As proof-of-principle, we perform an RNAi screen of 702 human kinases and identify potential candidate upstream splicing regulators of the FGFR2 gene. HiFENS should be a useful tool for the unbiased delineation of cellular pathways involved in alternative splicing regulation.
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Affiliation(s)
- Asaf Shilo
- Cell Biology of Genomes, Center for Cancer Research (CCR), National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility (HiTIF), Center for Cancer Research (CCR), National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Tom Misteli
- To whom correspondence should be addressed. Tel: +1 240 670 6669; Fax: +1 240 670 6670;
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12
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Beiter RM, Rivet-Noor C, Merchak AR, Bai R, Johanson DM, Slogar E, Sol-Church K, Overall CC, Gaultier A. Evidence for oligodendrocyte progenitor cell heterogeneity in the adult mouse brain. Sci Rep 2022; 12:12921. [PMID: 35902669 PMCID: PMC9334628 DOI: 10.1038/s41598-022-17081-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/20/2022] [Indexed: 12/25/2022] Open
Abstract
Oligodendrocyte progenitor cells (OPCs) account for approximately 5% of the adult brain and have been historically studied for their role in myelination. In the adult brain, OPCs maintain their proliferative capacity and ability to differentiate into oligodendrocytes throughout adulthood, even though relatively few mature oligodendrocytes are produced post-developmental myelination. Recent work has begun to demonstrate that OPCs likely perform multiple functions in both homeostasis and disease and can significantly impact behavioral phenotypes such as food intake and depressive symptoms. However, the exact mechanisms through which OPCs might influence brain function remain unclear. The first step in further exploration of OPC function is to profile the transcriptional repertoire and assess the heterogeneity of adult OPCs. In this work, we demonstrate that adult OPCs are transcriptionally diverse and separate into two distinct populations in the homeostatic brain. These two groups show distinct transcriptional signatures and enrichment of biological processes unique to individual OPC populations. We have validated these OPC populations using multiple methods, including multiplex RNA in situ hybridization and RNA flow cytometry. This study provides an important resource that profiles the transcriptome of adult OPCs and will provide a toolbox for further investigation into novel OPC functions.
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Affiliation(s)
- Rebecca M Beiter
- Department of Neuroscience, Center for Brain Immunology and Glia, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Graduate Program in Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Courtney Rivet-Noor
- Department of Neuroscience, Center for Brain Immunology and Glia, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Graduate Program in Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Andrea R Merchak
- Department of Neuroscience, Center for Brain Immunology and Glia, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Graduate Program in Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Robin Bai
- Department of Neuroscience, Center for Brain Immunology and Glia, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - David M Johanson
- Department of Neuroscience, Center for Brain Immunology and Glia, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Erica Slogar
- Department of Neuroscience, Center for Brain Immunology and Glia, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Katia Sol-Church
- Genome Analysis and Technology Core, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Christopher C Overall
- Department of Neuroscience, Center for Brain Immunology and Glia, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Alban Gaultier
- Department of Neuroscience, Center for Brain Immunology and Glia, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA. .,Graduate Program in Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
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13
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Hein RFC, Wu JH, Holloway EM, Frum T, Conchola AS, Tsai YH, Wu A, Fine AS, Miller AJ, Szenker-Ravi E, Yan KS, Kuo CJ, Glass I, Reversade B, Spence JR. R-SPONDIN2 + mesenchymal cells form the bud tip progenitor niche during human lung development. Dev Cell 2022; 57:1598-1614.e8. [PMID: 35679862 PMCID: PMC9283295 DOI: 10.1016/j.devcel.2022.05.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 01/23/2023]
Abstract
The human respiratory epithelium is derived from a progenitor cell in the distal buds of the developing lung. These "bud tip progenitors" are regulated by reciprocal signaling with surrounding mesenchyme; however, mesenchymal heterogeneity and function in the developing human lung are poorly understood. We interrogated single-cell RNA sequencing data from multiple human lung specimens and identified a mesenchymal cell population present during development that is highly enriched for expression of the WNT agonist RSPO2, and we found that the adjacent bud tip progenitors are enriched for the RSPO2 receptor LGR5. Functional experiments using organoid models, explant cultures, and FACS-isolated RSPO2+ mesenchyme show that RSPO2 is a critical niche cue that potentiates WNT signaling in bud tip progenitors to support their maintenance and multipotency.
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Affiliation(s)
- Renee F C Hein
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joshua H Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tristan Frum
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ansley S Conchola
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alexis S Fine
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alyssa J Miller
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Emmanuelle Szenker-Ravi
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Singapore 138648, Singapore
| | - Kelley S Yan
- Columbia Center for Human Development, Columbia Stem Cell Initiative, Departments of Medicine and Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Bruno Reversade
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Singapore 138648, Singapore; Laboratory of Human Genetics & Therapeutics, Institute of Molecular and Cell Biology (IMCB), A∗STAR, Singapore; Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA.
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14
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In situ hybridization assay for circular RNA visualization based on padlock probe and rolling circle amplification. Biochem Biophys Res Commun 2022; 610:30-34. [DOI: 10.1016/j.bbrc.2022.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 04/08/2022] [Indexed: 11/21/2022]
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15
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Erben L, Welday JP, Cronin ME, Murphy R, Skirzewski M, Vullhorst D, Carroll SL, Buonanno A. Developmental, neurochemical, and behavioral analyses of ErbB4 Cyt-1 knockout mice. J Neurochem 2022; 161:435-452. [PMID: 35523590 PMCID: PMC9149141 DOI: 10.1111/jnc.15612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 01/26/2023]
Abstract
Neuregulins (NRGs) and their cognate neuronal receptor ERBB4, which is expressed in GABAergic and dopaminergic neurons, regulate numerous behaviors in rodents and have been identified as schizophrenia at-risk genes. ErbB4 transcripts are alternatively spliced to generate isoforms that either include (Cyt-1) or exclude (Cyt-2) exon 26, which encodes a cytoplasmic domain that imparts ErbB4 receptors the ability to signal via the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) pathway. Although ErbB4 Cyt-1/2 isoforms have been studied in transfected cultured cells, their functions in vivo remain unknown. Here, we generated ErbB4-floxed (ErbB4-Cyt1fl/fl ) mice to investigate the effects of germline (constitutive) and conditional (acute) deletions of the Cyt-1 exon. Overall receptor mRNA levels remain unchanged in germline ErbB4 Cyt-1 knockouts (Cyt-1 KOs), with all transcripts encoding Cyt-2 variants. In contrast to mice lacking all ErbB4 receptor function, GABAergic interneuron migration and number are unaltered in Cyt-1 KOs. However, basal extracellular dopamine (DA) levels in the medial prefrontal cortex are increased in Cyt-1 heterozygotes. Despite these neurochemical changes, Cyt-1 heterozygous and homozygous mice do not manifest behavioral abnormalities previously reported to be altered in ErbB4 null mice. To address the possibility that Cyt-2 variants compensate for the lack of Cyt-1 during development, we microinjected an adeno-associated virus expressing Cre-recombinase (AAV-Cre) into the DA-rich ventral tegmental area of adult ErbB4-Cyt1fl/fl mice to acutely target exon 26. These conditional Cyt-1 KOs were found to exhibit behavioral abnormalities in the elevated plus maze and startle response, consistent with the idea that late exon 26 ablations may circumvent compensation by Cyt-2 variants. Taken together, our observations indicate that ErbB4 Cyt-1 function in vivo is important for DA balance and behaviors in adults.
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Affiliation(s)
- Larissa Erben
- Section on Molecular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Porter Neuroscience Research Center, Bethesda, Maryland, USA
| | - Jacqueline P Welday
- Section on Molecular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Porter Neuroscience Research Center, Bethesda, Maryland, USA
| | - Marie E Cronin
- Section on Molecular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Porter Neuroscience Research Center, Bethesda, Maryland, USA
| | - Ricardo Murphy
- Section on Molecular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Porter Neuroscience Research Center, Bethesda, Maryland, USA
| | - Miguel Skirzewski
- Section on Molecular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Porter Neuroscience Research Center, Bethesda, Maryland, USA
| | - Detlef Vullhorst
- Section on Molecular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Porter Neuroscience Research Center, Bethesda, Maryland, USA
| | - Steven L Carroll
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Andres Buonanno
- Section on Molecular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Porter Neuroscience Research Center, Bethesda, Maryland, USA
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16
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D'Ambra E, Santini T, Vitiello E, D'Uva S, Silenzi V, Morlando M, Bozzoni I. Circ-Hdgfrp3 shuttles along neurites and is trapped in aggregates formed by ALS-associated mutant FUS. iScience 2021; 24:103504. [PMID: 34934923 DOI: 10.1016/j.isci.2021.103504] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 10/12/2021] [Accepted: 11/21/2021] [Indexed: 12/17/2022] Open
Abstract
CircRNAs belong to a family of RNA molecules which are conserved in evolution, have tissue-specific expression, and are abundant in neuronal cells. Here, we define several features of circ-Hdgfrp3 and describe interesting alterations occurring in motor neurons (MNs) carrying ALS-associated FUS mutations. Through a highly sensitive in situ approach we describe that circ-Hdgfrp3 traffics along neurites, while upon oxidative stress it is retained in the perinuclear region. While in wild-type stressed MNs, circ-Hdgfrp3 localizes in stress granules (SGs), in MNs carrying mutant FUS, a higher proportion of circ-Hdgfrp3 was trapped into cytoplasmic aggregates. Upon stress removal, circ-Hdgfrp3 was easily freed from SGs whereas it was less efficiently released from FUS-aggregates. We found that the human circ-Hdgfrp3 counterpart was also similarly associated to mutant FUS-aggregates in stressed neuronal cells. Overall, the alteration of circ-Hdgfrp3 trafficking adds a further layer of complexity to the role of FUS-aggregates in ALS disease.
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Affiliation(s)
- Eleonora D'Ambra
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, Rome, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, Rome, Italy
| | - Erika Vitiello
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Center for Human Technology@ Istituto Italiano di Tecnologia, Genova, Italy
| | - Sara D'Uva
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Valentina Silenzi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, Rome, Italy
| | - Mariangela Morlando
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Perugia, Italy
| | - Irene Bozzoni
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, Rome, Italy
- Center for Human Technology@ Istituto Italiano di Tecnologia, Genova, Italy
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17
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Moore AM, Lohr DB, Coolen LM, Lehman MN. Prenatal Androgen Exposure Alters KNDy Neurons and Their Afferent Network in a Model of Polycystic Ovarian Syndrome. Endocrinology 2021; 162:bqab158. [PMID: 34346492 PMCID: PMC8402932 DOI: 10.1210/endocr/bqab158] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Indexed: 02/08/2023]
Abstract
Polycystic ovarian syndrome (PCOS), the most common endocrinopathy affecting women worldwide, is characterized by elevated luteinizing hormone (LH) pulse frequency due to the impaired suppression of gonadotrophin-releasing hormone (GnRH) release by steroid hormone negative feedback. Although neurons that co-express kisspeptin, neurokinin B, and dynorphin (KNDy cells) were recently defined as the GnRH/LH pulse generator, little is understood about their role in the pathogenesis of PCOS. We used a prenatal androgen-treated (PNA) mouse model of PCOS to determine whether changes in KNDy neurons or their afferent network underlie altered negative feedback. First, we identified elevated androgen receptor gene expression in KNDy cells of PNA mice, whereas progesterone receptor and dynorphin gene expression was significantly reduced, suggesting elevated androgens in PCOS disrupt progesterone negative feedback via direct actions upon KNDy cells. Second, we discovered GABAergic and glutamatergic synaptic input to KNDy neurons was reduced in PNA mice. Retrograde monosynaptic tract-tracing revealed a dramatic reduction in input originates from sexually dimorphic afferents in the preoptic area, anteroventral periventricular nucleus, anterior hypothalamic area and lateral hypothalamus. These results reveal 2 sites of neuronal alterations potentially responsible for defects in negative feedback in PCOS: changes in gene expression within KNDy neurons, and changes in synaptic inputs from steroid hormone-responsive hypothalamic regions. How each of these changes contribute to the neuroendocrine phenotype seen in in PCOS, and the role of specific sets of upstream KNDy afferents in the process, remains to be determined.
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Affiliation(s)
- Aleisha M Moore
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
- Brain Health Research Institute, Kent State University, Kent, OH 44242, USA
| | - Dayanara B Lohr
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
- Brain Health Research Institute, Kent State University, Kent, OH 44242, USA
| | - Lique M Coolen
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
- Brain Health Research Institute, Kent State University, Kent, OH 44242, USA
| | - Michael N Lehman
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
- Brain Health Research Institute, Kent State University, Kent, OH 44242, USA
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18
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Takahashi Y, Maynard KR, Tippani M, Jaffe AE, Martinowich K, Kleinman JE, Weinberger DR, Hyde TM. Single molecule in situ hybridization reveals distinct localizations of schizophrenia risk-related transcripts SNX19 and AS3MT in human brain. Mol Psychiatry 2021; 26:3536-3547. [PMID: 33649454 DOI: 10.1038/s41380-021-01046-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/20/2021] [Accepted: 02/02/2021] [Indexed: 11/09/2022]
Abstract
Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) associated with schizophrenia risk. Integration of RNA-sequencing data from postmortem human brains with these risk SNPs identified transcripts associated with increased schizophrenia susceptibility, including a class of exon 9-spliced isoforms of Sorting nexin-19 (SNX19d9) and an isoform of Arsenic methyltransferase (AS3MT) splicing out exons 2 and 3 (AS3MTd2d3). However, the biological function of these transcript variants is unclear. Defining the cell types where these risk transcripts are dominantly expressed is an important step to understand function, in prioritizing specific cell types and/or neural pathways in subsequent studies. To identify the cell type-specific localization of SNX19 and AS3MT in the human dorsolateral prefrontal cortex (DLPFC), we used single-molecule in situ hybridization techniques combined with automated quantification and machine learning approaches to analyze 10 postmortem brains of neurotypical individuals. These analyses revealed that both pan-SNX19 and pan-AS3MT were more highly expressed in neurons than non-neurons in layers II/III and VI of DLPFC. Furthermore, pan-SNX19 was preferentially expressed in glutamatergic neurons, while pan-AS3MT was preferentially expressed in GABAergic neurons. Finally, we utilized duplex BaseScope technology, to delineate the localization of SNX19d9 and AS3MTd2d3 splice variants, revealing consistent trends in spatial gene expression among pan-transcripts and schizophrenia risk-related transcript variants. These findings demonstrate that schizophrenia risk transcripts have distinct localization patterns in the healthy human brains, and suggest that SNX19 transcripts might disrupt the normal function of glutamatergic neurons, while AS3MT may lead to disturbances in the GABAergic system in the pathophysiology of schizophrenia.
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Affiliation(s)
- Yoichiro Takahashi
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Legal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Keri Martinowich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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19
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Beck J, Turnquist C, Horikawa I, Harris C. Targeting cellular senescence in cancer and aging: roles of p53 and its isoforms. Carcinogenesis 2021; 41:1017-1029. [PMID: 32619002 DOI: 10.1093/carcin/bgaa071] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/11/2022] Open
Abstract
Cellular senescence and the associated secretory phenotype (SASP) promote disease in the aged population. Targeting senescent cells by means of removal, modulation of SASP or through cellular reprogramming represents a novel therapeutic avenue for treating cancer- and age-related diseases such as neurodegeneration, pulmonary fibrosis and renal disease. Cellular senescence is partly regulated by the TP53 gene, a critical tumor suppressor gene which encodes 12 or more p53 protein isoforms. This review marks a significant milestone of 40 years of Carcinogenesis publication history and p53 research and 15 years of p53 isoform research. The p53 isoforms are produced through initiation at alternative transcriptional and translational start sites and alternative mRNA splicing. These truncated p53 isoform proteins are endogenously expressed in normal human cells and maintain important functional roles, including modulation of full-length p53-mediated cellular senescence, apoptosis and DNA repair. In this review, we discuss the mechanisms and functions of cellular senescence and SASP in health and disease, the regulation of cellular senescence by p53 isoforms, and the therapeutic potential of targeting cellular senescence to treat cancer- and age-associated diseases.
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Affiliation(s)
- Jessica Beck
- Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
| | - Casmir Turnquist
- Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,University of Oxford Medical School, John Radcliffe Hospital, Oxford, UK
| | - Izumi Horikawa
- Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Curtis Harris
- Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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20
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Marchisella F, Creutzberg KC, Begni V, Sanson A, Wearick-Silva LE, Tractenberg SG, Orso R, Kestering-Ferreira É, Grassi-Oliveira R, Riva MA. Exposure to Prenatal Stress Is Associated With an Excitatory/Inhibitory Imbalance in Rat Prefrontal Cortex and Amygdala and an Increased Risk for Emotional Dysregulation. Front Cell Dev Biol 2021; 9:653384. [PMID: 34141707 PMCID: PMC8204112 DOI: 10.3389/fcell.2021.653384] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/07/2021] [Indexed: 12/17/2022] Open
Abstract
Epidemiological studies have shown that environmental insults and maternal stress during pregnancy increase the risk of several psychiatric disorders in the offspring. Converging lines of evidence from humans, as well as from rodent models, suggest that prenatal stress (PNS) interferes with fetal development, ultimately determining changes in brain maturation and function that may lead to the onset of neuropsychiatric disorders. From a molecular standpoint, transcriptional alterations are thought to play a major role in this context and may contribute to the behavioral phenotype by shifting the expression of genes related to excitatory and inhibitory (E/I) transmission balance. Nevertheless, the exact neurophysiological mechanisms underlying the enhanced vulnerability to psychopathology following PNS exposure are not well understood. In the present study, we used a model of maternal stress in rats to investigate the distal effects of PNS on the expression of genes related to glutamatergic and GABAergic neurotransmissions. We inspected two critical brain regions involved in emotion regulation, namely, the prefrontal cortex (PFC) and the amygdala (AMY), which we show to relate with the mild behavioral effects detected in adult rat offspring. We observed that PNS exposure promotes E/I imbalance in the PFC of adult males only, by dysregulating the expression of glutamatergic-related genes. Moreover, such an effect is accompanied by increased expression of the activity-dependent synaptic modulator gene Npas4 specifically in the PFC parvalbumin (PV)-positive interneurons, suggesting an altered regulation of synapse formation promoting higher PV-dependent inhibitory transmission and increased overall circuit inhibition in the PFC of males. In the AMY, PNS more evidently affects the transcription of GABAergic-related genes, shifting the balance toward inhibition. Collectively, our findings suggest that the E/I dysregulation of the PFC-to-AMY transmission may be a long-term signature of PNS and may contribute to increase the risk for mood disorder upon further stress.
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Affiliation(s)
- Francesca Marchisella
- Laboratory of Psychopharmacology and Molecular Psychiatry, Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Kerstin Camile Creutzberg
- Laboratory of Psychopharmacology and Molecular Psychiatry, Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Veronica Begni
- Laboratory of Psychopharmacology and Molecular Psychiatry, Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Alice Sanson
- Laboratory of Psychopharmacology and Molecular Psychiatry, Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Luis Eduardo Wearick-Silva
- Developmental Cognitive Neuroscience Lab, Brain Institute, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Saulo Gantes Tractenberg
- Developmental Cognitive Neuroscience Lab, Brain Institute, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Rodrigo Orso
- Developmental Cognitive Neuroscience Lab, Brain Institute, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Érika Kestering-Ferreira
- Developmental Cognitive Neuroscience Lab, Brain Institute, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Rodrigo Grassi-Oliveira
- Developmental Cognitive Neuroscience Lab, Brain Institute, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil.,Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Marco Andrea Riva
- Laboratory of Psychopharmacology and Molecular Psychiatry, Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy.,Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli Brescia, Brescia, Italy
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21
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Mishra A, Lai GC, Yao LJ, Aung TT, Shental N, Rotter-Maskowitz A, Shepherdson E, Singh GSN, Pai R, Shanti A, Wong RMM, Lee A, Khyriem C, Dutertre CA, Chakarov S, Srinivasan KG, Shadan NB, Zhang XM, Khalilnezhad S, Cottier F, Tan ASM, Low G, Chen P, Fan Y, Hor PX, Lee AKM, Choolani M, Vermijlen D, Sharma A, Fuks G, Straussman R, Pavelka N, Malleret B, McGovern N, Albani S, Chan JKY, Ginhoux F. Microbial exposure during early human development primes fetal immune cells. Cell 2021; 184:3394-3409.e20. [PMID: 34077752 PMCID: PMC8240556 DOI: 10.1016/j.cell.2021.04.039] [Citation(s) in RCA: 144] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/09/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023]
Abstract
The human fetal immune system begins to develop early during gestation; however, factors responsible for fetal immune-priming remain elusive. We explored potential exposure to microbial agents in utero and their contribution toward activation of memory T cells in fetal tissues. We profiled microbes across fetal organs using 16S rRNA gene sequencing and detected low but consistent microbial signal in fetal gut, skin, placenta, and lungs in the 2nd trimester of gestation. We identified several live bacterial strains including Staphylococcus and Lactobacillus in fetal tissues, which induced in vitro activation of memory T cells in fetal mesenteric lymph node, supporting the role of microbial exposure in fetal immune-priming. Finally, using SEM and RNA-ISH, we visualized discrete localization of bacteria-like structures and eubacterial-RNA within 14th weeks fetal gut lumen. These findings indicate selective presence of live microbes in fetal organs during the 2nd trimester of gestation and have broader implications toward the establishment of immune competency and priming before birth.
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Affiliation(s)
- Archita Mishra
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Ghee Chuan Lai
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Leong Jing Yao
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore
| | - Thet Tun Aung
- Department of Microbiology and Immunology, Immunology Translational Research Programme, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117597, Singapore
| | - Noam Shental
- Department of Mathematics and Computer Science, Open University of Israel, Ra'anana 4353701, Israel
| | - Aviva Rotter-Maskowitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Edwin Shepherdson
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Gurmit Singh Naranjan Singh
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Rhea Pai
- Genome Institute of Singapore (GIS), A(∗)STAR, 60 Biopolis Street, Singapore 138672, Singapore
| | - Adhika Shanti
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Regina Men Men Wong
- Genome Institute of Singapore (GIS), A(∗)STAR, 60 Biopolis Street, Singapore 138672, Singapore
| | - Andrea Lee
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore
| | - Costerwell Khyriem
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Charles Antoine Dutertre
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore; Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore; Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Svetoslav Chakarov
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - K G Srinivasan
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Nurhidaya Binte Shadan
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Xiao-Meng Zhang
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Shabnam Khalilnezhad
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Fabien Cottier
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Alrina Shin Min Tan
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Gillian Low
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Phyllis Chen
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore
| | - Yiping Fan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore; Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Pei Xiang Hor
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Avery Khoo May Lee
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Mahesh Choolani
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block, 1E Kent Ridge Road, Singapore 119228, Singpore
| | - David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics, Institute for Medical Immunology, ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Ankur Sharma
- Genome Institute of Singapore (GIS), A(∗)STAR, 60 Biopolis Street, Singapore 138672, Singapore; Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, WA 6009, Australia; Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Norman Pavelka
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Benoit Malleret
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore; Department of Microbiology and Immunology, Immunology Translational Research Programme, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117597, Singapore
| | - Naomi McGovern
- Department of Pathology and Centre for Trophoblast Research, Tennis Court Road, Cambridge CB2 1QP, UK.
| | - Salvatore Albani
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore.
| | - Jerry Kok Yen Chan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore; Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; OBGYN-Academic Clinical Program, Duke-NUS, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore 119077, Singapore.
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore; Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China.
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22
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Kitamura Y, Uranishi K, Hirasaki M, Nishimoto M, Suzuki A, Okuda A. Identification of germ cell-specific Mga variant mRNA that promotes meiosis via impediment of a non-canonical PRC1. Sci Rep 2021; 11:9737. [PMID: 33958653 PMCID: PMC8102552 DOI: 10.1038/s41598-021-89123-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/19/2021] [Indexed: 02/03/2023] Open
Abstract
A non-canonical PRC1 (PRC1.6) prevents precocious meiotic onset. Germ cells alleviate its negative effect by reducing their amount of MAX, a component of PRC1.6, as a prerequisite for their bona fide meiosis. Here, we found that germ cells produced Mga variant mRNA bearing a premature termination codon (PTC) during meiosis as an additional mechanism to impede the function of PRC1.6. The variant mRNA encodes an anomalous MGA protein that lacks the bHLHZ domain and thus functions as a dominant negative regulator of PRC1.6. Notwithstanding the presence of PTC, the Mga variant mRNA are rather stably present in spermatocytes and spermatids due to their intrinsic inefficient background of nonsense-mediated mRNA decay. Thus, our data indicate that meiosis is controlled in a multi-layered manner in which both MAX and MGA, which constitute the core of PRC1.6, are at least used as targets to deteriorate the integrity of the complex to ensure progression of meiosis.
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Affiliation(s)
- Yuka Kitamura
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan
| | - Kousuke Uranishi
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan
| | - Masataka Hirasaki
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan
- Department of Clinical Cancer Genomics, International Medical Center, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan
| | - Masazumi Nishimoto
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan
- Biomedical Research Center, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan
| | - Ayumu Suzuki
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan.
| | - Akihiko Okuda
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan.
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23
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Seow JJW, Pai R, Mishra A, Shepherdson E, Lim TKH, Goh BKP, Chan JKY, Chow PKH, Ginhoux F, DasGupta R, Sharma A. Single-Cell RNA-seq Reveals Angiotensin-Converting Enzyme 2 and Transmembrane Serine Protease 2 Expression in TROP2 + Liver Progenitor Cells: Implications in Coronavirus Disease 2019-Associated Liver Dysfunction. Front Med (Lausanne) 2021; 8:603374. [PMID: 33968947 PMCID: PMC8100026 DOI: 10.3389/fmed.2021.603374] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 03/01/2021] [Indexed: 12/15/2022] Open
Abstract
The recent coronavirus disease 2019 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2. COVID-19 was first reported in China (December 2019) and is now prevalent across the globe. Entry of severe acute respiratory syndrome coronavirus 2 into mammalian cells requires the binding of viral Spike (S) proteins to the angiotensin-converting enzyme 2 receptor. Once entered, the S protein is primed by a specialized serine protease, transmembrane serine protease 2 in the host cell. Importantly, besides the respiratory symptoms that are consistent with other common respiratory virus infections when patients become viremic, a significant number of COVID-19 patients also develop liver comorbidities. We explored whether a specific target cell-type in the mammalian liver could be implicated in disease pathophysiology other than the general deleterious response to cytokine storms. Here, we used single-cell RNA-seq to survey the human liver and identified potentially implicated liver cell-type for viral ingress. We analyzed ~300,000 single cells across five different (i.e., human fetal, healthy, cirrhotic, tumor, and adjacent normal) liver tissue types. This study reports on the co-expression of angiotensin-converting enzyme 2 and transmembrane serine protease 2 in a TROP2+ liver progenitor population. Importantly, we detected enrichment of this cell population in the cirrhotic liver when compared with tumor tissue. These results indicated that in COVID-19-associated liver dysfunction and cell death, a viral infection of TROP2+ progenitors in the liver might significantly impair liver regeneration in patients with liver cirrhosis.
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Affiliation(s)
- Justine Jia Wen Seow
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Rhea Pai
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Archita Mishra
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Edwin Shepherdson
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Tony Kiat Hon Lim
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Brian K. P. Goh
- Department of Hepato-Pancreato-Biliary and Transplant Surgery, Singapore General Hospital, Singapore, Singapore
| | - Jerry K. Y. Chan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Pierce K. H. Chow
- Division of Surgical Oncology, National Cancer Centre, Singapore, Singapore
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai, China
- Translational Immunology Institute, SingHealth Duke-National University of Singapore Academic Medical Centre, Singapore, Singapore
| | - Ramanuj DasGupta
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Ankur Sharma
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre and Centre for Medical Research, Nedlands, WA, Australia
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
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24
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TRPM3 Channels Play Roles in Heat Hypersensitivity and Spontaneous Pain after Nerve Injury. J Neurosci 2021; 41:2457-2474. [PMID: 33478988 DOI: 10.1523/jneurosci.1551-20.2020] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/11/2020] [Accepted: 11/07/2020] [Indexed: 12/11/2022] Open
Abstract
Transient receptor potential melastatin 3 (TRPM3) is a heat-activated ion channel in primary sensory neurons of the dorsal root ganglia (DRGs). Pharmacological and genetic studies implicated TRPM3 in various pain modalities, but TRPM3 inhibitors were not validated in TRPM3-/- mice. Here we tested two inhibitors of TRPM3 in male and female wild-type and TRPM3-/- mice in nerve injury-induced neuropathic pain. We found that intraperitoneal injection of either isosakuranetin or primidone reduced heat hypersensitivity induced by chronic constriction injury (CCI) of the sciatic nerve in wild-type, but not in TRPM3-/- mice. Primidone was also effective when injected locally in the hindpaw or intrathecally. Consistently, intrathecal injection of the TRPM3 agonist CIM0216 reduced paw withdrawal latency to radiant heat in wild-type, but not in TRPM3-/- mice. Intraperitoneal injection of 2 mg/kg, but not 0.5 mg/kg isosakuranetin, inhibited cold and mechanical hypersensitivity in CCI, both in wild-type and TRPM3-/- mice, indicating a dose-dependent off-target effect. Primidone had no effect on cold sensitivity, and only a marginal effect on mechanical hypersensitivity. Genetic deletion or inhibitors of TRPM3 reduced the increase in the levels of the early genes c-Fos and pERK in the spinal cord and DRGs in CCI mice, suggesting spontaneous activity of the channel. Intraperitoneal isosakuranetin also inhibited spontaneous pain related behavior in CCI in the conditioned place preference assay, and this effect was eliminated in TRPM3-/- mice. Overall, our data indicate a role of TRPM3 in heat hypersensitivity and in spontaneous pain after nerve injury.SIGNIFICANCE STATEMENT Neuropathic pain is a major unsolved medical problem. The heat-activated TRPM3 ion channel is a potential target for novel pain medications, but the pain modalities in which it plays a role are not clear. Here we used a combination of genetic and pharmacological tools to assess the role of this channel in spontaneous pain, heat, cold, and mechanical hypersensitivity in a nerve injury model of neuropathic pain in mice. Our findings indicate a role for TRPM3 in heat hyperalgesia, and spontaneous pain, but not in cold and mechanical hypersensitivity. We also find that not only TRPM3 located in the peripheral nerve termini, but also TRPM3 in the spinal cord or proximal segments of DRG neurons are important for heat hypersensitivity.
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25
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Zeng T, Tang Z, Liang L, Suo D, Li L, Li J, Yuan Y, Guan XY, Li Y. PDSS2-Del2, a new variant of PDSS2, promotes tumor cell metastasis and angiogenesis in hepatocellular carcinoma via activating NF-κB. Mol Oncol 2020; 14:3184-3197. [PMID: 33064899 PMCID: PMC7718950 DOI: 10.1002/1878-0261.12826] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 09/08/2020] [Accepted: 09/25/2020] [Indexed: 12/28/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is among the leading causes of cancer‐related mortality worldwide. Our previous study identified a novel alternative splicing variant of prenyl diphosphate synthase subunit 2 (PDSS2) in HCC characterized by a deletion of exon 2, named PDSS2‐Del2, which is devoid of the tumor‐suppressive function of full‐length PDSS2 (PDSS2‐FL). To better understand the clinical significance of PDSS2‐Del2, we performed a BaseScope™ assay on an HCC tissue microarray and found that positive staining for PDSS2‐Del2 predicted a worse overall survival in patients with HCC (P = 0.02). PDSS2‐Del2 levels correlated significantly with microvessel counts in HCC tumor tissues. Importantly, PDSS2‐Del2 overexpression functionally promoted HCC metastasis, as demonstrated by in vitro and in vivo migration assays. In vivo assays also demonstrated that PDSS2‐Del2 increased angiogenesis in xenografts. Furthermore, we discovered that elevated PDSS2‐Del2 expression in HCC tumor cells decreased fumarate levels and activated the canonical nuclear factor‐κB pathway. The epithelial‐to‐mesenchymal transition (EMT) and WNT/β‐catenin signaling pathways were also activated by overexpression. Dimethyl fumarate (DMF), a fumaric acid ester, effectively reduced the metastasis induced by PDSS2‐Del2 as observed with in vivo spleen‐liver metastasis animal experiments. DMF is a prescribed oral therapy for multiple sclerosis and it might be a potential treatment for metastasis of patients with HCC. Early clinical trials are needed to validate its potential in this context.
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Affiliation(s)
- Tingting Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhi Tang
- School of Public Health, Guangdong Medical University, Dongguan, China
| | - Lili Liang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Daqin Suo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lei Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Clinical Oncology, The University of Hong Kong, China
| | - Jiangchao Li
- Vascular Biology Research Institute, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yunfei Yuan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xin-Yuan Guan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Clinical Oncology, The University of Hong Kong, China
| | - Yan Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
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26
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Sharma A, Seow JJW, Dutertre CA, Pai R, Blériot C, Mishra A, Wong RMM, Singh GSN, Sudhagar S, Khalilnezhad S, Erdal S, Teo HM, Khalilnezhad A, Chakarov S, Lim TKH, Fui ACY, Chieh AKW, Chung CP, Bonney GK, Goh BKP, Chan JK, Chow PK, Ginhoux F, DasGupta R. Onco-fetal Reprogramming of Endothelial Cells Drives Immunosuppressive Macrophages in Hepatocellular Carcinoma. Cell 2020; 183:377-394.e21. [DOI: 10.1016/j.cell.2020.08.040] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 04/29/2020] [Accepted: 08/21/2020] [Indexed: 12/19/2022]
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27
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CircRNAs in lung cancer - Biogenesis, function and clinical implication. Cancer Lett 2020; 492:106-115. [PMID: 32860847 DOI: 10.1016/j.canlet.2020.08.013] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/26/2020] [Accepted: 08/12/2020] [Indexed: 02/08/2023]
Abstract
Lung cancer is the leading cause of malignancy-related incidence and mortality worldwide. Molecular mechanisms underlying tumorigenesis and development of lung cancer are still warranted to be elucidated. Previous studies have shown that non-coding RNAs are related to the tumorigenesis and progression of various cancers. However, the expression patterns and clinical implications of circRNAs in lung cancer remain obscure. CircRNAs are a special class of non-coding RNAs with stable covalently closed circular structures, high abundance and tissue/cell/development-specific expression patterns. Thus, circRNAs are a new frontier in lung cancer research. Therefore, in this review, we elucidated the biological function and mechanism of circRNAs, as well as the role of aberrant expressed circRNAs in proliferation, invasion, drug resistance and tumor microenvironment. Furthermore, we discussed that circRNAs may serve as potential clinical biomarkers for the diagnosis, prognosis and treatment of lung cancer.
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28
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Di Timoteo G, Rossi F, Bozzoni I. Circular RNAs in cell differentiation and development. Development 2020; 147:147/16/dev182725. [PMID: 32839270 DOI: 10.1242/dev.182725] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In recent years, circular RNAs (circRNAs) - a novel class of RNA molecules characterized by their covalently closed circular structure - have emerged as a complex family of eukaryotic transcripts with important biological features. Besides their peculiar structure, which makes them particularly stable molecules, they have attracted much interest because their expression is strongly tissue and cell specific. Moreover, many circRNAs are conserved across eukaryotes, localized in particular subcellular compartments, and can play disparate molecular functions. The discovery of circRNAs has therefore added not only another layer of gene expression regulation but also an additional degree of complexity to our understanding of the structure, function and evolution of eukaryotic genomes. In this Review, we summarize current knowledge of circRNAs and discuss the possible functions of circRNAs in cell differentiation and development.
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Affiliation(s)
- Gaia Di Timoteo
- Department of Biology and Biotechnology Charles Darwin, Sapienza, University of Rome, Rome, Italy
| | - Francesca Rossi
- Department of Biology and Biotechnology Charles Darwin, Sapienza, University of Rome, Rome, Italy
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza, University of Rome, Rome, Italy .,Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
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29
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Eskra JN, Rabizadeh D, Mangold L, Fabian E, Brennen WN, Yeater DB, Pienta KJ, Partin AW, Isaacs WB, Pavlovich CP, Luo J. A novel method for detection of exfoliated prostate cancer cells in urine by RNA in situ hybridization. Prostate Cancer Prostatic Dis 2020; 24:220-232. [PMID: 32820256 DOI: 10.1038/s41391-020-00272-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 11/09/2022]
Abstract
BACKGROUND In the current study, we explore the feasibility of detecting exfoliated prostate cancer cells in urine using an RNA in situ hybridization (RISH) assay. We hypothesized that robust and specific labeling of prostate cancer cells could be achieved in post-digital rectal examination (DRE) urine samples using RISH. METHODS We focused on method development, optimization, and analytical evaluation of RISH-based detection of prostate cancer in urine. We optimized a sample collection, processing, and target detection workflow for urine cytology specimens in conjunction with RNA target detection by RISH. We screened a panel of 11 prostate-specific RNA targets, and selected NKX3-1 and PRAC1 as markers for cells of prostate origin and PCA3 as a marker of prostate malignancy. Following analytical validation of a multiplexed NKX3-1/PRAC1/PCA3 assay, we evaluated whether prostate cancer cells can be detected in a pilot cohort of 19 post-DRE specimens obtained from men diagnosed with prostate cancer. RESULTS Using cytology specimens prepared from spiked urine samples, we established the analytical validity of the RISH assay for detection and visualization of prostate cells in urine. Cells of prostate origin could be readily and specifically identified and separated into benign and malignant cell populations based on the multiplex test that consisted of markers specific for prostate cells (NKX3-1, PRAC1) and prostate cancer cells (PCA3). Upon evaluation of post-DRE urine from a pilot cohort of prostate cancer patients, we identified 11 samples in which prostate cells were present, 6 of which were also positive for prostate cancer cells. CONCLUSIONS Multiplex RISH enables the direct visualization and molecular characterization of individual exfoliated prostate cells in urine. This proof-of-principle study provides evidence supporting the application of RISH as a potential noninvasive tool for prostate cancer detection.
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Affiliation(s)
- Jillian N Eskra
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel Rabizadeh
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leslie Mangold
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Fabian
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - W Nathaniel Brennen
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David B Yeater
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth J Pienta
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alan W Partin
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William B Isaacs
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christian P Pavlovich
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jun Luo
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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30
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Gallo CM, Ho A, Beffert U. ApoER2: Functional Tuning Through Splicing. Front Mol Neurosci 2020; 13:144. [PMID: 32848602 PMCID: PMC7410921 DOI: 10.3389/fnmol.2020.00144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/13/2020] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing occurs in over 95% of protein-coding genes and contributes to the diversity of the human proteome. Apolipoprotein E receptor 2 (apoER2) is a critical modulator of neuronal development and synaptic plasticity in the brain and is enriched in cassette exon splicing events, in which functional exons are excluded from the final transcript. These alternative splicing events affect apoER2 function, as individual apoER2 exons tend to encode distinct protein functional domains. Although several apoER2 splice variants have been characterized, much work remains to understand how apoER2 splicing events modulate distinct apoER2 activities, including ligand binding specificity, synapse formation and plasticity. Additionally, little is known about how apoER2 splicing events are regulated. Often, alternative splicing events are regulated through the combinatorial action of RNA-binding proteins and other epigenetic mechanisms, however, the regulatory pathways corresponding to each specific exon are unknown in most cases. In this mini-review, we describe the structure of apoER2, highlight the unique functions of known isoforms, discuss what is currently known about the regulation of apoER2 splicing by RNA-binding proteins and pose new questions that will further our understanding of apoER2 splicing complexity.
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Affiliation(s)
- Christina M Gallo
- Department of Biology, Boston University, Boston, MA, United States.,Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States
| | - Angela Ho
- Department of Biology, Boston University, Boston, MA, United States.,Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States
| | - Uwe Beffert
- Department of Biology, Boston University, Boston, MA, United States
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31
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Ray TA, Cochran K, Kozlowski C, Wang J, Alexander G, Cady MA, Spencer WJ, Ruzycki PA, Clark BS, Laeremans A, He MX, Wang X, Park E, Hao Y, Iannaccone A, Hu G, Fedrigo O, Skiba NP, Arshavsky VY, Kay JN. Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease. Nat Commun 2020; 11:3328. [PMID: 32620864 PMCID: PMC7335077 DOI: 10.1038/s41467-020-17009-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/30/2020] [Indexed: 02/08/2023] Open
Abstract
Genes encoding cell-surface proteins control nervous system development and are implicated in neurological disorders. These genes produce alternative mRNA isoforms which remain poorly characterized, impeding understanding of how disease-associated mutations cause pathology. Here we introduce a strategy to define complete portfolios of full-length isoforms encoded by individual genes. Applying this approach to neural cell-surface molecules, we identify thousands of unannotated isoforms expressed in retina and brain. By mass spectrometry we confirm expression of newly-discovered proteins on the cell surface in vivo. Remarkably, we discover that the major isoform of a retinal degeneration gene, CRB1, was previously overlooked. This CRB1 isoform is the only one expressed by photoreceptors, the affected cells in CRB1 disease. Using mouse mutants, we identify a function for this isoform at photoreceptor-glial junctions and demonstrate that loss of this isoform accelerates photoreceptor death. Therefore, our isoform identification strategy enables discovery of new gene functions relevant to disease.
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Affiliation(s)
- Thomas A Ray
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kelly Cochran
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Chris Kozlowski
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jingjing Wang
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Graham Alexander
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27710, USA
| | | | | | - Philip A Ruzycki
- John F. Hardesty, M.D. Department of Ophthalmology and Visual Sciences, Washington University, St. Louis, MO, 63110, USA
| | - Brian S Clark
- John F. Hardesty, M.D. Department of Ophthalmology and Visual Sciences, Washington University, St. Louis, MO, 63110, USA
- Department of Developmental Biology, Washington University, St. Louis, MO, 63110, USA
| | | | - Ming-Xiao He
- Advanced Cell Diagnostics, Newark, CA, 94560, USA
| | | | - Emily Park
- Advanced Cell Diagnostics, Newark, CA, 94560, USA
| | - Ying Hao
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Alessandro Iannaccone
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Gary Hu
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Olivier Fedrigo
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27710, USA
- The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Nikolai P Skiba
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jeremy N Kay
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, 27710, USA.
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32
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Paterson C, Cumming B, Law AJ. Temporal Dynamics of the Neuregulin-ErbB Network in the Murine Prefrontal Cortex across the Lifespan. Cereb Cortex 2020; 30:3325-3339. [PMID: 31897479 DOI: 10.1093/cercor/bhz312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Neuregulin-ErbB signaling is essential for numerous functions in the developing, adult, and aging brain, particularly in the prefrontal cortex (PFC). Mouse models with disrupted Nrg and/or ErbB genes are relevant to psychiatric, developmental, and age-related disorders, displaying a range of abnormalities stemming from cortical circuitry impairment. Many of these models display nonoverlapping phenotypes dependent upon the gene target and timing of perturbation, suggesting that cortical expression of the Nrg-ErbB network undergoes temporal regulation across the lifespan. Here, we report a comprehensive temporal expression mapping study of the Nrg-ErbB signaling network in the mouse PFC across postnatal development through aging. We find that Nrg and ErbB genes display distinct expression profiles; moreover, splice isoforms of these genes are differentially expressed across the murine lifespan. We additionally find a developmental switch in ErbB4 splice isoform expression potentially mediated through coregulation of the lncRNA Miat expression. Our results are the first to comprehensively and quantitatively map the expression patterns of the Nrg-ErbB network in the mouse PFC across the postnatal lifespan and may help disentangle the pathway's involvement in normal cortical sequences of events across the lifespan, as well as shedding light on the pathophysiological mechanisms of abnormal Nrg-ErbB signaling in neurological disease.
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Affiliation(s)
- Clare Paterson
- Department of Psychiatry, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Brooke Cumming
- Department of Psychiatry, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Amanda J Law
- Department of Psychiatry, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA.,Department of Cell and Developmental Biology, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA.,Department of Medicine, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA
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33
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Gao C, Leng Y, Ma J, Rooke V, Rodriguez-Gonzalez S, Ramakrishnan C, Deisseroth K, Penzo MA. Two genetically, anatomically and functionally distinct cell types segregate across anteroposterior axis of paraventricular thalamus. Nat Neurosci 2020; 23:217-228. [PMID: 31932767 PMCID: PMC7007348 DOI: 10.1038/s41593-019-0572-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 12/06/2019] [Indexed: 12/16/2022]
Abstract
Unlike the sensory thalamus, studies on the functional organization of the midline and intralaminar nuclei are scarce, and this has hindered the establishment of conceptual models of the function of this brain region. We investigated the functional organization of the paraventricular nucleus of the thalamus (PVT), a midline thalamic structure that is increasingly being recognized as a critical node in the control of diverse processes such as arousal, stress, emotional memory and motivation, in mice. We identify two major classes of PVT neurons-termed type I and type II-that differ in terms of gene expression, anatomy and function. In addition, we demonstrate that type II neurons belong to a previously neglected class of PVT neurons that convey arousal-related information to corticothalamic neurons of the infralimbic cortex. Our results uncover the existence of an arousal-modulated thalamo-corticothalamic loop that links the PVT and the ventromedial prefrontal cortex.
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Affiliation(s)
- Claire Gao
- National Institute of Mental Health, Bethesda, MD, USA
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - Yan Leng
- National Institute of Mental Health, Bethesda, MD, USA
| | - Jun Ma
- National Institute of Mental Health, Bethesda, MD, USA
| | | | | | | | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Mario A Penzo
- National Institute of Mental Health, Bethesda, MD, USA.
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34
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Nielsen BS, Møller T, Kjems J. Automated One-Double-Z Pair BaseScope™ for CircRNA In Situ Hybridization. Methods Mol Biol 2020; 2148:379-388. [PMID: 32394395 DOI: 10.1007/978-1-0716-0623-0_24] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Circular RNAs (circRNAs) are single-stranded RNA, typically exons, connected head to tail by back-splicing. The functions of circRNAs include binding of microRNA, regulation of transcription, regulation of alternative splicing, and modulation of immune response. As for other RNA transcripts their levels vary during development and may also become deregulated during disease progression. Different from linear RNAs, the circRNAs are not susceptible to traditional exonuclease activity and therefore more stable in tissues and blood. This makes the circRNAs an attractive new group of potential biomarkers. Specific detection of circRNAs in situ is challenged by the need to discriminate bona fide circRNAs from the linear precursor forms and splice variants that contain largely overlapping sequences. Knowing the sequence around the splice junction site makes the branched DNA probe technology, BaseScope, suitable for selective detection of unique circRNAs. Here, we present the automated application of BaseScope with a one-double-Z pair probe set designed for the junction of circHIPK3.
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Affiliation(s)
| | - Trine Møller
- Molecular Histology, Bioneer A/S, Hørsholm, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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35
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Ravindranathan A, Diolaiti ME, Cimini BA, Stohr BA. In Situ Visualization of Telomere Length, Telomere Elongation, and TERT Expression in Single Cells. ACTA ACUST UNITED AC 2019; 85:e97. [PMID: 31763768 DOI: 10.1002/cpcb.97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Telomerase plays a critical role in cancer and aging by adding hexa-nucleotide repeats to the ends of telomeres and extending the cellular proliferative lifespan. The very low level of telomerase expression in most cell populations and the difficulty of detecting telomere elongation in single cells have limited the study of telomerase expression and function in individual cells of a heterogeneous population. The method described in this article combines single-molecule detection (RNAscope) of telomerase reverse transcriptase (TERT) with our previously described TSQ1 assay for in situ monitoring of telomere extension, thereby enabling detection of TERT expression, telomere length, and telomere elongation in single cells and providing a unique approach for studying the factors that regulate telomere elongation by telomerase. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: TSQ1 lentivirus production Basic Protocol 2: TSQ1 lentiviral infection and plating Basic Protocol 3: RNAscope analysis Basic Protocol 4: TSQ1 PNA-FISH detection.
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Affiliation(s)
- Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, California
| | - Morgan E Diolaiti
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | | | - Bradley A Stohr
- Department of Pathology, University of California, San Francisco, California
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36
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Kristensen LS, Andersen MS, Stagsted LVW, Ebbesen KK, Hansen TB, Kjems J. The biogenesis, biology and characterization of circular RNAs. Nat Rev Genet 2019; 20:675-691. [PMID: 31395983 DOI: 10.1038/s41576-019-0158-7] [Citation(s) in RCA: 2774] [Impact Index Per Article: 554.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2019] [Indexed: 02/06/2023]
Abstract
Circular RNAs (circRNAs) are covalently closed, endogenous biomolecules in eukaryotes with tissue-specific and cell-specific expression patterns, whose biogenesis is regulated by specific cis-acting elements and trans-acting factors. Some circRNAs are abundant and evolutionarily conserved, and many circRNAs exert important biological functions by acting as microRNA or protein inhibitors ('sponges'), by regulating protein function or by being translated themselves. Furthermore, circRNAs have been implicated in diseases such as diabetes mellitus, neurological disorders, cardiovascular diseases and cancer. Although the circular nature of these transcripts makes their detection, quantification and functional characterization challenging, recent advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of state-of-the-art approaches for their identification, and novel approaches to functional characterization are emerging.
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Affiliation(s)
- Lasse S Kristensen
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark.
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark.
| | - Maria S Andersen
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
| | - Lotte V W Stagsted
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark
| | - Karoline K Ebbesen
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
| | - Thomas B Hansen
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
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37
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Capponi S, Stöffler N, Irimia M, Van Schaik FMA, Ondik MM, Biniossek ML, Lehmann L, Mitschke J, Vermunt MW, Creyghton MP, Graybiel AM, Reinheckel T, Schilling O, Blencowe BJ, Crittenden JR, Timmers HTM. Neuronal-specific microexon splicing of TAF1 mRNA is directly regulated by SRRM4/nSR100. RNA Biol 2019; 17:62-74. [PMID: 31559909 PMCID: PMC6948980 DOI: 10.1080/15476286.2019.1667214] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Neuronal microexons represent the most highly conserved class of alternative splicing events and their timed expression shapes neuronal biology, including neuronal commitment and differentiation. The six-nt microexon 34ʹ is included in the neuronal form of TAF1 mRNA, which encodes the largest subunit of the basal transcription factor TFIID. In this study, we investigate the tissue distribution of TAF1-34ʹ mRNA and protein and the mechanism responsible for its neuronal-specific splicing. Using isoform-specific RNA probes and antibodies, we observe that canonical TAF1 and TAF1-34ʹ have different distributions in the brain, which distinguish proliferating from post-mitotic neurons. Knockdown and ectopic expression experiments demonstrate that the neuronal-specific splicing factor SRRM4/nSR100 promotes the inclusion of microexon 34ʹ into TAF1 mRNA, through the recognition of UGC sequences in the poly-pyrimidine tract upstream of the regulated microexon. These results show that SRRM4 regulates temporal and spatial expression of alternative TAF1 mRNAs to generate a neuronal-specific TFIID complex.
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Affiliation(s)
- Simona Capponi
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Nadja Stöffler
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Manuel Irimia
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Frederik M A Van Schaik
- Molecular Cancer Research and Stem Cells, Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mercedes M Ondik
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Martin L Biniossek
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lisa Lehmann
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julia Mitschke
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marit W Vermunt
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Menno P Creyghton
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ann M Graybiel
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas Reinheckel
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, and German Cancer Consortium (DKTK) partner site Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine-University of Freiburg, Freiburg, Germany
| | - Benjamin J Blencowe
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jill R Crittenden
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - H Th Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
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38
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Yu S, Shao H, Ban X, Zhang H, You Y, Zhou N, Mao X, Zhao H, Chen J, Lu Z. Detection of POLE Subtypes in High-Grade Endometrioid Carcinoma by BaseScope-ISH Assay. Front Oncol 2019; 9:831. [PMID: 31552169 PMCID: PMC6738085 DOI: 10.3389/fonc.2019.00831] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/13/2019] [Indexed: 12/11/2022] Open
Abstract
Objective: The identification of DNA polymerase epsilon (POLE) mutation subtypes in endometrial cancer is critical for molecular classification. The mutation of the POLE gene could only be detected by sequencing until now. We propose to validate and develop the feasibility of using BaseScope, an in situ hybridization (ISH) assay, for the detection of POLE mutations in high-grade endometrioid carcinomas (EC). Methods: Among 51 paraffin-embedded samples of high-grade EC, BaseScope-ISH assays were used to detect the RNA mutation status of the POLE gene, mainly focusing on two hotspot mutations of P286R and V411L. The number of positive signals in the cytoplasm was counted, setting the positive threshold and determining the in situ hybridization results. The sensitivity and specificity of BaseScope-ISH assay were compared with that of the Sanger sequencing results. Results: Based on the BaseScope assay, there were 19 positive samples and 32 negative samples in a total of 51 samples. Of the 19 positive samples, 10 samples showed P286R site mutations in the POLE gene, while the other nine samples were V411L site mutations. Only one sample with the V411L site mutation identified by Sanger sequencing showed negative signal value. The remaining 31 cases without the P286R site mutation or V411L site mutations all showed negative signal. This analysis result showed the sensitivity was 95% and the specificity was 100% for the BaseScope assay detecting POLE mutants in high-grade EC. Conclusion: In the case of high-grade EC, combined with morphological characteristics, the BaseScope assay can effectively and specifically identify POLE mutation cases, providing a reliable foundation for the application of clinical diagnosis and molecular classification.
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Affiliation(s)
- Shuangni Yu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Huilin Shao
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xinchao Ban
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hongkai Zhang
- Department of Pathology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yan You
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Na Zhou
- Department of Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xinxin Mao
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - He Zhao
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jie Chen
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhaohui Lu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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Wang Y, Xu W, Maddera L, Tsuchiya D, Thomas N, Yu CR, Parmely T. Alkaline phosphatase-based chromogenic and fluorescence detection method for BaseScope™ In Situ hybridization. J Histotechnol 2019; 42:193-201. [PMID: 31416394 DOI: 10.1080/01478885.2019.1620906] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The BaseScope™ assay is a novel, highly sensitive RNA in situ hybridization (ISH) technique, allowing detection of short RNA sequences as well as discrimination between single-nucleotide alterations. Multiplexing BaseScope™ ISH with immunofluorescence assay has proven challenging because the diffusion of colorimetric dyes such as Fast Red in aqueous solutions degrades spatial resolution. In this study, we explore alkaline phosphatase-based fluorescent signal detection methods and integrate it with BaseScope™ RNA ISH. We found that Fast Blue BB/NAMP can be used in BaseScope™ ISH for signal detection. Additionally, we found that the calcium binding fluorochromes calcein and xylenol orange can be used to localize alkaline phosphatase activity in both immunohistochemistry (IHC) and BaseScope™ ISH assays. When applied to mouse brain and intestine tissue sections, we successfully detected circular RNA molecules and cell proliferation antigen Ki-67 proteins. This technological advance expanded the substrate selection of alkaline phosphatase-based BaseScope™ RNA ISH to allow researchers and clinical professionals accurately assess RNA targets with immunofluorescent multiplexing.
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Affiliation(s)
- Yongfu Wang
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Wenjing Xu
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Lucinda Maddera
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Dai Tsuchiya
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Nancy Thomas
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - C Ron Yu
- Stowers Institute for Medical Research, Kansas City, MO, USA.,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Tari Parmely
- Stowers Institute for Medical Research, Kansas City, MO, USA
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Baker AM, Graham TA. Concurrent in situ analysis of point mutations and immune infiltrate in FFPE cancers. Methods Enzymol 2019; 636:287-297. [PMID: 32178822 DOI: 10.1016/bs.mie.2019.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Existing methodology for analysis of genetic heterogeneity generally involves digestion of the tumor tissue, followed by bulk DNA extraction or single cell preparation. Such methods destroy the tissue morphology, and therefore opportunities to analyze tumor heterogeneity and clonal architecture within the native spatial context are lost. Thus, there is a clear need for the development of generally applicable methods of in situ mutation detection (ISMD), in which tumor cells can be genetically analyzed in the context of their cellular microenvironment, including immune infiltrate. Furthermore, protocols in which ISMD can be combined with immunohistochemical analysis are highly sought after, as the combination of these two techniques enables insight not only into genetic heterogeneity, but is also permissive of genotype-phenotype analysis, whilst preserving tissue morphology and spatial context. Here we describe a novel method for in situ point mutation detection using commercially available BaseScope reagents, followed by immunohistochemical detection of immune infiltrate on the same tissue section.
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Affiliation(s)
- Ann-Marie Baker
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom.
| | - Trevor A Graham
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom.
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41
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Erben L, Buonanno A. Detection and Quantification of Multiple RNA Sequences Using Emerging Ultrasensitive Fluorescent In Situ Hybridization Techniques. ACTA ACUST UNITED AC 2019; 87:e63. [PMID: 30791216 DOI: 10.1002/cpns.63] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescent detection of transcripts using RNAscope has quickly become a standard in situ hybridization (ISH) approach in neuroscience with over 400 publications since its introduction in 2012. RNAscope's sensitivity and specificity allow the simultaneously detection of up to three low abundance mRNAs in single cells (i.e., multiplexing) and, in contrast to other ISH techniques, RNAscope is performed in 1 day. BaseScope, a newer ultrasensitive platform, uses improved amplification chemistry of single oligonucleotide probe pairs (∼50 bases). This technique allows discrimination of single nucleotide polymorphisms or splice variants that differ by short exons. A present limitation of BaseScope is that expression analysis is limited to a single gene (i.e., single-plexing). This article outlines detailed protocols for both RNAscope and BaseScope in neuronal tissue. We discuss how to perform ISH experiments using either fresh-frozen or formalin-fixed paraffin-embedded sections, as well as dissociated cultured neurons. We also outline how to obtain quantitative data from hybridized tissue sections. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Larissa Erben
- Section on Molecular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.,Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Andres Buonanno
- Section on Molecular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
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42
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Chung DW, Chung Y, Bazmi HH, Lewis DA. Altered ErbB4 splicing and cortical parvalbumin interneuron dysfunction in schizophrenia and mood disorders. Neuropsychopharmacology 2018; 43:2478-2486. [PMID: 30120408 PMCID: PMC6180093 DOI: 10.1038/s41386-018-0169-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/28/2018] [Accepted: 07/25/2018] [Indexed: 01/01/2023]
Abstract
Working memory requires the activity of parvalbumin (PV) interneurons in the dorsolateral prefrontal cortex (DLPFC). Impaired working memory and lower PV expression in the DLPFC are reported in schizophrenia and to a lesser degree in mood disorders. We previously proposed that activity-dependent PV expression is lower in schizophrenia due to a shift in the splicing of erb-b2 receptor tyrosine kinase 4 (ErbB4) transcripts from major to inactive minor variants that reduces excitatory drive to PV interneurons. Here, we tested the hypothesis that the degree of major-to-minor shift in ErbB4 splicing predicts the level of PV expression across schizophrenia and mood disorders. Levels of ErbB4 splice variants and PV mRNA were quantified by PCR in the DLPFC from 40 matched tetrads (N = 160 subjects) of schizophrenia, bipolar disorder (BD), major depressive disorder (MDD), and unaffected comparison subjects. Relative to unaffected comparison subjects, the magnitude of increases in minor variant levels and decreases in major variant levels was greatest in schizophrenia, intermediate in BD, and least in MDD. The same rank order was present for the magnitude of increases in the composite splicing score, which reflects the degree of major-to-minor shift across all ErbB4 splice loci, and for the magnitude of deficient PV expression. Finally, the composite splicing score negatively predicted PV expression across all subject groups. Together, these findings demonstrate a shared relationship between ErbB4 splicing and PV expression and suggest that scaling of the major-to-minor shift in ErbB4 splicing may influence the severity of deficient PV interneuron activity across diagnoses.
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Affiliation(s)
- Daniel W Chung
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Youjin Chung
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Jacobs School of Medicine and Biomedical Science, University at Buffalo, Buffalo, NY, 14260, USA
| | - H Holly Bazmi
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - David A Lewis
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
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Guo X, Zhao Y, Nguyen H, Liu T, Wang Z, Lou H. Quantitative Analysis of Alternative Pre-mRNA Splicing in Mouse Brain Sections Using RNA In Situ Hybridization Assay. J Vis Exp 2018. [PMID: 30199013 DOI: 10.3791/57889] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Alternative splicing (AS) occurs in more than 90% of human genes. The expression pattern of an alternatively spliced exon is often regulated in a cell type-specific fashion. AS expression patterns are typically analyzed by RT-PCR and RNA-seq using RNA samples isolated from a population of cells. In situ examination of AS expression patterns for a particular biological structure can be carried out by RNA in situ hybridization (ISH) using exon-specific probes. However, this particular use of ISH has been limited because alternative exons are generally too short to design exon-specific probes. In this report, the use of BaseScope, a recently developed technology that employs short antisense oligonucleotides in RNA ISH, is described to analyze AS expression patterns in mouse brain sections. Exon 23a of neurofibromatosis type 1 (Nf1) is used as an example to illustrate that short exon-exon junction probes exhibit robust hybridization signals with high specificity in RNA ISH analysis on mouse brain sections. More importantly, signals detected with exon inclusion- and skipping-specific probes can be used to reliably calculate the percent spliced in values of Nf1 exon 23a expression in different anatomical areas of a mouse brain. The experimental protocol and calculation method for AS analysis are presented. The results indicate that BaseScope provides a powerful new tool to assess AS expression patterns in situ.
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Affiliation(s)
- Xuan Guo
- Department of Genetics and Genome Sciences, Case Western Reserve University; Department of Endocrinology, Dongfang Hospital of Beijing University of Chinese Medicine
| | - Yiqing Zhao
- Department of Genetics and Genome Sciences, Case Western Reserve University; Case Comprehensive Cancer Center, Case Western Reserve University
| | - Hieu Nguyen
- Department of Genetics and Genome Sciences, Case Western Reserve University
| | - Tonghua Liu
- Department of Endocrinology, Dongfang Hospital of Beijing University of Chinese Medicine
| | - Zhenghe Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University; Case Comprehensive Cancer Center, Case Western Reserve University
| | - Hua Lou
- Department of Genetics and Genome Sciences, Case Western Reserve University; Case Comprehensive Cancer Center, Case Western Reserve University; Center for RNA Science and Therapeutics, Case Western Reserve University;
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Anderson CM, Laeremans A, Wang XMM, Wu X, Zhang B, Doolittle E, Kim J, Li N, Pimentel HXY, Park E, Ma XJ. Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay. J Vis Exp 2018. [PMID: 30176002 PMCID: PMC6126797 DOI: 10.3791/58097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Because precision medicine is highly dependent on the accurate detection of biomarkers, there is an increasing need for standardized and robust technologies that measure RNA biomarkers in situ in clinical specimens. While grind-and-bind assays like RNAseq and quantitative RT-PCR enable highly sensitive gene expression measurements, they also require RNA extraction and thus prevent valuable expression analysis within the morphological tissue context. The in situ hybridization (ISH) assay described here can detect RNA target sequences as short as 50 nucleotides at single-nucleotide resolution and at the single-cell level. This assay is complementary to the previously developed commercial assay and enables sensitive and specific in situ detection of splice variants, short targets, and point mutations within the tissue. In this protocol, probes were designed to target unique exon junctions for two clinically important splice variants, EGFRvIII and METΔ14. The detection of short target sequences was demonstrated by the specific detection of CDR3 sequences of T-cell receptors α and β in the Jurkat T-cell line. Also shown is the utility of this ISH assay for the distinction of RNA target sequences at single-nucleotide resolution (point mutations) through the visualization of EGFR L858R and KRAS G12A single-nucleotide variations in cell lines using automated staining platforms. In summary, the protocol shows a specialized RNA ISH assay that enables the detection of splice variants, short sequences, and mutations in situ for manual performance and on automated stainers.
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Affiliation(s)
| | | | | | | | | | | | | | - Na Li
- Advanced Cell Diagnostics, Inc
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